[INFO] Console - predicting pockets for proteins from dataset [tyk2.pdb] [INFO] PredictPocketsRoutine - outdir: /oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_tyk2 [INFO] FeatureSetup - enabledFeatures: [chem, volsite, protrusion, bfactor, atom_table] [INFO] Dataset - processing dataset [tyk2.pdb] using 0 threads [INFO] Dataset - ------------------------------------------------------------------------------------------------------------------------ processing [tyk2.pdb] (1/1) ------------------------------------------------------------------------------------------------------------------------ [INFO] Console - processing [tyk2.pdb] (1/1) [INFO] Protein - loading protein [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/proteins/tyk2.pdb] [INFO] PdbUtils - loading file [../proteins/tyk2.pdb] [INFO] Struct - groups in chain A: 1187 [INFO] Struct - groups in chain A: 1187 [INFO] Struct - 1187 groups in chain A [INFO] Protein - structure atoms: 9409 [INFO] Protein - protein atoms: 9183 [INFO] Protein - ignoring ligands [INFO] FeatureSetup - enabledFeatures: [chem, volsite, protrusion, bfactor, atom_table] [INFO] Protein - SAS points: 20020 [INFO] Protein - exposed protein atoms: 6164 of 9183 [INFO] InstancePredictor - Creating WekaInstancePredictor [INFO] SLinkClusterer - clustering [326] elements [INFO] SLinkClusterer - clusters: [id:21( 3 ), id:22( 2 ), id:31( 3 ), id:39( 1 ), id:40( 3 ), id:44( 1 ), id:46( 4 ), id:53( 22 ), id:60( 6 ), id:63( 8 ), id:64( 1 ), id:68( 4 ), id:69( 2 ), id:70( 1 ), id:73( 1 ), id:85( 14 ), id:87( 1 ), id:89( 2 ), id:95( 1 ), id:96( 1 ), id:100( 6 ), id:103( 9 ), id:105( 1 ), id:106( 2 ), id:113( 23 ), id:130( 4 ), id:138( 7 ), id:144( 8 ), id:146( 7 ), id:172( 2 ), id:188( 2 ), id:189( 6 ), id:205( 1 ), id:214( 14 ), id:224( 1 ), id:226( 42 ), id:227( 1 ), id:229( 6 ), id:230( 1 ), id:237( 1 ), id:245( 2 ), id:259( 24 ), id:263( 1 ), id:266( 1 ), id:268( 2 ), id:285( 1 ), id:287( 2 ), id:289( 2 ), id:296( 22 ), id:301( 17 ), id:306( 6 ), id:317( 4 ), id:318( 1 ), id:320( 2 ), id:322( 10 ), id:323( 2 ), id:324( 1 ), id:325( 1 )] [INFO] SLinkClusterer - clusters together: 326 / 326 [INFO] PocketPredictor - PREDICTING POCKETS.... ==================================== [INFO] PocketPredictor - SAS POINTS: 20020 [INFO] PocketPredictor - LIGANDABLE POINTS: 326 [INFO] PocketPredictor - CLUSTERS: 58 [INFO] PocketPredictor - FILTERED CLUSTERS: 26 [INFO] PocketPredictor - pocket 1 - surf_atoms: 67 points: 42 score: 12.2 [INFO] PocketPredictor - pocket 2 - surf_atoms: 34 points: 22 score: 8.5 [INFO] PocketPredictor - pocket 3 - surf_atoms: 36 points: 22 score: 7.5 [INFO] PocketPredictor - pocket 4 - surf_atoms: 43 points: 23 score: 7.3 [INFO] PocketPredictor - pocket 5 - surf_atoms: 26 points: 24 score: 7.1 [INFO] PocketPredictor - pocket 6 - surf_atoms: 41 points: 17 score: 6.8 [INFO] PocketPredictor - pocket 7 - surf_atoms: 38 points: 14 score: 4.8 [INFO] PocketPredictor - pocket 8 - surf_atoms: 37 points: 14 score: 4.8 [INFO] PocketPredictor - pocket 9 - surf_atoms: 22 points: 8 score: 3.2 [INFO] PocketPredictor - pocket10 - surf_atoms: 21 points: 6 score: 3.1 [INFO] PocketPredictor - pocket11 - surf_atoms: 28 points: 6 score: 3.1 [INFO] PocketPredictor - pocket12 - surf_atoms: 23 points: 6 score: 3.0 [INFO] PocketPredictor - pocket13 - surf_atoms: 22 points: 9 score: 2.8 [INFO] PocketPredictor - pocket14 - surf_atoms: 20 points: 10 score: 2.6 [INFO] PocketPredictor - pocket15 - surf_atoms: 21 points: 7 score: 2.5 [INFO] PocketPredictor - pocket16 - surf_atoms: 20 points: 4 score: 2.4 [INFO] PocketPredictor - pocket17 - surf_atoms: 19 points: 8 score: 2.3 [INFO] PocketPredictor - pocket18 - surf_atoms: 20 points: 7 score: 2.3 [INFO] PocketPredictor - pocket19 - surf_atoms: 25 points: 6 score: 2.1 [INFO] PocketPredictor - pocket20 - surf_atoms: 21 points: 6 score: 1.8 [INFO] PocketPredictor - pocket21 - surf_atoms: 17 points: 3 score: 1.6 [INFO] PocketPredictor - pocket22 - surf_atoms: 15 points: 3 score: 1.4 [INFO] PocketPredictor - pocket23 - surf_atoms: 10 points: 4 score: 1.3 [INFO] PocketPredictor - pocket24 - surf_atoms: 18 points: 3 score: 1.3 [INFO] PocketPredictor - pocket25 - surf_atoms: 17 points: 4 score: 1.2 [INFO] PocketPredictor - pocket26 - surf_atoms: 15 points: 4 score: 1.0 [INFO] OldPymolRenderer - copying [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/proteins/tyk2.pdb] to [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_tyk2/visualizations/data/tyk2.pdb] [INFO] Console - predicting pockets finished in 0 hours 0 minutes 19.628 seconds [INFO] Console - results saved to directory [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_tyk2] [INFO] Console - [INFO] Console - Finished successfully in 0 hours 0 minutes 20.963 seconds.