From mailer@bialko.llnl.gov Sun Aug 11 20:18:11 2002 Date: Sun, 11 Aug 2002 20:18:02 -0700 (PDT) From: Automatic Reply To: karplus@soe.ucsc.edu 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 Sun Aug 11 19:50:06 PDT 2002 by Adam Zemla # # The PIN number of your submission is: PIN_625021_20636 # (PIN number is not an ACCESSION CODE) # Thank you for your submission. Your prediction has been accepted with an ACCESSION CODE: T0176SS007_1 Current information on models submitted in prediction T0176SS007 MODEL_INDEX PIN CODE DATE E-mail T0176SS007_1 PIN_625021_20636 6269-7633-6117 08/11/02 19:50:06 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 T0176 MODEL_INDEX PIN CODE DATE E-mail T0176SS007_1 PIN_625021_20636 6269-7633-6117 08/11/02 19:50:06 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 T0176 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: 100 # Number of residues with nonzero confidence: 100 # Number of METHOD records: 42 # No errors. ################################ # # # SUBMISSION # # # ################################ # # # BEGIN # # # ################################ PFRMAT SS TARGET T0176 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-9103.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-2222//target-align-2222.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 25.3343 METHOD METHOD CHAIN 1 METHOD Method 1: METHOD Prediction using SAM HMM nearest-neighbor METHOD sequence: seed-seqs-9103.a2m(1) METHOD model_file: /projects/compbio/tmp/sam-nn-tmp.cc72.8621/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: Thu Aug 8 22:57:11 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-2222//target-align-2222.a2m METHOD METHOD guide seq name: seed-seqs-9103.a2m(1), 100 bases, EF164FA checksum. METHOD ###end 0 MODEL 1 M C 0.661 D C 0.624 G C 0.604 V C 0.549 M C 0.514 S C 0.455 A C 0.384 V E 0.358 T E 0.414 V E 0.38 N C 0.465 D C 0.62 D C 0.646 G C 0.543 L E 0.621 V E 0.696 L E 0.721 R E 0.716 L E 0.717 Y E 0.685 I E 0.594 Q C 0.621 P C 0.714 K C 0.689 A C 0.669 S C 0.649 R C 0.522 D C 0.515 S C 0.476 I C 0.461 V C 0.444 G C 0.461 L C 0.48 H C 0.572 G C 0.572 D C 0.537 E E 0.435 V E 0.555 K E 0.624 V E 0.655 A E 0.648 I E 0.623 T E 0.455 A C 0.633 P C 0.75 P C 0.659 V C 0.534 D C 0.493 G C 0.473 Q H 0.524 A H 0.602 N H 0.618 S H 0.763 H H 0.777 L H 0.788 V H 0.795 K H 0.808 F H 0.806 L H 0.795 G H 0.769 K H 0.751 Q H 0.714 F H 0.612 R C 0.592 V C 0.631 A C 0.641 K C 0.499 S C 0.497 Q C 0.459 V E 0.474 V E 0.579 I E 0.539 E E 0.397 K C 0.519 G C 0.66 E C 0.577 L C 0.54 G C 0.584 R C 0.444 H E 0.376 K E 0.463 Q E 0.573 I E 0.604 K E 0.602 I E 0.555 I C 0.408 N C 0.578 P C 0.572 Q C 0.534 Q C 0.53 I C 0.629 P H 0.662 P H 0.749 E H 0.756 V H 0.751 A H 0.756 A H 0.753 L H 0.726 I H 0.622 N C 0.651 END ################################ # # # END # # # ################################ From mailer@bialko.llnl.gov Thu Aug 15 14:18:18 2002 Date: Thu, 15 Aug 2002 14:18:12 -0700 (PDT) From: Automatic Reply To: karplus@soe.ucsc.edu Subject: T0176 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 13:50:09 PDT 2002 by Adam Zemla # # The PIN number of your submission is: PIN_632723_25152 # (PIN number is not an ACCESSION CODE) # Thank you for your submission. Your prediction has been accepted with an ACCESSION CODE: T0176TS007_1 Current information on models submitted in prediction T0176TS007 MODEL_INDEX PIN CODE DATE E-mail T0176TS007_1 PIN_632723_25152 6269-7633-6117 08/15/02 13:50:09 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 T0176 MODEL_INDEX PIN CODE DATE E-mail T0176TS007_1 PIN_632723_25152 6269-7633-6117 08/15/02 13:50:09 casp5@bialko.llnl.gov T0176SS007_1 PIN_625021_20636 6269-7633-6117 08/11/02 19:50:06 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 T0176 AUTHOR 6269-7633-6117 # Reading MODEL 1 PARENT 1JRM_A # Loading PARENT structure: 1jrm (chain: A) # Number of residues in PARENT structure: 104 # Reading prediction format TS (DONE) # Checking the TS prediction MODEL 1 # IMPORTANT NOTE! Not complete main chain atoms for residue G 3 # !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! # # 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 V 4 # IMPORTANT NOTE! Not complete main chain atoms for residue M 5 # IMPORTANT NOTE! Not complete main chain atoms for residue S 6 # IMPORTANT NOTE! Not complete main chain atoms for residue A 7 # IMPORTANT NOTE! Not complete main chain atoms for residue V 8 # IMPORTANT NOTE! Not complete main chain atoms for residue T 9 # IMPORTANT NOTE! Not complete main chain atoms for residue V 10 # IMPORTANT NOTE! Not complete main chain atoms for residue N 11 # IMPORTANT NOTE! Not complete main chain atoms for residue D 12 # IMPORTANT NOTE! Not complete main chain atoms for residue D 13 # IMPORTANT NOTE! Not complete main chain atoms for residue G 14 # IMPORTANT NOTE! Not complete main chain atoms for residue L 15 # IMPORTANT NOTE! Not complete main chain atoms for residue V 16 # IMPORTANT NOTE! Not complete main chain atoms for residue L 17 # IMPORTANT NOTE! Not complete main chain atoms for residue R 18 # IMPORTANT NOTE! Not complete main chain atoms for residue L 19 # IMPORTANT NOTE! Not complete main chain atoms for residue Y 20 # IMPORTANT NOTE! Not complete main chain atoms for residue I 21 # IMPORTANT NOTE! Not complete main chain atoms for residue Q 22 # IMPORTANT NOTE! Not complete main chain atoms for residue P 23 # IMPORTANT NOTE! Not complete main chain atoms for residue K 24 # IMPORTANT NOTE! Not complete main chain atoms for residue A 25 # IMPORTANT NOTE! Not complete main chain atoms for residue S 26 # IMPORTANT NOTE! Not complete main chain atoms for residue R 27 # IMPORTANT NOTE! Not complete main chain atoms for residue D 28 # IMPORTANT NOTE! Not complete main chain atoms for residue S 29 # IMPORTANT NOTE! Not complete main chain atoms for residue I 30 # IMPORTANT NOTE! Not complete main chain atoms for residue V 31 # IMPORTANT NOTE! Not complete main chain atoms for residue G 32 # IMPORTANT NOTE! Not complete main chain atoms for residue L 33 # IMPORTANT NOTE! Not complete main chain atoms for residue H 34 # IMPORTANT NOTE! Not complete main chain atoms for residue G 35 # IMPORTANT NOTE! Not complete main chain atoms for residue D 36 # IMPORTANT NOTE! Not complete main chain atoms for residue E 37 # IMPORTANT NOTE! Not complete main chain atoms for residue V 38 # IMPORTANT NOTE! Not complete main chain atoms for residue K 39 # IMPORTANT NOTE! Not complete main chain atoms for residue V 40 # IMPORTANT NOTE! Not complete main chain atoms for residue A 41 # IMPORTANT NOTE! Not complete main chain atoms for residue I 42 # IMPORTANT NOTE! Not complete main chain atoms for residue T 43 # IMPORTANT NOTE! Not complete main chain atoms for residue A 44 # IMPORTANT NOTE! Not complete main chain atoms for residue P 45 # IMPORTANT NOTE! Not complete main chain atoms for residue P 46 # IMPORTANT NOTE! Not complete main chain atoms for residue V 47 # IMPORTANT NOTE! Not complete main chain atoms for residue D 48 # IMPORTANT NOTE! Not complete main chain atoms for residue G 49 # IMPORTANT NOTE! Not complete main chain atoms for residue Q 50 # IMPORTANT NOTE! Not complete main chain atoms for residue A 51 # IMPORTANT NOTE! Not complete main chain atoms for residue N 52 # IMPORTANT NOTE! Not complete main chain atoms for residue S 53 # IMPORTANT NOTE! Not complete main chain atoms for residue H 54 # IMPORTANT NOTE! Not complete main chain atoms for residue L 55 # IMPORTANT NOTE! Not complete main chain atoms for residue V 56 # IMPORTANT NOTE! Not complete main chain atoms for residue K 57 # IMPORTANT NOTE! Not complete main chain atoms for residue F 58 # IMPORTANT NOTE! Not complete main chain atoms for residue L 59 # IMPORTANT NOTE! Not complete main chain atoms for residue G 60 # IMPORTANT NOTE! Not complete main chain atoms for residue K 61 # IMPORTANT NOTE! Not complete main chain atoms for residue Q 62 # IMPORTANT NOTE! Not complete main chain atoms for residue F 63 # IMPORTANT NOTE! Not complete main chain atoms for residue R 64 # IMPORTANT NOTE! Not complete main chain atoms for residue S 68 # IMPORTANT NOTE! Not complete main chain atoms for residue Q 69 # IMPORTANT NOTE! Not complete main chain atoms for residue V 70 # IMPORTANT NOTE! Not complete main chain atoms for residue V 71 # IMPORTANT NOTE! Not complete main chain atoms for residue I 72 # IMPORTANT NOTE! Not complete main chain atoms for residue E 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 E 76 # IMPORTANT NOTE! Not complete main chain atoms for residue L 77 # IMPORTANT NOTE! Not complete main chain atoms for residue G 78 # IMPORTANT NOTE! Not complete main chain atoms for residue R 79 # IMPORTANT NOTE! Not complete main chain atoms for residue H 80 # IMPORTANT NOTE! Not complete main chain atoms for residue K 81 # IMPORTANT NOTE! Not complete main chain atoms for residue Q 82 # IMPORTANT NOTE! Not complete main chain atoms for residue I 83 # IMPORTANT NOTE! Not complete main chain atoms for residue K 84 # IMPORTANT NOTE! Not complete main chain atoms for residue I 85 # IMPORTANT NOTE! Not complete main chain atoms for residue I 86 # IMPORTANT NOTE! Not complete main chain atoms for residue N 87 # IMPORTANT NOTE! Not complete main chain atoms for residue I 91 # IMPORTANT NOTE! Not complete main chain atoms for residue P 92 # IMPORTANT NOTE! Not complete main chain atoms for residue P 93 # IMPORTANT NOTE! Not complete main chain atoms for residue E 94 # IMPORTANT NOTE! Not complete main chain atoms for residue V 95 # IMPORTANT NOTE! Not complete main chain atoms for residue A 96 # IMPORTANT NOTE! Not complete main chain atoms for residue A 97 # IMPORTANT NOTE! Not complete main chain atoms for residue L 98 # IMPORTANT NOTE! Not complete main chain atoms for residue I 99 # Checking the TS prediction MODEL 1 (DONE) # MODEL index: 1 # Target name: T0176 # Total number of residues in target: 100 # Total number of residues in model: 91 # Total number of atoms in model: 91 # Number of atoms with 1.0 occupancy: 91 # Number of fragments in model: 1 # Number of METHOD records: 1 # No errors. # Number of Warnings: 91 ################################ # # # SUBMISSION # # # ################################ # # # BEGIN # # # ################################ PFRMAT TS TARGET T0176 AUTHOR 6269-7633-6117 METHOD CAFASP MODEL 1 PARENT 1JRM_A ATOM 2 CA GLY 3 0.927 0.868 -4.747 1.00 1.00 ATOM 3 CA VAL 4 -1.927 -1.271 -6.014 1.00 1.00 ATOM 4 CA MET 5 -4.893 1.068 -6.261 1.00 1.00 ATOM 5 CA SER 6 -6.631 2.801 -9.142 1.00 1.00 ATOM 6 CA ALA 7 -7.331 6.481 -9.687 1.00 1.00 ATOM 7 CA VAL 8 -6.334 7.060 -13.293 1.00 1.00 ATOM 8 CA THR 9 -9.200 7.115 -15.764 1.00 1.00 ATOM 9 CA VAL 10 -8.566 6.147 -19.368 1.00 1.00 ATOM 10 CA ASN 11 -10.472 8.625 -21.501 1.00 1.00 ATOM 11 CA ASP 12 -9.550 8.757 -25.170 1.00 1.00 ATOM 12 CA ASP 13 -6.042 9.919 -25.984 1.00 1.00 ATOM 13 CA GLY 14 -6.227 11.490 -22.546 1.00 1.00 ATOM 14 CA LEU 15 -6.160 10.122 -19.017 1.00 1.00 ATOM 15 CA VAL 16 -7.731 11.385 -15.814 1.00 1.00 ATOM 16 CA LEU 17 -6.153 10.854 -12.415 1.00 1.00 ATOM 17 CA ARG 18 -7.333 11.788 -8.942 1.00 1.00 ATOM 18 CA LEU 19 -4.630 13.567 -6.979 1.00 1.00 ATOM 19 CA TYR 20 -3.631 16.878 -5.442 1.00 1.00 ATOM 20 CA ILE 21 -2.584 19.997 -7.314 1.00 1.00 ATOM 21 CA GLN 22 1.030 19.019 -7.867 1.00 1.00 ATOM 22 CA PRO 23 3.112 17.507 -10.678 1.00 1.00 ATOM 23 CA LYS 24 6.194 15.745 -9.367 1.00 1.00 ATOM 24 CA ALA 25 9.609 16.988 -8.308 1.00 1.00 ATOM 25 CA SER 26 12.917 15.262 -8.946 1.00 1.00 ATOM 26 CA ARG 27 11.860 11.941 -10.424 1.00 1.00 ATOM 27 CA ASP 28 8.169 11.772 -11.241 1.00 1.00 ATOM 28 CA SER 29 6.744 11.005 -7.820 1.00 1.00 ATOM 29 CA ILE 30 3.053 10.219 -8.112 1.00 1.00 ATOM 30 CA VAL 31 1.743 7.075 -6.404 1.00 1.00 ATOM 31 CA GLY 32 -1.712 5.567 -6.749 1.00 1.00 ATOM 32 CA LEU 33 -4.773 7.271 -5.317 1.00 1.00 ATOM 33 CA HIS 34 -7.632 5.878 -3.266 1.00 1.00 ATOM 34 CA GLY 35 -11.260 6.911 -2.956 1.00 1.00 ATOM 35 CA ASP 36 -11.140 6.557 0.810 1.00 1.00 ATOM 38 CA GLU 37 -6.396 12.403 -2.276 1.00 1.00 ATOM 39 CA VAL 38 -2.993 11.245 -3.462 1.00 1.00 ATOM 40 CA LYS 39 0.389 12.481 -2.296 1.00 1.00 ATOM 41 CA VAL 40 2.585 13.803 -5.081 1.00 1.00 ATOM 42 CA ALA 41 6.164 15.021 -4.915 1.00 1.00 ATOM 43 CA ILE 42 7.133 18.527 -5.962 1.00 1.00 ATOM 44 CA THR 43 9.032 21.631 -4.920 1.00 1.00 ATOM 45 CA ALA 44 8.084 23.925 -2.063 1.00 1.00 ATOM 46 CA PRO 45 6.764 26.660 -4.364 1.00 1.00 ATOM 47 CA PRO 46 4.353 24.203 -5.999 1.00 1.00 ATOM 48 CA VAL 47 2.975 22.877 -2.733 1.00 1.00 ATOM 49 CA ASP 48 2.142 26.513 -2.092 1.00 1.00 ATOM 50 CA GLY 49 -0.331 26.631 -4.955 1.00 1.00 ATOM 51 CA GLN 50 2.007 26.975 -7.911 1.00 1.00 ATOM 52 CA ALA 51 1.768 23.199 -8.019 1.00 1.00 ATOM 53 CA ASN 52 -1.186 24.011 -10.242 1.00 1.00 ATOM 54 CA SER 53 0.780 25.789 -12.943 1.00 1.00 ATOM 55 CA HIS 54 3.879 23.834 -11.993 1.00 1.00 ATOM 56 CA LEU 55 1.981 20.622 -12.627 1.00 1.00 ATOM 57 CA VAL 56 1.878 21.172 -16.370 1.00 1.00 ATOM 58 CA LYS 57 5.417 22.447 -15.947 1.00 1.00 ATOM 59 CA PHE 58 6.803 19.481 -14.047 1.00 1.00 ATOM 60 CA LEU 59 4.162 16.872 -14.784 1.00 1.00 ATOM 61 CA GLY 60 4.376 17.658 -18.480 1.00 1.00 ATOM 62 CA LYS 61 8.144 17.751 -18.128 1.00 1.00 ATOM 63 CA GLN 62 8.317 14.709 -15.881 1.00 1.00 ATOM 64 CA PHE 63 6.695 12.571 -18.551 1.00 1.00 ATOM 65 CA ARG 64 6.400 15.030 -21.413 1.00 1.00 ATOM 66 CA SER 68 2.630 14.929 -21.731 1.00 1.00 ATOM 67 CA GLN 69 -0.214 17.327 -21.031 1.00 1.00 ATOM 68 CA VAL 70 -1.734 17.734 -17.589 1.00 1.00 ATOM 69 CA VAL 71 -4.588 19.699 -16.066 1.00 1.00 ATOM 70 CA ILE 72 -5.985 19.983 -12.560 1.00 1.00 ATOM 71 CA GLU 73 -9.581 18.811 -12.713 1.00 1.00 ATOM 72 CA LYS 74 -12.007 17.843 -9.973 1.00 1.00 ATOM 73 CA GLY 75 -11.993 20.744 -7.543 1.00 1.00 ATOM 74 CA GLU 76 -8.743 22.519 -6.758 1.00 1.00 ATOM 75 CA LEU 77 -10.755 24.881 -4.591 1.00 1.00 ATOM 76 CA GLY 78 -10.498 22.212 -1.919 1.00 1.00 ATOM 77 CA ARG 79 -7.007 21.268 -3.036 1.00 1.00 ATOM 78 CA HIS 80 -8.384 17.821 -3.775 1.00 1.00 ATOM 79 CA LYS 81 -8.943 17.630 -7.513 1.00 1.00 ATOM 80 CA GLN 82 -8.292 15.397 -10.499 1.00 1.00 ATOM 81 CA ILE 83 -5.256 15.685 -12.741 1.00 1.00 ATOM 82 CA LYS 84 -6.324 15.247 -16.346 1.00 1.00 ATOM 83 CA ILE 85 -3.523 14.150 -18.643 1.00 1.00 ATOM 84 CA ILE 86 -3.889 14.729 -22.366 1.00 1.00 ATOM 85 CA ASN 87 -2.373 12.400 -24.936 1.00 1.00 ATOM 86 CA ILE 91 -1.672 10.004 -22.090 1.00 1.00 ATOM 87 CA PRO 92 -3.411 6.891 -20.821 1.00 1.00 ATOM 88 CA PRO 93 -3.408 4.557 -17.842 1.00 1.00 ATOM 89 CA GLU 94 -0.418 2.376 -18.636 1.00 1.00 ATOM 90 CA VAL 95 1.386 5.610 -19.420 1.00 1.00 ATOM 91 CA ALA 96 0.875 7.170 -16.009 1.00 1.00 ATOM 92 CA ALA 97 1.495 3.786 -14.430 1.00 1.00 ATOM 93 CA LEU 98 4.516 3.198 -16.633 1.00 1.00 ATOM 94 CA ILE 99 6.112 6.356 -15.290 1.00 1.00 TER END ################################ # # # END # # # ################################