mqaprna.py ver: 52e618e-dirty start 2017-08-31 16:42:07 -------------------------- ---------------------------------------------------- Seq ss fn /home/mqapRNA/mqapRNAweb/media/jobs/db813e65-a24a-4cc8-b86d-de31ab500197/ss.txt Output csv /home/mqapRNA/mqapRNAweb/media/jobs/db813e65-a24a-4cc8-b86d-de31ab500197/db813e6_raw.csv Input files #5 ['input/1y26_rpr_refx.pdb', 'input/ade_npk_dca_slope_3-500f3ee2_ALL_thrs7.20A_clust01-000001_AA_refx.pdb', 'input/ade_npk_dca_slope_x2-0adc8423_ALL_thrs7.20A_clust01-000001_AA_refx.pdb'] RNAkb 5pt Model path /home/magnus/Dropbox/WORK_/mqaprna-papier/SVMlin.rda Multiprocessing on Verbose off Ignore pdb fn off Methods ClashScore,AnalyzeGeometry,FARNA,SimRNA_0,RNAscore,eSCORE,RNAkb,SSAgreement,FARNA_hires,RASP,RNAkb_all rmsd biopython_all Native pdb off RASP all -------------------------- ---------------------------------------------------- AnalyzeGeometry on SSAgreement on pdb_id >seq ref_seq CGCUUCAUAUAAUCCUAAUGAUAUGGUUUGGGAGUUUCUACCAAGAGCCUUAAACUCUUGAUUAUGAAGUG ref_ss (((((((((...((((((......[[.))))))........((((((]].....))))))..))))))))) to ignore 0 [] files to analyze: 5 ['input/1y26_rpr_refx.pdb', 'input/ade_npk_dca_slope_3-500f3ee2_ALL_thrs7.20A_clust01-000001_AA_refx.pdb', 'input/ade_npk_dca_slope_x2-0adc8423_ALL_thrs7.20A_clust01-000001_AA_refx.pdb', 'input/ade_pk-35b2a2c1_ALL_thrs7.20A_clust01-000001_AA_refx.pdb', 'input/ade_pk_dca_slope_3-23341152-thrs7.10A_clust01X_refx.pdb'] -------------------------------------------------------------------------------- 3dRNAscore::err [---------------- ] 1 20.0 % 5 10 True ade_npk_dca_slope_3-500f3ee2_ALL_thrs7.20A_clust01-000001_AA_refx.pdb {'AnalyzeGeometry': 14.0845, 'eSCORE': 1.77446, 'FARNA': ['-32.255', '-1.952', '-20.753', '-130.854', '-16.754', '-275.959', '26.195', '3.517', '-9.305', '-438.757', '0.0', '0.0', '19.364', '0.0'], 'ClashScore': 0.0, 'length': 71, 'SimRNA_0': ['0', '-693.471767', '-344.263', '-115.704', '-0.796', '-348.412395', '-48.116', '-54.918', '-49.798', '-42.659', '-152.922', '', '-693.471767'], 'FARNA_hires': ['0.0', '-392.788', '-5.977', '0.0', '1.504', '8.369', '-366.126', '5.265', '-175.636', '2.956', '-89.55', '16.324', '-2.028', '201.878', '10.232'], 'RNAscore': 16.9394, 'RASP': ['0.8899', '760', '0.00117092', '6.59976', '2.08903', '-2.73326', '-6858.28', '45502', '-0.150725', '-6699.4', '35.8965', '-4.42606', '-16249.1', '104809', '-0.155036', '-15622', '71.9584', '-8.71485', '-40716.5', '353945', '-0.115036', '0', '0', '0'], 'RNAkb': ['7.53723e+03', '4.19269e+03', '6.38102e+03', '2.08829e+00', '0.00000e+00', '0.00000e+00', '-1.23557e-03', '0.00000e+00', '1.81130e+04', '1.13060e-09', '1.81130e+04'], 'RNAkb_all': ['7.53723e+03', '4.19269e+03', '6.38102e+03', '2.08829e+00', '0.00000e+00', '0.00000e+00', '-7.83862e-04', '0.00000e+00', '1.81130e+04', '1.13060e-09', '1.81130e+04'], 'SSAgreement': '0.851'} [-------------------------------- ] 2 40.0 % 5 10 True ade_pk-35b2a2c1_ALL_thrs7.20A_clust01-000001_AA_refx.pdb {'AnalyzeGeometry': 19.7183, 'eSCORE': 1.79858, 'FARNA': ['-33.169', '-6.597', '-24.959', '-131.414', '-19.468', '-284.735', '27.602', '14.658', '-15.341', '-453.868', '0.0', '0.0', '19.555', '0.0'], 'ClashScore': 0.442674, 'length': 71, 'SimRNA_0': ['0', '-673.152581', '-352.086', '-112.029', '-0.940', '-320.125882', '-48.521', '-54.726', '-49.889', '-35.853', '-131.137', '', '-673.152581'], 'FARNA_hires': ['0.0', '-398.529', '-4.127', '0.0', '1.931', '8.514', '-344.912', '8.379', '-180.373', '3.999', '-92.734', '14.841', '-20.774', '190.763', '15.965'], 'RNAscore': 17.7447, 'RASP': ['1.557', '767', '0.00202999', '7.14028', '2.65452', '-2.10331', '-6219.04', '46354', '-0.134164', '-6101.16', '41.5393', '-2.8379', '-15379.6', '106103', '-0.14495', '-14716.3', '84.1742', '-7.88088', '-36942.7', '370942', '-0.0995915', '0', '0', '0'], 'RNAkb': ['7.51482e+03', '4.32335e+03', '6.45076e+03', '1.71689e+00', '0.00000e+00', '0.00000e+00', '-1.09492e-03', '0.00000e+00', '1.82906e+04', '1.12918e-09', '1.82906e+04'], 'RNAkb_all': ['7.51482e+03', '4.32335e+03', '6.45076e+03', '1.71689e+00', '0.00000e+00', '0.00000e+00', '-7.01357e-04', '0.00000e+00', '1.82906e+04', '1.12918e-09', '1.82906e+04'], 'SSAgreement': '0.906'} [------------------------------------------------ ] 3 60.0 % 5 10 True ade_npk_dca_slope_x2-0adc8423_ALL_thrs7.20A_clust01-000001_AA_refx.pdb {'AnalyzeGeometry': 12.6761, 'eSCORE': 1.73865, 'FARNA': ['-27.886', '-4.86', '-20.987', '-115.116', '-16.008', '-255.738', '23.716', '4.713', '-11.148', '-403.823', '0.0', '0.0', '19.49', '0.0'], 'ClashScore': 0.885347, 'length': 71, 'SimRNA_0': -1, 'FARNA_hires': ['0.0', '-380.52', '-2.816', '0.0', '1.592', '8.978', '-331.53', '6.477', '-174.652', '1.873', '-93.076', '18.858', '-9.082', '179.829', '13.028'], 'RNAscore': 16.8904, 'RASP': ['1.7436', '752', '0.00231862', '5.96169', '2.98301', '-1.41404', '-6606.15', '45095', '-0.146494', '-6520.79', '39.8378', '-2.14261', '-16247.1', '103172', '-0.157476', '-15699', '76.6124', '-7.15533', '-40429.3', '347639', '-0.116297', '0', '0', '0'], 'RNAkb': ['7.58961e+03', '4.37655e+03', '6.37781e+03', '1.51673e+00', '0.00000e+00', '0.00000e+00', '-2.24518e-03', '0.00000e+00', '1.83455e+04', '1.14091e-09', '1.83455e+04'], 'RNAkb_all': ['7.58961e+03', '4.37655e+03', '6.37781e+03', '1.51673e+00', '0.00000e+00', '0.00000e+00', '-7.55936e-04', '0.00000e+00', '1.83455e+04', '1.14091e-09', '1.83455e+04'], 'SSAgreement': '0.913'} [---------------------------------------------------------------- ] 4 80.0 % 5 10 True 1y26_rpr_refx.pdb {'AnalyzeGeometry': 25.3521, 'eSCORE': 1.71473, 'FARNA': ['-33.438', '-10.668', '-29.559', '-137.355', '-22.518', '-296.97', '12.091', '11.418', '-20.784', '-508.004', '0.0', '0.0', '19.779', '0.0'], 'ClashScore': 0.0, 'length': 71, 'SimRNA_0': ['0', '-641.440219', '-339.100', '-100.743', '-1.821', '-300.519704', '-43.907', '-52.824', '-35.182', '-33.611', '-134.995', '', '-641.440219'], 'FARNA_hires': ['0.0', '-448.893', '-1.362', '0.0', '2.066', '8.004', '-399.67', '4.702', '-184.38', '1.415', '-103.203', '11.771', '-11.643', '196.352', '27.056'], 'RNAscore': 17.6475, 'RASP': ['-5.7006', '790', '-0.00721595', '4.85766', '3.19223', '-3.30749', '-6188.76', '47391', '-0.130589', '-5807.48', '43.2824', '-8.80915', '-14543.4', '110366', '-0.131774', '-13261.2', '103.311', '-12.4109', '-35231.2', '383462', '-0.0918767', '0', '0', '0'], 'RNAkb': ['7.48774e+03', '4.28584e+03', '6.41421e+03', '1.46322e+00', '0.00000e+00', '0.00000e+00', '-9.43569e-04', '0.00000e+00', '1.81892e+04', '1.12456e-09', '1.81892e+04'], 'RNAkb_all': ['7.48774e+03', '4.28584e+03', '6.41421e+03', '1.46322e+00', '0.00000e+00', '0.00000e+00', '-7.27514e-04', '0.00000e+00', '1.81892e+04', '1.12456e-09', '1.81892e+04'], 'SSAgreement': '0.959'} [--------------------------------------------------------------------------------] 5 100.0 % 5 10 True ade_pk_dca_slope_3-23341152-thrs7.10A_clust01X_refx.pdb {'AnalyzeGeometry': 22.5352, 'eSCORE': 'error', 'FARNA': ['-30.339', '-2.311', '-21.1', '-128.181', '-17.672', '-282.391', '14.12', '18.12', '-29.839', '-459.716', '0.0', '0.0', '19.877', '0.0'], 'ClashScore': 0.449438, 'length': 71, 'SimRNA_0': -1, 'FARNA_hires': ['0.0', '-403.568', '-1.527', '0.0', '1.792', '9.299', '-340.44', '6.919', '-178.241', '3.144', '-99.749', '14.27', '-18.541', '181.357', '18.15'], 'RNAscore': -1, 'RASP': ['1.9613', '776', '0.00252745', '5.90139', '2.64192', '-1.49137', '-5894.42', '46627', '-0.126416', '-5818.91', '33.9354', '-2.22509', '-14842.1', '108212', '-0.137158', '-14280.3', '70.3573', '-7.98615', '-37470', '377806', '-0.0991778', '0', '0', '0'], 'RNAkb': -1, 'RNAkb_all': -1, 'SSAgreement': '0.883'} Cmd: mqaprna.py -s /home/mqapRNA/mqapRNAweb/media/jobs/db813e65-a24a-4cc8-b86d-de31ab500197/ss.txt -m 6 -f -o /home/mqapRNA/mqapRNAweb/media/jobs/db813e65-a24a-4cc8-b86d-de31ab500197/db813e6_raw.csv input/1y26_rpr_refx.pdb input/ade_npk_dca_slope_3-500f3ee2_ALL_thrs7.20A_clust01-000001_AA_refx.pdb input/ade_npk_dca_slope_x2-0adc8423_ALL_thrs7.20A_clust01-000001_AA_refx.pdb input/ade_pk-35b2a2c1_ALL_thrs7.20A_clust01-000001_AA_refx.pdb input/ade_pk_dca_slope_3-23341152-thrs7.10A_clust01X_refx.pdb Execution time: 0:04:51.536 process: 6 start: 16:42:07 end: 16:46:58 Output: /home/mqapRNA/mqapRNAweb/media/jobs/db813e65-a24a-4cc8-b86d-de31ab500197/db813e6_raw.csv logging: /home/mqapRNA/mqapRNAweb/media/jobs/db813e65-a24a-4cc8-b86d-de31ab500197/db813e6_raw.log logging wrappers /home/mqapRNA/mqaprna_env/log/ in: /home/mqapRNA/mqapRNAweb/media/jobs/db813e65-a24a-4cc8-b86d-de31ab500197/db813e6_raw.csv model_key: grid-8a6dfea4-1f6e-4354-9396-f727a5bd937a_model_14 Checking whether there is an H2O instance running at http://localhost:54321..... not found. Attempting to start a local H2O server... Java Version: java version "1.8.0_131"; Java(TM) SE Runtime Environment (build 1.8.0_131-b11); Java HotSpot(TM) 64-Bit Server VM (build 25.131-b11, mixed mode) Starting server from /usr/local/lib/python2.7/dist-packages/h2o/backend/bin/h2o.jar Ice root: /tmp/tmpncRen3 JVM stdout: /tmp/tmpncRen3/h2o_unknownUser_started_from_python.out JVM stderr: /tmp/tmpncRen3/h2o_unknownUser_started_from_python.err Server is running at http://127.0.0.1:54321 Connecting to H2O server at http://127.0.0.1:54321... successful. Warning: Your H2O cluster version is too old (4 months and 11 days)! Please download and install the latest version from http://h2o.ai/download/ -------------------------- ---------------------------------- H2O cluster uptime: 03 secs H2O cluster version: 3.10.4.5 H2O cluster version age: 4 months and 11 days !!! H2O cluster name: H2O_from_python_unknownUser_zcqhq7 H2O cluster total nodes: 1 H2O cluster free memory: 1.742 Gb H2O cluster total cores: 8 H2O cluster allowed cores: 8 H2O cluster status: accepting new members, healthy H2O connection url: http://127.0.0.1:54321 H2O connection proxy: H2O internal security: False Python version: 2.7.6 final -------------------------- ---------------------------------- Parse progress: [#########################################################] 100% fn clash_score analyze_geometry farna_rna_base_axis farna_rna_backbone_backbone farna_rna_base_stack_axis farna_rna_base_stagger farna_rna_base_stack farna_rna_base_pair farna_rna_repulsive farna_rna_vdw farna_rna_base_backbone farna_score_lowres farna_rna_data_backbone farna_linear_chainbreak farna_rna_rg farna_atom_pair_constraint simrna_steps simrna_total_energy simrna_base_base simrna_short_stacking simrna_base_backbone simrna_local_geometry simrna_bonds_dist_cp simrna_bonds_dist_pc simrna_flat_angles_cpc simrna_flat_angles_pcp simrna_tors_eta_theta simrna_sphere_penalty simrna_chain_energy x3rnascore escore rnakb_bond rnakb_angle rnakb_proper_dih rnakb_improper_dih rnakb_lj14 rnakb_coulomb14 rnakb_lj_sr rnakb_coulomb_sr rnakb_potential rnakb_kinetic_en rnakb_total_energy ss_disagreement farna_atom_pair_constraint_hires farna_score_hires farna_hbond_sr_bb_sc farna_linear_chainbreak_hires farna_fa_intra_rep farna_rna_sugar_close farna_hbond_sc farna_lk_nonpolar farna_fa_atr farna_fa_elec_rna_phos_phos farna_ch_bond farna_fa_rep farna_hbond_lr_bb_sc farna_geom_sol farna_rna_torsion rasp_c3_pdb_energy rasp_c3_no_contacts rasp_c3_norm_energy rasp_c3_mean_energy rasp_c3_sd_energy rasp_c3_zscore rasp_bb_pdb_energy rasp_bb_no_contacts rasp_bb_norm_energy rasp_bb_mean_energy rasp_bb_sd_energy rasp_bb_zscore rasp_bbr_pdb_energy rasp_bbr_no_contacts rasp_bbr_norm_energy rasp_bbr_mean_energy rasp_bbr_sd_energy rasp_bbr_zscore rasp_all_pdb_energy rasp_all_no_contacts rasp_all_norm_energy rasp_all_mean_energy rasp_all_sd_energy rasp_all_zscore rnakb_bond_all rnakb_angle_all rnakb_proper_dih_all rnakb_improper_dih_all rnakb_lj14_all rnakb_coulomb14_all rnakb_lj_sr_all rnakb_coulomb_sr_all rnakb_potential_all rnakb_kinetic_en_all rnakb_total_energy_all ---------------------------------------------------------------------- ------------- ------------------ --------------------- ----------------------------- --------------------------- ------------------------ ---------------------- --------------------- --------------------- --------------- ------------------------- -------------------- ------------------------- ------------------------- -------------- ---------------------------- -------------- --------------------- ------------------ ----------------------- ---------------------- ----------------------- ---------------------- ---------------------- ------------------------ ------------------------ ----------------------- ----------------------- --------------------- 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---------------------- ---------------------- -------------------- ----------------- ---------------- ----------------- ---------------------- ------------------------ ---------------- --------------------- ----------------- ---------------------- --------------------- ---------------------- ------------------------ ade_npk_dca_slope_3-500f3ee2_ALL_thrs7.20A_clust01-000001_AA_refx.pdb 0 14.0845 -32.255 -1.952 -20.753 -130.854 -16.754 -275.959 26.195 3.517 -9.305 -438.757 0 0 19.364 0 0 -693.472 -344.263 -115.704 -0.796 -348.412 -48.116 -54.918 -49.798 -42.659 -152.922 nan -693.472 16.9394 1.77446 7537.23 4192.69 6381.02 2.08829 0 0 -0.00123557 0 18113 1.1306e-09 18113 0.851 0 -392.788 -5.977 0 1.504 8.369 -366.126 5.265 -175.636 2.956 -89.55 16.324 -2.028 201.878 10.232 0.8899 760 0.00117092 6.59976 2.08903 -2.73326 -6858.28 45502 -0.150725 -6699.4 35.8965 -4.42606 -16249.1 104809 -0.155036 -15622 71.9584 -8.71485 -40716.5 353945 -0.115036 0 0 0 7537.23 4192.69 6381.02 2.08829 0 0 -0.000783862 0 18113 1.1306e-09 18113 ade_pk-35b2a2c1_ALL_thrs7.20A_clust01-000001_AA_refx.pdb 0.442674 19.7183 -33.169 -6.597 -24.959 -131.414 -19.468 -284.735 27.602 14.658 -15.341 -453.868 0 0 19.555 0 0 -673.153 -352.086 -112.029 -0.94 -320.126 -48.521 -54.726 -49.889 -35.853 -131.137 nan -673.153 17.7447 1.79858 7514.82 4323.35 6450.76 1.71689 0 0 -0.00109492 0 18290.6 1.12918e-09 18290.6 0.906 0 -398.529 -4.127 0 1.931 8.514 -344.912 8.379 -180.373 3.999 -92.734 14.841 -20.774 190.763 15.965 1.557 767 0.00202999 7.14028 2.65452 -2.10331 -6219.04 46354 -0.134164 -6101.16 41.5393 -2.8379 -15379.6 106103 -0.14495 -14716.3 84.1742 -7.88088 -36942.7 370942 -0.0995915 0 0 0 7514.82 4323.35 6450.76 1.71689 0 0 -0.000701357 0 18290.6 1.12918e-09 18290.6 ade_npk_dca_slope_x2-0adc8423_ALL_thrs7.20A_clust01-000001_AA_refx.pdb 0.885347 12.6761 -27.886 -4.86 -20.987 -115.116 -16.008 -255.738 23.716 4.713 -11.148 -403.823 0 0 19.49 0 -1 16.8904 1.73865 7589.61 4376.55 6377.81 1.51673 0 0 -0.00224518 0 18345.5 1.14091e-09 18345.5 0.913 0 -380.52 -2.816 0 1.592 8.978 -331.53 6.477 -174.652 1.873 -93.076 18.858 -9.082 179.829 13.028 1.7436 752 0.00231862 5.96169 2.98301 -1.41404 -6606.15 45095 -0.146494 -6520.79 39.8378 -2.14261 -16247.1 103172 -0.157476 -15699 76.6124 -7.15533 -40429.3 347639 -0.116297 0 0 0 7589.61 4376.55 6377.81 1.51673 0 0 -0.000755936 0 18345.5 1.14091e-09 18345.5 nan nan nan nan nan nan nan nan nan nan nan nan 1y26_rpr_refx.pdb 0 25.3521 -33.438 -10.668 -29.559 -137.355 -22.518 -296.97 12.091 11.418 -20.784 -508.004 0 0 19.779 0 0 -641.44 -339.1 -100.743 -1.821 -300.52 -43.907 -52.824 -35.182 -33.611 -134.995 nan -641.44 17.6475 1.71473 7487.74 4285.84 6414.21 1.46322 0 0 -0.000943569 0 18189.2 1.12456e-09 18189.2 0.959 0 -448.893 -1.362 0 2.066 8.004 -399.67 4.702 -184.38 1.415 -103.203 11.771 -11.643 196.352 27.056 -5.7006 790 -0.00721595 4.85766 3.19223 -3.30749 -6188.76 47391 -0.130589 -5807.48 43.2824 -8.80915 -14543.4 110366 -0.131774 -13261.2 103.311 -12.4109 -35231.2 383462 -0.0918767 0 0 0 7487.74 4285.84 6414.21 1.46322 0 0 -0.000727514 0 18189.2 1.12456e-09 18189.2 ade_pk_dca_slope_3-23341152-thrs7.10A_clust01X_refx.pdb 0.449438 22.5352 -30.339 -2.311 -21.1 -128.181 -17.672 -282.391 14.12 18.12 -29.839 -459.716 0 0 19.877 0 -1 -1 nan -1 0.883 0 -403.568 -1.527 0 1.792 9.299 -340.44 6.919 -178.241 3.144 -99.749 14.27 -18.541 181.357 18.15 1.9613 776 0.00252745 5.90139 2.64192 -1.49137 -5894.42 46627 -0.126416 -5818.91 33.9354 -2.22509 -14842.1 108212 -0.137158 -14280.3 70.3573 -7.98615 -37470 377806 -0.0991778 0 0 0 -1 nan nan nan nan nan nan nan nan nan nan nan nan nan nan nan nan nan nan nan nan nan nan nan nan nan nan nan nan nan nan nan nan [5 rows x 94 columns] deeplearning prediction progress: [#######################################] 100% deeplearning prediction progress: [#######################################] 100% mqapRNA ----------- 1.4921 1.68898 1.99861e+07 1.09063 2.8128e+07 [5 rows x 1 column] fn ---------------------------------------------------------------------- ade_npk_dca_slope_3-500f3ee2_ALL_thrs7.20A_clust01-000001_AA_refx.pdb ade_pk-35b2a2c1_ALL_thrs7.20A_clust01-000001_AA_refx.pdb ade_npk_dca_slope_x2-0adc8423_ALL_thrs7.20A_clust01-000001_AA_refx.pdb 1y26_rpr_refx.pdb ade_pk_dca_slope_3-23341152-thrs7.10A_clust01X_refx.pdb [5 rows x 1 column] Exporting to /home/mqapRNA/mqapRNAweb/media/jobs/db813e65-a24a-4cc8-b86d-de31ab500197/db813e6_raw_mqapRNA.csv Export File progress: [###################################################] 100% clash_score \ fn 1y26_rpr_refx.pdb 0.000000 ade_npk_dca_slope_3-500f3ee2_ALL_thrs7.20A_clus... 0.000000 ade_pk-35b2a2c1_ALL_thrs7.20A_clust01-000001_AA... 0.442674 ade_npk_dca_slope_x2-0adc8423_ALL_thrs7.20A_clu... 0.885347 ade_pk_dca_slope_3-23341152-thrs7.10A_clust01X_... 0.449438 analyze_geometry \ fn 1y26_rpr_refx.pdb 25.3521 ade_npk_dca_slope_3-500f3ee2_ALL_thrs7.20A_clus... 14.0845 ade_pk-35b2a2c1_ALL_thrs7.20A_clust01-000001_AA... 19.7183 ade_npk_dca_slope_x2-0adc8423_ALL_thrs7.20A_clu... 12.6761 ade_pk_dca_slope_3-23341152-thrs7.10A_clust01X_... 22.5352 farna_rna_base_axis \ fn 1y26_rpr_refx.pdb -33.438 ade_npk_dca_slope_3-500f3ee2_ALL_thrs7.20A_clus... -32.255 ade_pk-35b2a2c1_ALL_thrs7.20A_clust01-000001_AA... -33.169 ade_npk_dca_slope_x2-0adc8423_ALL_thrs7.20A_clu... -27.886 ade_pk_dca_slope_3-23341152-thrs7.10A_clust01X_... -30.339 farna_rna_backbone_backbone \ fn 1y26_rpr_refx.pdb -10.668 ade_npk_dca_slope_3-500f3ee2_ALL_thrs7.20A_clus... -1.952 ade_pk-35b2a2c1_ALL_thrs7.20A_clust01-000001_AA... -6.597 ade_npk_dca_slope_x2-0adc8423_ALL_thrs7.20A_clu... -4.860 ade_pk_dca_slope_3-23341152-thrs7.10A_clust01X_... -2.311 farna_rna_base_stack_axis \ fn 1y26_rpr_refx.pdb -29.559 ade_npk_dca_slope_3-500f3ee2_ALL_thrs7.20A_clus... -20.753 ade_pk-35b2a2c1_ALL_thrs7.20A_clust01-000001_AA... -24.959 ade_npk_dca_slope_x2-0adc8423_ALL_thrs7.20A_clu... -20.987 ade_pk_dca_slope_3-23341152-thrs7.10A_clust01X_... -21.100 farna_rna_base_stagger \ fn 1y26_rpr_refx.pdb -137.355 ade_npk_dca_slope_3-500f3ee2_ALL_thrs7.20A_clus... -130.854 ade_pk-35b2a2c1_ALL_thrs7.20A_clust01-000001_AA... -131.414 ade_npk_dca_slope_x2-0adc8423_ALL_thrs7.20A_clu... -115.116 ade_pk_dca_slope_3-23341152-thrs7.10A_clust01X_... -128.181 farna_rna_base_stack \ fn 1y26_rpr_refx.pdb -22.518 ade_npk_dca_slope_3-500f3ee2_ALL_thrs7.20A_clus... -16.754 ade_pk-35b2a2c1_ALL_thrs7.20A_clust01-000001_AA... -19.468 ade_npk_dca_slope_x2-0adc8423_ALL_thrs7.20A_clu... -16.008 ade_pk_dca_slope_3-23341152-thrs7.10A_clust01X_... -17.672 farna_rna_base_pair \ fn 1y26_rpr_refx.pdb -296.970 ade_npk_dca_slope_3-500f3ee2_ALL_thrs7.20A_clus... -275.959 ade_pk-35b2a2c1_ALL_thrs7.20A_clust01-000001_AA... -284.735 ade_npk_dca_slope_x2-0adc8423_ALL_thrs7.20A_clu... -255.738 ade_pk_dca_slope_3-23341152-thrs7.10A_clust01X_... -282.391 farna_rna_repulsive \ fn 1y26_rpr_refx.pdb 12.091 ade_npk_dca_slope_3-500f3ee2_ALL_thrs7.20A_clus... 26.195 ade_pk-35b2a2c1_ALL_thrs7.20A_clust01-000001_AA... 27.602 ade_npk_dca_slope_x2-0adc8423_ALL_thrs7.20A_clu... 23.716 ade_pk_dca_slope_3-23341152-thrs7.10A_clust01X_... 14.120 farna_rna_vdw \ fn 1y26_rpr_refx.pdb 11.418 ade_npk_dca_slope_3-500f3ee2_ALL_thrs7.20A_clus... 3.517 ade_pk-35b2a2c1_ALL_thrs7.20A_clust01-000001_AA... 14.658 ade_npk_dca_slope_x2-0adc8423_ALL_thrs7.20A_clu... 4.713 ade_pk_dca_slope_3-23341152-thrs7.10A_clust01X_... 18.120 ... \ fn ... 1y26_rpr_refx.pdb ... ade_npk_dca_slope_3-500f3ee2_ALL_thrs7.20A_clus... ... ade_pk-35b2a2c1_ALL_thrs7.20A_clust01-000001_AA... ... ade_npk_dca_slope_x2-0adc8423_ALL_thrs7.20A_clu... ... ade_pk_dca_slope_3-23341152-thrs7.10A_clust01X_... ... rnakb_proper_dih_all \ fn 1y26_rpr_refx.pdb 6414.21 ade_npk_dca_slope_3-500f3ee2_ALL_thrs7.20A_clus... 6381.02 ade_pk-35b2a2c1_ALL_thrs7.20A_clust01-000001_AA... 6450.76 ade_npk_dca_slope_x2-0adc8423_ALL_thrs7.20A_clu... NaN ade_pk_dca_slope_3-23341152-thrs7.10A_clust01X_... NaN rnakb_improper_dih_all \ fn 1y26_rpr_refx.pdb 1.46322 ade_npk_dca_slope_3-500f3ee2_ALL_thrs7.20A_clus... 2.08829 ade_pk-35b2a2c1_ALL_thrs7.20A_clust01-000001_AA... 1.71689 ade_npk_dca_slope_x2-0adc8423_ALL_thrs7.20A_clu... NaN ade_pk_dca_slope_3-23341152-thrs7.10A_clust01X_... NaN rnakb_lj14_all \ fn 1y26_rpr_refx.pdb 0.0 ade_npk_dca_slope_3-500f3ee2_ALL_thrs7.20A_clus... 0.0 ade_pk-35b2a2c1_ALL_thrs7.20A_clust01-000001_AA... 0.0 ade_npk_dca_slope_x2-0adc8423_ALL_thrs7.20A_clu... NaN ade_pk_dca_slope_3-23341152-thrs7.10A_clust01X_... NaN rnakb_coulomb14_all \ fn 1y26_rpr_refx.pdb 0.0 ade_npk_dca_slope_3-500f3ee2_ALL_thrs7.20A_clus... 0.0 ade_pk-35b2a2c1_ALL_thrs7.20A_clust01-000001_AA... 0.0 ade_npk_dca_slope_x2-0adc8423_ALL_thrs7.20A_clu... NaN ade_pk_dca_slope_3-23341152-thrs7.10A_clust01X_... NaN rnakb_lj_sr_all \ fn 1y26_rpr_refx.pdb -0.000728 ade_npk_dca_slope_3-500f3ee2_ALL_thrs7.20A_clus... -0.000784 ade_pk-35b2a2c1_ALL_thrs7.20A_clust01-000001_AA... -0.000701 ade_npk_dca_slope_x2-0adc8423_ALL_thrs7.20A_clu... NaN ade_pk_dca_slope_3-23341152-thrs7.10A_clust01X_... NaN rnakb_coulomb_sr_all \ fn 1y26_rpr_refx.pdb 0.0 ade_npk_dca_slope_3-500f3ee2_ALL_thrs7.20A_clus... 0.0 ade_pk-35b2a2c1_ALL_thrs7.20A_clust01-000001_AA... 0.0 ade_npk_dca_slope_x2-0adc8423_ALL_thrs7.20A_clu... NaN ade_pk_dca_slope_3-23341152-thrs7.10A_clust01X_... NaN rnakb_potential_all \ fn 1y26_rpr_refx.pdb 18189.2 ade_npk_dca_slope_3-500f3ee2_ALL_thrs7.20A_clus... 18113.0 ade_pk-35b2a2c1_ALL_thrs7.20A_clust01-000001_AA... 18290.6 ade_npk_dca_slope_x2-0adc8423_ALL_thrs7.20A_clu... NaN ade_pk_dca_slope_3-23341152-thrs7.10A_clust01X_... NaN rnakb_kinetic_en_all \ fn 1y26_rpr_refx.pdb 1.124560e-09 ade_npk_dca_slope_3-500f3ee2_ALL_thrs7.20A_clus... 1.130600e-09 ade_pk-35b2a2c1_ALL_thrs7.20A_clust01-000001_AA... 1.129180e-09 ade_npk_dca_slope_x2-0adc8423_ALL_thrs7.20A_clu... NaN ade_pk_dca_slope_3-23341152-thrs7.10A_clust01X_... NaN rnakb_total_energy_all \ fn 1y26_rpr_refx.pdb 18189.2 ade_npk_dca_slope_3-500f3ee2_ALL_thrs7.20A_clus... 18113.0 ade_pk-35b2a2c1_ALL_thrs7.20A_clust01-000001_AA... 18290.6 ade_npk_dca_slope_x2-0adc8423_ALL_thrs7.20A_clu... NaN ade_pk_dca_slope_3-23341152-thrs7.10A_clust01X_... NaN mqapRNA fn 1y26_rpr_refx.pdb 1.090631e+00 ade_npk_dca_slope_3-500f3ee2_ALL_thrs7.20A_clus... 1.492095e+00 ade_pk-35b2a2c1_ALL_thrs7.20A_clust01-000001_AA... 1.688980e+00 ade_npk_dca_slope_x2-0adc8423_ALL_thrs7.20A_clu... 1.998609e+07 ade_pk_dca_slope_3-23341152-thrs7.10A_clust01X_... 2.812800e+07 [5 rows x 94 columns] mqapRNA fn 1y26_rpr_refx.pdb 1.090631e+00 ade_npk_dca_slope_3-500f3ee2_ALL_thrs7.20A_clus... 1.492095e+00 ade_pk-35b2a2c1_ALL_thrs7.20A_clust01-000001_AA... 1.688980e+00 ade_npk_dca_slope_x2-0adc8423_ALL_thrs7.20A_clu... 1.998609e+07 ade_pk_dca_slope_3-23341152-thrs7.10A_clust01X_... 2.812800e+07 saved /home/mqapRNA/mqapRNAweb/media/jobs/db813e65-a24a-4cc8-b86d-de31ab500197/db813e6_mqapRNA.csv H2O session _sid_910d closed. fn clash_score escore mqapRNA \ 3 1y26_rpr_refx.pdb 0.000000 0.640641 0.000000e+00 0 ade_npk_dca_slope_3- 0.000000 0.613868 1.427276e-08 1 ade_pk-35b2a2c1_ALL_ 0.500001 0.603057 2.127235e-08 2 ade_npk_dca_slope_x2 1.000000 1.000000 7.105406e-01 4 ade_pk_dca_slope_3-2 0.507641 0.000000 1.000000e+00 farna_score_lowres ss_disagreement simrna_total_energy rnakb_lj_sr \ 3 0.000000 0.003027 0.073247 0.299341 0 0.664680 0.003045 0.000000 0.299341 1 0.519634 0.003036 0.028604 0.299341 2 1.000000 0.000000 1.000000 0.000000 4 0.463501 1.000000 0.974815 1.000000 x3rnascore analyze_geometry 3 0.010575 1.000000 0 0.010537 0.111108 1 0.010580 0.555554 2 1.000000 0.000000 4 0.000000 0.777777 ploting to /home/mqapRNA/mqapRNAweb/media/jobs/db813e65-a24a-4cc8-b86d-de31ab500197/plot.png [OK]