mqaprna.py ver: 346e445-dirty start 2020-11-24 04:22:06 -------------------------- ---------------------------------------------------- Seq ss fn /home/mqapRNA/mqapRNAweb/media/jobs/94afabf0-230c-45ac-9b1c-85ae3173cc09/ss.txt Output csv /home/mqapRNA/mqapRNAweb/media/jobs/94afabf0-230c-45ac-9b1c-85ae3173cc09/94afabf_raw.csv Input files #5 ['input/17_Bujnicki_7_rpr.pdb', 'input/17_Das_1_rpr.pdb', 'input/17_Das_4_rpr.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,RNA3DCNN,Dfire rmsd biopython_all Native pdb off RASP all -------------------------- ---------------------------------------------------- AnalyzeGeometry on SSAgreement on pdb_id >seq ref_seq CGUGGUUAGGGCCACGUUAAAUAGUUGCUUAAGCCCUAAGCGUUGAUAAAUAUCAGGUGCAA ref_ss ((((.[[[[[[.))))........((((.....]]]]]]...(((((....)))))..)))) to ignore 0 [] files to analyze: 5 ['input/17_Bujnicki_7_rpr.pdb', 'input/17_Das_1_rpr.pdb', 'input/17_Das_4_rpr.pdb', 'input/17_Dohkolyan_1_rpr.pdb', 'input/17_Major_6_rpr.pdb'] -------------------------------------------------------------------------------- unknown -- error, see /tmp/tmpTAAFVH/err.txt unknown -- error, see /tmp/tmpTAAFVH/err.txt unknown -- error, see /tmp/tmpTAAFVH/err.txt unknown -- error, see /tmp/tmpTAAFVH/err.txt unknown -- error, see /tmp/tmpTAAFVH/err.txt unknown -- error, see /tmp/tmpTAAFVH/err.txt unknown -- error, see /tmp/tmpTAAFVH/err.txt unknown -- error, see /tmp/tmpTAAFVH/err.txt unknown -- error, see /tmp/tmpTAAFVH/err.txt unknown -- error, see /tmp/tmpTAAFVH/err.txt unknown -- error, see /tmp/tmpTAAFVH/err.txt unknown -- error, see /tmp/tmpTAAFVH/err.txt unknown -- error, see /tmp/tmpTAAFVH/err.txt unknown -- error, see /tmp/tmpTAAFVH/err.txt unknown -- error, see /tmp/tmpTAAFVH/err.txt unknown -- error, see /tmp/tmpTAAFVH/err.txt unknown -- error, see /tmp/tmpTAAFVH/err.txt unknown -- error, see /tmp/tmpTAAFVH/err.txt unknown -- error, see /tmp/tmpTAAFVH/err.txt unknown -- error, see /tmp/tmpTAAFVH/err.txt unknown -- error, see /tmp/tmpTAAFVH/err.txt unknown -- error, see /tmp/tmpTAAFVH/err.txt unknown -- error, see /tmp/tmpTAAFVH/err.txt unknown -- error, see /tmp/tmpTAAFVH/err.txt unknown -- error, see /tmp/tmpTAAFVH/err.txt unknown -- error, see /tmp/tmpTAAFVH/err.txt unknown -- error, see /tmp/tmpTAAFVH/err.txt unknown -- error, see /tmp/tmpTAAFVH/err.txt unknown -- error, see /tmp/tmpPWxpD4/err.txt unknown -- error, see /tmp/tmpPWxpD4/err.txt unknown -- error, see /tmp/tmpPWxpD4/err.txt unknown -- error, see /tmp/tmpPWxpD4/err.txt unknown -- error, see /tmp/tmpPWxpD4/err.txt unknown -- error, see /tmp/tmpPWxpD4/err.txt unknown -- error, see /tmp/tmpPWxpD4/err.txt unknown -- error, see /tmp/tmpPWxpD4/err.txt unknown -- error, see /tmp/tmpPWxpD4/err.txt unknown -- error, see /tmp/tmpPWxpD4/err.txt unknown -- error, see /tmp/tmpPWxpD4/err.txt unknown -- error, see /tmp/tmpPWxpD4/err.txt unknown -- error, see /tmp/tmpPWxpD4/err.txt unknown -- error, see /tmp/tmpPWxpD4/err.txt unknown -- error, see /tmp/tmpPWxpD4/err.txt unknown -- error, see /tmp/tmpPWxpD4/err.txt unknown -- error, see /tmp/tmpPWxpD4/err.txt unknown -- error, see /tmp/tmpPWxpD4/err.txt unknown -- error, see /tmp/tmpPWxpD4/err.txt unknown -- error, see /tmp/tmpPWxpD4/err.txt unknown -- error, see /tmp/tmpPWxpD4/err.txt unknown -- error, see /tmp/tmpPWxpD4/err.txt unknown -- error, see /tmp/tmpPWxpD4/err.txt unknown -- error, see /tmp/tmpPWxpD4/err.txt unknown -- error, see /tmp/tmpPWxpD4/err.txt unknown -- error, see /tmp/tmpPWxpD4/err.txt unknown -- error, see /tmp/tmpPWxpD4/err.txt unknown -- error, see /tmp/tmpPWxpD4/err.txt unknown -- error, see /tmp/tmpvFK8j4/err.txt unknown -- error, see /tmp/tmpvFK8j4/err.txt unknown -- error, see /tmp/tmpvFK8j4/err.txt unknown -- error, see /tmp/tmpvFK8j4/err.txt unknown -- error, see /tmp/tmpvFK8j4/err.txt [---------------- ] 1 20.0 % 5 10 True 17_Das_4_rpr.pdb {'AnalyzeGeometry': 22.5806, 'Dfire': -47512.46249, 'eSCORE': 1.43315, 'FARNA': ['-26.525', '-1.027', '-17.909', '-108.973', '-14.302', '-221.889', '13.636', '0.96', '-11.373', '-368.764', '0.0', '0.0', '18.638', '0.0'], 'RNA3DCNN': 9.593173, 'ClashScore': 15.577889, 'length': 62, 'SimRNA_0': ['0', '-547.921961', '-298.538', '-84.436', '-1.117', '-248.266965', '-44.125', '-40.615', '-28.469', '-29.506', '-105.552', '', '-547.921961'], 'FARNA_hires': ['0.0', '-356.837', '-0.153', '0.0', '1.461', '4.543', '-314.55', '8.672', '-148.481', '2.224', '-90.612', '16.314', '-9.024', '168.925', '3.841'], 'RNAscore': 16.5026, 'RASP': ['-0.6548', '636', '-0.00102956', '6.56863', '3.35203', '-2.15494', '-5511.89', '39337', '-0.14012', '-5291.84', '40.8874', '-5.38196', '-12670.2', '89379', '-0.141758', '-11949.6', '78.2526', '-9.2091', '-29371.8', '309432', '-0.0949216', '0', '0', '0'], 'RNAkb': ['5.98349e+03', '2.50340e+03', '5.66775e+03', '6.23377e-01', '0.00000e+00', '0.00000e+00', '-1.75985e-02', '0.00000e+00', '1.41552e+04', '9.50833e-10', '1.41552e+04'], 'RNAkb_all': 255, 'SSAgreement': 'error'} unknown -- error, see /tmp/tmpvFK8j4/err.txt unknown -- error, see /tmp/tmpvFK8j4/err.txt unknown -- error, see /tmp/tmpvFK8j4/err.txt unknown -- error, see /tmp/tmpvFK8j4/err.txt unknown -- error, see /tmp/tmpvFK8j4/err.txt unknown -- error, see /tmp/tmpvFK8j4/err.txt unknown -- error, see /tmp/tmpvFK8j4/err.txt unknown -- error, see /tmp/tmpvFK8j4/err.txt unknown -- error, see /tmp/tmpvFK8j4/err.txt unknown -- error, see /tmp/tmpvFK8j4/err.txt unknown -- error, see /tmp/tmpvFK8j4/err.txt unknown -- error, see /tmp/tmpvFK8j4/err.txt unknown -- error, see /tmp/tmpvFK8j4/err.txt unknown -- error, see /tmp/tmpvFK8j4/err.txt unknown -- error, see /tmp/tmpvFK8j4/err.txt unknown -- error, see /tmp/tmpvFK8j4/err.txt unknown -- error, see /tmp/tmpvFK8j4/err.txt unknown -- error, see /tmp/tmpvFK8j4/err.txt unknown -- error, see /tmp/tmpvFK8j4/err.txt unknown -- error, see /tmp/tmpvFK8j4/err.txt unknown -- error, see /tmp/tmpvFK8j4/err.txt unknown -- error, see /tmp/tmpvFK8j4/err.txt unknown -- error, see /tmp/tmpvFK8j4/err.txt [-------------------------------- ] 2 40.0 % 5 10 True 17_Das_1_rpr.pdb {'AnalyzeGeometry': 17.7419, 'Dfire': -45764.238984, 'eSCORE': 1.43655, 'FARNA': ['-25.941', '-0.781', '-20.339', '-102.772', '-15.772', '-210.313', '10.926', '0.849', '-13.508', '-357.486', '0.0', '0.0', '20.165', '0.0'], 'RNA3DCNN': 6.6659923, 'ClashScore': 8.542714, 'length': 62, 'SimRNA_0': ['0', '-577.595885', '-304.467', '-96.772', '-0.145', '-272.983295', '-49.021', '-47.144', '-32.107', '-35.486', '-109.226', '', '-577.595885'], 'FARNA_hires': ['0.0', '-359.206', '0.0', '0.0', '1.471', '5.196', '-305.984', '7.254', '-156.252', '2.305', '-87.686', '12.931', '-4.166', '162.618', '3.105'], 'RNAscore': 16.1099, 'RASP': ['-3.1964', '583', '-0.00548268', '5.59871', '2.59159', '-3.39371', '-5591.36', '36005', '-0.155294', '-5301.94', '35.4', '-8.17565', '-12988.6', '81838', '-0.158711', '-12107.6', '69.736', '-12.6336', '-30282.5', '283765', '-0.106717', '0', '0', '0'], 'RNAkb': ['5.96636e+03', '2.50310e+03', '5.72950e+03', '6.46352e-01', '0.00000e+00', '0.00000e+00', '-1.66602e-02', '0.00000e+00', '1.41996e+04', '9.48439e-10', '1.41996e+04'], 'RNAkb_all': 255, 'SSAgreement': 'error'} unknown -- error, see /tmp/tmpuVFUrU/err.txt unknown -- error, see /tmp/tmpuVFUrU/err.txt unknown -- error, see /tmp/tmpuVFUrU/err.txt unknown -- error, see /tmp/tmpuVFUrU/err.txt unknown -- error, see /tmp/tmpuVFUrU/err.txt unknown -- error, see /tmp/tmpuVFUrU/err.txt unknown -- error, see /tmp/tmpuVFUrU/err.txt unknown -- error, see /tmp/tmpuVFUrU/err.txt unknown -- error, see /tmp/tmpuVFUrU/err.txt unknown -- error, see /tmp/tmpuVFUrU/err.txt unknown -- error, see /tmp/tmpuVFUrU/err.txt unknown -- error, see /tmp/tmpuVFUrU/err.txt unknown -- error, see /tmp/tmpuVFUrU/err.txt unknown -- error, see /tmp/tmpuVFUrU/err.txt unknown -- error, see /tmp/tmpuVFUrU/err.txt unknown -- error, see /tmp/tmpuVFUrU/err.txt unknown -- error, see /tmp/tmpuVFUrU/err.txt unknown -- error, see /tmp/tmpuVFUrU/err.txt unknown -- error, see /tmp/tmpuVFUrU/err.txt unknown -- error, see /tmp/tmpuVFUrU/err.txt unknown -- error, see /tmp/tmpuVFUrU/err.txt unknown -- error, see /tmp/tmpuVFUrU/err.txt unknown -- error, see /tmp/tmpuVFUrU/err.txt unknown -- error, see /tmp/tmpuVFUrU/err.txt unknown -- error, see /tmp/tmpuVFUrU/err.txt unknown -- error, see /tmp/tmpuVFUrU/err.txt unknown -- error, see /tmp/tmpuVFUrU/err.txt unknown -- error, see /tmp/tmpuVFUrU/err.txt [------------------------------------------------ ] 3 60.0 % 5 10 True 17_Bujnicki_7_rpr.pdb {'AnalyzeGeometry': 11.2903, 'Dfire': -44512.708442, 'eSCORE': 1.40036, 'FARNA': ['-26.41', '-5.748', '-18.393', '-104.358', '-14.32', '-215.78', '7.509', '6.818', '-7.173', '-359.656', '0.0', '0.0', '18.198', '0.0'], 'RNA3DCNN': 12.0295105, 'ClashScore': 1.507538, 'length': 62, 'SimRNA_0': ['0', '-536.728354', '-283.215', '-80.145', '-0.846', '-252.667248', '-37.963', '-47.092', '-36.305', '-27.303', '-104.003', '', '-536.728354'], 'FARNA_hires': ['0.0', '-296.586', '-1.87', '0.0', '1.195', '7.668', '-272.229', '7.609', '-140.549', '2.357', '-78.84', '10.195', '-6.769', '171.206', '3.44'], 'RNAscore': 17.3346, 'RASP': ['-1.5117', '640', '-0.00236203', '4.66615', '2.8368', '-2.17775', '-5280.66', '38946', '-0.135589', '-4999.56', '37.9202', '-7.41299', '-11803.8', '88867', '-0.132825', '-10953.1', '81.7044', '-10.4117', '-26922.2', '300533', '-0.0895815', '0', '0', '0'], 'RNAkb': ['6.63748e+03', '4.08482e+03', '5.46709e+03', '1.25895e+00', '0.00000e+00', '0.00000e+00', '-1.50119e-02', '0.00000e+00', '1.61906e+04', '9.94050e-10', '1.61906e+04'], 'RNAkb_all': 255, 'SSAgreement': 'error'} [---------------------------------------------------------------- ] 4 80.0 % 5 10 True 17_Dohkolyan_1_rpr.pdb {'AnalyzeGeometry': 30.6452, 'Dfire': -44918.363057, 'eSCORE': 0.86939, 'FARNA': ['-15.723', '-5.488', '-5.096', '-53.816', '-5.149', '-185.122', '13.116', '13.214', '-15.346', '-237.606', '0.0', '0.0', '21.803', '0.0'], 'RNA3DCNN': 14.10626, 'ClashScore': 23.61809, 'length': 62, 'SimRNA_0': ['0', '301.394848', '74.484', '-62.316', '111.484', '115.427166', '294.030', '-42.635', '-28.773', '-26.118', '-81.076', '', '301.394848'], 'FARNA_hires': ['0.0', '-234.484', '-1.808', '0.0', '1.534', '15.377', '-217.655', '9.049', '-137.537', '1.368', '-85.604', '10.77', '-17.58', '178.407', '9.196'], 'RNAscore': 18.8536, 'RASP': ['5.606', '636', '0.00881447', '5.70281', '2.8576', '-0.0338795', '-5369.01', '37749', '-0.142229', '-5229.39', '34.9112', '-3.99931', '-12368.4', '88312', '-0.140053', '-11986.5', '69.1014', '-5.52625', '-24195.1', '310238', '-0.0779888', '0', '0', '0'], 'RNAkb': ['6.51020e+03', '4.31257e+03', '7.69595e+03', '2.52520e+02', '0.00000e+00', '0.00000e+00', '-1.44351e-02', '0.00000e+00', '1.87712e+04', '1.01573e-09', '1.87712e+04'], 'RNAkb_all': 255, 'SSAgreement': 'error'} unknown -- error, see /tmp/tmpLpX3mB/err.txt unknown -- error, see /tmp/tmpLpX3mB/err.txt unknown -- error, see /tmp/tmpLpX3mB/err.txt unknown -- error, see /tmp/tmpLpX3mB/err.txt unknown -- error, see /tmp/tmpLpX3mB/err.txt unknown -- error, see /tmp/tmpLpX3mB/err.txt unknown -- error, see /tmp/tmpLpX3mB/err.txt unknown -- error, see /tmp/tmpLpX3mB/err.txt unknown -- error, see /tmp/tmpLpX3mB/err.txt unknown -- error, see /tmp/tmpLpX3mB/err.txt unknown -- error, see /tmp/tmpLpX3mB/err.txt unknown -- error, see /tmp/tmpLpX3mB/err.txt unknown -- error, see /tmp/tmpLpX3mB/err.txt unknown -- error, see /tmp/tmpLpX3mB/err.txt unknown -- error, see /tmp/tmpLpX3mB/err.txt unknown -- error, see /tmp/tmpLpX3mB/err.txt unknown -- error, see /tmp/tmpLpX3mB/err.txt unknown -- error, see /tmp/tmpLpX3mB/err.txt unknown -- error, see /tmp/tmpLpX3mB/err.txt unknown -- error, see /tmp/tmpLpX3mB/err.txt unknown -- error, see /tmp/tmpLpX3mB/err.txt unknown -- error, see /tmp/tmpLpX3mB/err.txt unknown -- error, see /tmp/tmpLpX3mB/err.txt unknown -- error, see /tmp/tmpLpX3mB/err.txt unknown -- error, see /tmp/tmpLpX3mB/err.txt unknown -- error, see /tmp/tmpLpX3mB/err.txt unknown -- error, see /tmp/tmpLpX3mB/err.txt unknown -- error, see /tmp/tmpLpX3mB/err.txt [--------------------------------------------------------------------------------] 5 100.0 % 5 10 True 17_Major_6_rpr.pdb {'AnalyzeGeometry': 51.6129, 'Dfire': -37862.936374, 'eSCORE': 0.58693, 'FARNA': ['-12.245', '-21.407', '-6.439', '-59.165', '-6.805', '-167.109', '53.658', '13.997', '-24.34', '-212.943', '0.0', '0.0', '16.912', '0.0'], 'RNA3DCNN': 25.758287, 'ClashScore': 3.015075, 'length': 62, 'SimRNA_0': ['0', '-213.643135', '-82.771', '-17.374', '0.912', '-131.784132', '-36.482', '-36.334', '-28.376', '4.459', '-35.051', '', '-213.643135'], 'FARNA_hires': ['0.0', '-272.798', '-0.373', '0.0', '2.493', '7.926', '-231.603', '12.324', '-144.355', '4.121', '-91.993', '15.009', '-3.029', '126.077', '30.605'], 'RNAscore': 24.4173, 'RASP': ['2.993', '757', '0.00395376', '6.22725', '3.25028', '-0.995068', '-2982.08', '44679', '-0.0667446', '-2941.01', '35.7732', '-1.14817', '-6128.49', '104153', '-0.0588412', '-6095.64', '74.4018', '-0.441467', '-9883.01', '353719', '-0.0279403', '0', '0', '0'], 'RNAkb': ['6.10016e+03', '3.79112e+03', '6.09487e+03', '1.63691e+01', '0.00000e+00', '0.00000e+00', '-1.25042e-03', '0.00000e+00', '1.60025e+04', '9.69265e-10', '1.60025e+04'], 'RNAkb_all': 255, 'SSAgreement': 'error'} Cmd: mqaprna.py -s /home/mqapRNA/mqapRNAweb/media/jobs/94afabf0-230c-45ac-9b1c-85ae3173cc09/ss.txt -m 6 -f -o /home/mqapRNA/mqapRNAweb/media/jobs/94afabf0-230c-45ac-9b1c-85ae3173cc09/94afabf_raw.csv input/17_Bujnicki_7_rpr.pdb input/17_Das_1_rpr.pdb input/17_Das_4_rpr.pdb input/17_Dohkolyan_1_rpr.pdb input/17_Major_6_rpr.pdb Execution time: 0:05:47.747 process: 6 start: 04:22:06 end: 04:27:54 Output: /home/mqapRNA/mqapRNAweb/media/jobs/94afabf0-230c-45ac-9b1c-85ae3173cc09/94afabf_raw.csv logging: /home/mqapRNA/mqapRNAweb/media/jobs/94afabf0-230c-45ac-9b1c-85ae3173cc09/94afabf_raw.log logging wrappers /home/mqapRNA/mqaprna_env/log/ in: /home/mqapRNA/mqapRNAweb/media/jobs/94afabf0-230c-45ac-9b1c-85ae3173cc09/94afabf_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/tmp1Z7xcM JVM stdout: /tmp/tmp1Z7xcM/h2o_unknownUser_started_from_python.out JVM stderr: /tmp/tmp1Z7xcM/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 (3 years, 7 months and 4 days)! Please download and install the latest version from http://h2o.ai/download/ -------------------------- ---------------------------------- H2O cluster uptime: 04 secs H2O cluster version: 3.10.4.5 H2O cluster version age: 3 years, 7 months and 4 days !!! H2O cluster name: H2O_from_python_unknownUser_2sdzpp 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 rna3dcnn dfire ---------------------- ------------- ------------------ --------------------- ----------------------------- --------------------------- ------------------------ ---------------------- --------------------- --------------------- --------------- ------------------------- -------------------- ------------------------- ------------------------- -------------- ---------------------------- -------------- --------------------- ------------------ ----------------------- ---------------------- ----------------------- ---------------------- ---------------------- ------------------------ ------------------------ ----------------------- ----------------------- --------------------- ------------ -------- ------------ 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-------------------- ----------------- ---------------- ----------------- ---------------------- ------------------------ ---------------- --------------------- ----------------- ---------------------- --------------------- ---------------------- ------------------------ ---------- ------- 17_Das_4_rpr.pdb 15.5779 22.5806 -26.525 -1.027 -17.909 -108.973 -14.302 -221.889 13.636 0.96 -11.373 -368.764 0 0 18.638 0 0 -547.922 -298.538 -84.436 -1.117 -248.267 -44.125 -40.615 -28.469 -29.506 -105.552 nan -547.922 16.5026 1.43315 5983.49 2503.4 5667.75 0.623377 0 0 -0.0175985 0 14155.2 9.50833e-10 14155.2 error 0 -356.837 -0.153 0 1.461 4.543 -314.55 8.672 -148.481 2.224 -90.612 16.314 -9.024 168.925 3.841 -0.6548 636 -0.00102956 6.56863 3.35203 -2.15494 -5511.89 39337 -0.14012 -5291.84 40.8874 -5.38196 -12670.2 89379 -0.141758 -11949.6 78.2526 -9.2091 -29371.8 309432 -0.0949216 0 0 0 255 9.59317 -47512.5 nan nan nan nan nan nan nan nan nan nan 17_Das_1_rpr.pdb 8.54271 17.7419 -25.941 -0.781 -20.339 -102.772 -15.772 -210.313 10.926 0.849 -13.508 -357.486 0 0 20.165 0 0 -577.596 -304.467 -96.772 -0.145 -272.983 -49.021 -47.144 -32.107 -35.486 -109.226 nan -577.596 16.1099 1.43655 5966.36 2503.1 5729.5 0.646352 0 0 -0.0166602 0 14199.6 9.48439e-10 14199.6 error 0 -359.206 0 0 1.471 5.196 -305.984 7.254 -156.252 2.305 -87.686 12.931 -4.166 162.618 3.105 -3.1964 583 -0.00548268 5.59871 2.59159 -3.39371 -5591.36 36005 -0.155294 -5301.94 35.4 -8.17565 -12988.6 81838 -0.158711 -12107.6 69.736 -12.6336 -30282.5 283765 -0.106717 0 0 0 255 6.66599 -45764.2 nan nan nan nan nan nan nan nan nan nan 17_Bujnicki_7_rpr.pdb 1.50754 11.2903 -26.41 -5.748 -18.393 -104.358 -14.32 -215.78 7.509 6.818 -7.173 -359.656 0 0 18.198 0 0 -536.728 -283.215 -80.145 -0.846 -252.667 -37.963 -47.092 -36.305 -27.303 -104.003 nan -536.728 17.3346 1.40036 6637.48 4084.82 5467.09 1.25895 0 0 -0.0150119 0 16190.6 9.9405e-10 16190.6 error 0 -296.586 -1.87 0 1.195 7.668 -272.229 7.609 -140.549 2.357 -78.84 10.195 -6.769 171.206 3.44 -1.5117 640 -0.00236203 4.66615 2.8368 -2.17775 -5280.66 38946 -0.135589 -4999.56 37.9202 -7.41299 -11803.8 88867 -0.132825 -10953.1 81.7044 -10.4117 -26922.2 300533 -0.0895815 0 0 0 255 12.0295 -44512.7 nan nan nan nan nan nan nan nan nan nan 17_Dohkolyan_1_rpr.pdb 23.6181 30.6452 -15.723 -5.488 -5.096 -53.816 -5.149 -185.122 13.116 13.214 -15.346 -237.606 0 0 21.803 0 0 301.395 74.484 -62.316 111.484 115.427 294.03 -42.635 -28.773 -26.118 -81.076 nan 301.395 18.8536 0.86939 6510.2 4312.57 7695.95 252.52 0 0 -0.0144351 0 18771.2 1.01573e-09 18771.2 error 0 -234.484 -1.808 0 1.534 15.377 -217.655 9.049 -137.537 1.368 -85.604 10.77 -17.58 178.407 9.196 5.606 636 0.00881447 5.70281 2.8576 -0.0338795 -5369.01 37749 -0.142229 -5229.39 34.9112 -3.99931 -12368.4 88312 -0.140053 -11986.5 69.1014 -5.52625 -24195.1 310238 -0.0779888 0 0 0 255 14.1063 -44918.4 nan nan nan nan nan nan nan nan nan nan 17_Major_6_rpr.pdb 3.01507 51.6129 -12.245 -21.407 -6.439 -59.165 -6.805 -167.109 53.658 13.997 -24.34 -212.943 0 0 16.912 0 0 -213.643 -82.771 -17.374 0.912 -131.784 -36.482 -36.334 -28.376 4.459 -35.051 nan -213.643 24.4173 0.58693 6100.16 3791.12 6094.87 16.3691 0 0 -0.00125042 0 16002.5 9.69265e-10 16002.5 error 0 -272.798 -0.373 0 2.493 7.926 -231.603 12.324 -144.355 4.121 -91.993 15.009 -3.029 126.077 30.605 2.993 757 0.00395376 6.22725 3.25028 -0.995068 -2982.08 44679 -0.0667446 -2941.01 35.7732 -1.14817 -6128.49 104153 -0.0588412 -6095.64 74.4018 -0.441467 -9883.01 353719 -0.0279403 0 0 0 255 25.7583 -37862.9 nan nan nan nan nan nan nan nan nan nan [5 rows x 96 columns] deeplearning prediction progress: [#######################################] 100% deeplearning prediction progress: [#######################################] 100% mqapRNA --------- 1.08304 0.914736 1.00656 2.13889 3.63882 [5 rows x 1 column] fn ---------------------- 17_Das_4_rpr.pdb 17_Das_1_rpr.pdb 17_Bujnicki_7_rpr.pdb 17_Dohkolyan_1_rpr.pdb 17_Major_6_rpr.pdb [5 rows x 1 column] Exporting to /home/mqapRNA/mqapRNAweb/media/jobs/94afabf0-230c-45ac-9b1c-85ae3173cc09/94afabf_raw_mqapRNA.csv Export File progress: [###################################################] 100% clash_score analyze_geometry farna_rna_base_axis \ fn 17_Das_1_rpr.pdb 8.54 17.74 -25.94 17_Bujnicki_7_rpr.pdb 1.51 11.29 -26.41 17_Das_4_rpr.pdb 15.58 22.58 -26.52 17_Dohkolyan_1_rpr.pdb 23.62 30.65 -15.72 17_Major_6_rpr.pdb 3.02 51.61 -12.24 farna_rna_backbone_backbone \ fn 17_Das_1_rpr.pdb -0.78 17_Bujnicki_7_rpr.pdb -5.75 17_Das_4_rpr.pdb -1.03 17_Dohkolyan_1_rpr.pdb -5.49 17_Major_6_rpr.pdb -21.41 farna_rna_base_stack_axis farna_rna_base_stagger \ fn 17_Das_1_rpr.pdb -20.34 -102.77 17_Bujnicki_7_rpr.pdb -18.39 -104.36 17_Das_4_rpr.pdb -17.91 -108.97 17_Dohkolyan_1_rpr.pdb -5.10 -53.82 17_Major_6_rpr.pdb -6.44 -59.16 farna_rna_base_stack farna_rna_base_pair \ fn 17_Das_1_rpr.pdb -15.77 -210.31 17_Bujnicki_7_rpr.pdb -14.32 -215.78 17_Das_4_rpr.pdb -14.30 -221.89 17_Dohkolyan_1_rpr.pdb -5.15 -185.12 17_Major_6_rpr.pdb -6.80 -167.11 farna_rna_repulsive farna_rna_vdw ... \ fn ... 17_Das_1_rpr.pdb 10.93 0.85 ... 17_Bujnicki_7_rpr.pdb 7.51 6.82 ... 17_Das_4_rpr.pdb 13.64 0.96 ... 17_Dohkolyan_1_rpr.pdb 13.12 13.21 ... 17_Major_6_rpr.pdb 53.66 14.00 ... rnakb_lj14_all rnakb_coulomb14_all rnakb_lj_sr_all \ fn 17_Das_1_rpr.pdb NaN NaN NaN 17_Bujnicki_7_rpr.pdb NaN NaN NaN 17_Das_4_rpr.pdb NaN NaN NaN 17_Dohkolyan_1_rpr.pdb NaN NaN NaN 17_Major_6_rpr.pdb NaN NaN NaN rnakb_coulomb_sr_all rnakb_potential_all \ fn 17_Das_1_rpr.pdb NaN NaN 17_Bujnicki_7_rpr.pdb NaN NaN 17_Das_4_rpr.pdb NaN NaN 17_Dohkolyan_1_rpr.pdb NaN NaN 17_Major_6_rpr.pdb NaN NaN rnakb_kinetic_en_all rnakb_total_energy_all \ fn 17_Das_1_rpr.pdb NaN NaN 17_Bujnicki_7_rpr.pdb NaN NaN 17_Das_4_rpr.pdb NaN NaN 17_Dohkolyan_1_rpr.pdb NaN NaN 17_Major_6_rpr.pdb NaN NaN rna3dcnn dfire mqapRNA fn 17_Das_1_rpr.pdb NaN NaN 0.91 17_Bujnicki_7_rpr.pdb NaN NaN 1.01 17_Das_4_rpr.pdb NaN NaN 1.08 17_Dohkolyan_1_rpr.pdb NaN NaN 2.14 17_Major_6_rpr.pdb NaN NaN 3.64 [5 rows x 96 columns] mqapRNA fn 17_Das_1_rpr.pdb 0.91 17_Bujnicki_7_rpr.pdb 1.01 17_Das_4_rpr.pdb 1.08 17_Dohkolyan_1_rpr.pdb 2.14 17_Major_6_rpr.pdb 3.64 saved /home/mqapRNA/mqapRNAweb/media/jobs/94afabf0-230c-45ac-9b1c-85ae3173cc09/94afabf_mqapRNA.csv H2O session _sid_baae closed.