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[INFO] Console - predicting pockets for proteins from dataset [map3k15.pdb] |
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[INFO] PredictPocketsRoutine - outdir: /oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_map3k15 |
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[INFO] FeatureSetup - enabledFeatures: [chem, volsite, protrusion, bfactor, atom_table] |
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[INFO] Dataset - processing dataset [map3k15.pdb] using 0 threads |
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[INFO] Dataset - |
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processing [map3k15.pdb] (1/1) |
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[INFO] Console - processing [map3k15.pdb] (1/1) |
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[INFO] Protein - loading protein [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/proteins/map3k15.pdb] |
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[INFO] PdbUtils - loading file [../proteins/map3k15.pdb] |
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[INFO] Struct - groups in chain A: 1313 |
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[INFO] Struct - groups in chain A: 1313 |
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[INFO] Struct - 1313 groups in chain A |
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[INFO] Protein - structure atoms: 10370 |
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[INFO] Protein - protein atoms: 10154 |
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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: 28287 |
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[INFO] Protein - exposed protein atoms: 7499 of 10154 |
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[INFO] InstancePredictor - Creating WekaInstancePredictor |
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[INFO] SLinkClusterer - clustering [143] elements |
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[INFO] SLinkClusterer - clusters: [id:0( 1 ), id:1( 1 ), id:3( 2 ), id:4( 1 ), id:7( 3 ), id:8( 1 ), id:42( 5 ), id:53( 2 ), id:58( 47 ), id:75( 3 ), id:76( 9 ), id:78( 4 ), id:82( 1 ), id:83( 1 ), id:84( 2 ), id:105( 2 ), id:108( 7 ), id:120( 20 ), id:123( 3 ), id:128( 4 ), id:133( 2 ), id:141( 21 ), id:142( 1 )] |
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[INFO] SLinkClusterer - clusters together: 143 / 143 |
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[INFO] PocketPredictor - PREDICTING POCKETS.... ==================================== |
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[INFO] PocketPredictor - SAS POINTS: 28287 |
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[INFO] PocketPredictor - LIGANDABLE POINTS: 143 |
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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: 58 points: 47 score: 16.0 |
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[INFO] PocketPredictor - pocket 2 - surf_atoms: 52 points: 20 score: 8.6 |
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[INFO] PocketPredictor - pocket 3 - surf_atoms: 40 points: 21 score: 6.6 |
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[INFO] PocketPredictor - pocket 4 - surf_atoms: 20 points: 9 score: 2.7 |
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[INFO] PocketPredictor - pocket 5 - surf_atoms: 18 points: 4 score: 2.7 |
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[INFO] PocketPredictor - pocket 6 - surf_atoms: 21 points: 7 score: 2.6 |
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[INFO] PocketPredictor - pocket 7 - surf_atoms: 17 points: 5 score: 1.9 |
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[INFO] PocketPredictor - pocket 8 - surf_atoms: 13 points: 4 score: 1.4 |
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[INFO] PocketPredictor - pocket 9 - surf_atoms: 14 points: 3 score: 1.2 |
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[INFO] PocketPredictor - pocket10 - surf_atoms: 17 points: 3 score: 1.0 |
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[INFO] PocketPredictor - pocket11 - surf_atoms: 9 points: 3 score: 0.8 |
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[INFO] OldPymolRenderer - copying [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/proteins/map3k15.pdb] to [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_map3k15/visualizations/data/map3k15.pdb] |
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[INFO] Console - predicting pockets finished in 0 hours 0 minutes 13.170 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_map3k15] |
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[INFO] Console - |
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[INFO] Console - Finished successfully in 0 hours 0 minutes 14.607 seconds. |
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