From mailer@bialko.llnl.gov Tue Jul 16 19:03:28 2002 Date: Tue, 16 Jul 2002 19:03:23 -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 18:36:32 PDT 2002 by Adam Zemla # # The PIN number of your submission is: PIN_478875_12196 # (PIN number is not an ACCESSION CODE) # Thank you for your submission. Your prediction has been accepted with an ACCESSION CODE: T0140SS389_1 Current information on models submitted in prediction T0140SS389 MODEL_INDEX PIN CODE DATE E-mail T0140SS389_1 PIN_478875_12196 1549-8716-6404 07/16/02 18:36:32 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 T0140 MODEL_INDEX PIN CODE DATE E-mail T0140SS389_1 PIN_478875_12196 1549-8716-6404 07/16/02 18:36:32 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 T0140 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: 103 # Number of residues with nonzero confidence: 103 # Number of METHOD records: 46 # No errors. ################################ # # # SUBMISSION # # # ################################ # # # BEGIN # # # ################################ PFRMAT SS TARGET T0140 AUTHOR 1549-8716-6404 METHOD CAFASP METHOD samt02_dssp_ehl METHOD This file is the result of combining several RDB files, specifically METHOD preds/T0140.t2k.dssp-ebghstl.rdb (weight 1.53986) METHOD preds/T0140.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/T0140.t2k.dssp-ebghstl.rdb METHOD ============================================ METHOD TARGET T0140 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 T0140.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 341 METHOD METHOD ============================================ METHOD Comments from preds/T0140.t2k.stride-ebghtl.rdb METHOD ============================================ METHOD TARGET T0140 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 T0140.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 341 METHOD METHOD ============================================ MODEL 1 M C 0.97 R C 0.75 G C 0.69 S C 0.60 H C 0.51 H C 0.48 H C 0.56 H C 0.69 H C 0.85 H C 0.60 G C 0.53 S C 0.42 R C 0.43 L E 0.43 Q C 0.49 S C 0.63 G C 0.59 K C 0.52 M E 0.64 T E 0.77 G E 0.91 I E 0.95 V E 0.95 K E 0.94 W E 0.89 F E 0.80 N E 0.78 A E 0.61 D C 0.46 K C 0.65 G C 0.81 F C 0.62 G E 0.72 F E 0.87 I E 0.85 T E 0.65 P C 0.57 D C 0.71 D C 0.69 G C 0.79 S C 0.63 K E 0.77 D E 0.87 V E 0.89 F E 0.90 V E 0.86 H E 0.82 F E 0.67 S E 0.47 A C 0.56 G C 0.63 S C 0.70 S C 0.50 G H 0.66 A H 0.72 A H 0.72 V H 0.66 R H 0.62 G H 0.50 N C 0.54 P C 0.80 Q C 0.85 Q C 0.87 G C 0.88 D E 0.54 R E 0.89 V E 0.93 E E 0.94 G E 0.94 K E 0.96 I E 0.96 K E 0.96 S E 0.94 I E 0.86 T E 0.59 D C 0.62 F C 0.69 G C 0.52 I E 0.79 F E 0.94 I E 0.94 G E 0.92 L E 0.76 D C 0.69 G C 0.91 G C 0.93 I C 0.73 D C 0.51 G E 0.80 L E 0.93 V E 0.92 H E 0.88 L E 0.43 S H 0.40 D H 0.57 I H 0.51 S C 0.49 W C 0.51 A C 0.49 Q C 0.50 A C 0.59 E C 0.72 A C 0.95 END ################################ # # # END # # # ################################ From mailer@bialko.llnl.gov Wed Jul 24 18:13:08 2002 Date: Wed, 24 Jul 2002 18:13:02 -0700 (PDT) From: Automatic Reply To: karplus@soe.ucsc.edu Subject: T0140 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 Wed Jul 24 17:45:35 PDT 2002 by Adam Zemla # # The PIN number of your submission is: PIN_572902_14271 # (PIN number is not an ACCESSION CODE) # Thank you for your submission. Your prediction has been accepted with an ACCESSION CODE: T0140TS189_1 Current information on models submitted in prediction T0140TS189 MODEL_INDEX PIN CODE DATE E-mail T0140TS189_1 PIN_572902_14271 5035-2079-5263 07/24/02 17:45:35 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 T0140 MODEL_INDEX PIN CODE DATE E-mail T0140TS189_1 PIN_572902_14271 5035-2079-5263 07/24/02 17:45:35 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 T0140 AUTHOR 5035-2079-5263 # Reading MODEL 1 PARENT 1MJC # Loading PARENT structure: 1mjc (chain: ) # Number of residues in PARENT structure: 69 # Reading prediction format TS (DONE) # Checking the TS prediction MODEL 1 # IMPORTANT NOTE! Not complete main chain atoms for residue S 16 # !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! # # 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 G 17 # IMPORTANT NOTE! Not complete main chain atoms for residue K 18 # IMPORTANT NOTE! Not complete main chain atoms for residue M 19 # IMPORTANT NOTE! Not complete main chain atoms for residue T 20 # IMPORTANT NOTE! Not complete main chain atoms for residue G 21 # IMPORTANT NOTE! Not complete main chain atoms for residue I 22 # IMPORTANT NOTE! Not complete main chain atoms for residue V 23 # IMPORTANT NOTE! Not complete main chain atoms for residue K 24 # IMPORTANT NOTE! Not complete main chain atoms for residue W 25 # IMPORTANT NOTE! Not complete main chain atoms for residue F 26 # IMPORTANT NOTE! Not complete main chain atoms for residue N 27 # IMPORTANT NOTE! Not complete main chain atoms for residue A 28 # IMPORTANT NOTE! Not complete main chain atoms for residue D 29 # IMPORTANT NOTE! Not complete main chain atoms for residue K 30 # IMPORTANT NOTE! Not complete main chain atoms for residue G 31 # IMPORTANT NOTE! Not complete main chain atoms for residue F 32 # IMPORTANT NOTE! Not complete main chain atoms for residue G 33 # IMPORTANT NOTE! Not complete main chain atoms for residue F 34 # IMPORTANT NOTE! Not complete main chain atoms for residue I 35 # IMPORTANT NOTE! Not complete main chain atoms for residue T 36 # IMPORTANT NOTE! Not complete main chain atoms for residue P 37 # IMPORTANT NOTE! Not complete main chain atoms for residue D 38 # IMPORTANT NOTE! Not complete main chain atoms for residue D 39 # IMPORTANT NOTE! Not complete main chain atoms for residue G 40 # IMPORTANT NOTE! Not complete main chain atoms for residue S 41 # IMPORTANT NOTE! Not complete main chain atoms for residue K 42 # IMPORTANT NOTE! Not complete main chain atoms for residue D 43 # IMPORTANT NOTE! Not complete main chain atoms for residue V 44 # IMPORTANT NOTE! Not complete main chain atoms for residue F 45 # IMPORTANT NOTE! Not complete main chain atoms for residue V 46 # IMPORTANT NOTE! Not complete main chain atoms for residue H 47 # IMPORTANT NOTE! Not complete main chain atoms for residue F 48 # IMPORTANT NOTE! Not complete main chain atoms for residue S 49 # IMPORTANT NOTE! Not complete main chain atoms for residue A 50 # IMPORTANT NOTE! Not complete main chain atoms for residue G 51 # IMPORTANT NOTE! Not complete main chain atoms for residue S 52 # IMPORTANT NOTE! Not complete main chain atoms for residue A 55 # IMPORTANT NOTE! Not complete main chain atoms for residue A 56 # IMPORTANT NOTE! Not complete main chain atoms for residue V 57 # IMPORTANT NOTE! Not complete main chain atoms for residue R 58 # IMPORTANT NOTE! Not complete main chain atoms for residue G 59 # IMPORTANT NOTE! Not complete main chain atoms for residue N 60 # IMPORTANT NOTE! Not complete main chain atoms for residue P 61 # IMPORTANT NOTE! Not complete main chain atoms for residue Q 62 # IMPORTANT NOTE! Not complete main chain atoms for residue Q 63 # IMPORTANT NOTE! Not complete main chain atoms for residue G 64 # IMPORTANT NOTE! Not complete main chain atoms for residue D 65 # IMPORTANT NOTE! Not complete main chain atoms for residue R 66 # IMPORTANT NOTE! Not complete main chain atoms for residue V 67 # IMPORTANT NOTE! Not complete main chain atoms for residue E 68 # IMPORTANT NOTE! Not complete main chain atoms for residue G 69 # IMPORTANT NOTE! Not complete main chain atoms for residue K 70 # IMPORTANT NOTE! Not complete main chain atoms for residue I 71 # IMPORTANT NOTE! Not complete main chain atoms for residue K 72 # IMPORTANT NOTE! Not complete main chain atoms for residue S 73 # IMPORTANT NOTE! Not complete main chain atoms for residue I 74 # IMPORTANT NOTE! Not complete main chain atoms for residue T 75 # IMPORTANT NOTE! Not complete main chain atoms for residue D 76 # IMPORTANT NOTE! Not complete main chain atoms for residue F 77 # IMPORTANT NOTE! Not complete main chain atoms for residue G 78 # IMPORTANT NOTE! Not complete main chain atoms for residue I 79 # IMPORTANT NOTE! Not complete main chain atoms for residue F 80 # IMPORTANT NOTE! Not complete main chain atoms for residue I 81 # IMPORTANT NOTE! Not complete main chain atoms for residue G 82 # IMPORTANT NOTE! Not complete main chain atoms for residue L 83 # IMPORTANT NOTE! Not complete main chain atoms for residue D 84 # IMPORTANT NOTE! Not complete main chain atoms for residue G 85 # Checking the TS prediction MODEL 1 (DONE) # MODEL index: 1 # Target name: T0140 # Total number of residues in target: 103 # Total number of residues in model: 68 # Total number of atoms in model: 68 # Number of atoms with 1.0 occupancy: 68 # Number of fragments in model: 1 # Number of METHOD records: 1 # No errors. # Number of Warnings: 68 ################################ # # # SUBMISSION # # # ################################ # # # BEGIN # # # ################################ PFRMAT TS TARGET T0140 AUTHOR 5035-2079-5263 METHOD CAFASP MODEL 1 PARENT 1MJC ATOM 2 CA SER 16 13.987 25.698 38.130 1.00 1.00 ATOM 3 CA GLY 17 13.710 24.742 34.442 1.00 1.00 ATOM 4 CA LYS 18 17.460 24.128 34.531 1.00 1.00 ATOM 5 CA MET 19 18.958 21.022 32.935 1.00 1.00 ATOM 6 CA THR 20 22.092 19.382 34.362 1.00 1.00 ATOM 7 CA GLY 21 24.906 17.886 32.277 1.00 1.00 ATOM 8 CA ILE 22 28.671 17.339 32.005 1.00 1.00 ATOM 9 CA VAL 23 31.222 19.420 30.035 1.00 1.00 ATOM 10 CA LYS 24 32.125 17.280 26.971 1.00 1.00 ATOM 11 CA TRP 25 34.998 19.635 26.091 1.00 1.00 ATOM 12 CA PHE 26 35.817 23.332 26.442 1.00 1.00 ATOM 13 CA ASN 27 38.312 25.273 24.243 1.00 1.00 ATOM 14 CA ALA 28 39.553 28.090 26.558 1.00 1.00 ATOM 15 CA ASP 29 41.411 29.708 23.596 1.00 1.00 ATOM 16 CA LYS 30 38.248 30.130 21.482 1.00 1.00 ATOM 17 CA GLY 31 35.956 30.452 24.537 1.00 1.00 ATOM 18 CA PHE 32 33.334 27.763 23.692 1.00 1.00 ATOM 19 CA GLY 33 32.600 24.059 24.031 1.00 1.00 ATOM 20 CA PHE 34 29.816 21.523 24.494 1.00 1.00 ATOM 21 CA ILE 35 27.756 20.102 27.301 1.00 1.00 ATOM 22 CA THR 36 26.232 16.583 27.242 1.00 1.00 ATOM 23 CA PRO 37 22.773 16.965 28.854 1.00 1.00 ATOM 24 CA ASP 38 21.734 14.350 31.387 1.00 1.00 ATOM 25 CA ASP 39 18.531 13.605 29.403 1.00 1.00 ATOM 26 CA GLY 40 20.456 11.995 26.478 1.00 1.00 ATOM 27 CA SER 41 19.488 14.870 24.124 1.00 1.00 ATOM 28 CA LYS 42 21.891 16.506 21.604 1.00 1.00 ATOM 29 CA ASP 43 25.093 18.193 22.897 1.00 1.00 ATOM 30 CA VAL 44 24.567 21.836 23.795 1.00 1.00 ATOM 31 CA PHE 45 26.907 24.614 22.694 1.00 1.00 ATOM 32 CA VAL 46 28.225 26.715 25.607 1.00 1.00 ATOM 33 CA HIS 47 29.825 30.169 24.991 1.00 1.00 ATOM 34 CA PHE 48 32.164 31.599 27.704 1.00 1.00 ATOM 35 CA SER 49 29.762 34.573 28.019 1.00 1.00 ATOM 36 CA ALA 50 26.985 32.194 29.281 1.00 1.00 ATOM 37 CA GLY 51 29.024 31.197 32.410 1.00 1.00 ATOM 38 CA SER 52 28.372 32.598 35.851 1.00 1.00 ATOM 39 CA ALA 55 31.596 34.614 35.817 1.00 1.00 ATOM 40 CA ALA 56 32.829 35.446 39.443 1.00 1.00 ATOM 41 CA VAL 57 36.336 35.584 37.930 1.00 1.00 ATOM 42 CA ARG 58 36.050 32.118 36.354 1.00 1.00 ATOM 43 CA GLY 59 34.329 31.964 32.937 1.00 1.00 ATOM 44 CA ASN 60 36.233 28.723 32.017 1.00 1.00 ATOM 45 CA PRO 61 35.124 25.008 32.321 1.00 1.00 ATOM 46 CA GLN 62 36.840 21.706 32.562 1.00 1.00 ATOM 47 CA GLN 63 36.073 18.562 30.711 1.00 1.00 ATOM 48 CA GLY 64 33.980 16.339 32.959 1.00 1.00 ATOM 49 CA ASP 65 32.578 19.093 35.208 1.00 1.00 ATOM 50 CA ARG 66 28.906 18.778 36.294 1.00 1.00 ATOM 51 CA VAL 67 27.016 21.971 35.287 1.00 1.00 ATOM 52 CA GLU 68 23.460 23.309 35.352 1.00 1.00 ATOM 53 CA GLY 69 22.139 25.556 32.635 1.00 1.00 ATOM 54 CA LYS 70 19.003 26.574 30.796 1.00 1.00 ATOM 55 CA ILE 71 18.475 25.605 27.134 1.00 1.00 ATOM 56 CA LYS 72 18.208 28.643 24.993 1.00 1.00 ATOM 57 CA SER 73 17.573 29.929 21.564 1.00 1.00 ATOM 58 CA ILE 74 20.894 29.531 19.808 1.00 1.00 ATOM 59 CA THR 75 22.268 30.933 16.596 1.00 1.00 ATOM 60 CA ASP 76 23.018 27.452 15.198 1.00 1.00 ATOM 61 CA PHE 77 21.461 24.869 17.629 1.00 1.00 ATOM 62 CA GLY 78 20.576 24.479 21.311 1.00 1.00 ATOM 63 CA ILE 79 22.688 26.755 23.544 1.00 1.00 ATOM 64 CA PHE 80 23.318 26.799 27.272 1.00 1.00 ATOM 65 CA ILE 81 22.383 29.927 29.234 1.00 1.00 ATOM 66 CA GLY 82 22.992 30.645 32.981 1.00 1.00 ATOM 67 CA LEU 83 25.709 28.020 33.327 1.00 1.00 ATOM 68 CA ASP 84 26.437 27.134 36.881 1.00 1.00 ATOM 69 CA GLY 85 28.896 24.653 38.406 1.00 1.00 TER END ################################ # # # END # # # ################################ From mailer@bialko.llnl.gov Wed Jul 24 18:13:39 2002 Date: Wed, 24 Jul 2002 18:13:34 -0700 (PDT) From: Automatic Reply To: karplus@soe.ucsc.edu Subject: T0140 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 Wed Jul 24 17:46:18 PDT 2002 by Adam Zemla # # The PIN number of your submission is: PIN_582815_14274 # (PIN number is not an ACCESSION CODE) # Thank you for your submission. Your prediction has been accepted with an ACCESSION CODE: T0140TS189_2 Current information on models submitted in prediction T0140TS189 MODEL_INDEX PIN CODE DATE E-mail T0140TS189_2 PIN_582815_14274 5035-2079-5263 07/24/02 17:46:18 casp5@bialko.llnl.gov T0140TS189_1 PIN_572902_14271 5035-2079-5263 07/24/02 17:45:35 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 T0140 MODEL_INDEX PIN CODE DATE E-mail T0140TS189_1 PIN_572902_14271 5035-2079-5263 07/24/02 17:45:35 casp5@bialko.llnl.gov T0140TS189_2 PIN_582815_14274 5035-2079-5263 07/24/02 17:46:18 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 T0140 AUTHOR 5035-2079-5263 # Reading MODEL 2 PARENT 1GO3_E # Loading PARENT structure: 1go3 (chain: E) # Number of residues in PARENT structure: 177 # Reading prediction format TS (DONE) # Checking the TS prediction MODEL 2 # 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 R 2 # IMPORTANT NOTE! Not complete main chain atoms for residue G 3 # IMPORTANT NOTE! Not complete main chain atoms for residue S 4 # IMPORTANT NOTE! Not complete main chain atoms for residue H 5 # IMPORTANT NOTE! Not complete main chain atoms for residue H 6 # IMPORTANT NOTE! Not complete main chain atoms for residue H 7 # IMPORTANT NOTE! Not complete main chain atoms for residue H 8 # IMPORTANT NOTE! Not complete main chain atoms for residue H 9 # IMPORTANT NOTE! Not complete main chain atoms for residue H 10 # IMPORTANT NOTE! Not complete main chain atoms for residue G 11 # IMPORTANT NOTE! Not complete main chain atoms for residue S 12 # IMPORTANT NOTE! Not complete main chain atoms for residue L 14 # IMPORTANT NOTE! Not complete main chain atoms for residue Q 15 # IMPORTANT NOTE! Not complete main chain atoms for residue S 16 # IMPORTANT NOTE! Not complete main chain atoms for residue G 17 # IMPORTANT NOTE! Not complete main chain atoms for residue K 18 # IMPORTANT NOTE! Not complete main chain atoms for residue M 19 # IMPORTANT NOTE! Not complete main chain atoms for residue T 20 # IMPORTANT NOTE! Not complete main chain atoms for residue G 21 # IMPORTANT NOTE! Not complete main chain atoms for residue I 22 # IMPORTANT NOTE! Not complete main chain atoms for residue V 23 # IMPORTANT NOTE! Not complete main chain atoms for residue K 24 # IMPORTANT NOTE! Not complete main chain atoms for residue W 25 # IMPORTANT NOTE! Not complete main chain atoms for residue A 28 # IMPORTANT NOTE! Not complete main chain atoms for residue D 29 # IMPORTANT NOTE! Not complete main chain atoms for residue K 30 # IMPORTANT NOTE! Not complete main chain atoms for residue G 31 # IMPORTANT NOTE! Not complete main chain atoms for residue F 32 # IMPORTANT NOTE! Not complete main chain atoms for residue G 33 # IMPORTANT NOTE! Not complete main chain atoms for residue F 34 # IMPORTANT NOTE! Not complete main chain atoms for residue I 35 # IMPORTANT NOTE! Not complete main chain atoms for residue T 36 # IMPORTANT NOTE! Not complete main chain atoms for residue P 37 # IMPORTANT NOTE! Not complete main chain atoms for residue D 38 # IMPORTANT NOTE! Not complete main chain atoms for residue D 39 # IMPORTANT NOTE! Not complete main chain atoms for residue G 40 # IMPORTANT NOTE! Not complete main chain atoms for residue S 41 # IMPORTANT NOTE! Not complete main chain atoms for residue K 42 # IMPORTANT NOTE! Not complete main chain atoms for residue D 43 # IMPORTANT NOTE! Not complete main chain atoms for residue V 44 # IMPORTANT NOTE! Not complete main chain atoms for residue F 45 # IMPORTANT NOTE! Not complete main chain atoms for residue V 46 # IMPORTANT NOTE! Not complete main chain atoms for residue H 47 # IMPORTANT NOTE! Not complete main chain atoms for residue F 48 # IMPORTANT NOTE! Not complete main chain atoms for residue A 55 # IMPORTANT NOTE! Not complete main chain atoms for residue A 56 # IMPORTANT NOTE! Not complete main chain atoms for residue V 57 # IMPORTANT NOTE! Not complete main chain atoms for residue R 58 # IMPORTANT NOTE! Not complete main chain atoms for residue G 59 # IMPORTANT NOTE! Not complete main chain atoms for residue N 60 # IMPORTANT NOTE! Not complete main chain atoms for residue P 61 # IMPORTANT NOTE! Not complete main chain atoms for residue Q 62 # IMPORTANT NOTE! Not complete main chain atoms for residue Q 63 # IMPORTANT NOTE! Not complete main chain atoms for residue G 64 # IMPORTANT NOTE! Not complete main chain atoms for residue D 65 # IMPORTANT NOTE! Not complete main chain atoms for residue R 66 # IMPORTANT NOTE! Not complete main chain atoms for residue V 67 # IMPORTANT NOTE! Not complete main chain atoms for residue E 68 # IMPORTANT NOTE! Not complete main chain atoms for residue G 69 # IMPORTANT NOTE! Not complete main chain atoms for residue K 70 # IMPORTANT NOTE! Not complete main chain atoms for residue I 71 # IMPORTANT NOTE! Not complete main chain atoms for residue K 72 # IMPORTANT NOTE! Not complete main chain atoms for residue S 73 # IMPORTANT NOTE! Not complete main chain atoms for residue I 74 # IMPORTANT NOTE! Not complete main chain atoms for residue T 75 # IMPORTANT NOTE! Not complete main chain atoms for residue D 76 # IMPORTANT NOTE! Not complete main chain atoms for residue F 77 # IMPORTANT NOTE! Not complete main chain atoms for residue G 78 # IMPORTANT NOTE! Not complete main chain atoms for residue I 79 # IMPORTANT NOTE! Not complete main chain atoms for residue F 80 # IMPORTANT NOTE! Not complete main chain atoms for residue I 81 # IMPORTANT NOTE! Not complete main chain atoms for residue G 82 # IMPORTANT NOTE! Not complete main chain atoms for residue L 83 # IMPORTANT NOTE! Not complete main chain atoms for residue G 85 # IMPORTANT NOTE! Not complete main chain atoms for residue G 86 # IMPORTANT NOTE! Not complete main chain atoms for residue I 87 # IMPORTANT NOTE! Not complete main chain atoms for residue D 88 # IMPORTANT NOTE! Not complete main chain atoms for residue G 89 # IMPORTANT NOTE! Not complete main chain atoms for residue L 90 # IMPORTANT NOTE! Not complete main chain atoms for residue V 91 # IMPORTANT NOTE! Not complete main chain atoms for residue H 92 # IMPORTANT NOTE! Not complete main chain atoms for residue L 93 # IMPORTANT NOTE! Not complete main chain atoms for residue S 94 # IMPORTANT NOTE! Not complete main chain atoms for residue D 95 # IMPORTANT NOTE! Not complete main chain atoms for residue I 96 # IMPORTANT NOTE! Not complete main chain atoms for residue S 97 # IMPORTANT NOTE! Not complete main chain atoms for residue W 98 # IMPORTANT NOTE! Not complete main chain atoms for residue A 99 # IMPORTANT NOTE! Not complete main chain atoms for residue Q 100 # IMPORTANT NOTE! Not complete main chain atoms for residue A 101 # IMPORTANT NOTE! Not complete main chain atoms for residue E 102 # Checking the TS prediction MODEL 2 (DONE) # MODEL index: 2 # Target name: T0140 # Total number of residues in target: 103 # Total number of residues in model: 92 # Total number of atoms in model: 92 # Number of atoms with 1.0 occupancy: 92 # Number of fragments in model: 1 # Number of METHOD records: 1 # No errors. # Number of Warnings: 92 ################################ # # # SUBMISSION # # # ################################ # # # BEGIN # # # ################################ PFRMAT TS TARGET T0140 AUTHOR 5035-2079-5263 METHOD CAFASP MODEL 2 PARENT 1GO3_E ATOM 1 CA MET 1 37.081 62.554 61.057 1.00 1.00 ATOM 2 CA ARG 2 33.814 61.097 62.323 1.00 1.00 ATOM 3 CA GLY 3 32.039 58.172 60.692 1.00 1.00 ATOM 4 CA SER 4 28.920 56.070 61.069 1.00 1.00 ATOM 5 CA HIS 5 29.705 52.409 60.381 1.00 1.00 ATOM 12 CA HIS 6 25.606 36.242 72.551 1.00 1.00 ATOM 13 CA HIS 7 22.465 36.596 74.675 1.00 1.00 ATOM 14 CA HIS 8 22.598 34.823 78.086 1.00 1.00 ATOM 15 CA HIS 9 19.492 32.877 79.216 1.00 1.00 ATOM 16 CA HIS 10 19.108 35.185 82.225 1.00 1.00 ATOM 17 CA GLY 11 18.007 37.851 79.738 1.00 1.00 ATOM 18 CA SER 12 15.436 35.847 77.759 1.00 1.00 ATOM 40 CA LEU 14 43.931 51.198 64.566 1.00 1.00 ATOM 41 CA GLN 15 41.798 50.662 61.453 1.00 1.00 ATOM 42 CA SER 16 38.306 51.463 62.747 1.00 1.00 ATOM 43 CA GLY 17 38.992 54.206 65.279 1.00 1.00 ATOM 44 CA LYS 18 37.457 55.038 68.667 1.00 1.00 ATOM 45 CA MET 19 33.990 53.522 69.179 1.00 1.00 ATOM 46 CA THR 20 31.837 56.333 70.582 1.00 1.00 ATOM 47 CA GLY 21 28.324 54.929 70.475 1.00 1.00 ATOM 48 CA ILE 22 26.153 52.035 69.359 1.00 1.00 ATOM 49 CA VAL 23 23.610 54.238 67.595 1.00 1.00 ATOM 50 CA LYS 24 21.074 51.540 66.817 1.00 1.00 ATOM 51 CA TRP 25 20.566 47.862 66.042 1.00 1.00 ATOM 52 CA ALA 28 19.175 47.556 62.524 1.00 1.00 ATOM 53 CA ASP 29 18.619 43.804 62.299 1.00 1.00 ATOM 54 CA LYS 30 18.501 40.813 64.644 1.00 1.00 ATOM 55 CA GLY 31 18.229 37.312 63.218 1.00 1.00 ATOM 56 CA PHE 32 16.919 34.154 64.847 1.00 1.00 ATOM 57 CA GLY 33 18.972 32.827 67.730 1.00 1.00 ATOM 58 CA PHE 34 21.232 29.808 67.347 1.00 1.00 ATOM 59 CA ILE 35 22.129 27.497 70.221 1.00 1.00 ATOM 60 CA THR 36 25.265 25.344 70.326 1.00 1.00 ATOM 61 CA PRO 37 25.780 22.363 72.637 1.00 1.00 ATOM 62 CA ASP 38 27.439 23.010 75.983 1.00 1.00 ATOM 63 CA ASP 39 26.348 26.647 75.785 1.00 1.00 ATOM 64 CA GLY 40 23.067 28.029 77.114 1.00 1.00 ATOM 65 CA SER 41 23.263 31.379 75.332 1.00 1.00 ATOM 66 CA LYS 42 21.379 32.327 72.178 1.00 1.00 ATOM 67 CA ASP 43 23.625 33.570 69.377 1.00 1.00 ATOM 68 CA VAL 44 21.852 36.119 67.192 1.00 1.00 ATOM 69 CA PHE 45 23.192 37.441 63.890 1.00 1.00 ATOM 70 CA VAL 46 22.924 41.227 63.956 1.00 1.00 ATOM 71 CA HIS 47 23.633 44.409 62.038 1.00 1.00 ATOM 72 CA PHE 48 24.278 47.501 64.127 1.00 1.00 ATOM 73 CA ALA 55 25.262 51.103 63.475 1.00 1.00 ATOM 74 CA ALA 56 28.100 52.801 65.329 1.00 1.00 ATOM 75 CA VAL 57 29.633 56.271 65.541 1.00 1.00 ATOM 76 CA ARG 58 33.433 56.353 65.545 1.00 1.00 ATOM 77 CA GLY 59 36.187 58.946 65.708 1.00 1.00 ATOM 78 CA ASN 60 39.070 58.306 63.335 1.00 1.00 ATOM 79 CA PRO 61 42.124 60.593 62.992 1.00 1.00 ATOM 80 CA GLN 62 43.585 60.613 59.480 1.00 1.00 ATOM 81 CA GLN 63 47.083 61.555 58.317 1.00 1.00 ATOM 82 CA GLY 64 47.427 65.142 57.071 1.00 1.00 ATOM 83 CA ASP 65 43.852 65.849 58.160 1.00 1.00 ATOM 84 CA ARG 66 42.840 69.458 58.820 1.00 1.00 ATOM 85 CA VAL 67 41.263 69.805 62.246 1.00 1.00 ATOM 86 CA GLU 68 39.930 72.392 64.652 1.00 1.00 ATOM 87 CA GLY 69 39.986 71.827 68.393 1.00 1.00 ATOM 88 CA LYS 70 40.329 73.295 71.874 1.00 1.00 ATOM 89 CA ILE 71 43.551 73.550 73.875 1.00 1.00 ATOM 90 CA LYS 72 43.073 71.594 77.107 1.00 1.00 ATOM 91 CA SER 73 46.605 71.663 78.518 1.00 1.00 ATOM 92 CA ILE 74 49.756 73.704 77.942 1.00 1.00 ATOM 93 CA THR 75 53.136 72.419 79.127 1.00 1.00 ATOM 94 CA ASP 76 56.779 73.208 78.380 1.00 1.00 ATOM 95 CA PHE 77 56.873 70.600 75.618 1.00 1.00 ATOM 96 CA GLY 78 53.671 71.557 73.825 1.00 1.00 ATOM 97 CA ILE 79 49.916 72.048 73.874 1.00 1.00 ATOM 98 CA PHE 80 47.309 69.297 74.040 1.00 1.00 ATOM 99 CA ILE 81 44.264 69.790 71.809 1.00 1.00 ATOM 100 CA GLY 82 40.952 67.955 72.208 1.00 1.00 ATOM 101 CA LEU 83 39.739 66.416 68.943 1.00 1.00 ATOM 102 CA GLY 85 36.921 64.369 70.439 1.00 1.00 ATOM 103 CA GLY 86 37.462 61.304 72.664 1.00 1.00 ATOM 104 CA ILE 87 41.188 61.642 71.952 1.00 1.00 ATOM 105 CA ASP 88 43.621 64.558 72.106 1.00 1.00 ATOM 106 CA GLY 89 46.429 65.566 69.789 1.00 1.00 ATOM 107 CA LEU 90 49.706 67.184 70.791 1.00 1.00 ATOM 108 CA VAL 91 51.257 70.213 69.141 1.00 1.00 ATOM 109 CA HIS 92 54.895 69.967 70.189 1.00 1.00 ATOM 110 CA LEU 93 56.174 73.328 71.462 1.00 1.00 ATOM 111 CA SER 94 58.299 73.845 68.336 1.00 1.00 ATOM 112 CA ASP 95 55.311 73.358 66.018 1.00 1.00 ATOM 113 CA ILE 96 53.041 76.051 67.453 1.00 1.00 ATOM 114 CA SER 97 54.385 79.111 65.636 1.00 1.00 ATOM 115 CA TRP 98 57.315 80.420 63.604 1.00 1.00 ATOM 116 CA ALA 99 58.901 82.331 66.475 1.00 1.00 ATOM 117 CA GLN 100 61.044 81.820 69.573 1.00 1.00 ATOM 118 CA ALA 101 58.681 80.471 72.220 1.00 1.00 ATOM 119 CA GLU 102 58.838 80.004 75.982 1.00 1.00 TER END ################################ # # # END # # # ################################ From mailer@bialko.llnl.gov Wed Jul 24 18:14:07 2002 Date: Wed, 24 Jul 2002 18:14:02 -0700 (PDT) From: Automatic Reply To: karplus@soe.ucsc.edu Subject: T0140 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 Wed Jul 24 17:46:32 PDT 2002 by Adam Zemla # # The PIN number of your submission is: PIN_580998_14275 # (PIN number is not an ACCESSION CODE) # Thank you for your submission. Your prediction has been accepted with an ACCESSION CODE: T0140TS189_3 Current information on models submitted in prediction T0140TS189 MODEL_INDEX PIN CODE DATE E-mail T0140TS189_3 PIN_580998_14275 5035-2079-5263 07/24/02 17:46:32 casp5@bialko.llnl.gov T0140TS189_2 PIN_582815_14274 5035-2079-5263 07/24/02 17:46:18 casp5@bialko.llnl.gov T0140TS189_1 PIN_572902_14271 5035-2079-5263 07/24/02 17:45:35 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 T0140 MODEL_INDEX PIN CODE DATE E-mail T0140TS189_1 PIN_572902_14271 5035-2079-5263 07/24/02 17:45:35 casp5@bialko.llnl.gov T0140TS189_2 PIN_582815_14274 5035-2079-5263 07/24/02 17:46:18 casp5@bialko.llnl.gov T0140TS189_3 PIN_580998_14275 5035-2079-5263 07/24/02 17:46:32 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 T0140 AUTHOR 5035-2079-5263 # Reading MODEL 3 PARENT 1SRO # Loading PARENT structure: 1sro (chain: ) # Number of residues in PARENT structure: 76 # Reading prediction format TS (DONE) # Checking the TS prediction MODEL 3 # IMPORTANT NOTE! Not complete main chain atoms for residue G 59 # !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! # # 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 N 60 # IMPORTANT NOTE! Not complete main chain atoms for residue P 61 # IMPORTANT NOTE! Not complete main chain atoms for residue Q 62 # IMPORTANT NOTE! Not complete main chain atoms for residue Q 63 # IMPORTANT NOTE! Not complete main chain atoms for residue G 64 # IMPORTANT NOTE! Not complete main chain atoms for residue D 65 # IMPORTANT NOTE! Not complete main chain atoms for residue R 66 # IMPORTANT NOTE! Not complete main chain atoms for residue V 67 # IMPORTANT NOTE! Not complete main chain atoms for residue E 68 # IMPORTANT NOTE! Not complete main chain atoms for residue G 69 # IMPORTANT NOTE! Not complete main chain atoms for residue K 70 # IMPORTANT NOTE! Not complete main chain atoms for residue I 71 # IMPORTANT NOTE! Not complete main chain atoms for residue K 72 # IMPORTANT NOTE! Not complete main chain atoms for residue S 73 # IMPORTANT NOTE! Not complete main chain atoms for residue I 74 # IMPORTANT NOTE! Not complete main chain atoms for residue T 75 # IMPORTANT NOTE! Not complete main chain atoms for residue D 76 # IMPORTANT NOTE! Not complete main chain atoms for residue F 77 # IMPORTANT NOTE! Not complete main chain atoms for residue G 78 # IMPORTANT NOTE! Not complete main chain atoms for residue I 79 # IMPORTANT NOTE! Not complete main chain atoms for residue F 80 # IMPORTANT NOTE! Not complete main chain atoms for residue I 81 # IMPORTANT NOTE! Not complete main chain atoms for residue G 82 # IMPORTANT NOTE! Not complete main chain atoms for residue L 83 # IMPORTANT NOTE! Not complete main chain atoms for residue D 84 # IMPORTANT NOTE! Not complete main chain atoms for residue G 85 # IMPORTANT NOTE! Not complete main chain atoms for residue G 86 # IMPORTANT NOTE! Not complete main chain atoms for residue I 87 # IMPORTANT NOTE! Not complete main chain atoms for residue D 88 # IMPORTANT NOTE! Not complete main chain atoms for residue G 89 # IMPORTANT NOTE! Not complete main chain atoms for residue L 90 # IMPORTANT NOTE! Not complete main chain atoms for residue V 91 # IMPORTANT NOTE! Not complete main chain atoms for residue H 92 # IMPORTANT NOTE! Not complete main chain atoms for residue L 93 # IMPORTANT NOTE! Not complete main chain atoms for residue S 94 # IMPORTANT NOTE! Not complete main chain atoms for residue D 95 # IMPORTANT NOTE! Not complete main chain atoms for residue I 96 # IMPORTANT NOTE! Not complete main chain atoms for residue S 97 # IMPORTANT NOTE! Not complete main chain atoms for residue W 98 # IMPORTANT NOTE! Not complete main chain atoms for residue A 99 # IMPORTANT NOTE! Not complete main chain atoms for residue Q 100 # IMPORTANT NOTE! Not complete main chain atoms for residue A 101 # IMPORTANT NOTE! Not complete main chain atoms for residue E 102 # Checking the TS prediction MODEL 3 (DONE) # MODEL index: 3 # Target name: T0140 # Total number of residues in target: 103 # Total number of residues in model: 44 # Total number of atoms in model: 44 # Number of atoms with 1.0 occupancy: 44 # Number of fragments in model: 1 # Number of METHOD records: 1 # No errors. # Number of Warnings: 44 ################################ # # # SUBMISSION # # # ################################ # # # BEGIN # # # ################################ PFRMAT TS TARGET T0140 AUTHOR 5035-2079-5263 METHOD CAFASP MODEL 3 PARENT 1SRO ATOM 1 CA GLY 59 17.499 11.108 0.818 1.00 1.00 ATOM 2 CA ASN 60 15.262 8.377 -0.667 1.00 1.00 ATOM 3 CA PRO 61 15.265 5.084 1.264 1.00 1.00 ATOM 4 CA GLN 62 16.444 1.461 0.964 1.00 1.00 ATOM 5 CA GLN 63 14.337 -1.509 -0.204 1.00 1.00 ATOM 6 CA GLY 64 13.973 -4.651 1.938 1.00 1.00 ATOM 7 CA ASP 65 12.853 -2.608 4.965 1.00 1.00 ATOM 8 CA ARG 66 9.345 -2.430 6.474 1.00 1.00 ATOM 9 CA VAL 67 7.167 0.651 5.870 1.00 1.00 ATOM 10 CA GLU 68 4.130 1.856 7.831 1.00 1.00 ATOM 11 CA GLY 69 1.701 2.522 4.968 1.00 1.00 ATOM 12 CA LYS 70 -0.845 5.172 5.995 1.00 1.00 ATOM 13 CA ILE 71 -4.092 5.480 4.036 1.00 1.00 ATOM 14 CA LYS 72 -4.040 8.718 2.031 1.00 1.00 ATOM 15 CA SER 73 -6.174 7.677 -0.978 1.00 1.00 ATOM 16 CA ILE 74 -8.474 4.850 -2.174 1.00 1.00 ATOM 17 CA THR 75 -9.854 3.822 -5.585 1.00 1.00 ATOM 18 CA ASP 76 -12.914 1.857 -6.774 1.00 1.00 ATOM 19 CA PHE 77 -10.557 -0.582 -8.554 1.00 1.00 ATOM 20 CA GLY 78 -8.196 -0.763 -5.543 1.00 1.00 ATOM 21 CA ILE 79 -6.696 1.528 -2.873 1.00 1.00 ATOM 22 CA PHE 80 -3.814 4.017 -2.727 1.00 1.00 ATOM 23 CA ILE 81 -1.403 4.489 0.200 1.00 1.00 ATOM 24 CA GLY 82 1.442 6.816 1.275 1.00 1.00 ATOM 25 CA LEU 83 4.438 6.427 3.638 1.00 1.00 ATOM 26 CA ASP 84 5.263 10.140 4.021 1.00 1.00 ATOM 27 CA GLY 85 8.768 11.468 3.270 1.00 1.00 ATOM 28 CA GLY 86 8.202 11.846 -0.494 1.00 1.00 ATOM 29 CA ILE 87 7.266 8.204 -1.174 1.00 1.00 ATOM 30 CA ASP 88 3.832 6.557 -1.216 1.00 1.00 ATOM 31 CA GLY 89 2.538 2.968 -1.346 1.00 1.00 ATOM 32 CA LEU 90 -0.554 1.512 -3.049 1.00 1.00 ATOM 33 CA VAL 91 -3.167 -0.951 -1.794 1.00 1.00 ATOM 34 CA HIS 92 -4.481 -1.848 -5.251 1.00 1.00 ATOM 35 CA LEU 93 -7.622 -4.025 -5.050 1.00 1.00 ATOM 36 CA SER 94 -5.519 -7.184 -5.555 1.00 1.00 ATOM 37 CA ASP 95 -3.106 -6.099 -2.780 1.00 1.00 ATOM 38 CA ILE 96 -4.788 -6.337 0.652 1.00 1.00 ATOM 39 CA SER 97 -4.997 -9.549 2.707 1.00 1.00 ATOM 40 CA TRP 98 -5.241 -13.251 1.807 1.00 1.00 ATOM 41 CA ALA 99 -8.978 -12.758 2.429 1.00 1.00 ATOM 42 CA GLN 100 -10.878 -11.640 -0.690 1.00 1.00 ATOM 43 CA ALA 101 -11.082 -7.843 -0.340 1.00 1.00 ATOM 44 CA GLU 102 -13.605 -7.305 -3.156 1.00 1.00 TER END ################################ # # # END # # # ################################