[INFO] Console - predicting pockets for proteins from dataset [dpp4.pdb]
[INFO] PredictPocketsRoutine - outdir: /oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_dpp4
[INFO] FeatureSetup - enabledFeatures: [chem, volsite, protrusion, bfactor, atom_table]
[INFO] Dataset - processing dataset [dpp4.pdb] using 0 threads
[INFO] Dataset - 
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processing [dpp4.pdb] (1/1)
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[INFO] Console - processing [dpp4.pdb] (1/1)
[INFO] Protein - loading protein [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/proteins/dpp4.pdb]
[INFO] PdbUtils - loading file [../proteins/dpp4.pdb]
[INFO] Struct - groups in chain A: 766
[INFO] Struct - groups in chain A: 766
[INFO] Struct - 766 groups in chain A
[INFO] Protein - structure atoms: 6238
[INFO] Protein - protein   atoms: 6101
[INFO] Protein - ignoring ligands
[INFO] FeatureSetup - enabledFeatures: [chem, volsite, protrusion, bfactor, atom_table]
[INFO] Protein - SAS points: 10904
[INFO] Protein - exposed protein atoms: 3759 of 6101
[INFO] InstancePredictor - Creating WekaInstancePredictor
[INFO] SLinkClusterer - clustering [143] elements
[INFO] SLinkClusterer - clusters: [id:0( 1 ), id:1( 1 ), id:2( 1 ), id:3( 1 ), id:6( 1 ), id:13( 5 ), id:17( 2 ), id:22( 11 ), id:23( 1 ), id:29( 2 ), id:30( 1 ), id:36( 5 ), id:38( 3 ), id:39( 1 ), id:45( 37 ), id:50( 4 ), id:52( 4 ), id:54( 4 ), id:57( 1 ), id:60( 2 ), id:61( 2 ), id:63( 1 ), id:69( 6 ), id:91( 7 ), id:98( 28 ), id:138( 8 ), id:140( 3 )]
[INFO] SLinkClusterer - clusters together: 143 / 143
[INFO] PocketPredictor - PREDICTING POCKETS.... ====================================
[INFO] PocketPredictor - SAS POINTS: 10904
[INFO] PocketPredictor - LIGANDABLE POINTS: 143
[INFO] PocketPredictor - CLUSTERS: 27
[INFO] PocketPredictor - FILTERED CLUSTERS: 13
[INFO] PocketPredictor - pocket 1 -  surf_atoms:  41   points:  37   score:   11.5
[INFO] PocketPredictor - pocket 2 -  surf_atoms:  47   points:  28   score:    8.8
[INFO] PocketPredictor - pocket 3 -  surf_atoms:  22   points:   8   score:    3.2
[INFO] PocketPredictor - pocket 4 -  surf_atoms:  18   points:  11   score:    3.1
[INFO] PocketPredictor - pocket 5 -  surf_atoms:  26   points:   7   score:    3.0
[INFO] PocketPredictor - pocket 6 -  surf_atoms:  16   points:   5   score:    2.2
[INFO] PocketPredictor - pocket 7 -  surf_atoms:  10   points:   6   score:    1.9
[INFO] PocketPredictor - pocket 8 -  surf_atoms:  18   points:   5   score:    1.8
[INFO] PocketPredictor - pocket 9 -  surf_atoms:  16   points:   4   score:    1.7
[INFO] PocketPredictor - pocket10 -  surf_atoms:  16   points:   4   score:    1.6
[INFO] PocketPredictor - pocket11 -  surf_atoms:  11   points:   4   score:    1.6
[INFO] PocketPredictor - pocket12 -  surf_atoms:  16   points:   3   score:    1.1
[INFO] PocketPredictor - pocket13 -  surf_atoms:   7   points:   3   score:    0.9
[INFO] OldPymolRenderer - copying [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/proteins/dpp4.pdb] to [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_dpp4/visualizations/data/dpp4.pdb]
[INFO] Console - predicting pockets finished in 0 hours 0 minutes 11.892 seconds
[INFO] Console - results saved to directory [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_dpp4]
[INFO] Console - 
[INFO] Console - Finished successfully in 0 hours 0 minutes 13.572 seconds.