[INFO] Console - predicting pockets for proteins from dataset [dpp9.pdb]
[INFO] PredictPocketsRoutine - outdir: /oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_dpp9
[INFO] FeatureSetup - enabledFeatures: [chem, volsite, protrusion, bfactor, atom_table]
[INFO] Dataset - processing dataset [dpp9.pdb] using 0 threads
[INFO] Dataset - 
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processing [dpp9.pdb] (1/1)
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[INFO] Console - processing [dpp9.pdb] (1/1)
[INFO] Protein - loading protein [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/proteins/dpp9.pdb]
[INFO] PdbUtils - loading file [../proteins/dpp9.pdb]
[INFO] Struct - groups in chain A: 863
[INFO] Struct - groups in chain A: 863
[INFO] Struct - 863 groups in chain A
[INFO] Protein - structure atoms: 6944
[INFO] Protein - protein   atoms: 6805
[INFO] Protein - ignoring ligands
[INFO] FeatureSetup - enabledFeatures: [chem, volsite, protrusion, bfactor, atom_table]
[INFO] Protein - SAS points: 11568
[INFO] Protein - exposed protein atoms: 4221 of 6805
[INFO] InstancePredictor - Creating WekaInstancePredictor
[INFO] SLinkClusterer - clustering [198] elements
[INFO] SLinkClusterer - clusters: [id:4( 7 ), id:5( 1 ), id:11( 2 ), id:22( 2 ), id:37( 41 ), id:54( 1 ), id:56( 7 ), id:67( 1 ), id:68( 1 ), id:73( 1 ), id:76( 1 ), id:80( 7 ), id:85( 4 ), id:121( 31 ), id:123( 17 ), id:132( 21 ), id:147( 1 ), id:148( 3 ), id:156( 1 ), id:176( 34 ), id:177( 1 ), id:178( 1 ), id:186( 9 ), id:187( 1 ), id:188( 1 ), id:195( 1 )]
[INFO] SLinkClusterer - clusters together: 198 / 198
[INFO] PocketPredictor - PREDICTING POCKETS.... ====================================
[INFO] PocketPredictor - SAS POINTS: 11568
[INFO] PocketPredictor - LIGANDABLE POINTS: 198
[INFO] PocketPredictor - CLUSTERS: 26
[INFO] PocketPredictor - FILTERED CLUSTERS: 11
[INFO] PocketPredictor - pocket 1 -  surf_atoms:  69   points:  41   score:   13.7
[INFO] PocketPredictor - pocket 2 -  surf_atoms:  32   points:  34   score:   13.1
[INFO] PocketPredictor - pocket 3 -  surf_atoms:  51   points:  31   score:    9.7
[INFO] PocketPredictor - pocket 4 -  surf_atoms:  34   points:  21   score:    8.6
[INFO] PocketPredictor - pocket 5 -  surf_atoms:  22   points:  17   score:    4.4
[INFO] PocketPredictor - pocket 6 -  surf_atoms:  18   points:   9   score:    2.7
[INFO] PocketPredictor - pocket 7 -  surf_atoms:  21   points:   7   score:    2.2
[INFO] PocketPredictor - pocket 8 -  surf_atoms:  13   points:   7   score:    2.2
[INFO] PocketPredictor - pocket 9 -  surf_atoms:  17   points:   7   score:    2.1
[INFO] PocketPredictor - pocket10 -  surf_atoms:  23   points:   4   score:    1.4
[INFO] PocketPredictor - pocket11 -  surf_atoms:   8   points:   3   score:    0.8
[INFO] OldPymolRenderer - copying [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/proteins/dpp9.pdb] to [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_dpp9/visualizations/data/dpp9.pdb]
[INFO] Console - predicting pockets finished in 0 hours 0 minutes 11.498 seconds
[INFO] Console - results saved to directory [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_dpp9]
[INFO] Console - 
[INFO] Console - Finished successfully in 0 hours 0 minutes 13.029 seconds.