From mailer@bialko.llnl.gov Wed Jul 24 09:47:08 2002 Date: Wed, 24 Jul 2002 09:47:02 -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 Wed Jul 24 09:19:37 PDT 2002 by Adam Zemla # # The PIN number of your submission is: PIN_312035_13827 # (PIN number is not an ACCESSION CODE) # Thank you for your submission. Your prediction has been accepted with an ACCESSION CODE: T0161SS007_1 Current information on models submitted in prediction T0161SS007 MODEL_INDEX PIN CODE DATE E-mail T0161SS007_1 PIN_312035_13827 6269-7633-6117 07/24/02 09:19:37 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 T0161 MODEL_INDEX PIN CODE DATE E-mail T0161SS007_1 PIN_312035_13827 6269-7633-6117 07/24/02 09:19:37 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 T0161 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: 156 # Number of residues with nonzero confidence: 156 # Number of METHOD records: 42 # No errors. ################################ # # # SUBMISSION # # # ################################ # # # BEGIN # # # ################################ PFRMAT SS TARGET T0161 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-2728.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-14601//target-align-14601.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 1.86607 METHOD METHOD CHAIN 1 METHOD Method 1: METHOD Prediction using SAM HMM nearest-neighbor METHOD sequence: seed-seqs-2728.a2m(1) METHOD model_file: /projects/compbio/tmp/sam-nn-tmp.cc54.21019/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: Tue Jul 23 13:40:34 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-14601//target-align-14601.a2m METHOD METHOD guide seq name: seed-seqs-2728.a2m(1), 156 bases, DB63B92E checksum. METHOD ###end 0 MODEL 1 M C 0.709 S C 0.687 E H 0.485 T H 0.565 D H 0.631 L H 0.64 L H 0.642 L H 0.639 K H 0.616 M H 0.565 V H 0.485 R C 0.459 Q C 0.637 P C 0.618 V C 0.431 K E 0.351 L E 0.417 Y E 0.403 S H 0.372 V H 0.602 A H 0.657 T H 0.688 L H 0.699 F H 0.732 H H 0.732 E H 0.737 F H 0.741 S H 0.732 E H 0.75 V H 0.729 I H 0.719 T H 0.699 K H 0.683 L H 0.622 E H 0.575 H H 0.523 S H 0.447 V H 0.421 Q C 0.439 K C 0.482 E C 0.64 P C 0.61 T C 0.493 S C 0.408 L H 0.413 L C 0.406 S C 0.496 E H 0.617 E H 0.633 N H 0.654 W H 0.677 H H 0.764 K H 0.821 Q H 0.818 F H 0.814 L H 0.812 K H 0.81 F H 0.794 A H 0.783 Q H 0.745 A H 0.691 L H 0.512 P C 0.496 A C 0.504 H C 0.537 G C 0.591 S C 0.547 A H 0.467 S H 0.465 W H 0.497 L H 0.441 N C 0.433 L H 0.654 D H 0.699 D H 0.788 A H 0.787 L H 0.788 Q H 0.771 A H 0.742 V H 0.714 V H 0.657 G H 0.48 N C 0.488 S C 0.457 R H 0.627 S H 0.696 A H 0.778 F H 0.775 L H 0.803 H H 0.814 Q H 0.822 L H 0.819 I H 0.834 A H 0.841 K H 0.834 L H 0.819 K H 0.794 S H 0.77 R H 0.723 H H 0.681 L H 0.66 Q H 0.648 V H 0.633 L H 0.594 E H 0.535 L H 0.509 N C 0.479 K C 0.477 I C 0.511 G C 0.699 S C 0.709 E C 0.702 P C 0.651 L C 0.579 D C 0.597 L C 0.498 S C 0.593 N C 0.627 L C 0.724 P C 0.742 A C 0.711 P C 0.629 F E 0.444 Y E 0.558 V E 0.571 L E 0.483 L C 0.546 P C 0.489 E H 0.51 S H 0.565 F H 0.572 A H 0.544 A H 0.509 R H 0.474 I H 0.444 T E 0.476 L E 0.506 L E 0.496 V E 0.44 Q H 0.389 D C 0.447 K C 0.537 A C 0.552 L C 0.614 P C 0.584 Y E 0.439 V E 0.54 R E 0.594 V E 0.602 S E 0.571 F E 0.57 E E 0.534 Y E 0.494 W E 0.427 H C 0.436 A C 0.674 END ################################ # # # END # # # ################################ From mailer@bialko.llnl.gov Thu Aug 15 02:40:08 2002 Date: Thu, 15 Aug 2002 02:40:02 -0700 (PDT) From: Automatic Reply To: karplus@soe.ucsc.edu Subject: T0161 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 Thu Aug 15 02:12:04 PDT 2002 by Adam Zemla # # The PIN number of your submission is: PIN_246945_24309 # (PIN number is not an ACCESSION CODE) # Thank you for your submission. Your prediction has been accepted with an ACCESSION CODE: T0161TS007_1 Current information on models submitted in prediction T0161TS007 MODEL_INDEX PIN CODE DATE E-mail T0161TS007_1 PIN_246945_24309 6269-7633-6117 08/15/02 02:12:04 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 T0161 MODEL_INDEX PIN CODE DATE E-mail T0161TS007_1 PIN_246945_24309 6269-7633-6117 08/15/02 02:12:04 casp5@bialko.llnl.gov T0161SS007_1 PIN_312035_13827 6269-7633-6117 07/24/02 09:19:37 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 T0161 AUTHOR 6269-7633-6117 # Reading MODEL 1 PARENT 1A16 # Loading PARENT structure: 1a16 (chain: ) # Number of residues in PARENT structure: 439 # Reading prediction format TS (DONE) # Checking the TS prediction MODEL 1 # IMPORTANT NOTE! Not complete main chain atoms for residue H 65 # !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! # # 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 66 # IMPORTANT NOTE! Not complete main chain atoms for residue S 67 # IMPORTANT NOTE! Not complete main chain atoms for residue A 68 # IMPORTANT NOTE! Not complete main chain atoms for residue S 69 # IMPORTANT NOTE! Not complete main chain atoms for residue W 70 # IMPORTANT NOTE! Not complete main chain atoms for residue L 71 # IMPORTANT NOTE! Not complete main chain atoms for residue N 72 # IMPORTANT NOTE! Not complete main chain atoms for residue L 73 # IMPORTANT NOTE! Not complete main chain atoms for residue D 74 # IMPORTANT NOTE! Not complete main chain atoms for residue D 75 # IMPORTANT NOTE! Not complete main chain atoms for residue A 76 # IMPORTANT NOTE! Not complete main chain atoms for residue L 77 # IMPORTANT NOTE! Not complete main chain atoms for residue Q 78 # IMPORTANT NOTE! Not complete main chain atoms for residue A 79 # IMPORTANT NOTE! Not complete main chain atoms for residue V 80 # IMPORTANT NOTE! Not complete main chain atoms for residue V 81 # IMPORTANT NOTE! Not complete main chain atoms for residue G 82 # IMPORTANT NOTE! Not complete main chain atoms for residue N 83 # IMPORTANT NOTE! Not complete main chain atoms for residue S 84 # IMPORTANT NOTE! Not complete main chain atoms for residue R 85 # IMPORTANT NOTE! Not complete main chain atoms for residue S 86 # IMPORTANT NOTE! Not complete main chain atoms for residue A 87 # IMPORTANT NOTE! Not complete main chain atoms for residue F 88 # IMPORTANT NOTE! Not complete main chain atoms for residue L 89 # Checking the TS prediction MODEL 1 (DONE) # MODEL index: 1 # Target name: T0161 # Total number of residues in target: 156 # Total number of residues in model: 25 # Total number of atoms in model: 25 # Number of atoms with 1.0 occupancy: 25 # Number of fragments in model: 1 # Number of METHOD records: 1 # No errors. # Number of Warnings: 25 ################################ # # # SUBMISSION # # # ################################ # # # BEGIN # # # ################################ PFRMAT TS TARGET T0161 AUTHOR 6269-7633-6117 METHOD CAFASP MODEL 1 PARENT 1A16 ATOM 350 CA HIS 65 55.547 44.641 50.957 1.00 1.00 ATOM 351 CA GLY 66 56.319 45.931 47.474 1.00 1.00 ATOM 352 CA SER 67 59.335 44.796 45.475 1.00 1.00 ATOM 353 CA ALA 68 60.433 48.341 44.631 1.00 1.00 ATOM 354 CA SER 69 60.025 51.878 45.299 1.00 1.00 ATOM 355 CA TRP 70 61.627 55.074 43.584 1.00 1.00 ATOM 356 CA LEU 71 64.866 56.372 45.126 1.00 1.00 ATOM 357 CA ASN 72 66.261 59.938 45.202 1.00 1.00 ATOM 358 CA LEU 73 66.188 62.983 47.542 1.00 1.00 ATOM 359 CA ASP 74 63.841 60.824 49.659 1.00 1.00 ATOM 360 CA ASP 75 64.346 57.106 50.319 1.00 1.00 ATOM 361 CA ALA 76 60.683 56.562 49.257 1.00 1.00 ATOM 362 CA LEU 77 61.050 59.026 46.403 1.00 1.00 ATOM 363 CA GLN 78 58.333 61.046 44.722 1.00 1.00 ATOM 364 CA ALA 79 56.897 60.100 41.336 1.00 1.00 ATOM 365 CA VAL 80 53.746 58.427 40.010 1.00 1.00 ATOM 366 CA VAL 81 53.786 54.620 40.144 1.00 1.00 ATOM 367 CA GLY 82 50.688 54.023 38.047 1.00 1.00 ATOM 368 CA ASN 83 47.998 51.732 39.416 1.00 1.00 ATOM 369 CA SER 84 49.615 48.768 41.178 1.00 1.00 ATOM 370 CA ARG 85 52.994 50.250 40.240 1.00 1.00 ATOM 371 CA SER 86 52.347 49.456 36.562 1.00 1.00 ATOM 372 CA ALA 87 53.961 52.539 35.029 1.00 1.00 ATOM 373 CA PHE 88 56.315 51.628 32.188 1.00 1.00 ATOM 374 CA LEU 89 59.953 52.061 33.274 1.00 1.00 TER END ################################ # # # END # # # ################################ From mailer@bialko.llnl.gov Thu Aug 15 02:41:17 2002 Date: Thu, 15 Aug 2002 02:41:12 -0700 (PDT) From: Automatic Reply To: karplus@soe.ucsc.edu Subject: T0161 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 Thu Aug 15 02:13:11 PDT 2002 by Adam Zemla # # The PIN number of your submission is: PIN_257649_24313 # (PIN number is not an ACCESSION CODE) # Thank you for your submission. Your prediction has been accepted with an ACCESSION CODE: T0161TS007_2 Current information on models submitted in prediction T0161TS007 MODEL_INDEX PIN CODE DATE E-mail T0161TS007_2 PIN_257649_24313 6269-7633-6117 08/15/02 02:13:11 casp5@bialko.llnl.gov T0161TS007_1 PIN_246945_24309 6269-7633-6117 08/15/02 02:12:04 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 T0161 MODEL_INDEX PIN CODE DATE E-mail T0161TS007_1 PIN_246945_24309 6269-7633-6117 08/15/02 02:12:04 casp5@bialko.llnl.gov T0161TS007_2 PIN_257649_24313 6269-7633-6117 08/15/02 02:13:11 casp5@bialko.llnl.gov T0161SS007_1 PIN_312035_13827 6269-7633-6117 07/24/02 09:19:37 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 T0161 AUTHOR 6269-7633-6117 # Reading MODEL 2 PARENT 1JAW # Loading PARENT structure: 1jaw (chain: ) # Number of residues in PARENT structure: 440 # Reading prediction format TS (DONE) # Checking the TS prediction MODEL 2 # IMPORTANT NOTE! Not complete main chain atoms for residue H 65 # !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! # # 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 66 # IMPORTANT NOTE! Not complete main chain atoms for residue S 67 # IMPORTANT NOTE! Not complete main chain atoms for residue A 68 # IMPORTANT NOTE! Not complete main chain atoms for residue S 69 # IMPORTANT NOTE! Not complete main chain atoms for residue W 70 # IMPORTANT NOTE! Not complete main chain atoms for residue L 71 # IMPORTANT NOTE! Not complete main chain atoms for residue N 72 # IMPORTANT NOTE! Not complete main chain atoms for residue L 73 # IMPORTANT NOTE! Not complete main chain atoms for residue D 74 # IMPORTANT NOTE! Not complete main chain atoms for residue D 75 # IMPORTANT NOTE! Not complete main chain atoms for residue A 76 # IMPORTANT NOTE! Not complete main chain atoms for residue L 77 # IMPORTANT NOTE! Not complete main chain atoms for residue Q 78 # IMPORTANT NOTE! Not complete main chain atoms for residue A 79 # IMPORTANT NOTE! Not complete main chain atoms for residue V 80 # IMPORTANT NOTE! Not complete main chain atoms for residue V 81 # IMPORTANT NOTE! Not complete main chain atoms for residue G 82 # IMPORTANT NOTE! Not complete main chain atoms for residue N 83 # IMPORTANT NOTE! Not complete main chain atoms for residue S 84 # IMPORTANT NOTE! Not complete main chain atoms for residue R 85 # IMPORTANT NOTE! Not complete main chain atoms for residue S 86 # IMPORTANT NOTE! Not complete main chain atoms for residue A 87 # IMPORTANT NOTE! Not complete main chain atoms for residue F 88 # IMPORTANT NOTE! Not complete main chain atoms for residue L 89 # Checking the TS prediction MODEL 2 (DONE) # MODEL index: 2 # Target name: T0161 # Total number of residues in target: 156 # Total number of residues in model: 25 # Total number of atoms in model: 25 # Number of atoms with 1.0 occupancy: 25 # Number of fragments in model: 1 # Number of METHOD records: 1 # No errors. # Number of Warnings: 25 ################################ # # # SUBMISSION # # # ################################ # # # BEGIN # # # ################################ PFRMAT TS TARGET T0161 AUTHOR 6269-7633-6117 METHOD CAFASP MODEL 2 PARENT 1JAW ATOM 350 CA HIS 65 27.866 60.785 35.529 1.00 1.00 ATOM 351 CA GLY 66 30.295 63.211 37.176 1.00 1.00 ATOM 352 CA SER 67 34.003 62.432 37.608 1.00 1.00 ATOM 353 CA ALA 68 34.121 63.614 41.214 1.00 1.00 ATOM 354 CA SER 69 31.910 64.419 44.286 1.00 1.00 ATOM 355 CA TRP 70 32.922 66.087 47.585 1.00 1.00 ATOM 356 CA LEU 71 33.500 63.509 50.344 1.00 1.00 ATOM 357 CA ASN 72 33.032 63.849 54.119 1.00 1.00 ATOM 358 CA LEU 73 30.333 63.155 56.720 1.00 1.00 ATOM 359 CA ASP 74 28.068 62.330 53.763 1.00 1.00 ATOM 360 CA ASP 75 29.407 60.325 50.750 1.00 1.00 ATOM 361 CA ALA 76 28.007 63.011 48.492 1.00 1.00 ATOM 362 CA LEU 77 29.237 65.711 50.825 1.00 1.00 ATOM 363 CA GLN 78 28.083 69.266 51.231 1.00 1.00 ATOM 364 CA ALA 79 29.874 72.290 49.782 1.00 1.00 ATOM 365 CA VAL 80 29.403 74.587 46.772 1.00 1.00 ATOM 366 CA VAL 81 30.673 73.132 43.466 1.00 1.00 ATOM 367 CA GLY 82 30.377 76.165 41.221 1.00 1.00 ATOM 368 CA ASN 83 28.687 76.115 37.795 1.00 1.00 ATOM 369 CA SER 84 29.428 72.748 36.104 1.00 1.00 ATOM 370 CA ARG 85 31.662 71.971 39.080 1.00 1.00 ATOM 371 CA SER 86 34.179 74.622 38.027 1.00 1.00 ATOM 372 CA ALA 87 35.278 75.764 41.514 1.00 1.00 ATOM 373 CA PHE 88 39.035 76.090 42.010 1.00 1.00 ATOM 374 CA LEU 89 40.395 73.281 44.182 1.00 1.00 TER END ################################ # # # END # # # ################################ From mailer@bialko.llnl.gov Thu Aug 15 02:45:18 2002 Date: Thu, 15 Aug 2002 02:45:12 -0700 (PDT) From: Automatic Reply To: karplus@soe.ucsc.edu Subject: T0161 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 Thu Aug 15 02:17:28 PDT 2002 by Adam Zemla # # The PIN number of your submission is: PIN_299361_24325 # (PIN number is not an ACCESSION CODE) # Thank you for your submission. Your prediction has been accepted with an ACCESSION CODE: T0161TS007_3 Current information on models submitted in prediction T0161TS007 MODEL_INDEX PIN CODE DATE E-mail T0161TS007_3 PIN_299361_24325 6269-7633-6117 08/15/02 02:17:28 casp5@bialko.llnl.gov T0161TS007_4 PIN_264304_24314 6269-7633-6117 08/15/02 02:13:40 casp5@bialko.llnl.gov T0161TS007_2 PIN_257649_24313 6269-7633-6117 08/15/02 02:13:11 casp5@bialko.llnl.gov T0161TS007_1 PIN_246945_24309 6269-7633-6117 08/15/02 02:12:04 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 T0161 MODEL_INDEX PIN CODE DATE E-mail T0161TS007_1 PIN_246945_24309 6269-7633-6117 08/15/02 02:12:04 casp5@bialko.llnl.gov T0161TS007_2 PIN_257649_24313 6269-7633-6117 08/15/02 02:13:11 casp5@bialko.llnl.gov T0161TS007_3 PIN_299361_24325 6269-7633-6117 08/15/02 02:17:28 casp5@bialko.llnl.gov T0161TS007_4 PIN_264304_24314 6269-7633-6117 08/15/02 02:13:40 casp5@bialko.llnl.gov T0161SS007_1 PIN_312035_13827 6269-7633-6117 07/24/02 09:19:37 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 T0161 AUTHOR 6269-7633-6117 # Reading MODEL 3 PARENT 1AZ9 # Loading PARENT structure: 1az9 (chain: ) # Number of residues in PARENT structure: 440 # Reading prediction format TS (DONE) # Checking the TS prediction MODEL 3 # IMPORTANT NOTE! Not complete main chain atoms for residue H 65 # !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! # # 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 66 # IMPORTANT NOTE! Not complete main chain atoms for residue S 67 # IMPORTANT NOTE! Not complete main chain atoms for residue A 68 # IMPORTANT NOTE! Not complete main chain atoms for residue S 69 # IMPORTANT NOTE! Not complete main chain atoms for residue W 70 # IMPORTANT NOTE! Not complete main chain atoms for residue L 71 # IMPORTANT NOTE! Not complete main chain atoms for residue N 72 # IMPORTANT NOTE! Not complete main chain atoms for residue L 73 # IMPORTANT NOTE! Not complete main chain atoms for residue D 74 # IMPORTANT NOTE! Not complete main chain atoms for residue D 75 # IMPORTANT NOTE! Not complete main chain atoms for residue A 76 # IMPORTANT NOTE! Not complete main chain atoms for residue L 77 # IMPORTANT NOTE! Not complete main chain atoms for residue Q 78 # IMPORTANT NOTE! Not complete main chain atoms for residue A 79 # IMPORTANT NOTE! Not complete main chain atoms for residue V 80 # IMPORTANT NOTE! Not complete main chain atoms for residue V 81 # IMPORTANT NOTE! Not complete main chain atoms for residue G 82 # IMPORTANT NOTE! Not complete main chain atoms for residue N 83 # IMPORTANT NOTE! Not complete main chain atoms for residue S 84 # IMPORTANT NOTE! Not complete main chain atoms for residue R 85 # IMPORTANT NOTE! Not complete main chain atoms for residue S 86 # IMPORTANT NOTE! Not complete main chain atoms for residue A 87 # IMPORTANT NOTE! Not complete main chain atoms for residue F 88 # IMPORTANT NOTE! Not complete main chain atoms for residue L 89 # Checking the TS prediction MODEL 3 (DONE) # MODEL index: 3 # Target name: T0161 # Total number of residues in target: 156 # Total number of residues in model: 25 # Total number of atoms in model: 25 # Number of atoms with 1.0 occupancy: 25 # Number of fragments in model: 1 # Number of METHOD records: 1 # No errors. # Number of Warnings: 25 ################################ # # # SUBMISSION # # # ################################ # # # BEGIN # # # ################################ PFRMAT TS TARGET T0161 AUTHOR 6269-7633-6117 METHOD CAFASP MODEL 3 PARENT 1AZ9 ATOM 350 CA HIS 65 55.535 44.583 50.961 1.00 1.00 ATOM 351 CA GLY 66 56.351 45.963 47.520 1.00 1.00 ATOM 352 CA SER 67 59.352 44.817 45.483 1.00 1.00 ATOM 353 CA ALA 68 60.493 48.303 44.508 1.00 1.00 ATOM 354 CA SER 69 60.177 51.950 45.310 1.00 1.00 ATOM 355 CA TRP 70 61.652 55.099 43.529 1.00 1.00 ATOM 356 CA LEU 71 64.858 56.381 45.118 1.00 1.00 ATOM 357 CA ASN 72 66.320 59.904 45.175 1.00 1.00 ATOM 358 CA LEU 73 66.217 62.963 47.472 1.00 1.00 ATOM 359 CA ASP 74 63.888 60.840 49.627 1.00 1.00 ATOM 360 CA ASP 75 64.388 57.123 50.266 1.00 1.00 ATOM 361 CA ALA 76 60.746 56.576 49.227 1.00 1.00 ATOM 362 CA LEU 77 61.101 58.985 46.362 1.00 1.00 ATOM 363 CA GLN 78 58.421 61.041 44.666 1.00 1.00 ATOM 364 CA ALA 79 56.915 60.143 41.293 1.00 1.00 ATOM 365 CA VAL 80 53.735 58.529 39.943 1.00 1.00 ATOM 366 CA VAL 81 53.809 54.714 40.071 1.00 1.00 ATOM 367 CA GLY 82 50.706 54.040 38.015 1.00 1.00 ATOM 368 CA ASN 83 48.002 51.682 39.313 1.00 1.00 ATOM 369 CA SER 84 49.680 48.785 41.160 1.00 1.00 ATOM 370 CA ARG 85 53.066 50.241 40.163 1.00 1.00 ATOM 371 CA SER 86 52.319 49.454 36.513 1.00 1.00 ATOM 372 CA ALA 87 54.039 52.506 35.025 1.00 1.00 ATOM 373 CA PHE 88 56.374 51.604 32.140 1.00 1.00 ATOM 374 CA LEU 89 60.005 52.081 33.169 1.00 1.00 TER END ################################ # # # END # # # ################################ From mailer@bialko.llnl.gov Thu Aug 15 02:41:38 2002 Date: Thu, 15 Aug 2002 02:41:33 -0700 (PDT) From: Automatic Reply To: karplus@soe.ucsc.edu Subject: T0161 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 Thu Aug 15 02:13:40 PDT 2002 by Adam Zemla # # The PIN number of your submission is: PIN_264304_24314 # (PIN number is not an ACCESSION CODE) # Thank you for your submission. Your prediction has been accepted with an ACCESSION CODE: T0161TS007_4 Current information on models submitted in prediction T0161TS007 MODEL_INDEX PIN CODE DATE E-mail T0161TS007_4 PIN_264304_24314 6269-7633-6117 08/15/02 02:13:40 casp5@bialko.llnl.gov T0161TS007_2 PIN_257649_24313 6269-7633-6117 08/15/02 02:13:11 casp5@bialko.llnl.gov T0161TS007_1 PIN_246945_24309 6269-7633-6117 08/15/02 02:12:04 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 T0161 MODEL_INDEX PIN CODE DATE E-mail T0161TS007_1 PIN_246945_24309 6269-7633-6117 08/15/02 02:12:04 casp5@bialko.llnl.gov T0161TS007_2 PIN_257649_24313 6269-7633-6117 08/15/02 02:13:11 casp5@bialko.llnl.gov T0161TS007_4 PIN_264304_24314 6269-7633-6117 08/15/02 02:13:40 casp5@bialko.llnl.gov T0161SS007_1 PIN_312035_13827 6269-7633-6117 07/24/02 09:19:37 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 T0161 AUTHOR 6269-7633-6117 # Reading MODEL 4 PARENT 1ITX_A # Loading PARENT structure: 1itx (chain: A) # Number of residues in PARENT structure: 419 # Reading prediction format TS (DONE) # Checking the TS prediction MODEL 4 # IMPORTANT NOTE! Not complete main chain atoms for residue S 69 # !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! # # 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 W 70 # IMPORTANT NOTE! Not complete main chain atoms for residue L 71 # IMPORTANT NOTE! Not complete main chain atoms for residue N 72 # IMPORTANT NOTE! Not complete main chain atoms for residue L 73 # IMPORTANT NOTE! Not complete main chain atoms for residue D 74 # IMPORTANT NOTE! Not complete main chain atoms for residue D 75 # IMPORTANT NOTE! Not complete main chain atoms for residue A 76 # IMPORTANT NOTE! Not complete main chain atoms for residue L 77 # IMPORTANT NOTE! Not complete main chain atoms for residue Q 78 # IMPORTANT NOTE! Not complete main chain atoms for residue A 79 # IMPORTANT NOTE! Not complete main chain atoms for residue V 80 # IMPORTANT NOTE! Not complete main chain atoms for residue V 81 # IMPORTANT NOTE! Not complete main chain atoms for residue G 82 # IMPORTANT NOTE! Not complete main chain atoms for residue N 83 # IMPORTANT NOTE! Not complete main chain atoms for residue S 84 # IMPORTANT NOTE! Not complete main chain atoms for residue R 85 # IMPORTANT NOTE! Not complete main chain atoms for residue S 86 # IMPORTANT NOTE! Not complete main chain atoms for residue A 87 # IMPORTANT NOTE! Not complete main chain atoms for residue F 88 # IMPORTANT NOTE! Not complete main chain atoms for residue L 89 # IMPORTANT NOTE! Not complete main chain atoms for residue H 90 # IMPORTANT NOTE! Not complete main chain atoms for residue Q 91 # IMPORTANT NOTE! Not complete main chain atoms for residue L 92 # IMPORTANT NOTE! Not complete main chain atoms for residue I 93 # IMPORTANT NOTE! Not complete main chain atoms for residue A 94 # IMPORTANT NOTE! Not complete main chain atoms for residue K 95 # IMPORTANT NOTE! Not complete main chain atoms for residue L 96 # IMPORTANT NOTE! Not complete main chain atoms for residue K 97 # IMPORTANT NOTE! Not complete main chain atoms for residue S 98 # IMPORTANT NOTE! Not complete main chain atoms for residue R 99 # IMPORTANT NOTE! Not complete main chain atoms for residue H 100 # IMPORTANT NOTE! Not complete main chain atoms for residue L 101 # IMPORTANT NOTE! Not complete main chain atoms for residue Q 102 # IMPORTANT NOTE! Not complete main chain atoms for residue V 103 # IMPORTANT NOTE! Not complete main chain atoms for residue L 104 # IMPORTANT NOTE! Not complete main chain atoms for residue E 105 # IMPORTANT NOTE! Not complete main chain atoms for residue L 106 # IMPORTANT NOTE! Not complete main chain atoms for residue N 107 # IMPORTANT NOTE! Not complete main chain atoms for residue K 108 # IMPORTANT NOTE! Not complete main chain atoms for residue I 109 # IMPORTANT NOTE! Not complete main chain atoms for residue G 110 # IMPORTANT NOTE! Not complete main chain atoms for residue S 111 # IMPORTANT NOTE! Not complete main chain atoms for residue E 112 # IMPORTANT NOTE! Not complete main chain atoms for residue P 113 # IMPORTANT NOTE! Not complete main chain atoms for residue L 119 # IMPORTANT NOTE! Not complete main chain atoms for residue P 120 # IMPORTANT NOTE! Not complete main chain atoms for residue A 121 # IMPORTANT NOTE! Not complete main chain atoms for residue P 122 # IMPORTANT NOTE! Not complete main chain atoms for residue F 123 # IMPORTANT NOTE! Not complete main chain atoms for residue Y 124 # IMPORTANT NOTE! Not complete main chain atoms for residue V 125 # IMPORTANT NOTE! Not complete main chain atoms for residue L 126 # IMPORTANT NOTE! Not complete main chain atoms for residue L 127 # IMPORTANT NOTE! Not complete main chain atoms for residue P 128 # IMPORTANT NOTE! Not complete main chain atoms for residue E 129 # IMPORTANT NOTE! Not complete main chain atoms for residue S 130 # IMPORTANT NOTE! Not complete main chain atoms for residue F 131 # IMPORTANT NOTE! Not complete main chain atoms for residue A 132 # IMPORTANT NOTE! Not complete main chain atoms for residue A 133 # IMPORTANT NOTE! Not complete main chain atoms for residue R 134 # IMPORTANT NOTE! Not complete main chain atoms for residue I 135 # IMPORTANT NOTE! Not complete main chain atoms for residue T 136 # IMPORTANT NOTE! Not complete main chain atoms for residue L 137 # IMPORTANT NOTE! Not complete main chain atoms for residue L 138 # IMPORTANT NOTE! Not complete main chain atoms for residue V 139 # IMPORTANT NOTE! Not complete main chain atoms for residue Q 140 # IMPORTANT NOTE! Not complete main chain atoms for residue D 141 # IMPORTANT NOTE! Not complete main chain atoms for residue K 142 # IMPORTANT NOTE! Not complete main chain atoms for residue A 143 # IMPORTANT NOTE! Not complete main chain atoms for residue L 144 # IMPORTANT NOTE! Not complete main chain atoms for residue P 145 # IMPORTANT NOTE! Not complete main chain atoms for residue Y 146 # IMPORTANT NOTE! Not complete main chain atoms for residue V 147 # IMPORTANT NOTE! Not complete main chain atoms for residue R 148 # IMPORTANT NOTE! Not complete main chain atoms for residue V 149 # IMPORTANT NOTE! Not complete main chain atoms for residue S 150 # IMPORTANT NOTE! Not complete main chain atoms for residue F 151 # IMPORTANT NOTE! Not complete main chain atoms for residue E 152 # IMPORTANT NOTE! Not complete main chain atoms for residue Y 153 # IMPORTANT NOTE! Not complete main chain atoms for residue W 154 # Checking the TS prediction MODEL 4 (DONE) # MODEL index: 4 # Target name: T0161 # Total number of residues in target: 156 # Total number of residues in model: 81 # Total number of atoms in model: 81 # Number of atoms with 1.0 occupancy: 81 # Number of fragments in model: 1 # Number of METHOD records: 1 # No errors. # Number of Warnings: 81 ################################ # # # SUBMISSION # # # ################################ # # # BEGIN # # # ################################ PFRMAT TS TARGET T0161 AUTHOR 6269-7633-6117 METHOD CAFASP MODEL 4 PARENT 1ITX_A ATOM 121 CA SER 69 15.200 14.563 43.817 1.00 1.00 ATOM 122 CA TRP 70 18.028 17.029 43.348 1.00 1.00 ATOM 123 CA LEU 71 17.002 18.128 39.872 1.00 1.00 ATOM 124 CA ASN 72 13.305 17.482 40.381 1.00 1.00 ATOM 125 CA LEU 73 12.823 19.536 43.576 1.00 1.00 ATOM 126 CA ASP 74 16.160 20.609 45.065 1.00 1.00 ATOM 127 CA ASP 75 18.007 22.957 42.637 1.00 1.00 ATOM 128 CA ALA 76 16.985 26.597 42.773 1.00 1.00 ATOM 129 CA LEU 77 16.162 28.726 39.767 1.00 1.00 ATOM 130 CA GLN 78 15.218 32.364 39.119 1.00 1.00 ATOM 131 CA ALA 79 12.235 33.323 41.254 1.00 1.00 ATOM 132 CA VAL 80 12.831 30.747 43.946 1.00 1.00 ATOM 133 CA VAL 81 13.531 31.882 47.458 1.00 1.00 ATOM 134 CA GLY 82 14.424 30.075 50.610 1.00 1.00 ATOM 135 CA ASN 83 10.781 30.335 51.774 1.00 1.00 ATOM 136 CA SER 84 9.112 27.816 49.550 1.00 1.00 ATOM 137 CA ARG 85 8.454 24.077 49.924 1.00 1.00 ATOM 138 CA SER 86 10.001 22.887 46.681 1.00 1.00 ATOM 139 CA ALA 87 12.303 24.123 44.008 1.00 1.00 ATOM 140 CA PHE 88 13.840 22.190 41.080 1.00 1.00 ATOM 141 CA LEU 89 12.378 21.445 37.719 1.00 1.00 ATOM 142 CA HIS 90 8.965 20.651 39.229 1.00 1.00 ATOM 143 CA GLN 91 8.534 24.060 40.825 1.00 1.00 ATOM 144 CA LEU 92 9.574 25.558 37.473 1.00 1.00 ATOM 145 CA ILE 93 6.772 23.593 35.783 1.00 1.00 ATOM 146 CA ALA 94 4.348 25.134 38.214 1.00 1.00 ATOM 147 CA LYS 95 5.828 28.563 37.387 1.00 1.00 ATOM 148 CA LEU 96 5.044 27.994 33.715 1.00 1.00 ATOM 149 CA LYS 97 1.390 27.654 34.754 1.00 1.00 ATOM 150 CA SER 98 1.383 30.794 36.829 1.00 1.00 ATOM 151 CA ARG 99 2.604 32.624 33.720 1.00 1.00 ATOM 152 CA HIS 100 0.544 30.520 31.288 1.00 1.00 ATOM 153 CA LEU 101 -2.592 29.524 33.171 1.00 1.00 ATOM 154 CA GLN 102 -4.039 27.241 30.479 1.00 1.00 ATOM 155 CA VAL 103 -1.158 24.666 30.790 1.00 1.00 ATOM 156 CA LEU 104 -1.537 21.283 32.545 1.00 1.00 ATOM 157 CA GLU 105 1.349 19.189 33.941 1.00 1.00 ATOM 158 CA LEU 106 1.429 15.415 34.178 1.00 1.00 ATOM 159 CA ASN 107 3.976 13.219 35.961 1.00 1.00 ATOM 160 CA LYS 108 5.150 10.286 33.839 1.00 1.00 ATOM 161 CA ILE 109 6.103 7.153 35.746 1.00 1.00 ATOM 162 CA GLY 110 8.473 4.605 34.232 1.00 1.00 ATOM 163 CA SER 111 9.730 4.734 30.671 1.00 1.00 ATOM 164 CA GLU 112 12.291 2.492 29.021 1.00 1.00 ATOM 165 CA PRO 113 14.702 2.399 31.988 1.00 1.00 ATOM 166 CA LEU 119 12.223 2.410 34.910 1.00 1.00 ATOM 167 CA PRO 120 9.641 -0.127 33.798 1.00 1.00 ATOM 168 CA ALA 121 11.254 -2.965 35.760 1.00 1.00 ATOM 169 CA PRO 122 8.806 -2.920 38.718 1.00 1.00 ATOM 170 CA PHE 123 5.417 -2.252 37.001 1.00 1.00 ATOM 171 CA TYR 124 4.637 -5.961 36.769 1.00 1.00 ATOM 172 CA VAL 125 5.362 -6.410 40.479 1.00 1.00 ATOM 173 CA LEU 126 3.182 -3.405 41.396 1.00 1.00 ATOM 174 CA LEU 127 0.291 -4.521 39.186 1.00 1.00 ATOM 180 CA PRO 128 -1.950 -1.577 43.207 1.00 1.00 ATOM 181 CA GLU 129 -3.493 0.216 46.191 1.00 1.00 ATOM 182 CA SER 130 -0.156 1.598 47.381 1.00 1.00 ATOM 183 CA PHE 131 0.723 2.821 43.900 1.00 1.00 ATOM 184 CA ALA 132 -2.691 4.435 43.320 1.00 1.00 ATOM 185 CA ALA 133 -2.722 6.215 46.673 1.00 1.00 ATOM 186 CA ARG 134 0.883 7.351 46.077 1.00 1.00 ATOM 187 CA ILE 135 -0.133 8.872 42.732 1.00 1.00 ATOM 188 CA THR 136 -2.670 11.022 44.579 1.00 1.00 ATOM 189 CA LEU 137 -0.016 11.904 47.149 1.00 1.00 ATOM 190 CA LEU 138 2.448 12.965 44.428 1.00 1.00 ATOM 191 CA VAL 139 -0.083 15.006 42.451 1.00 1.00 ATOM 192 CA GLN 140 -1.233 16.763 45.606 1.00 1.00 ATOM 193 CA ASP 141 2.232 17.508 46.953 1.00 1.00 ATOM 194 CA LYS 142 3.774 18.717 43.706 1.00 1.00 ATOM 195 CA ALA 143 0.678 20.269 42.062 1.00 1.00 ATOM 196 CA LEU 144 0.539 17.961 39.054 1.00 1.00 ATOM 197 CA PRO 145 -2.698 17.850 37.078 1.00 1.00 ATOM 198 CA TYR 146 -2.397 14.161 36.236 1.00 1.00 ATOM 199 CA VAL 147 -0.361 10.976 36.169 1.00 1.00 ATOM 200 CA ARG 148 0.884 9.051 33.120 1.00 1.00 ATOM 201 CA VAL 149 2.075 5.443 33.156 1.00 1.00 ATOM 202 CA SER 150 4.797 4.566 30.652 1.00 1.00 ATOM 203 CA PHE 151 5.003 0.805 31.178 1.00 1.00 ATOM 204 CA GLU 152 7.408 -0.517 28.569 1.00 1.00 ATOM 205 CA TYR 153 5.924 -3.125 28.399 1.00 1.00 ATOM 206 CA TRP 154 3.311 -5.467 29.860 1.00 1.00 TER END ################################ # # # END # # # ################################