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[INFO] Console - predicting pockets for proteins from dataset [tbc1d1.pdb] |
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[INFO] PredictPocketsRoutine - outdir: /oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_tbc1d1 |
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[INFO] FeatureSetup - enabledFeatures: [chem, volsite, protrusion, bfactor, atom_table] |
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[INFO] Dataset - processing dataset [tbc1d1.pdb] using 0 threads |
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[INFO] Dataset - |
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processing [tbc1d1.pdb] (1/1) |
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[INFO] Console - processing [tbc1d1.pdb] (1/1) |
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[INFO] Protein - loading protein [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/proteins/tbc1d1.pdb] |
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[INFO] PdbUtils - loading file [../proteins/tbc1d1.pdb] |
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[INFO] Struct - groups in chain A: 1168 |
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[INFO] Struct - groups in chain A: 1168 |
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[INFO] Struct - 1168 groups in chain A |
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[INFO] Protein - structure atoms: 9349 |
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[INFO] Protein - protein atoms: 9182 |
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[INFO] Protein - ignoring ligands |
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[INFO] FeatureSetup - enabledFeatures: [chem, volsite, protrusion, bfactor, atom_table] |
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[INFO] Protein - SAS points: 30597 |
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[INFO] Protein - exposed protein atoms: 7350 of 9182 |
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[INFO] InstancePredictor - Creating WekaInstancePredictor |
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[INFO] SLinkClusterer - clustering [106] elements |
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[INFO] SLinkClusterer - clusters: [id:5( 3 ), id:6( 1 ), id:7( 2 ), id:27( 11 ), id:28( 1 ), id:30( 2 ), id:37( 3 ), id:38( 13 ), id:41( 3 ), id:42( 2 ), id:47( 4 ), id:48( 4 ), id:57( 1 ), id:58( 1 ), id:59( 1 ), id:61( 1 ), id:63( 1 ), id:65( 4 ), id:69( 17 ), id:87( 1 ), id:101( 1 ), id:103( 5 ), id:104( 24 )] |
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[INFO] SLinkClusterer - clusters together: 106 / 106 |
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[INFO] PocketPredictor - PREDICTING POCKETS.... ==================================== |
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[INFO] PocketPredictor - SAS POINTS: 30597 |
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[INFO] PocketPredictor - LIGANDABLE POINTS: 106 |
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[INFO] PocketPredictor - CLUSTERS: 23 |
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[INFO] PocketPredictor - FILTERED CLUSTERS: 11 |
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[INFO] PocketPredictor - pocket 1 - surf_atoms: 55 points: 24 score: 7.6 |
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[INFO] PocketPredictor - pocket 2 - surf_atoms: 31 points: 17 score: 5.3 |
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[INFO] PocketPredictor - pocket 3 - surf_atoms: 24 points: 11 score: 4.6 |
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[INFO] PocketPredictor - pocket 4 - surf_atoms: 22 points: 13 score: 4.6 |
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[INFO] PocketPredictor - pocket 5 - surf_atoms: 24 points: 5 score: 2.1 |
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[INFO] PocketPredictor - pocket 6 - surf_atoms: 17 points: 4 score: 2.0 |
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[INFO] PocketPredictor - pocket 7 - surf_atoms: 20 points: 4 score: 1.7 |
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[INFO] PocketPredictor - pocket 8 - surf_atoms: 14 points: 3 score: 1.6 |
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[INFO] PocketPredictor - pocket 9 - surf_atoms: 15 points: 4 score: 1.4 |
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[INFO] PocketPredictor - pocket10 - surf_atoms: 19 points: 3 score: 1.1 |
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[INFO] PocketPredictor - pocket11 - surf_atoms: 19 points: 3 score: 1.0 |
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[INFO] OldPymolRenderer - copying [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/proteins/tbc1d1.pdb] to [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_tbc1d1/visualizations/data/tbc1d1.pdb] |
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[INFO] Console - predicting pockets finished in 0 hours 0 minutes 15.786 seconds |
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[INFO] Console - results saved to directory [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_tbc1d1] |
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[INFO] Console - |
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[INFO] Console - Finished successfully in 0 hours 0 minutes 17.240 seconds. |
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