mqapRNA


Results for job: 62d2e3ea-f7b4-4e56-b3f1-13f84c84c110

The lower score, the better. SS: Secondary Structure Penalty, RST: Distance Restraints Penalty

Filename mqapRNA Score Secondary Structure Penalty Restraints Penalty mqapRNA Score + All Penalties
17_Das_1_rpr.pdb 1.340.020.01.36
17_Bujnicki_7_rpr.pdb 1.530.020.01.56
17_Das_4_rpr.pdb 1.550.020.01.58
17_Major_6_rpr.pdb 3.570.490.04.06
17_Dohkolyan_1_rpr.pdb 3.720.470.04.18
5k7c_clean_onechain_renumber_as_puzzle_rpr.pdb 8.00.140.08.14


Distance restraints (from experimental data or coevolution analysis)
Select file with distance restraints Change Remove

The raw output files for each step of the pipeline can be found here


  
mqaprna.py

ver: 52e618e-dirty

start  2017-10-06 16:16:44
--------------------------  ----------------------------------------------------
Seq ss fn                   /home/mqapRNA/mqapRNAweb/media/jobs/62d2e3ea-f7b4-4e56-b3f1-13f84c84c110/ss.txt
Output csv                  /home/mqapRNA/mqapRNAweb/media/jobs/62d2e3ea-f7b4-4e56-b3f1-13f84c84c110/62d2e3e_raw.csv
Input files                 #6 ['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
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: 6 ['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']
--------------------------------------------------------------------------------
[-------------                                                                   ]      1 16.67 % 6 10
True 17_Das_4_rpr.pdb     {'AnalyzeGeometry': 22.5806, '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'], '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', '6.8104', '3.46301', '-2.1557', '-5511.89', '39337', '-0.14012', '-5290.65', '42.323', '-5.22752', '-12670.2', '89379', '-0.141758', '-11933.4', '77.4955', '-9.5072', '-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', '-2.05920e-03', '0.00000e+00', '1.41553e+04', '9.50833e-10', '1.41553e+04'], 'RNAkb_all': ['5.98349e+03', '2.50340e+03', '5.66775e+03', '6.23377e-01', '0.00000e+00', '0.00000e+00', '-7.84210e-04', '0.00000e+00', '1.41553e+04', '9.50833e-10', '1.41553e+04'], 'SSAgreement': 'error'}
[--------------------------                                                      ]      2 33.33 % 6 10
True 17_Das_1_rpr.pdb     {'AnalyzeGeometry': 17.7419, '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'], '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', '4.77178', '2.36214', '-3.37328', '-5591.36', '36005', '-0.155294', '-5305.38', '32.8831', '-8.69686', '-12988.6', '81838', '-0.158711', '-12103.4', '73.5883', '-12.029', '-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', '-1.54358e-03', '0.00000e+00', '1.41996e+04', '9.48439e-10', '1.41996e+04'], 'RNAkb_all': ['5.96636e+03', '2.50310e+03', '5.72950e+03', '6.46352e-01', '0.00000e+00', '0.00000e+00', '-7.57241e-04', '0.00000e+00', '1.41996e+04', '9.48439e-10', '1.41996e+04'], 'SSAgreement': 'error'}
[----------------------------------------                                        ]      3 50.0 % 6 10
True 17_Bujnicki_7_rpr.pdb {'AnalyzeGeometry': 11.2903, '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'], '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', '7.41012', '3.72668', '-2.39404', '-5280.66', '38946', '-0.135589', '-5000.6', '38.2625', '-7.31958', '-11803.8', '88867', '-0.132825', '-10956.8', '79.3093', '-10.6789', '-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', '-1.04038e-03', '0.00000e+00', '1.61906e+04', '9.94050e-10', '1.61906e+04'], 'RNAkb_all': ['6.63748e+03', '4.08482e+03', '5.46709e+03', '1.25895e+00', '0.00000e+00', '0.00000e+00', '-7.12617e-04', '0.00000e+00', '1.61906e+04', '9.94050e-10', '1.61906e+04'], 'SSAgreement': 'error'}
[-----------------------------------------------------                           ]      4 66.67 % 6 10
True 17_Dohkolyan_1_rpr.pdb {'AnalyzeGeometry': 30.6452, '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'], 'ClashScore': 23.61809, 'length': 62, 'SimRNA_0': ['0', '-411.437674', '-155.543', '-60.544', '4.715', '-260.609821', '-48.614', '-52.227', '-39.264', '-30.590', '-89.914', '', '-411.437674'], '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', '5.07149', '3.13486', '0.170504', '-5369.01', '37749', '-0.142229', '-5229.89', '34.8523', '-3.99167', '-12368.4', '88312', '-0.140053', '-11990.9', '65.0115', '-5.8056', '-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', '-1.65685e-03', '0.00000e+00', '1.87712e+04', '1.01573e-09', '1.87712e+04'], 'RNAkb_all': ['6.51020e+03', '4.31257e+03', '7.69595e+03', '2.52520e+02', '0.00000e+00', '0.00000e+00', '-5.62285e-04', '0.00000e+00', '1.87712e+04', '1.01573e-09', '1.87712e+04'], 'SSAgreement': 'error'}
[------------------------------------------------------------------              ]      5 83.33 % 6 10
True 5k7c_clean_onechain_renumber_as_puzzle_rpr.pdb {'AnalyzeGeometry': 18.9655, 'eSCORE': 1.18242, 'FARNA': ['-24.402', '-18.584', '-23.731', '-92.703', '-18.527', '-224.685', '20.866', '8.959', '-35.264', '-392.161', '0.0', '0.0', '15.91', '0.0'], 'ClashScore': 22.031166, 'length': 62, 'SimRNA_0': ['0', '-310.065637', '-230.308', '-68.038', '-3.207', '-76.550649', '119.627', '-46.804', '-30.228', '-20.818', '-98.328', '', '-310.065637'], 'FARNA_hires': ['0.0', '-406.345', '0.0', '0.0', '1.437', '6.281', '-362.292', '10.09', '-155.932', '2.326', '-90.583', '11.494', '-15.183', '180.695', '5.322'], 'RNAscore': 17.6751, 'RASP': ['-3.5107', '682', '-0.00514765', '4.72163', '3.71742', '-2.21452', '-4452.3', '41509', '-0.107261', '-4272.11', '44.1156', '-4.08462', '-10471.5', '94496', '-0.110814', '-9753.98', '77.0364', '-9.31428', '-23564.5', '330384', '-0.0713245', '0', '0', '0'], 'RNAkb': -1, 'RNAkb_all': -1, 'SSAgreement': 'error'}
[--------------------------------------------------------------------------------]      6 100.0 % 6 10
True 17_Major_6_rpr.pdb   {'AnalyzeGeometry': 51.6129, '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'], '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', '-270.911', '-0.315', '0.0', '2.259', '7.679', '-233.986', '11.287', '-142.774', '3.988', '-88.829', '15.689', '-2.789', '126.992', '29.886'], 'RNAscore': 24.4173, 'RASP': ['2.993', '757', '0.00395376', '5.95724', '3.28124', '-0.903391', '-2982.08', '44679', '-0.0667446', '-2941.63', '38.5309', '-1.04971', '-6128.49', '104153', '-0.0588412', '-6089.17', '79.392', '-0.495189', '-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', '1.60955e-03', '0.00000e+00', '1.60025e+04', '9.69265e-10', '1.60025e+04'], 'RNAkb_all': ['6.10016e+03', '3.79112e+03', '6.09487e+03', '1.63691e+01', '0.00000e+00', '0.00000e+00', '-4.90915e-04', '0.00000e+00', '1.60025e+04', '9.69265e-10', '1.60025e+04'], 'SSAgreement': 'error'}

Cmd: mqaprna.py -s /home/mqapRNA/mqapRNAweb/media/jobs/62d2e3ea-f7b4-4e56-b3f1-13f84c84c110/ss.txt -m 6 -f -o /home/mqapRNA/mqapRNAweb/media/jobs/62d2e3ea-f7b4-4e56-b3f1-13f84c84c110/62d2e3e_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 input/5k7c_clean_onechain_renumber_as_puzzle_rpr.pdb
Execution time: 0:03:34.636 process: 6 start: 16:16:44 end: 16:20:19  
Output: /home/mqapRNA/mqapRNAweb/media/jobs/62d2e3ea-f7b4-4e56-b3f1-13f84c84c110/62d2e3e_raw.csv 

logging: /home/mqapRNA/mqapRNAweb/media/jobs/62d2e3ea-f7b4-4e56-b3f1-13f84c84c110/62d2e3e_raw.log
logging wrappers /home/mqapRNA/mqaprna_env/log/