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[INFO] Console - predicting pockets for proteins from dataset [lrp2.pdb] |
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[INFO] PredictPocketsRoutine - outdir: /oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_lrp2 |
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[INFO] FeatureSetup - enabledFeatures: [chem, volsite, protrusion, bfactor, atom_table] |
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[INFO] Dataset - processing dataset [lrp2.pdb] using 0 threads |
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[INFO] Dataset - |
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processing [lrp2.pdb] (1/1) |
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[INFO] Console - processing [lrp2.pdb] (1/1) |
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[INFO] Protein - loading protein [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/proteins/lrp2.pdb] |
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[INFO] PdbUtils - loading file [../proteins/lrp2.pdb] |
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[INFO] Struct - groups in chain A: 1225 |
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[INFO] Struct - groups in chain A: 1225 |
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[INFO] Struct - 1225 groups in chain A |
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[INFO] Protein - structure atoms: 9491 |
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[INFO] Protein - protein atoms: 9319 |
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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: 25950 |
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[INFO] Protein - exposed protein atoms: 7174 of 9319 |
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[INFO] InstancePredictor - Creating WekaInstancePredictor |
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[INFO] SLinkClusterer - clustering [140] elements |
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[INFO] SLinkClusterer - clusters: [id:1( 2 ), id:2( 1 ), id:4( 2 ), id:5( 1 ), id:13( 1 ), id:23( 1 ), id:27( 20 ), id:30( 3 ), id:46( 9 ), id:50( 1 ), id:57( 1 ), id:60( 2 ), id:64( 9 ), id:66( 1 ), id:68( 6 ), id:80( 22 ), id:82( 1 ), id:91( 6 ), id:96( 1 ), id:99( 7 ), id:114( 1 ), id:117( 3 ), id:118( 1 ), id:119( 1 ), id:124( 23 ), id:126( 1 ), id:128( 1 ), id:129( 2 ), id:134( 5 ), id:136( 2 ), id:137( 1 ), id:138( 1 ), id:139( 1 )] |
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[INFO] SLinkClusterer - clusters together: 140 / 140 |
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[INFO] PocketPredictor - PREDICTING POCKETS.... ==================================== |
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[INFO] PocketPredictor - SAS POINTS: 25950 |
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[INFO] PocketPredictor - LIGANDABLE POINTS: 140 |
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[INFO] PocketPredictor - CLUSTERS: 33 |
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[INFO] PocketPredictor - FILTERED CLUSTERS: 11 |
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[INFO] PocketPredictor - pocket 1 - surf_atoms: 38 points: 23 score: 9.4 |
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[INFO] PocketPredictor - pocket 2 - surf_atoms: 37 points: 22 score: 6.9 |
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[INFO] PocketPredictor - pocket 3 - surf_atoms: 34 points: 20 score: 5.7 |
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[INFO] PocketPredictor - pocket 4 - surf_atoms: 17 points: 9 score: 4.0 |
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[INFO] PocketPredictor - pocket 5 - surf_atoms: 28 points: 9 score: 3.4 |
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[INFO] PocketPredictor - pocket 6 - surf_atoms: 18 points: 6 score: 3.0 |
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[INFO] PocketPredictor - pocket 7 - surf_atoms: 19 points: 6 score: 2.7 |
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[INFO] PocketPredictor - pocket 8 - surf_atoms: 19 points: 7 score: 1.8 |
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[INFO] PocketPredictor - pocket 9 - surf_atoms: 14 points: 5 score: 1.5 |
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[INFO] PocketPredictor - pocket10 - surf_atoms: 11 points: 3 score: 1.1 |
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[INFO] PocketPredictor - pocket11 - surf_atoms: 16 points: 3 score: 1.1 |
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[INFO] OldPymolRenderer - copying [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/proteins/lrp2.pdb] to [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_lrp2/visualizations/data/lrp2.pdb] |
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[INFO] Console - predicting pockets finished in 0 hours 0 minutes 15.607 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_lrp2] |
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[INFO] Console - |
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[INFO] Console - Finished successfully in 0 hours 0 minutes 17.336 seconds. |
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