From mailer@bialko.llnl.gov Mon Jun 24 08:47:07 2002 Date: Mon, 24 Jun 2002 08:47:01 -0700 (PDT) From: Automatic Reply To: karplus@soe.ucsc.edu X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK # # Protein Structure Prediction Center, LLNL, Livermore, CA # Verification system Mon Jun 24 08:20:19 PDT 2002 by Adam Zemla # # The PIN number of your submission is: PIN_314936_10885 # (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 T0140 AUTHOR 2491-6940-1261 # Reading MODEL 1 H T 0.429 # ERROR! Check the line NB = 9 in the MODEL section. # Check the SS format description. # Number of Warnings: 0 # Number of Errors: 1 ################################ # # # SUBMISSION # # # ################################ # # # BEGIN # # # ################################ PFRMAT SS TARGET T0140 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 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 276 METHOD MODEL 1 M C 0.999 R C 0.770 G C 0.486 S C 0.459 H C 0.391 H C 0.568 H C 0.448 H C 0.636 H T 0.429 H T 0.503 G G 0.236 S C 0.316 R E 0.373 L E 0.482 Q E 0.360 S S 0.254 G C 0.351 K E 0.701 M E 0.904 T E 0.941 G E 0.958 I E 0.983 V E 0.977 K E 0.977 W E 0.967 F E 0.898 N E 0.659 A T 0.642 D T 0.736 K T 0.469 G T 0.458 F E 0.451 G E 0.677 F E 0.809 I E 0.814 T E 0.556 P T 0.387 D T 0.757 D T 0.607 G S 0.429 S C 0.435 K E 0.717 D E 0.779 V E 0.777 F E 0.800 V E 0.725 H E 0.698 F E 0.480 S E 0.333 A E 0.221 G C 0.351 S C 0.521 S H 0.422 G H 0.576 A H 0.617 A H 0.593 V H 0.539 R H 0.433 G H 0.299 N E 0.311 P C 0.691 Q C 0.703 Q T 0.732 G T 0.673 D C 0.506 R E 0.922 V E 0.955 E E 0.965 G E 0.959 K E 0.981 I E 0.969 K E 0.974 S E 0.955 I E 0.839 T E 0.567 D E 0.356 F T 0.377 G E 0.603 I E 0.830 F E 0.968 I E 0.955 G E 0.923 L E 0.771 D C 0.373 G T 0.651 G T 0.600 I C 0.498 D C 0.393 G E 0.563 L E 0.885 V E 0.909 H E 0.823 L H 0.548 S G 0.498 D G 0.594 I H 0.535 S H 0.342 W H 0.302 A H 0.342 Q H 0.242 A C 0.360 E C 0.572 A C 0.994 END ################################ # # # END # # # ################################ From mailer@bialko.llnl.gov Mon Jun 24 08:47:18 2002 Date: Mon, 24 Jun 2002 08:47:12 -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 Mon Jun 24 08:20:32 PDT 2002 by Adam Zemla # # The PIN number of your submission is: PIN_316237_10886 # (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 T0140 AUTHOR 5144-8387-2760 # Reading MODEL 1 S T 0.394 # ERROR! Check the line NB = 4 in the MODEL section. # Check the SS format description. # Number of Warnings: 0 # Number of Errors: 1 ################################ # # # SUBMISSION # # # ################################ # # # BEGIN # # # ################################ PFRMAT SS TARGET T0140 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 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 276 METHOD MODEL 1 M C 0.762 R C 0.605 G C 0.387 S T 0.394 H T 0.356 H C 0.367 H C 0.555 H T 0.495 H T 0.573 H T 0.489 G T 0.400 S E 0.331 R E 0.504 L E 0.635 Q E 0.449 S T 0.649 G T 0.395 K E 0.744 M E 0.903 T E 0.975 G E 0.987 I E 0.989 V E 0.989 K E 0.970 W E 0.934 F E 0.827 N E 0.634 A T 0.708 D T 0.673 K T 0.653 G T 0.456 F E 0.475 G E 0.755 F E 0.794 I E 0.622 T E 0.453 P T 0.615 D T 0.664 D T 0.742 G T 0.653 S C 0.492 K E 0.546 D E 0.649 V E 0.755 F E 0.799 V E 0.803 H E 0.725 F E 0.611 S E 0.499 A E 0.281 G H 0.373 S C 0.319 S H 0.353 G H 0.485 A H 0.407 A H 0.429 V H 0.367 R H 0.320 G E 0.301 N E 0.322 P C 0.423 Q T 0.784 Q T 0.886 G T 0.919 D E 0.579 R E 0.847 V E 0.956 E E 0.979 G E 0.981 K E 0.984 I E 0.989 K E 0.981 S E 0.964 I E 0.920 T E 0.623 D T 0.542 F T 0.562 G E 0.443 I E 0.904 F E 0.971 I E 0.971 G E 0.922 L E 0.587 D T 0.789 G T 0.837 G T 0.734 I T 0.447 D E 0.515 G E 0.909 L E 0.934 V E 0.900 H E 0.754 L E 0.410 S C 0.314 D G 0.360 I H 0.303 S H 0.381 W H 0.523 A H 0.532 Q H 0.545 A C 0.415 E C 0.568 A C 0.915 END ################################ # # # END # # # ################################