From mailer@bialko.llnl.gov Thu Aug 15 06:36:29 2002 Date: Thu, 15 Aug 2002 06:36:24 -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 Thu Aug 15 06:08:31 PDT 2002 by Adam Zemla # # The PIN number of your submission is: PIN_211582_24558 # (PIN number is not an ACCESSION CODE) # Thank you for your submission. Your prediction has been accepted with an ACCESSION CODE: T0181SS007_1 Current information on models submitted in prediction T0181SS007 MODEL_INDEX PIN CODE DATE E-mail T0181SS007_1 PIN_211582_24558 6269-7633-6117 08/15/02 06:08:31 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 T0181 MODEL_INDEX PIN CODE DATE E-mail T0181SS007_1 PIN_211582_24558 6269-7633-6117 08/15/02 06:08:31 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 T0181 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: 111 # Number of residues with nonzero confidence: 111 # Number of METHOD records: 42 # No errors. ################################ # # # SUBMISSION # # # ################################ # # # BEGIN # # # ################################ PFRMAT SS TARGET T0181 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-31448.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-12858//target-align-12858.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 2.68788 METHOD METHOD CHAIN 1 METHOD Method 1: METHOD Prediction using SAM HMM nearest-neighbor METHOD sequence: seed-seqs-31448.a2m(1) METHOD model_file: /projects/compbio/tmp/sam-nn-tmp.cc74.19643/model.mod METHOD database_files: /projects/compbio/programs/hmm-server-2.0/src/pcc/data/overrep-2260.verify.mixed.seq /projects/compbio/programs/hmm-server-2.0/src/pcc/data/overrep-2260.verify.mixed.2d METHOD scoring_mode: local METHOD null_model: reverse METHOD scoring_algorithm: EM METHOD adjust_score: 2 METHOD date: Wed Aug 14 01:41:07 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-12858//target-align-12858.a2m METHOD METHOD guide seq name: seed-seqs-31448.a2m(1), 111 bases, 161F3D1E checksum. METHOD ###end 0 MODEL 1 M C 0.7 S C 0.646 T C 0.578 V C 0.458 T E 0.403 K E 0.476 Y E 0.532 F E 0.517 Y E 0.435 K C 0.546 G C 0.684 E C 0.692 N C 0.689 T C 0.551 D E 0.501 L E 0.675 I E 0.739 V E 0.738 F E 0.689 A E 0.493 A C 0.561 S C 0.655 E C 0.598 E C 0.473 L H 0.49 V H 0.572 D H 0.592 E H 0.605 Y H 0.547 L H 0.477 K C 0.454 N C 0.711 P C 0.701 S C 0.645 I C 0.546 G C 0.59 K C 0.525 L H 0.409 S H 0.413 E H 0.444 V H 0.427 V H 0.416 E H 0.392 L E 0.388 F E 0.461 E E 0.5 V E 0.541 F E 0.503 T C 0.51 P C 0.635 Q C 0.684 D C 0.714 G C 0.735 R C 0.713 G C 0.697 A C 0.646 E C 0.531 G C 0.466 E C 0.398 L H 0.368 G H 0.356 A H 0.371 A C 0.43 S C 0.494 K H 0.705 A H 0.724 Q H 0.715 V H 0.701 E H 0.694 N H 0.644 E H 0.568 F C 0.464 G C 0.656 K C 0.64 G C 0.648 K C 0.58 K C 0.509 I H 0.64 E H 0.669 E H 0.739 V H 0.672 I H 0.667 D H 0.67 L H 0.671 I H 0.655 L H 0.628 R H 0.545 N C 0.519 G C 0.748 K C 0.673 P C 0.584 N C 0.627 S C 0.657 T C 0.615 T C 0.55 S C 0.522 S C 0.541 L C 0.554 K C 0.548 T C 0.521 K C 0.519 G C 0.538 G C 0.561 N C 0.668 A C 0.612 G C 0.608 T C 0.511 K C 0.462 A C 0.458 Y C 0.546 N C 0.733 END ################################ # # # END # # # ################################ From mailer@bialko.llnl.gov Tue Aug 20 11:07:09 2002 Date: Tue, 20 Aug 2002 11:07:03 -0700 (PDT) From: Automatic Reply To: karplus@soe.ucsc.edu Subject: T0181 TS samt99.pdb 1 X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK # # Protein Structure Prediction Center, LLNL, Livermore, CA # Verification system Tue Aug 20 10:38:56 PDT 2002 by Adam Zemla # # The PIN number of your submission is: PIN_518100_28713 # (PIN number is not an ACCESSION CODE) # Thank you for your submission. Your prediction has been accepted with an ACCESSION CODE: T0181TS007_1 Current information on models submitted in prediction T0181TS007 MODEL_INDEX PIN CODE DATE E-mail T0181TS007_1 PIN_518100_28713 6269-7633-6117 08/20/02 10:38:56 casp5@bialko.llnl.gov T0181TS007_2 PIN_486389_28704 6269-7633-6117 08/20/02 10:35:39 casp5@bialko.llnl.gov T0181TS007_3 PIN_486667_28703 6269-7633-6117 08/20/02 10:35:21 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 T0181 MODEL_INDEX PIN CODE DATE E-mail T0181TS007_1 PIN_518100_28713 6269-7633-6117 08/20/02 10:38:56 casp5@bialko.llnl.gov T0181TS007_2 PIN_486389_28704 6269-7633-6117 08/20/02 10:35:39 casp5@bialko.llnl.gov T0181TS007_3 PIN_486667_28703 6269-7633-6117 08/20/02 10:35:21 casp5@bialko.llnl.gov T0181SS007_1 PIN_211582_24558 6269-7633-6117 08/15/02 06:08:31 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 T0181 AUTHOR 6269-7633-6117 # Reading MODEL 1 PARENT 1UWO_A # Loading PARENT structure: 1uwo (chain: A) # Number of residues in PARENT structure: 91 # Reading prediction format TS (DONE) # Checking the TS prediction MODEL 1 # IMPORTANT NOTE! Not complete main chain atoms for residue L 38 # !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! # # 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 39 # IMPORTANT NOTE! Not complete main chain atoms for residue E 40 # IMPORTANT NOTE! Not complete main chain atoms for residue V 41 # IMPORTANT NOTE! Not complete main chain atoms for residue V 42 # IMPORTANT NOTE! Not complete main chain atoms for residue E 43 # IMPORTANT NOTE! Not complete main chain atoms for residue L 44 # IMPORTANT NOTE! Not complete main chain atoms for residue F 45 # IMPORTANT NOTE! Not complete main chain atoms for residue E 46 # IMPORTANT NOTE! Not complete main chain atoms for residue V 47 # IMPORTANT NOTE! Not complete main chain atoms for residue F 48 # IMPORTANT NOTE! Not complete main chain atoms for residue T 49 # IMPORTANT NOTE! Not complete main chain atoms for residue P 50 # IMPORTANT NOTE! Not complete main chain atoms for residue Q 51 # IMPORTANT NOTE! Not complete main chain atoms for residue D 52 # IMPORTANT NOTE! Not complete main chain atoms for residue G 53 # IMPORTANT NOTE! Not complete main chain atoms for residue R 54 # IMPORTANT NOTE! Not complete main chain atoms for residue G 55 # IMPORTANT NOTE! Not complete main chain atoms for residue A 56 # IMPORTANT NOTE! Not complete main chain atoms for residue E 57 # IMPORTANT NOTE! Not complete main chain atoms for residue G 58 # IMPORTANT NOTE! Not complete main chain atoms for residue E 59 # IMPORTANT NOTE! Not complete main chain atoms for residue L 60 # IMPORTANT NOTE! Not complete main chain atoms for residue G 61 # IMPORTANT NOTE! Not complete main chain atoms for residue A 62 # IMPORTANT NOTE! Not complete main chain atoms for residue A 63 # IMPORTANT NOTE! Not complete main chain atoms for residue S 64 # IMPORTANT NOTE! Not complete main chain atoms for residue K 65 # IMPORTANT NOTE! Not complete main chain atoms for residue A 66 # IMPORTANT NOTE! Not complete main chain atoms for residue Q 67 # IMPORTANT NOTE! Not complete main chain atoms for residue V 68 # IMPORTANT NOTE! Not complete main chain atoms for residue E 69 # IMPORTANT NOTE! Not complete main chain atoms for residue N 70 # IMPORTANT NOTE! Not complete main chain atoms for residue E 71 # IMPORTANT NOTE! Not complete main chain atoms for residue F 72 # IMPORTANT NOTE! Not complete main chain atoms for residue G 73 # IMPORTANT NOTE! Not complete main chain atoms for residue K 74 # IMPORTANT NOTE! Not complete main chain atoms for residue G 75 # IMPORTANT NOTE! Not complete main chain atoms for residue K 76 # IMPORTANT NOTE! Not complete main chain atoms for residue K 77 # IMPORTANT NOTE! Not complete main chain atoms for residue I 78 # IMPORTANT NOTE! Not complete main chain atoms for residue E 79 # IMPORTANT NOTE! Not complete main chain atoms for residue E 80 # IMPORTANT NOTE! Not complete main chain atoms for residue V 81 # IMPORTANT NOTE! Not complete main chain atoms for residue I 82 # IMPORTANT NOTE! Not complete main chain atoms for residue D 83 # IMPORTANT NOTE! Not complete main chain atoms for residue L 84 # IMPORTANT NOTE! Not complete main chain atoms for residue I 85 # Checking the TS prediction MODEL 1 (DONE) # MODEL index: 1 # Target name: T0181 # Total number of residues in target: 111 # Total number of residues in model: 48 # Total number of atoms in model: 48 # Number of atoms with 1.0 occupancy: 48 # Number of fragments in model: 1 # Number of METHOD records: 1 # No errors. # Number of Warnings: 48 ################################ # # # SUBMISSION # # # ################################ # # # BEGIN # # # ################################ PFRMAT TS TARGET T0181 AUTHOR 6269-7633-6117 METHOD CAFASP MODEL 1 PARENT 1UWO_A ATOM 7 CA LEU 38 79.789 -5.305 -19.974 1.00 1.00 ATOM 8 CA SER 39 81.915 -7.724 -17.917 1.00 1.00 ATOM 9 CA GLU 40 81.990 -5.264 -14.992 1.00 1.00 ATOM 10 CA VAL 41 78.418 -3.907 -15.068 1.00 1.00 ATOM 11 CA VAL 42 77.327 -7.554 -15.401 1.00 1.00 ATOM 12 CA GLU 43 79.307 -8.544 -12.286 1.00 1.00 ATOM 13 CA LEU 44 77.255 -5.876 -10.477 1.00 1.00 ATOM 14 CA PHE 45 73.953 -7.319 -11.766 1.00 1.00 ATOM 15 CA GLU 46 74.604 -10.737 -10.181 1.00 1.00 ATOM 16 CA VAL 47 76.576 -9.300 -7.238 1.00 1.00 ATOM 17 CA PHE 48 73.902 -6.846 -6.038 1.00 1.00 ATOM 18 CA THR 49 71.133 -9.252 -7.109 1.00 1.00 ATOM 19 CA PRO 50 72.885 -11.822 -4.887 1.00 1.00 ATOM 20 CA GLN 51 71.836 -9.832 -1.798 1.00 1.00 ATOM 21 CA ASP 52 68.235 -10.919 -2.470 1.00 1.00 ATOM 22 CA GLY 53 68.671 -14.577 -1.447 1.00 1.00 ATOM 23 CA ARG 54 69.307 -15.860 -4.989 1.00 1.00 ATOM 24 CA GLY 55 71.513 -13.795 -7.330 1.00 1.00 ATOM 25 CA ALA 56 70.041 -12.512 -10.616 1.00 1.00 ATOM 29 CA GLU 57 63.684 -2.706 -5.066 1.00 1.00 ATOM 30 CA GLY 58 66.055 -1.599 -2.276 1.00 1.00 ATOM 31 CA GLU 59 68.752 -3.550 -4.157 1.00 1.00 ATOM 32 CA LEU 60 68.413 -1.117 -7.059 1.00 1.00 ATOM 33 CA GLY 61 68.588 1.936 -4.770 1.00 1.00 ATOM 34 CA ALA 62 71.893 0.512 -3.482 1.00 1.00 ATOM 35 CA ALA 63 73.470 0.435 -6.959 1.00 1.00 ATOM 36 CA SER 64 72.205 4.007 -7.456 1.00 1.00 ATOM 37 CA LYS 65 74.068 5.114 -4.305 1.00 1.00 ATOM 38 CA ALA 66 76.883 2.629 -3.574 1.00 1.00 ATOM 39 CA GLN 67 77.657 3.075 -7.294 1.00 1.00 ATOM 40 CA VAL 68 75.996 6.361 -8.323 1.00 1.00 ATOM 41 CA GLU 69 76.537 8.396 -5.134 1.00 1.00 ATOM 42 CA ASN 70 78.887 10.970 -6.699 1.00 1.00 ATOM 43 CA GLU 71 77.675 11.951 -10.188 1.00 1.00 ATOM 44 CA PHE 72 74.029 12.004 -9.046 1.00 1.00 ATOM 45 CA GLY 73 73.820 13.089 -5.387 1.00 1.00 ATOM 46 CA LYS 74 70.079 13.709 -5.865 1.00 1.00 ATOM 47 CA GLY 75 67.605 11.045 -4.653 1.00 1.00 ATOM 48 CA LYS 76 67.053 11.077 -0.855 1.00 1.00 ATOM 49 CA LYS 77 63.296 11.535 -1.399 1.00 1.00 ATOM 50 CA ILE 78 63.010 8.742 -3.995 1.00 1.00 ATOM 51 CA GLU 79 63.648 10.710 -7.211 1.00 1.00 ATOM 52 CA GLU 80 65.433 8.326 -9.604 1.00 1.00 ATOM 53 CA VAL 81 65.375 5.456 -7.090 1.00 1.00 ATOM 54 CA ILE 82 61.558 5.556 -7.075 1.00 1.00 ATOM 55 CA ASP 83 61.073 6.513 -10.742 1.00 1.00 ATOM 56 CA LEU 84 63.353 3.631 -11.765 1.00 1.00 ATOM 57 CA ILE 85 61.036 0.962 -10.289 1.00 1.00 TER END ################################ # # # END # # # ################################ From mailer@bialko.llnl.gov Tue Aug 20 11:03:28 2002 Date: Tue, 20 Aug 2002 11:03:23 -0700 (PDT) From: Automatic Reply To: karplus@soe.ucsc.edu Subject: T0181 TS samt99.pdb 2 X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK # # Protein Structure Prediction Center, LLNL, Livermore, CA # Verification system Tue Aug 20 10:35:39 PDT 2002 by Adam Zemla # # The PIN number of your submission is: PIN_486389_28704 # (PIN number is not an ACCESSION CODE) # Thank you for your submission. Your prediction has been accepted with an ACCESSION CODE: T0181TS007_2 Current information on models submitted in prediction T0181TS007 MODEL_INDEX PIN CODE DATE E-mail T0181TS007_2 PIN_486389_28704 6269-7633-6117 08/20/02 10:35:39 casp5@bialko.llnl.gov T0181TS007_3 PIN_486667_28703 6269-7633-6117 08/20/02 10:35:21 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 T0181 MODEL_INDEX PIN CODE DATE E-mail T0181TS007_2 PIN_486389_28704 6269-7633-6117 08/20/02 10:35:39 casp5@bialko.llnl.gov T0181TS007_3 PIN_486667_28703 6269-7633-6117 08/20/02 10:35:21 casp5@bialko.llnl.gov T0181SS007_1 PIN_211582_24558 6269-7633-6117 08/15/02 06:08:31 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 T0181 AUTHOR 6269-7633-6117 # Reading MODEL 2 PARENT 1MHO # Loading PARENT structure: 1mho (chain: ) # Number of residues in PARENT structure: 88 # Reading prediction format TS (DONE) # Checking the TS prediction MODEL 2 # IMPORTANT NOTE! Not complete main chain atoms for residue L 38 # !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! # # 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 39 # IMPORTANT NOTE! Not complete main chain atoms for residue E 40 # IMPORTANT NOTE! Not complete main chain atoms for residue V 41 # IMPORTANT NOTE! Not complete main chain atoms for residue V 42 # IMPORTANT NOTE! Not complete main chain atoms for residue E 43 # IMPORTANT NOTE! Not complete main chain atoms for residue L 44 # IMPORTANT NOTE! Not complete main chain atoms for residue F 45 # IMPORTANT NOTE! Not complete main chain atoms for residue E 46 # IMPORTANT NOTE! Not complete main chain atoms for residue V 47 # IMPORTANT NOTE! Not complete main chain atoms for residue F 48 # IMPORTANT NOTE! Not complete main chain atoms for residue T 49 # IMPORTANT NOTE! Not complete main chain atoms for residue P 50 # IMPORTANT NOTE! Not complete main chain atoms for residue Q 51 # IMPORTANT NOTE! Not complete main chain atoms for residue D 52 # IMPORTANT NOTE! Not complete main chain atoms for residue G 53 # IMPORTANT NOTE! Not complete main chain atoms for residue R 54 # IMPORTANT NOTE! Not complete main chain atoms for residue G 55 # IMPORTANT NOTE! Not complete main chain atoms for residue A 56 # IMPORTANT NOTE! Not complete main chain atoms for residue E 57 # IMPORTANT NOTE! Not complete main chain atoms for residue G 58 # IMPORTANT NOTE! Not complete main chain atoms for residue E 59 # IMPORTANT NOTE! Not complete main chain atoms for residue L 60 # IMPORTANT NOTE! Not complete main chain atoms for residue G 61 # IMPORTANT NOTE! Not complete main chain atoms for residue A 62 # IMPORTANT NOTE! Not complete main chain atoms for residue A 63 # IMPORTANT NOTE! Not complete main chain atoms for residue S 64 # IMPORTANT NOTE! Not complete main chain atoms for residue K 65 # IMPORTANT NOTE! Not complete main chain atoms for residue A 66 # IMPORTANT NOTE! Not complete main chain atoms for residue Q 67 # IMPORTANT NOTE! Not complete main chain atoms for residue V 68 # IMPORTANT NOTE! Not complete main chain atoms for residue E 69 # IMPORTANT NOTE! Not complete main chain atoms for residue N 70 # IMPORTANT NOTE! Not complete main chain atoms for residue E 71 # IMPORTANT NOTE! Not complete main chain atoms for residue F 72 # IMPORTANT NOTE! Not complete main chain atoms for residue G 73 # IMPORTANT NOTE! Not complete main chain atoms for residue K 74 # IMPORTANT NOTE! Not complete main chain atoms for residue G 75 # IMPORTANT NOTE! Not complete main chain atoms for residue K 76 # IMPORTANT NOTE! Not complete main chain atoms for residue K 77 # IMPORTANT NOTE! Not complete main chain atoms for residue I 78 # IMPORTANT NOTE! Not complete main chain atoms for residue E 79 # IMPORTANT NOTE! Not complete main chain atoms for residue E 80 # IMPORTANT NOTE! Not complete main chain atoms for residue V 81 # IMPORTANT NOTE! Not complete main chain atoms for residue I 82 # IMPORTANT NOTE! Not complete main chain atoms for residue D 83 # IMPORTANT NOTE! Not complete main chain atoms for residue L 84 # IMPORTANT NOTE! Not complete main chain atoms for residue I 85 # Checking the TS prediction MODEL 2 (DONE) # MODEL index: 2 # Target name: T0181 # Total number of residues in target: 111 # Total number of residues in model: 48 # Total number of atoms in model: 48 # Number of atoms with 1.0 occupancy: 48 # Number of fragments in model: 1 # Number of METHOD records: 1 # No errors. # Number of Warnings: 48 ################################ # # # SUBMISSION # # # ################################ # # # BEGIN # # # ################################ PFRMAT TS TARGET T0181 AUTHOR 6269-7633-6117 METHOD CAFASP MODEL 2 PARENT 1MHO ATOM 7 CA LEU 38 16.428 1.452 -4.585 1.00 1.00 ATOM 8 CA SER 39 18.628 -0.417 -7.033 1.00 1.00 ATOM 9 CA GLU 40 19.555 -3.042 -4.376 1.00 1.00 ATOM 10 CA VAL 41 15.796 -3.801 -4.035 1.00 1.00 ATOM 11 CA VAL 42 15.397 -4.385 -7.726 1.00 1.00 ATOM 12 CA GLU 43 18.670 -6.371 -7.921 1.00 1.00 ATOM 13 CA LEU 44 17.797 -8.690 -5.011 1.00 1.00 ATOM 14 CA PHE 45 14.241 -9.338 -6.370 1.00 1.00 ATOM 15 CA GLU 46 15.683 -10.232 -9.792 1.00 1.00 ATOM 16 CA VAL 47 18.298 -12.610 -8.354 1.00 1.00 ATOM 17 CA PHE 48 15.515 -14.718 -6.828 1.00 1.00 ATOM 18 CA THR 49 12.597 -14.309 -9.231 1.00 1.00 ATOM 19 CA PRO 50 14.485 -15.540 -12.259 1.00 1.00 ATOM 20 CA GLN 51 15.636 -18.922 -10.836 1.00 1.00 ATOM 21 CA ASP 52 12.540 -20.898 -11.801 1.00 1.00 ATOM 22 CA GLY 53 9.430 -20.733 -13.916 1.00 1.00 ATOM 23 CA ARG 54 8.146 -17.165 -14.264 1.00 1.00 ATOM 24 CA GLY 55 11.214 -14.912 -14.310 1.00 1.00 ATOM 28 CA ALA 56 7.169 -18.733 -6.268 1.00 1.00 ATOM 29 CA GLU 57 7.280 -20.303 -2.815 1.00 1.00 ATOM 30 CA GLY 58 10.712 -21.912 -3.176 1.00 1.00 ATOM 31 CA GLU 59 12.337 -18.694 -4.439 1.00 1.00 ATOM 32 CA LEU 60 10.665 -16.590 -1.694 1.00 1.00 ATOM 33 CA GLY 61 11.898 -19.078 0.931 1.00 1.00 ATOM 34 CA ALA 62 15.557 -18.875 -0.185 1.00 1.00 ATOM 35 CA ALA 63 15.346 -15.047 -0.421 1.00 1.00 ATOM 36 CA SER 64 14.229 -14.894 3.208 1.00 1.00 ATOM 37 CA LYS 65 16.762 -17.428 4.541 1.00 1.00 ATOM 38 CA ALA 66 19.734 -16.118 2.560 1.00 1.00 ATOM 39 CA GLN 67 19.034 -12.369 2.632 1.00 1.00 ATOM 40 CA VAL 68 16.924 -11.658 5.750 1.00 1.00 ATOM 41 CA GLU 69 18.762 -13.720 8.344 1.00 1.00 ATOM 42 CA ASN 70 19.262 -10.803 10.763 1.00 1.00 ATOM 43 CA GLU 71 15.651 -9.654 10.805 1.00 1.00 ATOM 44 CA PHE 72 13.583 -12.798 10.286 1.00 1.00 ATOM 45 CA GLY 73 13.707 -16.339 11.663 1.00 1.00 ATOM 46 CA LYS 74 14.940 -18.985 9.237 1.00 1.00 ATOM 47 CA GLY 75 12.042 -20.729 7.489 1.00 1.00 ATOM 48 CA LYS 76 12.106 -24.528 7.785 1.00 1.00 ATOM 49 CA LYS 77 8.406 -25.671 7.883 1.00 1.00 ATOM 50 CA ILE 78 6.297 -25.812 4.722 1.00 1.00 ATOM 51 CA GLU 79 3.383 -24.344 6.628 1.00 1.00 ATOM 52 CA GLU 80 5.397 -21.166 7.321 1.00 1.00 ATOM 53 CA VAL 81 6.326 -20.722 3.694 1.00 1.00 ATOM 54 CA ILE 82 2.674 -21.285 2.735 1.00 1.00 ATOM 55 CA ASP 83 1.488 -18.723 5.273 1.00 1.00 ATOM 56 CA LEU 84 4.007 -16.043 4.211 1.00 1.00 ATOM 57 CA ILE 85 3.000 -16.445 0.570 1.00 1.00 TER END ################################ # # # END # # # ################################ From mailer@bialko.llnl.gov Tue Aug 20 11:03:18 2002 Date: Tue, 20 Aug 2002 11:03:12 -0700 (PDT) From: Automatic Reply To: karplus@soe.ucsc.edu Subject: T0181 TS samt99.pdb 3 X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK # # Protein Structure Prediction Center, LLNL, Livermore, CA # Verification system Tue Aug 20 10:35:21 PDT 2002 by Adam Zemla # # The PIN number of your submission is: PIN_486667_28703 # (PIN number is not an ACCESSION CODE) # Thank you for your submission. Your prediction has been accepted with an ACCESSION CODE: T0181TS007_3 Current information on models submitted in prediction T0181TS007 MODEL_INDEX PIN CODE DATE E-mail T0181TS007_3 PIN_486667_28703 6269-7633-6117 08/20/02 10:35:21 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 T0181 MODEL_INDEX PIN CODE DATE E-mail T0181TS007_3 PIN_486667_28703 6269-7633-6117 08/20/02 10:35:21 casp5@bialko.llnl.gov T0181SS007_1 PIN_211582_24558 6269-7633-6117 08/15/02 06:08:31 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 T0181 AUTHOR 6269-7633-6117 # Reading MODEL 3 PARENT 1B4C_A # Loading PARENT structure: 1b4c (chain: A) # Number of residues in PARENT structure: 91 # Reading prediction format TS (DONE) # Checking the TS prediction MODEL 3 # IMPORTANT NOTE! Not complete main chain atoms for residue S 2 # !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! # # It is requested that coordinate data be supplied for at least # # all non-hydrogen main chain atoms, i.e. the N, CA, C and O # # atoms of every residue. Specifically, if only CA atoms are # # predicted by the method, predictors are encouraged to build # # the main chain atoms for every residue before submission to # # CASP. If only CA atoms were submitted it would not be possible # # to run most of the analysis software, which would severely # # limit the evaluation of that prediction. # # !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! # # IMPORTANT NOTE! Not complete main chain atoms for residue T 3 # IMPORTANT NOTE! Not complete main chain atoms for residue V 4 # IMPORTANT NOTE! Not complete main chain atoms for residue T 5 # IMPORTANT NOTE! Not complete main chain atoms for residue K 6 # IMPORTANT NOTE! Not complete main chain atoms for residue Y 7 # IMPORTANT NOTE! Not complete main chain atoms for residue F 8 # IMPORTANT NOTE! Not complete main chain atoms for residue Y 9 # IMPORTANT NOTE! Not complete main chain atoms for residue K 10 # IMPORTANT NOTE! Not complete main chain atoms for residue G 11 # IMPORTANT NOTE! Not complete main chain atoms for residue E 12 # IMPORTANT NOTE! Not complete main chain atoms for residue N 13 # IMPORTANT NOTE! Not complete main chain atoms for residue T 14 # IMPORTANT NOTE! Not complete main chain atoms for residue D 15 # IMPORTANT NOTE! Not complete main chain atoms for residue L 16 # IMPORTANT NOTE! Not complete main chain atoms for residue I 17 # IMPORTANT NOTE! Not complete main chain atoms for residue V 18 # IMPORTANT NOTE! Not complete main chain atoms for residue F 19 # IMPORTANT NOTE! Not complete main chain atoms for residue A 20 # IMPORTANT NOTE! Not complete main chain atoms for residue A 21 # IMPORTANT NOTE! Not complete main chain atoms for residue S 22 # IMPORTANT NOTE! Not complete main chain atoms for residue E 23 # IMPORTANT NOTE! Not complete main chain atoms for residue E 24 # IMPORTANT NOTE! Not complete main chain atoms for residue L 25 # IMPORTANT NOTE! Not complete main chain atoms for residue V 26 # IMPORTANT NOTE! Not complete main chain atoms for residue D 27 # IMPORTANT NOTE! Not complete main chain atoms for residue E 28 # IMPORTANT NOTE! Not complete main chain atoms for residue Y 29 # IMPORTANT NOTE! Not complete main chain atoms for residue L 30 # IMPORTANT NOTE! Not complete main chain atoms for residue K 31 # IMPORTANT NOTE! Not complete main chain atoms for residue N 32 # IMPORTANT NOTE! Not complete main chain atoms for residue P 33 # IMPORTANT NOTE! Not complete main chain atoms for residue S 34 # IMPORTANT NOTE! Not complete main chain atoms for residue I 35 # IMPORTANT NOTE! Not complete main chain atoms for residue G 36 # IMPORTANT NOTE! Not complete main chain atoms for residue K 37 # IMPORTANT NOTE! Not complete main chain atoms for residue L 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 V 41 # IMPORTANT NOTE! Not complete main chain atoms for residue V 42 # IMPORTANT NOTE! Not complete main chain atoms for residue E 43 # IMPORTANT NOTE! Not complete main chain atoms for residue L 44 # IMPORTANT NOTE! Not complete main chain atoms for residue F 45 # IMPORTANT NOTE! Not complete main chain atoms for residue E 46 # IMPORTANT NOTE! Not complete main chain atoms for residue V 47 # IMPORTANT NOTE! Not complete main chain atoms for residue F 48 # IMPORTANT NOTE! Not complete main chain atoms for residue T 49 # IMPORTANT NOTE! Not complete main chain atoms for residue P 50 # IMPORTANT NOTE! Not complete main chain atoms for residue Q 51 # IMPORTANT NOTE! Not complete main chain atoms for residue D 52 # IMPORTANT NOTE! Not complete main chain atoms for residue G 53 # IMPORTANT NOTE! Not complete main chain atoms for residue R 54 # IMPORTANT NOTE! Not complete main chain atoms for residue G 55 # IMPORTANT NOTE! Not complete main chain atoms for residue A 56 # IMPORTANT NOTE! Not complete main chain atoms for residue E 57 # IMPORTANT NOTE! Not complete main chain atoms for residue G 58 # IMPORTANT NOTE! Not complete main chain atoms for residue E 59 # IMPORTANT NOTE! Not complete main chain atoms for residue L 60 # IMPORTANT NOTE! Not complete main chain atoms for residue G 61 # IMPORTANT NOTE! Not complete main chain atoms for residue A 62 # IMPORTANT NOTE! Not complete main chain atoms for residue A 63 # IMPORTANT NOTE! Not complete main chain atoms for residue S 64 # IMPORTANT NOTE! Not complete main chain atoms for residue K 65 # IMPORTANT NOTE! Not complete main chain atoms for residue A 66 # IMPORTANT NOTE! Not complete main chain atoms for residue Q 67 # IMPORTANT NOTE! Not complete main chain atoms for residue V 68 # IMPORTANT NOTE! Not complete main chain atoms for residue E 69 # IMPORTANT NOTE! Not complete main chain atoms for residue N 70 # IMPORTANT NOTE! Not complete main chain atoms for residue E 71 # IMPORTANT NOTE! Not complete main chain atoms for residue F 72 # IMPORTANT NOTE! Not complete main chain atoms for residue G 73 # IMPORTANT NOTE! Not complete main chain atoms for residue K 74 # IMPORTANT NOTE! Not complete main chain atoms for residue G 75 # IMPORTANT NOTE! Not complete main chain atoms for residue K 76 # IMPORTANT NOTE! Not complete main chain atoms for residue K 77 # IMPORTANT NOTE! Not complete main chain atoms for residue I 78 # IMPORTANT NOTE! Not complete main chain atoms for residue E 79 # IMPORTANT NOTE! Not complete main chain atoms for residue E 80 # Checking the TS prediction MODEL 3 (DONE) # MODEL index: 3 # Target name: T0181 # Total number of residues in target: 111 # Total number of residues in model: 79 # Total number of atoms in model: 79 # Number of atoms with 1.0 occupancy: 79 # Number of fragments in model: 1 # Number of METHOD records: 1 # No errors. # Number of Warnings: 79 ################################ # # # SUBMISSION # # # ################################ # # # BEGIN # # # ################################ PFRMAT TS TARGET T0181 AUTHOR 6269-7633-6117 METHOD CAFASP MODEL 3 PARENT 1B4C_A ATOM 1 CA SER 2 -10.725 3.515 12.506 1.00 1.00 ATOM 2 CA THR 3 -8.047 0.954 13.429 1.00 1.00 ATOM 3 CA VAL 4 -6.850 1.193 9.809 1.00 1.00 ATOM 4 CA THR 5 -6.196 4.961 10.023 1.00 1.00 ATOM 5 CA LYS 6 -4.010 4.289 13.081 1.00 1.00 ATOM 6 CA TYR 7 -1.912 2.002 10.857 1.00 1.00 ATOM 7 CA PHE 8 -2.057 4.344 7.835 1.00 1.00 ATOM 8 CA TYR 9 -0.297 7.062 9.860 1.00 1.00 ATOM 21 CA LYS 10 17.913 14.589 6.151 1.00 1.00 ATOM 22 CA GLY 11 14.639 13.991 4.266 1.00 1.00 ATOM 23 CA GLU 12 16.029 16.844 2.127 1.00 1.00 ATOM 24 CA ASN 13 14.805 15.082 -1.035 1.00 1.00 ATOM 25 CA THR 14 11.722 12.816 -1.296 1.00 1.00 ATOM 26 CA ASP 15 13.253 9.886 -3.223 1.00 1.00 ATOM 27 CA LEU 16 14.555 6.444 -2.094 1.00 1.00 ATOM 28 CA ILE 17 17.253 4.386 -3.882 1.00 1.00 ATOM 29 CA VAL 18 16.743 0.670 -4.648 1.00 1.00 ATOM 30 CA PHE 19 19.953 -0.288 -2.807 1.00 1.00 ATOM 31 CA ALA 20 18.577 1.262 0.408 1.00 1.00 ATOM 32 CA ALA 21 15.004 0.166 -0.360 1.00 1.00 ATOM 33 CA SER 22 16.138 -3.474 -0.557 1.00 1.00 ATOM 34 CA GLU 23 17.789 -3.228 2.882 1.00 1.00 ATOM 35 CA GLU 24 14.363 -2.033 4.126 1.00 1.00 ATOM 36 CA LEU 25 12.828 -5.270 2.747 1.00 1.00 ATOM 37 CA VAL 26 15.456 -7.264 4.689 1.00 1.00 ATOM 38 CA ASP 27 14.267 -5.725 8.015 1.00 1.00 ATOM 39 CA GLU 28 10.605 -4.953 7.105 1.00 1.00 ATOM 40 CA TYR 29 9.447 -7.993 5.035 1.00 1.00 ATOM 41 CA LEU 30 11.700 -10.594 6.716 1.00 1.00 ATOM 42 CA LYS 31 8.817 -11.733 8.962 1.00 1.00 ATOM 43 CA ASN 32 6.277 -12.450 6.192 1.00 1.00 ATOM 44 CA PRO 33 9.080 -14.206 4.275 1.00 1.00 ATOM 45 CA SER 34 7.982 -17.341 6.162 1.00 1.00 ATOM 46 CA ILE 35 4.337 -17.108 5.007 1.00 1.00 ATOM 47 CA GLY 36 5.125 -17.098 1.240 1.00 1.00 ATOM 48 CA LYS 37 4.799 -19.756 -1.502 1.00 1.00 ATOM 49 CA LEU 38 5.164 -18.229 -4.989 1.00 1.00 ATOM 50 CA SER 39 8.943 -17.986 -4.434 1.00 1.00 ATOM 51 CA GLU 40 9.099 -17.133 -8.161 1.00 1.00 ATOM 52 CA VAL 41 7.074 -13.954 -7.527 1.00 1.00 ATOM 53 CA VAL 42 9.521 -12.694 -4.883 1.00 1.00 ATOM 54 CA GLU 43 12.385 -13.782 -7.153 1.00 1.00 ATOM 55 CA LEU 44 11.207 -11.359 -9.860 1.00 1.00 ATOM 56 CA PHE 45 10.809 -8.603 -7.235 1.00 1.00 ATOM 57 CA GLU 46 14.455 -8.758 -6.107 1.00 1.00 ATOM 58 CA VAL 47 15.272 -8.585 -9.846 1.00 1.00 ATOM 59 CA PHE 48 12.800 -5.751 -10.499 1.00 1.00 ATOM 60 CA THR 49 14.288 -3.674 -7.649 1.00 1.00 ATOM 61 CA PRO 50 17.868 -4.375 -8.783 1.00 1.00 ATOM 62 CA GLN 51 16.518 -3.347 -12.231 1.00 1.00 ATOM 63 CA ASP 52 15.286 0.017 -11.004 1.00 1.00 ATOM 64 CA GLY 53 16.294 1.355 -14.434 1.00 1.00 ATOM 65 CA ARG 54 15.142 4.782 -13.031 1.00 1.00 ATOM 66 CA GLY 55 18.168 5.744 -10.803 1.00 1.00 ATOM 67 CA ALA 56 15.713 6.646 -7.994 1.00 1.00 ATOM 68 CA GLU 57 12.583 4.922 -6.574 1.00 1.00 ATOM 69 CA GLY 58 9.839 7.181 -5.147 1.00 1.00 ATOM 70 CA GLU 59 7.415 6.263 -2.333 1.00 1.00 ATOM 71 CA LEU 60 4.766 5.252 -4.892 1.00 1.00 ATOM 72 CA GLY 61 7.181 2.548 -6.112 1.00 1.00 ATOM 73 CA ALA 62 7.679 1.404 -2.488 1.00 1.00 ATOM 74 CA ALA 63 3.941 1.004 -1.837 1.00 1.00 ATOM 75 CA SER 64 3.726 -1.127 -5.026 1.00 1.00 ATOM 76 CA LYS 65 6.753 -3.415 -4.446 1.00 1.00 ATOM 77 CA ALA 66 5.500 -3.810 -0.862 1.00 1.00 ATOM 78 CA GLN 67 2.074 -4.925 -2.156 1.00 1.00 ATOM 79 CA VAL 68 3.351 -7.511 -4.671 1.00 1.00 ATOM 80 CA GLU 69 5.566 -9.116 -2.015 1.00 1.00 ATOM 81 CA ASN 70 2.661 -9.088 0.466 1.00 1.00 ATOM 82 CA GLU 71 0.116 -10.210 -2.156 1.00 1.00 ATOM 83 CA PHE 72 2.727 -12.641 -3.546 1.00 1.00 ATOM 84 CA GLY 73 1.520 -15.110 -0.902 1.00 1.00 ATOM 85 CA LYS 74 -1.738 -16.000 -2.702 1.00 1.00 ATOM 86 CA GLY 75 -4.585 -16.172 -0.157 1.00 1.00 ATOM 87 CA LYS 76 -2.623 -14.584 2.712 1.00 1.00 ATOM 88 CA LYS 77 -5.866 -14.600 4.734 1.00 1.00 ATOM 89 CA ILE 78 -5.277 -18.349 5.162 1.00 1.00 ATOM 90 CA GLU 79 -2.678 -17.705 7.888 1.00 1.00 ATOM 91 CA GLU 80 -1.623 -21.105 9.283 1.00 1.00 TER END ################################ # # # END # # # ################################