mqaprna.py ver: 52e618e-dirty start 2017-08-28 08:25:07 -------------------------- ---------------------------------------------------- Seq ss fn /home/mqapRNA/mqapRNAweb/media/jobs/9269cbde-c5fb-49bf-a82b-88318ba5fff0/ss.txt Output csv /home/mqapRNA/mqapRNAweb/media/jobs/9269cbde-c5fb-49bf-a82b-88318ba5fff0/9269cbd_raw.csv Input files #5 ['input/1y26_rpr.pdb', 'input/ade_npk_dca_slope_3-500f3ee2_ALL_thrs7.20A_clust01-000001_AA.pdb', 'input/ade_npk_dca_slope_x2-0adc8423_ALL_thrs7.20A_clust01-000001_AA.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.pdb', 'input/ade_npk_dca_slope_3-500f3ee2_ALL_thrs7.20A_clust01-000001_AA.pdb', 'input/ade_npk_dca_slope_x2-0adc8423_ALL_thrs7.20A_clust01-000001_AA.pdb', 'input/ade_pk-35b2a2c1_ALL_thrs7.20A_clust01-000001_AA.pdb', 'input/ade_pk_dca_slope_3-23341152-thrs7.10A_clust01X.pdb'] -------------------------------------------------------------------------------- [---------------- ] 1 20.0 % 5 10 True ade_npk_dca_slope_x2-0adc8423_ALL_thrs7.20A_clust01-000001_AA.pdb {'AnalyzeGeometry': 22.2222, 'eSCORE': 1.53788, 'FARNA': ['-28.861', '-4.685', '-22.788', '-113.696', '-18.582', '-258.927', '21.76', '91.148', '-14.091', '-329.208', '0.0', '0.0', '19.514', '0.0'], 'ClashScore': 145.724258, 'length': 71, 'SimRNA_0': ['0', '-578.060510', '-236.383', '-60.046', '-1.935', '-339.742936', '-45.871', '-62.686', '-42.175', '-33.958', '-155.053', '', '-578.060510'], 'FARNA_hires': ['0.0', '-259.496', '-2.019', '0.0', '1.757', '11.32', '-229.892', '14.831', '-181.196', '-0.273', '-104.416', '32.722', '0.0', '190.787', '6.882'], 'RNAscore': 18.0098, 'RASP': ['-2.8509', '798', '-0.00357256', '8.52881', '3.25662', '-3.49434', '-6481.01', '49427', '-0.131123', '-6256.19', '45.2469', '-4.96863', '-14702', '111612', '-0.131724', '-13887.7', '74.6943', '-10.902', '-37508.7', '368372', '-0.101823', '0', '0', '0'], 'RNAkb': ['9.41914e+03', '1.08061e+04', '6.94714e+03', '2.06254e+01', '0.00000e+00', '0.00000e+00', '-2.25907e-03', '0.00000e+00', '2.71930e+04', '1.18644e-09', '2.71930e+04'], 'RNAkb_all': ['9.41914e+03', '1.08061e+04', '6.94714e+03', '2.06254e+01', '0.00000e+00', '0.00000e+00', '-8.88927e-04', '0.00000e+00', '2.71930e+04', '1.18644e-09', '2.71930e+04'], 'SSAgreement': '0.913'} [-------------------------------- ] 2 40.0 % 5 10 True 1y26_rpr.pdb {'AnalyzeGeometry': 7.0423, 'eSCORE': 1.58377, 'FARNA': ['-32.498', '-9.216', '-25.049', '-124.295', '-19.1', '-286.132', '13.582', '7.706', '-24.24', '-479.731', '0.0', '0.0', '19.512', '0.0'], 'ClashScore': 9.734513, 'length': 71, 'SimRNA_0': ['0', '-652.721063', '-319.845', '-103.484', '-1.721', '-331.154974', '-54.950', '-59.570', '-38.539', '-32.558', '-145.537', '', '-652.721063'], 'FARNA_hires': ['0.0', '-447.908', '-0.286', '0.0', '1.424', '9.214', '-402.41', '7.559', '-190.821', '1.088', '-108.859', '17.514', '-7.884', '221.398', '4.155'], 'RNAscore': 17.5408, 'RASP': ['-8.8894', '811', '-0.010961', '7.63726', '3.40637', '-4.85169', '-6534.41', '49729', '-0.1314', '-6089.58', '45.1783', '-9.84593', '-15020.5', '114620', '-0.131046', '-13601.2', '95.5433', '-14.8551', '-34978.1', '393447', '-0.0889016', '0', '0', '0'], 'RNAkb': ['7.69605e+03', '3.88256e+03', '6.51332e+03', '2.62954e+00', '0.00000e+00', '0.00000e+00', '-1.25692e-03', '0.00000e+00', '1.80946e+04', '1.12920e-09', '1.80946e+04'], 'RNAkb_all': ['7.69605e+03', '3.88256e+03', '6.51332e+03', '2.62954e+00', '0.00000e+00', '0.00000e+00', '-8.57504e-04', '0.00000e+00', '1.80946e+04', '1.12920e-09', '1.80946e+04'], 'SSAgreement': '0.959'} [------------------------------------------------ ] 3 60.0 % 5 10 True ade_npk_dca_slope_3-500f3ee2_ALL_thrs7.20A_clust01-000001_AA.pdb {'AnalyzeGeometry': 20.8333, 'eSCORE': 1.52705, 'FARNA': ['-33.05', '-1.02', '-27.579', '-116.364', '-22.447', '-275.299', '11.723', '39.043', '-11.861', '-416.479', '0.0', '0.0', '20.376', '0.0'], 'ClashScore': 128.216311, 'length': 71, 'SimRNA_0': ['0', '-597.790659', '-266.218', '-59.160', '-0.707', '-330.865957', '-35.453', '-63.057', '-43.495', '-30.047', '-158.814', '', '-597.790659'], 'FARNA_hires': ['0.0', '-367.614', '-2.553', '0.0', '1.752', '8.191', '-326.342', '10.401', '-177.353', '-0.02', '-99.591', '26.226', '-2.55', '188.332', '5.893'], 'RNAscore': 18.0992, 'RASP': ['1.1401', '791', '0.00144134', '7.09717', '2.33673', '-2.54931', '-6487.25', '49013', '-0.132358', '-6315.95', '37.5764', '-4.55867', '-14562.3', '111488', '-0.130618', '-14025.7', '72.3299', '-7.41906', '-37762.8', '372001', '-0.101513', '0', '0', '0'], 'RNAkb': ['1.74007e+04', '1.21154e+04', '6.97063e+03', '1.87531e+01', '0.00000e+00', '0.00000e+00', '-1.58203e-03', '0.00000e+00', '3.65055e+04', '1.37343e-09', '3.65055e+04'], 'RNAkb_all': ['1.74007e+04', '1.21154e+04', '6.97063e+03', '1.87531e+01', '0.00000e+00', '0.00000e+00', '-7.13643e-04', '0.00000e+00', '3.65055e+04', '1.37343e-09', '3.65055e+04'], 'SSAgreement': '0.819'} [---------------------------------------------------------------- ] 4 80.0 % 5 10 True ade_pk-35b2a2c1_ALL_thrs7.20A_clust01-000001_AA.pdb {'AnalyzeGeometry': 25.0, 'eSCORE': 1.63347, 'FARNA': ['-35.05', '-4.479', '-22.826', '-132.923', '-18.623', '-293.32', '26.565', '90.83', '-19.482', '-389.683', '0.0', '0.0', '19.624', '0.0'], 'ClashScore': 136.938509, 'length': 71, 'SimRNA_0': ['0', '-640.020990', '-317.295', '-88.092', '-1.592', '-321.133766', '-31.777', '-61.202', '-39.849', '-27.183', '-161.123', '', '-640.020990'], 'FARNA_hires': ['0.0', '-185.617', '-1.037', '0.0', '2.285', '9.794', '-88.949', '22.11', '-158.245', '2.455', '-116.247', '22.793', '-41.807', '148.22', '13.012'], 'RNAscore': 18.4008, 'RASP': ['3.6856', '839', '0.00439285', '7.22507', '3.4257', '-1.03321', '-6313.77', '51379', '-0.122886', '-6138.68', '39.2418', '-4.46183', '-14221.7', '116249', '-0.122338', '-13574.1', '86.0764', '-7.52298', '-36115.5', '397499', '-0.0908569', '0', '0', '0'], 'RNAkb': ['1.50256e+04', '1.26909e+04', '6.99712e+03', '1.58944e+01', '0.00000e+00', '0.00000e+00', '-1.59388e-03', '0.00000e+00', '3.47295e+04', '1.31953e-09', '3.47295e+04'], 'RNAkb_all': ['1.50256e+04', '1.26909e+04', '6.99712e+03', '1.58944e+01', '0.00000e+00', '0.00000e+00', '-8.69993e-04', '0.00000e+00', '3.47295e+04', '1.31953e-09', '3.47295e+04'], 'SSAgreement': '0.906'} [--------------------------------------------------------------------------------] 5 100.0 % 5 10 True ade_pk_dca_slope_3-23341152-thrs7.10A_clust01X.pdb {'AnalyzeGeometry': 25.3521, 'eSCORE': 1.62504, 'FARNA': ['-28.795', '-2.969', '-23.292', '-125.91', '-21.161', '-278.86', '14.916', '39.474', '-25.202', '-432.944', '0.0', '0.0', '18.855', '0.0'], 'ClashScore': 146.589903, 'length': 71, 'SimRNA_0': ['0', '-591.341797', '-287.115', '-83.857', '0.954', '-305.180561', '-28.392', '-56.733', '-41.143', '-30.928', '-147.985', '', '-591.341797'], 'FARNA_hires': ['0.0', '-401.503', '-2.047', '0.0', '2.099', '6.371', '-335.301', '10.895', '-187.695', '2.414', '-100.615', '28.375', '-14.194', '180.69', '7.505'], 'RNAscore': 18.2898, 'RASP': ['1.3187', '826', '0.00159649', '6.69676', '3.33138', '-1.61436', '-5796.23', '50770', '-0.114166', '-5687.93', '43.1968', '-2.50716', '-13393.7', '115774', '-0.115688', '-12812.1', '67.8332', '-8.57483', '-34945.2', '396081', '-0.0882275', '0', '0', '0'], 'RNAkb': ['2.66271e+04', '1.17210e+04', '6.87669e+03', '2.16790e+01', '0.00000e+00', '0.00000e+00', '-1.23604e-03', '0.00000e+00', '4.52465e+04', '1.57929e-09', '4.52465e+04'], 'RNAkb_all': ['2.66271e+04', '1.17210e+04', '6.87669e+03', '2.16790e+01', '0.00000e+00', '0.00000e+00', '-9.09573e-04', '0.00000e+00', '4.52465e+04', '1.57929e-09', '4.52465e+04'], 'SSAgreement': '0.894'} Cmd: mqaprna.py -s /home/mqapRNA/mqapRNAweb/media/jobs/9269cbde-c5fb-49bf-a82b-88318ba5fff0/ss.txt -m 6 -f -o /home/mqapRNA/mqapRNAweb/media/jobs/9269cbde-c5fb-49bf-a82b-88318ba5fff0/9269cbd_raw.csv input/1y26_rpr.pdb input/ade_npk_dca_slope_3-500f3ee2_ALL_thrs7.20A_clust01-000001_AA.pdb input/ade_npk_dca_slope_x2-0adc8423_ALL_thrs7.20A_clust01-000001_AA.pdb input/ade_pk-35b2a2c1_ALL_thrs7.20A_clust01-000001_AA.pdb input/ade_pk_dca_slope_3-23341152-thrs7.10A_clust01X.pdb Execution time: 0:04:36.592 process: 6 start: 08:25:07 end: 08:29:44 Output: /home/mqapRNA/mqapRNAweb/media/jobs/9269cbde-c5fb-49bf-a82b-88318ba5fff0/9269cbd_raw.csv logging: /home/mqapRNA/mqapRNAweb/media/jobs/9269cbde-c5fb-49bf-a82b-88318ba5fff0/9269cbd_raw.log logging wrappers /home/mqapRNA/mqaprna_env/log/ in: /home/mqapRNA/mqapRNAweb/media/jobs/9269cbde-c5fb-49bf-a82b-88318ba5fff0/9269cbd_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/tmp3ZINwi JVM stdout: /tmp/tmp3ZINwi/h2o_unknownUser_started_from_python.out JVM stderr: /tmp/tmp3ZINwi/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 8 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: 4 months and 8 days !!! H2O cluster name: H2O_from_python_unknownUser_ph3jza 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_x2-0adc8423_ALL_thrs7.20A_clust01-000001_AA.pdb 145.724 22.2222 -28.861 -4.685 -22.788 -113.696 -18.582 -258.927 21.76 91.148 -14.091 -329.208 0 0 19.514 0 0 -578.061 -236.383 -60.046 -1.935 -339.743 -45.871 -62.686 -42.175 -33.958 -155.053 nan -578.061 18.0098 1.53788 9419.14 10806.1 6947.14 20.6254 0 0 -0.00225907 0 27193 1.18644e-09 27193 0.913 0 -259.496 -2.019 0 1.757 11.32 -229.892 14.831 -181.196 -0.273 -104.416 32.722 0 190.787 6.882 -2.8509 798 -0.00357256 8.52881 3.25662 -3.49434 -6481.01 49427 -0.131123 -6256.19 45.2469 -4.96863 -14702 111612 -0.131724 -13887.7 74.6943 -10.902 -37508.7 368372 -0.101823 0 0 0 9419.14 10806.1 6947.14 20.6254 0 0 -0.000888927 0 27193 1.18644e-09 27193 1y26_rpr.pdb 9.73451 7.0423 -32.498 -9.216 -25.049 -124.295 -19.1 -286.132 13.582 7.706 -24.24 -479.731 0 0 19.512 0 0 -652.721 -319.845 -103.484 -1.721 -331.155 -54.95 -59.57 -38.539 -32.558 -145.537 nan -652.721 17.5408 1.58377 7696.05 3882.56 6513.32 2.62954 0 0 -0.00125692 0 18094.6 1.1292e-09 18094.6 0.959 0 -447.908 -0.286 0 1.424 9.214 -402.41 7.559 -190.821 1.088 -108.859 17.514 -7.884 221.398 4.155 -8.8894 811 -0.010961 7.63726 3.40637 -4.85169 -6534.41 49729 -0.1314 -6089.58 45.1783 -9.84593 -15020.5 114620 -0.131046 -13601.2 95.5433 -14.8551 -34978.1 393447 -0.0889016 0 0 0 7696.05 3882.56 6513.32 2.62954 0 0 -0.000857504 0 18094.6 1.1292e-09 18094.6 ade_npk_dca_slope_3-500f3ee2_ALL_thrs7.20A_clust01-000001_AA.pdb 128.216 20.8333 -33.05 -1.02 -27.579 -116.364 -22.447 -275.299 11.723 39.043 -11.861 -416.479 0 0 20.376 0 0 -597.791 -266.218 -59.16 -0.707 -330.866 -35.453 -63.057 -43.495 -30.047 -158.814 nan -597.791 18.0992 1.52705 17400.7 12115.4 6970.63 18.7531 0 0 -0.00158203 0 36505.5 1.37343e-09 36505.5 0.819 0 -367.614 -2.553 0 1.752 8.191 -326.342 10.401 -177.353 -0.02 -99.591 26.226 -2.55 188.332 5.893 1.1401 791 0.00144134 7.09717 2.33673 -2.54931 -6487.25 49013 -0.132358 -6315.95 37.5764 -4.55867 -14562.3 111488 -0.130618 -14025.7 72.3299 -7.41906 -37762.8 372001 -0.101513 0 0 0 17400.7 12115.4 6970.63 18.7531 0 0 -0.000713643 0 36505.5 1.37343e-09 36505.5 ade_pk-35b2a2c1_ALL_thrs7.20A_clust01-000001_AA.pdb 136.939 25 -35.05 -4.479 -22.826 -132.923 -18.623 -293.32 26.565 90.83 -19.482 -389.683 0 0 19.624 0 0 -640.021 -317.295 -88.092 -1.592 -321.134 -31.777 -61.202 -39.849 -27.183 -161.123 nan -640.021 18.4008 1.63347 15025.6 12690.9 6997.12 15.8944 0 0 -0.00159388 0 34729.5 1.31953e-09 34729.5 0.906 0 -185.617 -1.037 0 2.285 9.794 -88.949 22.11 -158.245 2.455 -116.247 22.793 -41.807 148.22 13.012 3.6856 839 0.00439285 7.22507 3.4257 -1.03321 -6313.77 51379 -0.122886 -6138.68 39.2418 -4.46183 -14221.7 116249 -0.122338 -13574.1 86.0764 -7.52298 -36115.5 397499 -0.0908569 0 0 0 15025.6 12690.9 6997.12 15.8944 0 0 -0.000869993 0 34729.5 1.31953e-09 34729.5 ade_pk_dca_slope_3-23341152-thrs7.10A_clust01X.pdb 146.59 25.3521 -28.795 -2.969 -23.292 -125.91 -21.161 -278.86 14.916 39.474 -25.202 -432.944 0 0 18.855 0 0 -591.342 -287.115 -83.857 0.954 -305.181 -28.392 -56.733 -41.143 -30.928 -147.985 nan -591.342 18.2898 1.62504 26627.1 11721 6876.69 21.679 0 0 -0.00123604 0 45246.5 1.57929e-09 45246.5 0.894 0 -401.503 -2.047 0 2.099 6.371 -335.301 10.895 -187.695 2.414 -100.615 28.375 -14.194 180.69 7.505 1.3187 826 0.00159649 6.69676 3.33138 -1.61436 -5796.23 50770 -0.114166 -5687.93 43.1968 -2.50716 -13393.7 115774 -0.115688 -12812.1 67.8332 -8.57483 -34945.2 396081 -0.0882275 0 0 0 26627.1 11721 6876.69 21.679 0 0 -0.000909573 0 45246.5 1.57929e-09 45246.5 [5 rows x 94 columns] deeplearning prediction progress: [#######################################] 100% deeplearning prediction progress: [#######################################] 100% mqapRNA --------- 0.793662 0.777395 1.32754 1.21239 1.15272 [5 rows x 1 column] fn ----------------------------------------------------------------- ade_npk_dca_slope_x2-0adc8423_ALL_thrs7.20A_clust01-000001_AA.pdb 1y26_rpr.pdb ade_npk_dca_slope_3-500f3ee2_ALL_thrs7.20A_clust01-000001_AA.pdb ade_pk-35b2a2c1_ALL_thrs7.20A_clust01-000001_AA.pdb ade_pk_dca_slope_3-23341152-thrs7.10A_clust01X.pdb [5 rows x 1 column] Exporting to /home/mqapRNA/mqapRNAweb/media/jobs/9269cbde-c5fb-49bf-a82b-88318ba5fff0/9269cbd_raw_mqapRNA.csv Export File progress: [###################################################] 100% clash_score \ fn 1y26_rpr.pdb 9.734513 ade_npk_dca_slope_x2-0adc8423_ALL_thrs7.20A_clu... 145.724258 ade_pk_dca_slope_3-23341152-thrs7.10A_clust01X.pdb 146.589903 ade_pk-35b2a2c1_ALL_thrs7.20A_clust01-000001_AA... 136.938509 ade_npk_dca_slope_3-500f3ee2_ALL_thrs7.20A_clus... 128.216311 analyze_geometry \ fn 1y26_rpr.pdb 7.0423 ade_npk_dca_slope_x2-0adc8423_ALL_thrs7.20A_clu... 22.2222 ade_pk_dca_slope_3-23341152-thrs7.10A_clust01X.pdb 25.3521 ade_pk-35b2a2c1_ALL_thrs7.20A_clust01-000001_AA... 25.0000 ade_npk_dca_slope_3-500f3ee2_ALL_thrs7.20A_clus... 20.8333 farna_rna_base_axis \ fn 1y26_rpr.pdb -32.498 ade_npk_dca_slope_x2-0adc8423_ALL_thrs7.20A_clu... -28.861 ade_pk_dca_slope_3-23341152-thrs7.10A_clust01X.pdb -28.795 ade_pk-35b2a2c1_ALL_thrs7.20A_clust01-000001_AA... -35.050 ade_npk_dca_slope_3-500f3ee2_ALL_thrs7.20A_clus... -33.050 farna_rna_backbone_backbone \ fn 1y26_rpr.pdb -9.216 ade_npk_dca_slope_x2-0adc8423_ALL_thrs7.20A_clu... -4.685 ade_pk_dca_slope_3-23341152-thrs7.10A_clust01X.pdb -2.969 ade_pk-35b2a2c1_ALL_thrs7.20A_clust01-000001_AA... -4.479 ade_npk_dca_slope_3-500f3ee2_ALL_thrs7.20A_clus... -1.020 farna_rna_base_stack_axis \ fn 1y26_rpr.pdb -25.049 ade_npk_dca_slope_x2-0adc8423_ALL_thrs7.20A_clu... -22.788 ade_pk_dca_slope_3-23341152-thrs7.10A_clust01X.pdb -23.292 ade_pk-35b2a2c1_ALL_thrs7.20A_clust01-000001_AA... -22.826 ade_npk_dca_slope_3-500f3ee2_ALL_thrs7.20A_clus... -27.579 farna_rna_base_stagger \ fn 1y26_rpr.pdb -124.295 ade_npk_dca_slope_x2-0adc8423_ALL_thrs7.20A_clu... -113.696 ade_pk_dca_slope_3-23341152-thrs7.10A_clust01X.pdb -125.910 ade_pk-35b2a2c1_ALL_thrs7.20A_clust01-000001_AA... -132.923 ade_npk_dca_slope_3-500f3ee2_ALL_thrs7.20A_clus... -116.364 farna_rna_base_stack \ fn 1y26_rpr.pdb -19.100 ade_npk_dca_slope_x2-0adc8423_ALL_thrs7.20A_clu... -18.582 ade_pk_dca_slope_3-23341152-thrs7.10A_clust01X.pdb -21.161 ade_pk-35b2a2c1_ALL_thrs7.20A_clust01-000001_AA... -18.623 ade_npk_dca_slope_3-500f3ee2_ALL_thrs7.20A_clus... -22.447 farna_rna_base_pair \ fn 1y26_rpr.pdb -286.132 ade_npk_dca_slope_x2-0adc8423_ALL_thrs7.20A_clu... -258.927 ade_pk_dca_slope_3-23341152-thrs7.10A_clust01X.pdb -278.860 ade_pk-35b2a2c1_ALL_thrs7.20A_clust01-000001_AA... -293.320 ade_npk_dca_slope_3-500f3ee2_ALL_thrs7.20A_clus... -275.299 farna_rna_repulsive \ fn 1y26_rpr.pdb 13.582 ade_npk_dca_slope_x2-0adc8423_ALL_thrs7.20A_clu... 21.760 ade_pk_dca_slope_3-23341152-thrs7.10A_clust01X.pdb 14.916 ade_pk-35b2a2c1_ALL_thrs7.20A_clust01-000001_AA... 26.565 ade_npk_dca_slope_3-500f3ee2_ALL_thrs7.20A_clus... 11.723 farna_rna_vdw ... \ fn ... 1y26_rpr.pdb 7.706 ... ade_npk_dca_slope_x2-0adc8423_ALL_thrs7.20A_clu... 91.148 ... ade_pk_dca_slope_3-23341152-thrs7.10A_clust01X.pdb 39.474 ... ade_pk-35b2a2c1_ALL_thrs7.20A_clust01-000001_AA... 90.830 ... ade_npk_dca_slope_3-500f3ee2_ALL_thrs7.20A_clus... 39.043 ... rnakb_proper_dih_all \ fn 1y26_rpr.pdb 6513.32 ade_npk_dca_slope_x2-0adc8423_ALL_thrs7.20A_clu... 6947.14 ade_pk_dca_slope_3-23341152-thrs7.10A_clust01X.pdb 6876.69 ade_pk-35b2a2c1_ALL_thrs7.20A_clust01-000001_AA... 6997.12 ade_npk_dca_slope_3-500f3ee2_ALL_thrs7.20A_clus... 6970.63 rnakb_improper_dih_all \ fn 1y26_rpr.pdb 2.62954 ade_npk_dca_slope_x2-0adc8423_ALL_thrs7.20A_clu... 20.62540 ade_pk_dca_slope_3-23341152-thrs7.10A_clust01X.pdb 21.67900 ade_pk-35b2a2c1_ALL_thrs7.20A_clust01-000001_AA... 15.89440 ade_npk_dca_slope_3-500f3ee2_ALL_thrs7.20A_clus... 18.75310 rnakb_lj14_all \ fn 1y26_rpr.pdb 0 ade_npk_dca_slope_x2-0adc8423_ALL_thrs7.20A_clu... 0 ade_pk_dca_slope_3-23341152-thrs7.10A_clust01X.pdb 0 ade_pk-35b2a2c1_ALL_thrs7.20A_clust01-000001_AA... 0 ade_npk_dca_slope_3-500f3ee2_ALL_thrs7.20A_clus... 0 rnakb_coulomb14_all \ fn 1y26_rpr.pdb 0 ade_npk_dca_slope_x2-0adc8423_ALL_thrs7.20A_clu... 0 ade_pk_dca_slope_3-23341152-thrs7.10A_clust01X.pdb 0 ade_pk-35b2a2c1_ALL_thrs7.20A_clust01-000001_AA... 0 ade_npk_dca_slope_3-500f3ee2_ALL_thrs7.20A_clus... 0 rnakb_lj_sr_all \ fn 1y26_rpr.pdb -0.000858 ade_npk_dca_slope_x2-0adc8423_ALL_thrs7.20A_clu... -0.000889 ade_pk_dca_slope_3-23341152-thrs7.10A_clust01X.pdb -0.000910 ade_pk-35b2a2c1_ALL_thrs7.20A_clust01-000001_AA... -0.000870 ade_npk_dca_slope_3-500f3ee2_ALL_thrs7.20A_clus... -0.000714 rnakb_coulomb_sr_all \ fn 1y26_rpr.pdb 0 ade_npk_dca_slope_x2-0adc8423_ALL_thrs7.20A_clu... 0 ade_pk_dca_slope_3-23341152-thrs7.10A_clust01X.pdb 0 ade_pk-35b2a2c1_ALL_thrs7.20A_clust01-000001_AA... 0 ade_npk_dca_slope_3-500f3ee2_ALL_thrs7.20A_clus... 0 rnakb_potential_all \ fn 1y26_rpr.pdb 18094.6 ade_npk_dca_slope_x2-0adc8423_ALL_thrs7.20A_clu... 27193.0 ade_pk_dca_slope_3-23341152-thrs7.10A_clust01X.pdb 45246.5 ade_pk-35b2a2c1_ALL_thrs7.20A_clust01-000001_AA... 34729.5 ade_npk_dca_slope_3-500f3ee2_ALL_thrs7.20A_clus... 36505.5 rnakb_kinetic_en_all \ fn 1y26_rpr.pdb 1.129200e-09 ade_npk_dca_slope_x2-0adc8423_ALL_thrs7.20A_clu... 1.186440e-09 ade_pk_dca_slope_3-23341152-thrs7.10A_clust01X.pdb 1.579290e-09 ade_pk-35b2a2c1_ALL_thrs7.20A_clust01-000001_AA... 1.319530e-09 ade_npk_dca_slope_3-500f3ee2_ALL_thrs7.20A_clus... 1.373430e-09 rnakb_total_energy_all \ fn 1y26_rpr.pdb 18094.6 ade_npk_dca_slope_x2-0adc8423_ALL_thrs7.20A_clu... 27193.0 ade_pk_dca_slope_3-23341152-thrs7.10A_clust01X.pdb 45246.5 ade_pk-35b2a2c1_ALL_thrs7.20A_clust01-000001_AA... 34729.5 ade_npk_dca_slope_3-500f3ee2_ALL_thrs7.20A_clus... 36505.5 mqapRNA fn 1y26_rpr.pdb 0.777395 ade_npk_dca_slope_x2-0adc8423_ALL_thrs7.20A_clu... 0.793662 ade_pk_dca_slope_3-23341152-thrs7.10A_clust01X.pdb 1.152722 ade_pk-35b2a2c1_ALL_thrs7.20A_clust01-000001_AA... 1.212393 ade_npk_dca_slope_3-500f3ee2_ALL_thrs7.20A_clus... 1.327542 [5 rows x 94 columns] mqapRNA fn 1y26_rpr.pdb 0.777395 ade_npk_dca_slope_x2-0adc8423_ALL_thrs7.20A_clu... 0.793662 ade_pk_dca_slope_3-23341152-thrs7.10A_clust01X.pdb 1.152722 ade_pk-35b2a2c1_ALL_thrs7.20A_clust01-000001_AA... 1.212393 ade_npk_dca_slope_3-500f3ee2_ALL_thrs7.20A_clus... 1.327542 saved /home/mqapRNA/mqapRNAweb/media/jobs/9269cbde-c5fb-49bf-a82b-88318ba5fff0/9269cbd_mqapRNA.csv H2O session _sid_bc40 closed. fn clash_score escore mqapRNA farna_score_lowres \ 1 1y26_rpr.pdb 0.000000 0.467017 0.000000 0.000000 0 ade_npk_dca_slope_x2 0.993675 0.898233 0.029569 1.000000 4 ade_pk_dca_slope_3-2 1.000000 0.079214 0.682230 0.310830 3 ade_pk-35b2a2c1_ALL_ 0.929477 0.000000 0.790693 0.598234 2 ade_npk_dca_slope_3- 0.865744 1.000000 1.000000 0.420215 ss_disagreement simrna_total_energy rnakb_lj_sr x3rnascore \ 1 0.000000 0.000000 0.979590 0.000000 0 0.328571 1.000000 0.000000 0.545349 4 0.464286 0.822111 1.000000 0.870930 3 0.378571 0.170104 0.650216 1.000000 2 1.000000 0.735735 0.661799 0.649302 analyze_geometry 1 0.000000 0 0.829059 4 1.000000 3 0.980770 2 0.753203 ploting to /home/mqapRNA/mqapRNAweb/media/jobs/9269cbde-c5fb-49bf-a82b-88318ba5fff0/plot.png [OK]