From mailer@bialko.llnl.gov Sat Jun 15 15:31:07 2002 Date: Sat, 15 Jun 2002 15:31:02 -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 15:04:32 PDT 2002 by Adam Zemla # # The PIN number of your submission is: PIN_156096_10769 # (PIN number is not an ACCESSION CODE) # YOUR SUBMISSION CANNOT BE ACCEPTED THE FORMAT OF YOUR PREDICTION IS NOT CORRECT The following is an error report generated by the CASP prediction verifier for one of your server submissions. The attached file is the version of your prediction that was processed. This has been preprocessed by CAFASP, adding the required CASP records, and in some cases, co-ordinates generated from alignments, using the standard CAFASP procedure. Please address the errors, add the following record to your model REMARK Corrected submission: PIN_number and submit the corrected file to submit@predictioncenter.llnl.gov Please ONLY change the records indicated as an ERROR. The returned file will be checked for consistency with the original (current PIN_number). A gentle reminder is that your prediction is not considered accepted as part of CAFASP until it has passed this verification process and a CASP server prediction accession number is issued. Any queries should be sent to casp5@predictioncenter.llnl.gov Please check the format required for submissions of CASP5 predictions: http://PredictionCenter.llnl.gov/casp5/doc/casp5-format.html ################################################################# # # # Each submission may contain only one model, beginning with # # the MODEL record, ending with END, and no target residue # # repetitions. # # # # All submissions should contain the records described below: # # # # PFRMAT Format specification # TS , AL , SS , DR or RR # # TARGET Target identifier from the CASP5 target table # # AUTHOR XXXX-XXXX-XXXX The Group Leader registration code # # REMARK Comment record (may appear anywhere, optional) # # METHOD Records describing the methods used # # MODEL Beginning of the data section for the submitted model # # PARENT Structure template used to generate the TS/AL model # # ------ data submitted as a model ------ # # TER Terminates independent segments of the TS/AL model # # END End of the submitted model # # # # In all submissions the standard keywords # # must begin in the first column of a record. # # # # Sometimes an error may arise due to a # # TAB separator used instead of a SPACE! # # # ################################################################# PLEASE CHECK THE OUTPUT FROM THE VERIFICATION SERVER BELOW # Reading prediction format SS PFRMAT SS TARGET T0131 AUTHOR 2491-6940-1261 # Reading MODEL 1 G S 0.370 # ERROR! Check the line NB = 12 in the MODEL section. # Check the SS format description. # Number of Warnings: 0 # Number of Errors: 1 ################################ # # # SUBMISSION # # # ################################ # # # BEGIN # # # ################################ PFRMAT SS TARGET T0131 AUTHOR 2491-6940-1261 METHOD CAFASP METHOD samt02_dssp METHOD Using neural net t2k-5740-IDaaHr-5-15-7-15-9-15-13-ebghstl-seeded.net METHOD This is a 4-layer network, with METHOD window units METHOD 5 15 METHOD 7 15 METHOD 9 15 METHOD 13 7 (1 EBGHSTL ) METHOD The input amino acid frequencies were determined from METHOD alignment T0131.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 12 METHOD MODEL 1 M C 0.998 S C 0.877 L C 0.491 K C 0.373 L E 0.464 V E 0.839 E E 0.955 I E 0.951 L E 0.980 V E 0.960 L E 0.734 G S 0.370 Q C 0.421 V E 0.720 L E 0.908 R E 0.890 L E 0.861 N E 0.462 V C 0.683 P C 0.793 I H 0.545 E H 0.611 Q H 0.751 E H 0.920 E H 0.924 L H 0.932 L H 0.974 R H 0.984 Q H 0.978 A H 0.973 A H 0.971 R H 0.929 N H 0.919 L H 0.911 D H 0.813 I H 0.869 L H 0.916 V H 0.965 S H 0.973 E H 0.964 M H 0.967 K H 0.940 E H 0.868 K H 0.627 T T 0.541 G C 0.304 L C 0.382 I C 0.438 Q C 0.387 L H 0.585 D H 0.757 R H 0.845 V H 0.897 L H 0.938 S H 0.972 I H 0.977 V H 0.991 A H 0.992 L H 0.993 N H 0.988 L H 0.985 S H 0.975 F H 0.945 E H 0.917 L H 0.896 S H 0.869 Q H 0.820 E H 0.829 K H 0.831 N H 0.750 K H 0.732 T H 0.710 A H 0.701 K H 0.685 I H 0.811 E H 0.915 E H 0.927 V H 0.940 L H 0.964 R H 0.974 T H 0.968 G H 0.968 I H 0.981 Q H 0.981 Q H 0.964 L H 0.941 D H 0.914 H H 0.873 S H 0.787 L H 0.811 E H 0.678 N H 0.580 I H 0.416 R C 0.294 V C 0.368 T C 0.529 K C 0.379 E C 0.552 P C 0.869 H C 0.996 END ################################ # # # END # # # ################################ From mailer@bialko.llnl.gov Sat Jun 15 15:31:18 2002 Date: Sat, 15 Jun 2002 15:31:12 -0700 (PDT) From: Automatic Reply To: karplus@soe.ucsc.edu X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK # # Protein Structure Prediction Center, LLNL, Livermore, CA # Verification system Sat Jun 15 15:04:45 PDT 2002 by Adam Zemla # # The PIN number of your submission is: PIN_157397_10770 # (PIN number is not an ACCESSION CODE) # YOUR SUBMISSION CANNOT BE ACCEPTED THE FORMAT OF YOUR PREDICTION IS NOT CORRECT The following is an error report generated by the CASP prediction verifier for one of your server submissions. The attached file is the version of your prediction that was processed. This has been preprocessed by CAFASP, adding the required CASP records, and in some cases, co-ordinates generated from alignments, using the standard CAFASP procedure. Please address the errors, add the following record to your model REMARK Corrected submission: PIN_number and submit the corrected file to submit@predictioncenter.llnl.gov Please ONLY change the records indicated as an ERROR. The returned file will be checked for consistency with the original (current PIN_number). A gentle reminder is that your prediction is not considered accepted as part of CAFASP until it has passed this verification process and a CASP server prediction accession number is issued. Any queries should be sent to casp5@predictioncenter.llnl.gov Please check the format required for submissions of CASP5 predictions: http://PredictionCenter.llnl.gov/casp5/doc/casp5-format.html ################################################################# # # # Each submission may contain only one model, beginning with # # the MODEL record, ending with END, and no target residue # # repetitions. # # # # All submissions should contain the records described below: # # # # PFRMAT Format specification # TS , AL , SS , DR or RR # # TARGET Target identifier from the CASP5 target table # # AUTHOR XXXX-XXXX-XXXX The Group Leader registration code # # REMARK Comment record (may appear anywhere, optional) # # METHOD Records describing the methods used # # MODEL Beginning of the data section for the submitted model # # PARENT Structure template used to generate the TS/AL model # # ------ data submitted as a model ------ # # TER Terminates independent segments of the TS/AL model # # END End of the submitted model # # # # In all submissions the standard keywords # # must begin in the first column of a record. # # # # Sometimes an error may arise due to a # # TAB separator used instead of a SPACE! # # # ################################################################# PLEASE CHECK THE OUTPUT FROM THE VERIFICATION SERVER BELOW # Reading prediction format SS PFRMAT SS TARGET T0131 AUTHOR 5144-8387-2760 # Reading MODEL 1 G T 0.530 # ERROR! Check the line NB = 12 in the MODEL section. # Check the SS format description. # Number of Warnings: 0 # Number of Errors: 1 ################################ # # # SUBMISSION # # # ################################ # # # BEGIN # # # ################################ PFRMAT SS TARGET T0131 AUTHOR 5144-8387-2760 METHOD CAFASP METHOD samt02_stride METHOD Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-ebghtl-seeded.net METHOD This is a 4-layer network, with METHOD window units METHOD 5 15 METHOD 7 15 METHOD 9 15 METHOD 13 6 (1 EBGHTL ) METHOD The input amino acid frequencies were determined from METHOD alignment T0131.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 12 METHOD MODEL 1 M C 0.757 S C 0.593 L C 0.394 K E 0.409 L E 0.717 V E 0.863 E E 0.946 I E 0.973 L E 0.969 V E 0.919 L E 0.514 G T 0.530 Q E 0.638 V E 0.840 L E 0.885 R E 0.810 L E 0.762 N E 0.611 V C 0.697 P C 0.591 I H 0.820 E H 0.809 Q H 0.833 E H 0.925 E H 0.927 L H 0.943 L H 0.965 R H 0.987 Q H 0.988 A H 0.990 A H 0.978 R H 0.951 N H 0.899 L H 0.899 D H 0.854 I H 0.895 L H 0.925 V H 0.983 S H 0.985 E H 0.990 M H 0.986 K H 0.979 E H 0.957 K H 0.849 T H 0.614 G C 0.497 L T 0.405 I C 0.338 Q T 0.406 L H 0.945 D H 0.976 R H 0.985 V H 0.985 L H 0.990 S H 0.988 I H 0.992 V H 0.994 A H 0.994 L H 0.987 N H 0.981 L H 0.983 S H 0.981 F H 0.970 E H 0.956 L H 0.966 S H 0.942 Q H 0.946 E H 0.942 K H 0.917 N H 0.886 K H 0.828 T H 0.805 A H 0.708 K H 0.630 I H 0.893 E H 0.930 E H 0.934 V H 0.965 L H 0.985 R H 0.989 T H 0.985 G H 0.979 I H 0.987 Q H 0.980 Q H 0.974 L H 0.969 D H 0.951 H H 0.884 S H 0.676 L H 0.739 E H 0.708 N H 0.564 I H 0.428 R C 0.312 V E 0.353 T C 0.408 K C 0.411 E C 0.552 P C 0.733 H C 0.975 END ################################ # # # END # # # ################################ From mailer@bialko.llnl.gov Wed Jun 26 12:10:08 2002 Date: Wed, 26 Jun 2002 12:10:02 -0700 (PDT) From: Automatic Reply To: karplus@soe.ucsc.edu Subject: T0131 TS samt02.pdb 1 X-SpamBouncer: 1.4 (10/07/01) X-SBNote: From Admin X-SBNote: FROM_DAEMON/Listserv X-SBPass: No Freemail Filtering X-SBClass: Admin # # Protein Structure Prediction Center, LLNL, Livermore, CA # Verification system Wed Jun 26 11:43:15 PDT 2002 by Adam Zemla # # The PIN number of your submission is: PIN_546149_10996 # (PIN number is not an ACCESSION CODE) # Thank you for your submission. Your prediction has been accepted with an ACCESSION CODE: T0131TS189_1 Current information on models submitted in prediction T0131TS189 MODEL_INDEX PIN CODE DATE E-mail T0131TS189_1 PIN_546149_10996 5035-2079-5263 06/26/02 11:43:15 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 T0131 MODEL_INDEX PIN CODE DATE E-mail T0131TS189_1 PIN_546149_10996 5035-2079-5263 06/26/02 11:43:15 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 T0131 AUTHOR 5035-2079-5263 # Reading MODEL 1 PARENT 1AFR_A # Loading PARENT structure: 1afr (chain: A) # Number of residues in PARENT structure: 345 # Reading prediction format TS (DONE) # Checking the TS prediction MODEL 1 # IMPORTANT NOTE! Not complete main chain atoms for residue V 19 # !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! # # 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 P 20 # IMPORTANT NOTE! Not complete main chain atoms for residue I 21 # IMPORTANT NOTE! Not complete main chain atoms for residue E 22 # IMPORTANT NOTE! Not complete main chain atoms for residue Q 23 # IMPORTANT NOTE! Not complete main chain atoms for residue E 24 # IMPORTANT NOTE! Not complete main chain atoms for residue E 25 # IMPORTANT NOTE! Not complete main chain atoms for residue L 26 # IMPORTANT NOTE! Not complete main chain atoms for residue L 27 # IMPORTANT NOTE! Not complete main chain atoms for residue R 28 # IMPORTANT NOTE! Not complete main chain atoms for residue Q 29 # IMPORTANT NOTE! Not complete main chain atoms for residue A 30 # IMPORTANT NOTE! Not complete main chain atoms for residue A 31 # IMPORTANT NOTE! Not complete main chain atoms for residue R 32 # IMPORTANT NOTE! Not complete main chain atoms for residue N 33 # IMPORTANT NOTE! Not complete main chain atoms for residue L 34 # IMPORTANT NOTE! Not complete main chain atoms for residue D 35 # IMPORTANT NOTE! Not complete main chain atoms for residue I 36 # IMPORTANT NOTE! Not complete main chain atoms for residue L 37 # IMPORTANT NOTE! Not complete main chain atoms for residue V 38 # IMPORTANT NOTE! Not complete main chain atoms for residue S 39 # IMPORTANT NOTE! Not complete main chain atoms for residue E 40 # IMPORTANT NOTE! Not complete main chain atoms for residue M 41 # IMPORTANT NOTE! Not complete main chain atoms for residue K 42 # IMPORTANT NOTE! Not complete main chain atoms for residue E 43 # IMPORTANT NOTE! Not complete main chain atoms for residue K 44 # IMPORTANT NOTE! Not complete main chain atoms for residue T 45 # IMPORTANT NOTE! Not complete main chain atoms for residue G 46 # IMPORTANT NOTE! Not complete main chain atoms for residue L 47 # IMPORTANT NOTE! Not complete main chain atoms for residue I 48 # IMPORTANT NOTE! Not complete main chain atoms for residue Q 49 # IMPORTANT NOTE! Not complete main chain atoms for residue L 50 # IMPORTANT NOTE! Not complete main chain atoms for residue D 51 # IMPORTANT NOTE! Not complete main chain atoms for residue R 52 # IMPORTANT NOTE! Not complete main chain atoms for residue V 53 # IMPORTANT NOTE! Not complete main chain atoms for residue L 54 # IMPORTANT NOTE! Not complete main chain atoms for residue S 55 # IMPORTANT NOTE! Not complete main chain atoms for residue I 56 # IMPORTANT NOTE! Not complete main chain atoms for residue V 57 # IMPORTANT NOTE! Not complete main chain atoms for residue A 58 # IMPORTANT NOTE! Not complete main chain atoms for residue L 59 # IMPORTANT NOTE! Not complete main chain atoms for residue N 60 # IMPORTANT NOTE! Not complete main chain atoms for residue L 61 # IMPORTANT NOTE! Not complete main chain atoms for residue S 62 # IMPORTANT NOTE! Not complete main chain atoms for residue F 63 # IMPORTANT NOTE! Not complete main chain atoms for residue E 64 # Checking the TS prediction MODEL 1 (DONE) # MODEL index: 1 # Target name: T0131 # Total number of residues in target: 100 # Total number of residues in model: 46 # Total number of atoms in model: 46 # Number of atoms with 1.0 occupancy: 46 # Number of fragments in model: 1 # Number of METHOD records: 1 # No errors. # Number of Warnings: 46 ################################ # # # SUBMISSION # # # ################################ # # # BEGIN # # # ################################ PFRMAT TS TARGET T0131 AUTHOR 5035-2079-5263 METHOD CAFASP MODEL 1 PARENT 1AFR_A ATOM 61 CA VAL 19 81.146 19.390 15.387 1.00 1.00 ATOM 62 CA PRO 20 79.090 18.291 18.387 1.00 1.00 ATOM 63 CA ILE 21 76.552 15.554 17.667 1.00 1.00 ATOM 64 CA GLU 22 73.177 14.982 19.398 1.00 1.00 ATOM 65 CA GLN 23 74.574 11.893 21.174 1.00 1.00 ATOM 66 CA GLU 24 76.978 14.213 22.970 1.00 1.00 ATOM 67 CA GLU 25 74.111 15.561 25.058 1.00 1.00 ATOM 68 CA LEU 26 71.785 12.572 25.417 1.00 1.00 ATOM 69 CA LEU 27 71.847 9.470 27.597 1.00 1.00 ATOM 70 CA ARG 28 74.281 6.930 26.175 1.00 1.00 ATOM 71 CA GLN 29 72.377 3.781 25.120 1.00 1.00 ATOM 72 CA ALA 30 75.614 1.828 24.894 1.00 1.00 ATOM 73 CA ALA 31 76.632 2.604 28.479 1.00 1.00 ATOM 74 CA ARG 32 75.874 0.820 31.764 1.00 1.00 ATOM 75 CA ASN 33 74.652 4.159 33.046 1.00 1.00 ATOM 76 CA LEU 34 71.917 4.485 30.400 1.00 1.00 ATOM 77 CA ASP 35 69.050 3.680 32.798 1.00 1.00 ATOM 78 CA ILE 36 70.064 6.022 35.588 1.00 1.00 ATOM 79 CA LEU 37 70.833 8.687 32.968 1.00 1.00 ATOM 80 CA VAL 38 67.322 8.406 31.518 1.00 1.00 ATOM 81 CA SER 39 65.785 8.291 35.019 1.00 1.00 ATOM 82 CA GLU 40 67.621 11.476 36.049 1.00 1.00 ATOM 83 CA MET 41 66.679 13.234 32.826 1.00 1.00 ATOM 84 CA LYS 42 63.051 12.414 33.648 1.00 1.00 ATOM 85 CA GLU 43 63.208 13.491 37.303 1.00 1.00 ATOM 86 CA LYS 44 64.615 16.920 36.379 1.00 1.00 ATOM 87 CA THR 45 61.901 17.255 33.689 1.00 1.00 ATOM 88 CA GLY 46 59.196 17.051 36.357 1.00 1.00 ATOM 89 CA LEU 47 60.690 20.207 37.931 1.00 1.00 ATOM 90 CA ILE 48 60.174 21.993 34.592 1.00 1.00 ATOM 91 CA GLN 49 56.718 23.581 34.173 1.00 1.00 ATOM 92 CA LEU 50 54.358 22.949 31.236 1.00 1.00 ATOM 93 CA ASP 51 54.725 26.608 30.251 1.00 1.00 ATOM 94 CA ARG 52 58.361 26.002 29.396 1.00 1.00 ATOM 95 CA VAL 53 57.571 22.757 27.568 1.00 1.00 ATOM 96 CA LEU 54 55.063 24.411 25.223 1.00 1.00 ATOM 97 CA SER 55 57.788 26.879 24.156 1.00 1.00 ATOM 98 CA ILE 56 60.473 24.229 23.957 1.00 1.00 ATOM 99 CA VAL 57 58.115 22.121 21.796 1.00 1.00 ATOM 100 CA ALA 58 57.343 25.033 19.492 1.00 1.00 ATOM 101 CA LEU 59 61.065 25.629 19.046 1.00 1.00 ATOM 102 CA ASN 60 61.626 21.921 18.311 1.00 1.00 ATOM 103 CA LEU 61 58.790 21.796 15.747 1.00 1.00 ATOM 104 CA SER 62 60.259 24.770 13.918 1.00 1.00 ATOM 105 CA PHE 63 63.680 23.038 13.784 1.00 1.00 ATOM 106 CA GLU 64 62.189 19.796 12.478 1.00 1.00 TER END ################################ # # # END # # # ################################ From mailer@bialko.llnl.gov Wed Jun 26 12:10:18 2002 Date: Wed, 26 Jun 2002 12:10:13 -0700 (PDT) From: Automatic Reply To: karplus@soe.ucsc.edu Subject: T0131 TS samt02.pdb 2 X-SpamBouncer: 1.4 (10/07/01) X-SBNote: From Admin X-SBNote: FROM_DAEMON/Listserv X-SBPass: No Freemail Filtering X-SBClass: Admin # # Protein Structure Prediction Center, LLNL, Livermore, CA # Verification system Wed Jun 26 11:43:29 PDT 2002 by Adam Zemla # # The PIN number of your submission is: PIN_551168_10997 # (PIN number is not an ACCESSION CODE) # Thank you for your submission. Your prediction has been accepted with an ACCESSION CODE: T0131TS189_2 Current information on models submitted in prediction T0131TS189 MODEL_INDEX PIN CODE DATE E-mail T0131TS189_2 PIN_551168_10997 5035-2079-5263 06/26/02 11:43:29 casp5@bialko.llnl.gov T0131TS189_1 PIN_546149_10996 5035-2079-5263 06/26/02 11:43:15 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 T0131 MODEL_INDEX PIN CODE DATE E-mail T0131TS189_1 PIN_546149_10996 5035-2079-5263 06/26/02 11:43:15 casp5@bialko.llnl.gov T0131TS189_2 PIN_551168_10997 5035-2079-5263 06/26/02 11:43:29 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 T0131 AUTHOR 5035-2079-5263 # Reading MODEL 2 PARENT 1NSE_A # Loading PARENT structure: 1nse (chain: A) # Number of residues in PARENT structure: 416 # 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 S 2 # IMPORTANT NOTE! Not complete main chain atoms for residue L 3 # IMPORTANT NOTE! Not complete main chain atoms for residue K 4 # IMPORTANT NOTE! Not complete main chain atoms for residue L 5 # IMPORTANT NOTE! Not complete main chain atoms for residue V 6 # IMPORTANT NOTE! Not complete main chain atoms for residue E 7 # IMPORTANT NOTE! Not complete main chain atoms for residue I 8 # IMPORTANT NOTE! Not complete main chain atoms for residue L 9 # IMPORTANT NOTE! Not complete main chain atoms for residue V 10 # IMPORTANT NOTE! Not complete main chain atoms for residue L 11 # IMPORTANT NOTE! Not complete main chain atoms for residue G 12 # IMPORTANT NOTE! Not complete main chain atoms for residue Q 13 # IMPORTANT NOTE! Not complete main chain atoms for residue V 14 # IMPORTANT NOTE! Not complete main chain atoms for residue L 15 # IMPORTANT NOTE! Not complete main chain atoms for residue R 16 # IMPORTANT NOTE! Not complete main chain atoms for residue L 17 # IMPORTANT NOTE! Not complete main chain atoms for residue N 18 # IMPORTANT NOTE! Not complete main chain atoms for residue V 19 # IMPORTANT NOTE! Not complete main chain atoms for residue P 20 # IMPORTANT NOTE! Not complete main chain atoms for residue I 21 # IMPORTANT NOTE! Not complete main chain atoms for residue E 22 # IMPORTANT NOTE! Not complete main chain atoms for residue Q 23 # IMPORTANT NOTE! Not complete main chain atoms for residue E 24 # IMPORTANT NOTE! Not complete main chain atoms for residue E 25 # IMPORTANT NOTE! Not complete main chain atoms for residue L 26 # IMPORTANT NOTE! Not complete main chain atoms for residue L 27 # IMPORTANT NOTE! Not complete main chain atoms for residue R 28 # IMPORTANT NOTE! Not complete main chain atoms for residue Q 29 # IMPORTANT NOTE! Not complete main chain atoms for residue A 30 # IMPORTANT NOTE! Not complete main chain atoms for residue A 31 # IMPORTANT NOTE! Not complete main chain atoms for residue R 32 # IMPORTANT NOTE! Not complete main chain atoms for residue N 33 # IMPORTANT NOTE! Not complete main chain atoms for residue L 34 # IMPORTANT NOTE! Not complete main chain atoms for residue D 35 # IMPORTANT NOTE! Not complete main chain atoms for residue I 36 # IMPORTANT NOTE! Not complete main chain atoms for residue L 37 # IMPORTANT NOTE! Not complete main chain atoms for residue V 38 # IMPORTANT NOTE! Not complete main chain atoms for residue S 39 # IMPORTANT NOTE! Not complete main chain atoms for residue E 40 # IMPORTANT NOTE! Not complete main chain atoms for residue M 41 # IMPORTANT NOTE! Not complete main chain atoms for residue K 42 # IMPORTANT NOTE! Not complete main chain atoms for residue E 43 # IMPORTANT NOTE! Not complete main chain atoms for residue K 44 # IMPORTANT NOTE! Not complete main chain atoms for residue T 45 # IMPORTANT NOTE! Not complete main chain atoms for residue G 46 # IMPORTANT NOTE! Not complete main chain atoms for residue L 47 # IMPORTANT NOTE! Not complete main chain atoms for residue I 48 # IMPORTANT NOTE! Not complete main chain atoms for residue Q 49 # IMPORTANT NOTE! Not complete main chain atoms for residue L 50 # IMPORTANT NOTE! Not complete main chain atoms for residue D 51 # IMPORTANT NOTE! Not complete main chain atoms for residue R 52 # IMPORTANT NOTE! Not complete main chain atoms for residue V 53 # IMPORTANT NOTE! Not complete main chain atoms for residue L 54 # IMPORTANT NOTE! Not complete main chain atoms for residue S 55 # IMPORTANT NOTE! Not complete main chain atoms for residue I 56 # IMPORTANT NOTE! Not complete main chain atoms for residue V 57 # IMPORTANT NOTE! Not complete main chain atoms for residue A 58 # IMPORTANT NOTE! Not complete main chain atoms for residue L 59 # IMPORTANT NOTE! Not complete main chain atoms for residue N 60 # IMPORTANT NOTE! Not complete main chain atoms for residue L 61 # IMPORTANT NOTE! Not complete main chain atoms for residue S 62 # IMPORTANT NOTE! Not complete main chain atoms for residue F 63 # IMPORTANT NOTE! Not complete main chain atoms for residue E 64 # IMPORTANT NOTE! Not complete main chain atoms for residue L 65 # IMPORTANT NOTE! Not complete main chain atoms for residue S 66 # IMPORTANT NOTE! Not complete main chain atoms for residue Q 67 # IMPORTANT NOTE! Not complete main chain atoms for residue E 68 # IMPORTANT NOTE! Not complete main chain atoms for residue K 69 # IMPORTANT NOTE! Not complete main chain atoms for residue N 70 # IMPORTANT NOTE! Not complete main chain atoms for residue K 71 # IMPORTANT NOTE! Not complete main chain atoms for residue T 72 # IMPORTANT NOTE! Not complete main chain atoms for residue A 73 # IMPORTANT NOTE! Not complete main chain atoms for residue K 74 # IMPORTANT NOTE! Not complete main chain atoms for residue I 75 # IMPORTANT NOTE! Not complete main chain atoms for residue E 76 # IMPORTANT NOTE! Not complete main chain atoms for residue E 77 # IMPORTANT NOTE! Not complete main chain atoms for residue V 78 # IMPORTANT NOTE! Not complete main chain atoms for residue L 79 # IMPORTANT NOTE! Not complete main chain atoms for residue R 80 # IMPORTANT NOTE! Not complete main chain atoms for residue T 81 # IMPORTANT NOTE! Not complete main chain atoms for residue G 82 # IMPORTANT NOTE! Not complete main chain atoms for residue I 83 # IMPORTANT NOTE! Not complete main chain atoms for residue Q 84 # IMPORTANT NOTE! Not complete main chain atoms for residue Q 85 # IMPORTANT NOTE! Not complete main chain atoms for residue L 86 # IMPORTANT NOTE! Not complete main chain atoms for residue D 87 # IMPORTANT NOTE! Not complete main chain atoms for residue H 88 # IMPORTANT NOTE! Not complete main chain atoms for residue S 89 # IMPORTANT NOTE! Not complete main chain atoms for residue L 90 # IMPORTANT NOTE! Not complete main chain atoms for residue E 91 # IMPORTANT NOTE! Not complete main chain atoms for residue N 92 # IMPORTANT NOTE! Not complete main chain atoms for residue I 93 # IMPORTANT NOTE! Not complete main chain atoms for residue R 94 # IMPORTANT NOTE! Not complete main chain atoms for residue V 95 # IMPORTANT NOTE! Not complete main chain atoms for residue T 96 # IMPORTANT NOTE! Not complete main chain atoms for residue K 97 # IMPORTANT NOTE! Not complete main chain atoms for residue E 98 # IMPORTANT NOTE! Not complete main chain atoms for residue P 99 # IMPORTANT NOTE! Not complete main chain atoms for residue H 100 # Checking the TS prediction MODEL 2 (DONE) # MODEL index: 2 # Target name: T0131 # Total number of residues in target: 100 # Total number of residues in model: 100 # Total number of atoms in model: 100 # Number of atoms with 1.0 occupancy: 100 # Number of fragments in model: 1 # Number of METHOD records: 1 # No errors. # Number of Warnings: 100 ################################ # # # SUBMISSION # # # ################################ # # # BEGIN # # # ################################ PFRMAT TS TARGET T0131 AUTHOR 5035-2079-5263 METHOD CAFASP MODEL 2 PARENT 1NSE_A ATOM 67 CA MET 1 8.638 -18.910 53.218 1.00 1.00 ATOM 68 CA SER 2 10.202 -18.026 49.868 1.00 1.00 ATOM 70 CA LEU 3 12.497 -13.336 48.357 1.00 1.00 ATOM 71 CA LYS 4 10.956 -10.051 49.509 1.00 1.00 ATOM 72 CA LEU 5 7.378 -10.567 50.611 1.00 1.00 ATOM 73 CA VAL 6 5.275 -7.676 49.306 1.00 1.00 ATOM 74 CA GLU 7 1.897 -6.662 50.687 1.00 1.00 ATOM 75 CA ILE 8 -1.043 -4.566 49.531 1.00 1.00 ATOM 100 CA LEU 9 20.607 2.688 56.426 1.00 1.00 ATOM 101 CA VAL 10 18.091 3.214 53.648 1.00 1.00 ATOM 102 CA LEU 11 18.825 5.847 51.018 1.00 1.00 ATOM 103 CA GLY 12 15.595 5.202 49.095 1.00 1.00 ATOM 104 CA GLN 13 14.451 8.837 49.204 1.00 1.00 ATOM 105 CA VAL 14 17.600 10.310 47.609 1.00 1.00 ATOM 106 CA LEU 15 17.053 11.742 44.129 1.00 1.00 ATOM 107 CA ARG 16 20.574 11.104 42.890 1.00 1.00 ATOM 116 CA LEU 17 33.653 6.997 30.448 1.00 1.00 ATOM 117 CA ASN 18 36.574 8.961 29.046 1.00 1.00 ATOM 118 CA VAL 19 37.972 5.458 28.414 1.00 1.00 ATOM 119 CA PRO 20 36.376 2.365 26.805 1.00 1.00 ATOM 120 CA ILE 21 34.864 -0.047 29.316 1.00 1.00 ATOM 121 CA GLU 22 37.171 -3.007 30.042 1.00 1.00 ATOM 122 CA GLN 23 36.547 -5.659 27.411 1.00 1.00 ATOM 123 CA GLU 24 35.816 -8.271 30.034 1.00 1.00 ATOM 124 CA GLU 25 33.342 -6.014 31.784 1.00 1.00 ATOM 125 CA LEU 26 31.775 -5.120 28.457 1.00 1.00 ATOM 126 CA LEU 27 31.387 -8.700 27.290 1.00 1.00 ATOM 127 CA ARG 28 29.624 -10.010 30.408 1.00 1.00 ATOM 128 CA GLN 29 27.124 -7.154 30.082 1.00 1.00 ATOM 129 CA ALA 30 26.813 -7.853 26.371 1.00 1.00 ATOM 130 CA ALA 31 26.352 -11.600 26.800 1.00 1.00 ATOM 131 CA ARG 32 23.725 -10.983 29.462 1.00 1.00 ATOM 132 CA ASN 33 21.792 -8.660 27.188 1.00 1.00 ATOM 133 CA LEU 34 22.092 -11.037 24.262 1.00 1.00 ATOM 134 CA ASP 35 20.770 -13.823 26.485 1.00 1.00 ATOM 135 CA ILE 36 17.866 -11.524 27.311 1.00 1.00 ATOM 136 CA LEU 37 17.148 -10.894 23.663 1.00 1.00 ATOM 137 CA VAL 38 17.142 -14.591 22.734 1.00 1.00 ATOM 138 CA SER 39 14.962 -15.502 25.728 1.00 1.00 ATOM 139 CA GLU 40 12.449 -12.861 24.679 1.00 1.00 ATOM 140 CA MET 41 12.047 -14.376 21.222 1.00 1.00 ATOM 141 CA LYS 42 12.191 -17.831 22.838 1.00 1.00 ATOM 142 CA GLU 43 15.301 -19.097 21.013 1.00 1.00 ATOM 143 CA LYS 44 17.505 -19.396 24.055 1.00 1.00 ATOM 162 CA THR 45 37.581 -3.381 18.049 1.00 1.00 ATOM 163 CA GLY 46 36.874 -3.158 21.789 1.00 1.00 ATOM 164 CA LEU 47 33.178 -2.518 21.163 1.00 1.00 ATOM 165 CA ILE 48 30.216 -4.027 19.362 1.00 1.00 ATOM 166 CA GLN 49 26.987 -3.048 17.610 1.00 1.00 ATOM 167 CA LEU 50 23.340 -3.966 18.091 1.00 1.00 ATOM 168 CA ASP 51 21.064 -5.417 15.430 1.00 1.00 ATOM 169 CA ARG 52 17.998 -3.282 14.754 1.00 1.00 ATOM 170 CA VAL 53 15.587 -5.630 16.525 1.00 1.00 ATOM 171 CA LEU 54 17.924 -5.839 19.509 1.00 1.00 ATOM 172 CA SER 55 17.845 -2.027 19.850 1.00 1.00 ATOM 173 CA ILE 56 14.026 -1.998 19.723 1.00 1.00 ATOM 174 CA VAL 57 13.891 -4.711 22.408 1.00 1.00 ATOM 175 CA ALA 58 16.495 -3.053 24.595 1.00 1.00 ATOM 176 CA LEU 59 14.752 0.323 24.415 1.00 1.00 ATOM 310 CA ASN 60 4.214 25.247 14.857 1.00 1.00 ATOM 311 CA LEU 61 5.933 22.092 16.019 1.00 1.00 ATOM 312 CA SER 62 5.653 22.877 19.714 1.00 1.00 ATOM 313 CA PHE 63 2.035 22.313 20.697 1.00 1.00 ATOM 314 CA GLU 64 0.958 24.286 23.770 1.00 1.00 ATOM 315 CA LEU 65 -2.271 24.363 25.796 1.00 1.00 ATOM 316 CA SER 66 -3.505 27.620 27.329 1.00 1.00 ATOM 317 CA GLN 67 -4.902 26.867 30.793 1.00 1.00 ATOM 318 CA GLU 68 -8.472 27.617 31.697 1.00 1.00 ATOM 319 CA LYS 69 -10.759 26.318 34.460 1.00 1.00 ATOM 320 CA ASN 70 -14.189 24.732 33.871 1.00 1.00 ATOM 321 CA LYS 71 -16.105 26.965 36.290 1.00 1.00 ATOM 322 CA THR 72 -13.697 29.652 37.534 1.00 1.00 ATOM 376 CA ALA 73 5.105 28.803 42.557 1.00 1.00 ATOM 377 CA LYS 74 1.531 29.901 41.771 1.00 1.00 ATOM 378 CA ILE 75 -0.264 28.564 44.860 1.00 1.00 ATOM 379 CA GLU 76 -0.649 31.897 46.619 1.00 1.00 ATOM 380 CA GLU 77 -1.659 33.696 43.425 1.00 1.00 ATOM 381 CA VAL 78 -4.489 31.281 42.773 1.00 1.00 ATOM 413 CA LEU 79 -9.294 17.730 27.344 1.00 1.00 ATOM 414 CA ARG 80 -10.851 20.788 25.675 1.00 1.00 ATOM 415 CA THR 81 -7.773 21.188 23.455 1.00 1.00 ATOM 416 CA GLY 82 -8.039 17.419 22.785 1.00 1.00 ATOM 417 CA ILE 83 -4.432 16.821 23.812 1.00 1.00 ATOM 418 CA GLN 84 -3.583 13.523 25.509 1.00 1.00 ATOM 419 CA GLN 85 -3.409 13.592 29.295 1.00 1.00 ATOM 420 CA LEU 86 -3.960 11.172 32.187 1.00 1.00 ATOM 421 CA ASP 87 -5.156 12.151 35.667 1.00 1.00 ATOM 422 CA HIS 88 -3.300 10.693 38.671 1.00 1.00 ATOM 423 CA SER 89 -6.213 8.423 39.641 1.00 1.00 ATOM 424 CA LEU 90 -6.442 6.823 36.231 1.00 1.00 ATOM 425 CA GLU 91 -2.655 6.578 35.970 1.00 1.00 ATOM 474 CA ASN 92 18.337 0.945 31.746 1.00 1.00 ATOM 475 CA ILE 93 17.712 4.669 31.580 1.00 1.00 ATOM 476 CA ARG 94 20.478 6.259 33.703 1.00 1.00 ATOM 477 CA VAL 95 21.362 9.782 34.811 1.00 1.00 ATOM 478 CA THR 96 24.684 11.073 33.384 1.00 1.00 ATOM 479 CA LYS 97 26.779 14.147 34.121 1.00 1.00 ATOM 480 CA GLU 98 26.088 17.484 32.468 1.00 1.00 ATOM 481 CA PRO 99 28.188 17.928 29.315 1.00 1.00 ATOM 482 CA HIS 100 29.489 21.342 30.386 1.00 1.00 TER END ################################ # # # END # # # ################################ From mailer@bialko.llnl.gov Wed Jun 26 12:11:18 2002 Date: Wed, 26 Jun 2002 12:11:12 -0700 (PDT) From: Automatic Reply To: karplus@soe.ucsc.edu Subject: T0131 TS samt02.pdb 3 X-SpamBouncer: 1.4 (10/07/01) X-SBNote: From Admin X-SBNote: FROM_DAEMON/Listserv X-SBPass: No Freemail Filtering X-SBClass: Admin # # Protein Structure Prediction Center, LLNL, Livermore, CA # Verification system Wed Jun 26 11:44:24 PDT 2002 by Adam Zemla # # The PIN number of your submission is: PIN_556250_11001 # (PIN number is not an ACCESSION CODE) # Thank you for your submission. Your prediction has been accepted with an ACCESSION CODE: T0131TS189_3 Current information on models submitted in prediction T0131TS189 MODEL_INDEX PIN CODE DATE E-mail T0131TS189_3 PIN_556250_11001 5035-2079-5263 06/26/02 11:44:24 casp5@bialko.llnl.gov T0131TS189_2 PIN_551168_10997 5035-2079-5263 06/26/02 11:43:29 casp5@bialko.llnl.gov T0131TS189_1 PIN_546149_10996 5035-2079-5263 06/26/02 11:43:15 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 T0131 MODEL_INDEX PIN CODE DATE E-mail T0131TS189_1 PIN_546149_10996 5035-2079-5263 06/26/02 11:43:15 casp5@bialko.llnl.gov T0131TS189_2 PIN_551168_10997 5035-2079-5263 06/26/02 11:43:29 casp5@bialko.llnl.gov T0131TS189_3 PIN_556250_11001 5035-2079-5263 06/26/02 11:44:24 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 T0131 AUTHOR 5035-2079-5263 # Reading MODEL 3 PARENT 1D0C_A # Loading PARENT structure: 1d0c (chain: A) # Number of residues in PARENT structure: 416 # Reading prediction format TS (DONE) # Checking the TS prediction MODEL 3 # IMPORTANT NOTE! Not complete main chain atoms for residue P 20 # !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! # # It is requested that coordinate data be supplied for at least # # all non-hydrogen main chain atoms, i.e. the N, CA, C and O # # atoms of every residue. Specifically, if only CA atoms are # # predicted by the method, predictors are encouraged to build # # the main chain atoms for every residue before submission to # # CASP. If only CA atoms were submitted it would not be possible # # to run most of the analysis software, which would severely # # limit the evaluation of that prediction. # # !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! # # IMPORTANT NOTE! Not complete main chain atoms for residue I 21 # IMPORTANT NOTE! Not complete main chain atoms for residue E 22 # IMPORTANT NOTE! Not complete main chain atoms for residue Q 23 # IMPORTANT NOTE! Not complete main chain atoms for residue E 24 # IMPORTANT NOTE! Not complete main chain atoms for residue E 25 # IMPORTANT NOTE! Not complete main chain atoms for residue L 26 # IMPORTANT NOTE! Not complete main chain atoms for residue L 27 # IMPORTANT NOTE! Not complete main chain atoms for residue R 28 # IMPORTANT NOTE! Not complete main chain atoms for residue Q 29 # IMPORTANT NOTE! Not complete main chain atoms for residue A 30 # IMPORTANT NOTE! Not complete main chain atoms for residue A 31 # IMPORTANT NOTE! Not complete main chain atoms for residue R 32 # IMPORTANT NOTE! Not complete main chain atoms for residue N 33 # IMPORTANT NOTE! Not complete main chain atoms for residue L 34 # IMPORTANT NOTE! Not complete main chain atoms for residue D 35 # IMPORTANT NOTE! Not complete main chain atoms for residue I 36 # IMPORTANT NOTE! Not complete main chain atoms for residue L 37 # IMPORTANT NOTE! Not complete main chain atoms for residue V 38 # IMPORTANT NOTE! Not complete main chain atoms for residue S 39 # IMPORTANT NOTE! Not complete main chain atoms for residue E 40 # IMPORTANT NOTE! Not complete main chain atoms for residue M 41 # IMPORTANT NOTE! Not complete main chain atoms for residue K 42 # IMPORTANT NOTE! Not complete main chain atoms for residue E 43 # IMPORTANT NOTE! Not complete main chain atoms for residue K 44 # IMPORTANT NOTE! Not complete main chain atoms for residue T 45 # IMPORTANT NOTE! Not complete main chain atoms for residue G 46 # IMPORTANT NOTE! Not complete main chain atoms for residue L 47 # IMPORTANT NOTE! Not complete main chain atoms for residue I 48 # IMPORTANT NOTE! Not complete main chain atoms for residue Q 49 # IMPORTANT NOTE! Not complete main chain atoms for residue L 50 # IMPORTANT NOTE! Not complete main chain atoms for residue D 51 # IMPORTANT NOTE! Not complete main chain atoms for residue R 52 # IMPORTANT NOTE! Not complete main chain atoms for residue V 53 # Checking the TS prediction MODEL 3 (DONE) # MODEL index: 3 # Target name: T0131 # Total number of residues in target: 100 # Total number of residues in model: 34 # Total number of atoms in model: 34 # Number of atoms with 1.0 occupancy: 34 # Number of fragments in model: 1 # Number of METHOD records: 1 # No errors. # Number of Warnings: 34 ################################ # # # SUBMISSION # # # ################################ # # # BEGIN # # # ################################ PFRMAT TS TARGET T0131 AUTHOR 5035-2079-5263 METHOD CAFASP MODEL 3 PARENT 1D0C_A ATOM 119 CA PRO 20 35.918 2.201 26.353 1.00 1.00 ATOM 120 CA ILE 21 34.824 -0.147 29.120 1.00 1.00 ATOM 121 CA GLU 22 37.072 -2.893 30.438 1.00 1.00 ATOM 122 CA GLN 23 36.793 -5.533 27.729 1.00 1.00 ATOM 123 CA GLU 24 35.648 -8.057 30.330 1.00 1.00 ATOM 124 CA GLU 25 33.200 -5.690 32.044 1.00 1.00 ATOM 125 CA LEU 26 31.691 -4.738 28.678 1.00 1.00 ATOM 126 CA LEU 27 31.689 -8.370 27.579 1.00 1.00 ATOM 127 CA ARG 28 29.910 -9.457 30.748 1.00 1.00 ATOM 128 CA GLN 29 27.223 -6.825 30.173 1.00 1.00 ATOM 129 CA ALA 30 26.973 -7.640 26.465 1.00 1.00 ATOM 130 CA ALA 31 26.611 -11.380 27.070 1.00 1.00 ATOM 131 CA ARG 32 23.881 -10.729 29.596 1.00 1.00 ATOM 132 CA ASN 33 22.062 -8.449 27.209 1.00 1.00 ATOM 133 CA LEU 34 22.296 -10.853 24.321 1.00 1.00 ATOM 134 CA ASP 35 21.021 -13.584 26.594 1.00 1.00 ATOM 135 CA ILE 36 18.026 -11.411 27.497 1.00 1.00 ATOM 136 CA LEU 37 17.380 -10.778 23.826 1.00 1.00 ATOM 137 CA VAL 38 17.404 -14.456 22.795 1.00 1.00 ATOM 138 CA SER 39 15.231 -15.333 25.785 1.00 1.00 ATOM 139 CA GLU 40 12.790 -12.668 24.725 1.00 1.00 ATOM 140 CA MET 41 12.382 -14.159 21.271 1.00 1.00 ATOM 141 CA LYS 42 12.373 -17.705 22.716 1.00 1.00 ATOM 142 CA GLU 43 15.625 -18.916 21.126 1.00 1.00 ATOM 143 CA LYS 44 17.963 -19.189 24.116 1.00 1.00 ATOM 144 CA THR 45 20.673 -21.846 23.681 1.00 1.00 ATOM 145 CA GLY 46 20.022 -21.878 19.952 1.00 1.00 ATOM 146 CA LEU 47 22.537 -21.905 17.116 1.00 1.00 ATOM 147 CA ILE 48 21.666 -18.273 16.265 1.00 1.00 ATOM 148 CA GLN 49 22.153 -17.304 19.920 1.00 1.00 ATOM 149 CA LEU 50 25.618 -18.886 20.150 1.00 1.00 ATOM 150 CA ASP 51 26.734 -17.255 16.925 1.00 1.00 ATOM 151 CA ARG 52 25.557 -13.840 18.122 1.00 1.00 ATOM 152 CA VAL 53 27.554 -14.240 21.363 1.00 1.00 TER END ################################ # # # END # # # ################################ From mailer@bialko.llnl.gov Tue Jul 16 19:00:29 2002 Date: Tue, 16 Jul 2002 19:00:23 -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 18:33:34 PDT 2002 by Adam Zemla # # The PIN number of your submission is: PIN_449037_12187 # (PIN number is not an ACCESSION CODE) # Thank you for your submission. Your prediction has been accepted with an ACCESSION CODE: T0131SS389_1 Current information on models submitted in prediction T0131SS389 MODEL_INDEX PIN CODE DATE E-mail T0131SS389_1 PIN_449037_12187 1549-8716-6404 07/16/02 18:33:34 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 T0131 MODEL_INDEX PIN CODE DATE E-mail T0131SS389_1 PIN_449037_12187 1549-8716-6404 07/16/02 18:33:34 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 T0131 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: 100 # Number of residues with nonzero confidence: 100 # Number of METHOD records: 46 # No errors. ################################ # # # SUBMISSION # # # ################################ # # # BEGIN # # # ################################ PFRMAT SS TARGET T0131 AUTHOR 1549-8716-6404 METHOD CAFASP METHOD samt02_dssp_ehl METHOD This file is the result of combining several RDB files, specifically METHOD preds/T0131.t2k.dssp-ebghstl.rdb (weight 1.53986) METHOD preds/T0131.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/T0131.t2k.dssp-ebghstl.rdb METHOD ============================================ METHOD TARGET T0131 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 T0131.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 12 METHOD METHOD ============================================ METHOD Comments from preds/T0131.t2k.stride-ebghtl.rdb METHOD ============================================ METHOD TARGET T0131 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 T0131.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 12 METHOD METHOD ============================================ MODEL 1 M C 0.96 S C 0.86 L C 0.79 K C 0.64 L E 0.57 V E 0.84 E E 0.93 I E 0.94 L E 0.96 V E 0.93 L E 0.63 G C 0.69 Q C 0.53 V E 0.77 L E 0.89 R E 0.85 L E 0.81 N E 0.54 V C 0.86 P C 0.91 I H 0.75 E H 0.79 Q H 0.84 E H 0.91 E H 0.91 L H 0.92 L H 0.95 R H 0.96 Q H 0.96 A H 0.96 A H 0.95 R H 0.93 N H 0.90 L H 0.89 D H 0.82 I H 0.87 L H 0.90 V H 0.95 S H 0.96 E H 0.96 M H 0.95 K H 0.94 E H 0.90 K H 0.73 T C 0.53 G C 0.79 L C 0.64 I C 0.66 Q C 0.71 L H 0.76 D H 0.84 R H 0.89 V H 0.91 L H 0.94 S H 0.95 I H 0.96 V H 0.97 A H 0.97 L H 0.97 N H 0.96 L H 0.96 S H 0.95 F H 0.94 E H 0.91 L H 0.91 S H 0.88 Q H 0.86 E H 0.86 K H 0.85 N H 0.80 K H 0.77 T H 0.74 A H 0.70 K H 0.66 I H 0.84 E H 0.91 E H 0.91 V H 0.93 L H 0.95 R H 0.96 T H 0.95 G H 0.95 I H 0.96 Q H 0.96 Q H 0.95 L H 0.94 D H 0.92 H H 0.87 S H 0.75 L H 0.82 E H 0.77 N H 0.65 I H 0.45 R C 0.46 V C 0.50 T C 0.72 K C 0.74 E C 0.80 P C 0.90 H C 0.98 END ################################ # # # END # # # ################################