From mailer@bialko.llnl.gov Mon Aug 12 21:23:18 2002 Date: Mon, 12 Aug 2002 21:23:13 -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 Mon Aug 12 20:55:18 PDT 2002 by Adam Zemla # # The PIN number of your submission is: PIN_676805_21248 # (PIN number is not an ACCESSION CODE) # Thank you for your submission. Your prediction has been accepted with an ACCESSION CODE: T0180SS389_1 Current information on models submitted in prediction T0180SS389 MODEL_INDEX PIN CODE DATE E-mail T0180SS389_1 PIN_676805_21248 1549-8716-6404 08/12/02 20:55:18 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 T0180 MODEL_INDEX PIN CODE DATE E-mail T0180SS389_1 PIN_676805_21248 1549-8716-6404 08/12/02 20:55:18 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 T0180 AUTHOR 1549-8716-6404 # Reading MODEL 1 # Reading prediction format SS (DONE) # Checking the SS prediction MODEL 1 # Checking the SS prediction MODEL 1 (DONE) # MODEL index: 1 # Total number of residues in model: 53 # Number of residues with nonzero confidence: 53 # Number of METHOD records: 65 # No errors. ################################ # # # SUBMISSION # # # ################################ # # # BEGIN # # # ################################ PFRMAT SS TARGET T0180 AUTHOR 1549-8716-6404 METHOD CAFASP METHOD samt02_dssp_ehl METHOD This file is the result of combining several RDB files, specifically METHOD T0180.t2k.dssp-ebghstl.rdb (weight 1.53986) METHOD T0180.t2k.stride-ebghtl.rdb (weight 1.24869) METHOD T0180.t2k.str.rdb (weight 1.53983) METHOD These files were combined by translating their predictions into EHL METHOD predictions with tables generated by compare-real, and then combining METHOD those predictions with weights proportional to their mutual information METHOD with the EHL alphabet. The comments from the individual files follow. METHOD METHOD Comments from T0180.t2k.dssp-ebghstl.rdb METHOD ============================================ METHOD TARGET T0180 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 T0180.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 1 METHOD METHOD ============================================ METHOD Comments from T0180.t2k.stride-ebghtl.rdb METHOD ============================================ METHOD TARGET T0180 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 T0180.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 1 METHOD METHOD ============================================ METHOD Comments from T0180.t2k.str.rdb METHOD ============================================ METHOD TARGET T0180 METHOD Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str-seeded.net METHOD This is a 4-layer network, with METHOD window units METHOD 5 15 METHOD 7 15 METHOD 9 15 METHOD 13 13 (1 str ) METHOD The input amino acid frequencies were determined from METHOD alignment T0180.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 1 METHOD METHOD ============================================ MODEL 1 M C 0.95 V C 0.77 G C 0.78 R C 0.74 R C 0.80 P C 0.84 G C 0.87 G C 0.87 G C 0.79 L C 0.67 K C 0.68 D C 0.74 T C 0.77 K C 0.74 P C 0.59 V E 0.79 V E 0.89 V E 0.90 R E 0.88 L E 0.68 Y C 0.69 P C 0.60 D C 0.50 E H 0.67 I H 0.72 E H 0.70 A H 0.69 L H 0.67 K H 0.63 S H 0.49 R C 0.57 V C 0.74 P C 0.81 A C 0.69 N C 0.67 T C 0.56 S H 0.48 M H 0.73 S H 0.81 A H 0.86 Y H 0.88 I H 0.90 R H 0.91 R H 0.90 I H 0.90 I H 0.86 L H 0.83 N H 0.70 H H 0.58 L C 0.49 E C 0.62 D C 0.80 D C 0.98 END END ################################ # # # END # # # ################################ From mailer@bialko.llnl.gov Mon Aug 19 12:47:08 2002 Date: Mon, 19 Aug 2002 12:47:02 -0700 (PDT) From: Automatic Reply To: karplus@soe.ucsc.edu Subject: T0180 TS samt02.pdb 1 X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK # # Protein Structure Prediction Center, LLNL, Livermore, CA # Verification system Mon Aug 19 12:19:03 PDT 2002 by Adam Zemla # # The PIN number of your submission is: PIN_320892_27875 # (PIN number is not an ACCESSION CODE) # Thank you for your submission. Your prediction has been accepted with an ACCESSION CODE: T0180TS189_1 Current information on models submitted in prediction T0180TS189 MODEL_INDEX PIN CODE DATE E-mail T0180TS189_1 PIN_320892_27875 5035-2079-5263 08/19/02 12:19:03 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 T0180 MODEL_INDEX PIN CODE DATE E-mail T0180TS189_1 PIN_320892_27875 5035-2079-5263 08/19/02 12:19:03 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 T0180 AUTHOR 5035-2079-5263 # Reading MODEL 1 PARENT 1D2Z_A # Loading PARENT structure: 1d2z (chain: A) # Number of residues in PARENT structure: 102 # Reading prediction format TS (DONE) # Checking the TS prediction MODEL 1 # IMPORTANT NOTE! Not complete main chain atoms for residue V 18 # !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! # # 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 R 19 # IMPORTANT NOTE! Not complete main chain atoms for residue L 20 # IMPORTANT NOTE! Not complete main chain atoms for residue Y 21 # IMPORTANT NOTE! Not complete main chain atoms for residue P 22 # IMPORTANT NOTE! Not complete main chain atoms for residue D 23 # IMPORTANT NOTE! Not complete main chain atoms for residue E 24 # IMPORTANT NOTE! Not complete main chain atoms for residue I 25 # IMPORTANT NOTE! Not complete main chain atoms for residue E 26 # IMPORTANT NOTE! Not complete main chain atoms for residue A 27 # IMPORTANT NOTE! Not complete main chain atoms for residue L 28 # IMPORTANT NOTE! Not complete main chain atoms for residue K 29 # IMPORTANT NOTE! Not complete main chain atoms for residue S 30 # IMPORTANT NOTE! Not complete main chain atoms for residue R 31 # IMPORTANT NOTE! Not complete main chain atoms for residue V 32 # IMPORTANT NOTE! Not complete main chain atoms for residue P 33 # IMPORTANT NOTE! Not complete main chain atoms for residue A 34 # IMPORTANT NOTE! Not complete main chain atoms for residue N 35 # IMPORTANT NOTE! Not complete main chain atoms for residue T 36 # IMPORTANT NOTE! Not complete main chain atoms for residue S 37 # IMPORTANT NOTE! Not complete main chain atoms for residue M 38 # IMPORTANT NOTE! Not complete main chain atoms for residue S 39 # IMPORTANT NOTE! Not complete main chain atoms for residue A 40 # IMPORTANT NOTE! Not complete main chain atoms for residue Y 41 # IMPORTANT NOTE! Not complete main chain atoms for residue I 42 # IMPORTANT NOTE! Not complete main chain atoms for residue R 43 # IMPORTANT NOTE! Not complete main chain atoms for residue R 44 # IMPORTANT NOTE! Not complete main chain atoms for residue I 45 # IMPORTANT NOTE! Not complete main chain atoms for residue I 46 # IMPORTANT NOTE! Not complete main chain atoms for residue L 47 # IMPORTANT NOTE! Not complete main chain atoms for residue N 48 # IMPORTANT NOTE! Not complete main chain atoms for residue H 49 # Checking the TS prediction MODEL 1 (DONE) # MODEL index: 1 # Target name: T0180 # Total number of residues in target: 53 # Total number of residues in model: 32 # Total number of atoms in model: 32 # Number of atoms with 1.0 occupancy: 32 # Number of fragments in model: 1 # Number of METHOD records: 1 # No errors. # Number of Warnings: 32 ################################ # # # SUBMISSION # # # ################################ # # # BEGIN # # # ################################ PFRMAT TS TARGET T0180 AUTHOR 5035-2079-5263 METHOD CAFASP MODEL 1 PARENT 1D2Z_A ATOM 62 CA VAL 18 23.447 42.480 34.925 1.00 1.00 ATOM 63 CA ARG 19 20.041 40.782 34.728 1.00 1.00 ATOM 64 CA LEU 20 20.776 38.324 31.910 1.00 1.00 ATOM 65 CA TYR 21 17.658 36.563 30.613 1.00 1.00 ATOM 66 CA PRO 22 16.770 32.895 31.342 1.00 1.00 ATOM 67 CA ASP 23 17.993 31.658 27.956 1.00 1.00 ATOM 68 CA GLU 24 21.329 33.472 28.459 1.00 1.00 ATOM 69 CA ILE 25 21.707 32.094 32.002 1.00 1.00 ATOM 70 CA GLU 26 20.942 28.585 30.725 1.00 1.00 ATOM 71 CA ALA 27 23.435 28.985 27.868 1.00 1.00 ATOM 72 CA LEU 28 26.149 29.710 30.465 1.00 1.00 ATOM 73 CA LYS 29 25.073 26.880 32.783 1.00 1.00 ATOM 74 CA SER 30 24.939 24.609 29.736 1.00 1.00 ATOM 75 CA ARG 31 28.453 25.491 28.565 1.00 1.00 ATOM 76 CA VAL 32 29.776 24.878 32.074 1.00 1.00 ATOM 77 CA PRO 33 28.245 21.386 32.253 1.00 1.00 ATOM 78 CA ALA 34 30.074 20.665 28.978 1.00 1.00 ATOM 79 CA ASN 35 33.390 21.415 30.707 1.00 1.00 ATOM 80 CA THR 36 33.779 24.950 29.334 1.00 1.00 ATOM 81 CA SER 37 34.479 28.192 31.190 1.00 1.00 ATOM 82 CA MET 38 31.319 29.656 32.697 1.00 1.00 ATOM 83 CA SER 39 32.771 33.148 33.026 1.00 1.00 ATOM 84 CA ALA 40 34.102 33.140 29.458 1.00 1.00 ATOM 85 CA TYR 41 30.571 32.347 28.273 1.00 1.00 ATOM 86 CA ILE 42 29.263 35.207 30.418 1.00 1.00 ATOM 87 CA ARG 43 31.768 37.527 28.694 1.00 1.00 ATOM 88 CA ARG 44 30.732 36.109 25.299 1.00 1.00 ATOM 89 CA ILE 45 27.092 37.009 26.007 1.00 1.00 ATOM 90 CA ILE 46 27.366 40.262 27.977 1.00 1.00 ATOM 91 CA LEU 47 30.396 41.588 26.101 1.00 1.00 ATOM 92 CA ASN 48 29.499 40.160 22.717 1.00 1.00 ATOM 93 CA HIS 49 25.860 41.109 22.254 1.00 1.00 TER END ################################ # # # END # # # ################################ From mailer@bialko.llnl.gov Mon Aug 19 12:52:29 2002 Date: Mon, 19 Aug 2002 12:52:23 -0700 (PDT) From: Automatic Reply To: karplus@soe.ucsc.edu Subject: T0180 TS samt02.pdb 2 X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK # # Protein Structure Prediction Center, LLNL, Livermore, CA # Verification system Mon Aug 19 12:24:25 PDT 2002 by Adam Zemla # # The PIN number of your submission is: PIN_373644_27891 # (PIN number is not an ACCESSION CODE) # Thank you for your submission. Your prediction has been accepted with an ACCESSION CODE: T0180TS189_2 Current information on models submitted in prediction T0180TS189 MODEL_INDEX PIN CODE DATE E-mail T0180TS189_2 PIN_373644_27891 5035-2079-5263 08/19/02 12:24:25 casp5@bialko.llnl.gov T0180TS189_1 PIN_320892_27875 5035-2079-5263 08/19/02 12:19:03 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 T0180 MODEL_INDEX PIN CODE DATE E-mail T0180TS189_1 PIN_320892_27875 5035-2079-5263 08/19/02 12:19:03 casp5@bialko.llnl.gov T0180TS189_2 PIN_373644_27891 5035-2079-5263 08/19/02 12:24:25 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 T0180 AUTHOR 5035-2079-5263 # Reading MODEL 2 PARENT 1QQF_A # Loading PARENT structure: 1qqf (chain: A) # Number of residues in PARENT structure: 276 # Reading prediction format TS (DONE) # Checking the TS prediction MODEL 2 # IMPORTANT NOTE! Not complete main chain atoms for residue R 4 # !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! # # 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 R 5 # IMPORTANT NOTE! Not complete main chain atoms for residue P 6 # IMPORTANT NOTE! Not complete main chain atoms for residue G 7 # IMPORTANT NOTE! Not complete main chain atoms for residue G 8 # IMPORTANT NOTE! Not complete main chain atoms for residue G 9 # IMPORTANT NOTE! Not complete main chain atoms for residue L 10 # IMPORTANT NOTE! Not complete main chain atoms for residue K 11 # IMPORTANT NOTE! Not complete main chain atoms for residue D 12 # IMPORTANT NOTE! Not complete main chain atoms for residue T 13 # IMPORTANT NOTE! Not complete main chain atoms for residue K 14 # IMPORTANT NOTE! Not complete main chain atoms for residue P 15 # IMPORTANT NOTE! Not complete main chain atoms for residue V 16 # IMPORTANT NOTE! Not complete main chain atoms for residue V 17 # IMPORTANT NOTE! Not complete main chain atoms for residue Y 21 # IMPORTANT NOTE! Not complete main chain atoms for residue P 22 # IMPORTANT NOTE! Not complete main chain atoms for residue D 23 # IMPORTANT NOTE! Not complete main chain atoms for residue E 24 # IMPORTANT NOTE! Not complete main chain atoms for residue I 25 # IMPORTANT NOTE! Not complete main chain atoms for residue E 26 # IMPORTANT NOTE! Not complete main chain atoms for residue A 27 # IMPORTANT NOTE! Not complete main chain atoms for residue L 28 # IMPORTANT NOTE! Not complete main chain atoms for residue K 29 # IMPORTANT NOTE! Not complete main chain atoms for residue S 30 # IMPORTANT NOTE! Not complete main chain atoms for residue R 31 # IMPORTANT NOTE! Not complete main chain atoms for residue V 32 # IMPORTANT NOTE! Not complete main chain atoms for residue P 33 # IMPORTANT NOTE! Not complete main chain atoms for residue A 34 # IMPORTANT NOTE! Not complete main chain atoms for residue N 35 # IMPORTANT NOTE! Not complete main chain atoms for residue T 36 # IMPORTANT NOTE! Not complete main chain atoms for residue S 37 # IMPORTANT NOTE! Not complete main chain atoms for residue M 38 # IMPORTANT NOTE! Not complete main chain atoms for residue S 39 # IMPORTANT NOTE! Not complete main chain atoms for residue A 40 # IMPORTANT NOTE! Not complete main chain atoms for residue Y 41 # IMPORTANT NOTE! Not complete main chain atoms for residue I 42 # IMPORTANT NOTE! Not complete main chain atoms for residue R 43 # IMPORTANT NOTE! Not complete main chain atoms for residue R 44 # IMPORTANT NOTE! Not complete main chain atoms for residue I 45 # IMPORTANT NOTE! Not complete main chain atoms for residue I 46 # Checking the TS prediction MODEL 2 (DONE) # MODEL index: 2 # Target name: T0180 # Total number of residues in target: 53 # Total number of residues in model: 40 # Total number of atoms in model: 40 # Number of atoms with 1.0 occupancy: 40 # Number of fragments in model: 1 # Number of METHOD records: 1 # No errors. # Number of Warnings: 40 ################################ # # # SUBMISSION # # # ################################ # # # BEGIN # # # ################################ PFRMAT TS TARGET T0180 AUTHOR 5035-2079-5263 METHOD CAFASP MODEL 2 PARENT 1QQF_A ATOM 1112 CA ARG 4 68.918 41.204 17.898 1.00 1.00 ATOM 1113 CA ARG 5 70.076 42.834 14.672 1.00 1.00 ATOM 1114 CA PRO 6 71.719 46.291 14.471 1.00 1.00 ATOM 1115 CA GLY 7 68.404 47.865 13.371 1.00 1.00 ATOM 1116 CA GLY 8 66.784 46.577 16.566 1.00 1.00 ATOM 1117 CA GLY 9 64.791 43.711 15.043 1.00 1.00 ATOM 1118 CA LEU 10 64.762 40.291 16.670 1.00 1.00 ATOM 1119 CA LYS 11 65.127 37.261 14.411 1.00 1.00 ATOM 1120 CA ASP 12 63.684 33.806 14.752 1.00 1.00 ATOM 1121 CA THR 13 66.119 31.090 13.554 1.00 1.00 ATOM 1122 CA LYS 14 64.187 28.111 15.021 1.00 1.00 ATOM 1123 CA PRO 15 60.450 28.538 14.681 1.00 1.00 ATOM 1124 CA VAL 16 58.284 26.712 17.194 1.00 1.00 ATOM 1125 CA VAL 17 56.559 23.463 16.248 1.00 1.00 ATOM 1126 CA TYR 21 53.409 24.492 18.057 1.00 1.00 ATOM 1127 CA PRO 22 52.520 27.430 15.810 1.00 1.00 ATOM 1128 CA ASP 23 49.133 27.720 17.509 1.00 1.00 ATOM 1129 CA GLU 24 50.771 28.965 20.755 1.00 1.00 ATOM 1130 CA ILE 25 52.182 32.200 19.302 1.00 1.00 ATOM 1131 CA GLU 26 48.925 34.065 18.646 1.00 1.00 ATOM 1132 CA ALA 27 48.786 36.666 15.871 1.00 1.00 ATOM 1133 CA LEU 28 52.506 36.267 15.080 1.00 1.00 ATOM 1134 CA LYS 29 51.432 33.106 13.256 1.00 1.00 ATOM 1135 CA SER 30 50.139 35.393 10.474 1.00 1.00 ATOM 1136 CA ARG 31 53.566 36.250 9.096 1.00 1.00 ATOM 1137 CA VAL 32 52.559 39.535 7.609 1.00 1.00 ATOM 1138 CA PRO 33 54.541 42.261 9.471 1.00 1.00 ATOM 1139 CA ALA 34 56.346 39.527 11.371 1.00 1.00 ATOM 1140 CA ASN 35 59.478 41.593 12.162 1.00 1.00 ATOM 1141 CA THR 36 57.205 43.991 13.995 1.00 1.00 ATOM 1142 CA SER 37 55.201 41.255 15.711 1.00 1.00 ATOM 1143 CA MET 38 58.300 39.503 16.956 1.00 1.00 ATOM 1144 CA SER 39 60.256 42.642 17.872 1.00 1.00 ATOM 1145 CA ALA 40 57.259 44.040 19.810 1.00 1.00 ATOM 1146 CA TYR 41 56.694 40.671 21.534 1.00 1.00 ATOM 1147 CA ILE 42 60.346 40.385 22.578 1.00 1.00 ATOM 1148 CA ARG 43 60.535 44.056 23.618 1.00 1.00 ATOM 1149 CA ARG 44 57.505 43.570 25.916 1.00 1.00 ATOM 1150 CA ILE 45 59.032 40.367 27.421 1.00 1.00 ATOM 1151 CA ILE 46 62.288 42.223 27.993 1.00 1.00 TER END ################################ # # # END # # # ################################