|
|
[INFO] Console - predicting pockets for proteins from dataset [scn10a.pdb] |
|
|
[INFO] PredictPocketsRoutine - outdir: /oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_scn10a |
|
|
[INFO] FeatureSetup - enabledFeatures: [chem, volsite, protrusion, bfactor, atom_table] |
|
|
[INFO] Dataset - processing dataset [scn10a.pdb] using 0 threads |
|
|
[INFO] Dataset - |
|
|
------------------------------------------------------------------------------------------------------------------------ |
|
|
processing [scn10a.pdb] (1/1) |
|
|
------------------------------------------------------------------------------------------------------------------------ |
|
|
|
|
|
[INFO] Console - processing [scn10a.pdb] (1/1) |
|
|
[INFO] Protein - loading protein [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/proteins/scn10a.pdb] |
|
|
[INFO] PdbUtils - loading file [../proteins/scn10a.pdb] |
|
|
[INFO] Struct - groups in chain A: 1956 |
|
|
[INFO] Struct - groups in chain A: 1956 |
|
|
[INFO] Struct - 1956 groups in chain A |
|
|
[INFO] Protein - structure atoms: 15534 |
|
|
[INFO] Protein - protein atoms: 15276 |
|
|
[INFO] Protein - ignoring ligands |
|
|
[INFO] FeatureSetup - enabledFeatures: [chem, volsite, protrusion, bfactor, atom_table] |
|
|
[INFO] Protein - SAS points: 44369 |
|
|
[INFO] Protein - exposed protein atoms: 12132 of 15276 |
|
|
[INFO] InstancePredictor - Creating WekaInstancePredictor |
|
|
[INFO] SLinkClusterer - clustering [680] elements |
|
|
[INFO] SLinkClusterer - clusters: [id:8( 1 ), id:9( 1 ), id:25( 27 ), id:32( 2 ), id:41( 3 ), id:42( 6 ), id:52( 10 ), id:67( 1 ), id:81( 1 ), id:83( 1 ), id:86( 2 ), id:88( 2 ), id:89( 1 ), id:91( 1 ), id:92( 2 ), id:117( 2 ), id:135( 36 ), id:140( 2 ), id:172( 1 ), id:173( 1 ), id:174( 1 ), id:180( 1 ), id:181( 1 ), id:184( 4 ), id:192( 1 ), id:197( 1 ), id:209( 2 ), id:215( 26 ), id:256( 8 ), id:270( 12 ), id:277( 6 ), id:280( 7 ), id:286( 2 ), id:287( 1 ), id:293( 1 ), id:304( 2 ), id:308( 87 ), id:323( 13 ), id:333( 1 ), id:344( 4 ), id:348( 2 ), id:352( 6 ), id:353( 3 ), id:354( 1 ), id:357( 3 ), id:358( 1 ), id:359( 1 ), id:368( 3 ), id:378( 7 ), id:419( 31 ), id:421( 1 ), id:422( 1 ), id:440( 30 ), id:441( 1 ), id:489( 4 ), id:490( 10 ), id:491( 70 ), id:513( 14 ), id:515( 1 ), id:519( 2 ), id:524( 1 ), id:526( 37 ), id:537( 1 ), id:552( 22 ), id:576( 12 ), id:577( 1 ), id:580( 4 ), id:602( 1 ), id:604( 1 ), id:608( 16 ), id:620( 40 ), id:621( 1 ), id:625( 8 ), id:634( 4 ), id:635( 1 ), id:641( 7 ), id:644( 11 ), id:661( 7 ), id:671( 2 ), id:674( 21 ), id:676( 2 ), id:678( 3 ), id:679( 1 )] |
|
|
[INFO] SLinkClusterer - clusters together: 680 / 680 |
|
|
[INFO] PocketPredictor - PREDICTING POCKETS.... ==================================== |
|
|
[INFO] PocketPredictor - SAS POINTS: 44369 |
|
|
[INFO] PocketPredictor - LIGANDABLE POINTS: 680 |
|
|
[INFO] PocketPredictor - CLUSTERS: 83 |
|
|
[INFO] PocketPredictor - FILTERED CLUSTERS: 38 |
|
|
[INFO] PocketPredictor - pocket 1 - surf_atoms: 49 points: 70 score: 34.0 |
|
|
[INFO] PocketPredictor - pocket 2 - surf_atoms: 88 points: 87 score: 27.4 |
|
|
[INFO] PocketPredictor - pocket 3 - surf_atoms: 31 points: 40 score: 21.3 |
|
|
[INFO] PocketPredictor - pocket 4 - surf_atoms: 36 points: 36 score: 17.2 |
|
|
[INFO] PocketPredictor - pocket 5 - surf_atoms: 46 points: 31 score: 14.3 |
|
|
[INFO] PocketPredictor - pocket 6 - surf_atoms: 32 points: 37 score: 12.1 |
|
|
[INFO] PocketPredictor - pocket 7 - surf_atoms: 41 points: 30 score: 10.3 |
|
|
[INFO] PocketPredictor - pocket 8 - surf_atoms: 42 points: 26 score: 9.7 |
|
|
[INFO] PocketPredictor - pocket 9 - surf_atoms: 37 points: 21 score: 8.5 |
|
|
[INFO] PocketPredictor - pocket10 - surf_atoms: 43 points: 27 score: 7.9 |
|
|
[INFO] PocketPredictor - pocket11 - surf_atoms: 27 points: 22 score: 6.8 |
|
|
[INFO] PocketPredictor - pocket12 - surf_atoms: 29 points: 12 score: 5.3 |
|
|
[INFO] PocketPredictor - pocket13 - surf_atoms: 19 points: 10 score: 4.8 |
|
|
[INFO] PocketPredictor - pocket14 - surf_atoms: 20 points: 16 score: 4.7 |
|
|
[INFO] PocketPredictor - pocket15 - surf_atoms: 43 points: 13 score: 4.1 |
|
|
[INFO] PocketPredictor - pocket16 - surf_atoms: 38 points: 14 score: 4.1 |
|
|
[INFO] PocketPredictor - pocket17 - surf_atoms: 25 points: 12 score: 4.1 |
|
|
[INFO] PocketPredictor - pocket18 - surf_atoms: 40 points: 11 score: 3.8 |
|
|
[INFO] PocketPredictor - pocket19 - surf_atoms: 17 points: 8 score: 3.7 |
|
|
[INFO] PocketPredictor - pocket20 - surf_atoms: 21 points: 10 score: 3.4 |
|
|
[INFO] PocketPredictor - pocket21 - surf_atoms: 17 points: 7 score: 3.1 |
|
|
[INFO] PocketPredictor - pocket22 - surf_atoms: 22 points: 7 score: 3.0 |
|
|
[INFO] PocketPredictor - pocket23 - surf_atoms: 25 points: 7 score: 2.9 |
|
|
[INFO] PocketPredictor - pocket24 - surf_atoms: 15 points: 6 score: 2.6 |
|
|
[INFO] PocketPredictor - pocket25 - surf_atoms: 20 points: 8 score: 2.6 |
|
|
[INFO] PocketPredictor - pocket26 - surf_atoms: 21 points: 7 score: 2.3 |
|
|
[INFO] PocketPredictor - pocket27 - surf_atoms: 19 points: 6 score: 2.3 |
|
|
[INFO] PocketPredictor - pocket28 - surf_atoms: 21 points: 4 score: 2.2 |
|
|
[INFO] PocketPredictor - pocket29 - surf_atoms: 12 points: 6 score: 1.6 |
|
|
[INFO] PocketPredictor - pocket30 - surf_atoms: 10 points: 4 score: 1.6 |
|
|
[INFO] PocketPredictor - pocket31 - surf_atoms: 10 points: 4 score: 1.6 |
|
|
[INFO] PocketPredictor - pocket32 - surf_atoms: 13 points: 3 score: 1.6 |
|
|
[INFO] PocketPredictor - pocket33 - surf_atoms: 11 points: 3 score: 1.4 |
|
|
[INFO] PocketPredictor - pocket34 - surf_atoms: 12 points: 4 score: 1.3 |
|
|
[INFO] PocketPredictor - pocket35 - surf_atoms: 13 points: 3 score: 0.9 |
|
|
[INFO] PocketPredictor - pocket36 - surf_atoms: 9 points: 3 score: 0.9 |
|
|
[INFO] PocketPredictor - pocket37 - surf_atoms: 12 points: 3 score: 0.8 |
|
|
[INFO] PocketPredictor - pocket38 - surf_atoms: 7 points: 4 score: 0.7 |
|
|
[INFO] OldPymolRenderer - copying [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/proteins/scn10a.pdb] to [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_scn10a/visualizations/data/scn10a.pdb] |
|
|
[INFO] Console - predicting pockets finished in 0 hours 0 minutes 28.114 seconds |
|
|
[INFO] Console - results saved to directory [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_scn10a] |
|
|
[INFO] Console - |
|
|
[INFO] Console - Finished successfully in 0 hours 0 minutes 29.622 seconds. |
|
|
|
