2026-04-26 20:07:03 NPdock start 2026-04-26 20:07:03 ver: server 2026-04-26 20:07:03 mode: 11111 2026-04-26 20:07:03 is RNA? 1 2026-04-26 20:07:03 Interface: prot: '25:A,26:A,92:A,104:A,107:A,134:A' na: '31-39:A' 2026-04-26 20:07:03 Curr dir:/home/rpdock/web/media/jobs/e928101a-6fc1-4ee9-b29a-f0fc85335d1c/ 2026-04-26 20:07:03 GRAMM in progress... 2026-04-26 20:07:03 python /home/rpdock/run_gramm//run_gramm1.py -d 20000 -p prot.pdb -r na.pdb -pi '25:A,26:A,92:A,104:A,107:A,134:A' -ri '31-39:A' -n 3 -pf 'A' -rf 'A' 2026-04-26 20:44:25 GRAMM done 2026-04-26 20:44:25 DARS scoring in progress... 2026-04-26 20:44:25 time python /home/rpdock/run_gramm//DARS-RNP_v3//DARS_potential_v3_scoring.py -m 100 -f list.txt -o dars_out.txt 2026-04-26 20:44:26 DARS start [DARS_potential_v3_scoring.py] 2026-04-26 20:44:26 Show log every 100 structures [DARS_potential_v3_scoring.py] 2026-04-26 20:44:26 1/128 na-prot_199.pdb -3772593.97 2026-04-26 20:44:44 100/128 na-prot_14404.pdb -2082387.72 2026-04-26 20:44:50 DARS scoring end 2026-04-26 20:44:50 Clustering (cuttoff: 5, nr_clust: 100 ) in progress... 2026-04-26 20:44:50 time python /home/rpdock/run_gramm//clustering_v4.py dars_out.txt list.txt 5 100 2026-04-26 20:44:50 100 best scored structures 2026-04-26 20:44:50 1 na-prot_6128.pdb -3927906.15 2026-04-26 20:44:50 2 na-prot_199.pdb -3772593.97 2026-04-26 20:44:50 3 na-prot_9203.pdb -3478834.31 2026-04-26 20:44:50 4 na-prot_1492.pdb -3374897.11 2026-04-26 20:44:50 5 na-prot_11908.pdb -3229869.24 2026-04-26 20:44:50 6 na-prot_10428.pdb -3219284.12 2026-04-26 20:44:50 7 na-prot_17850.pdb -3123924.1 2026-04-26 20:44:50 8 na-prot_9728.pdb -2957086.98 2026-04-26 20:44:50 9 na-prot_601.pdb -2899349.93 2026-04-26 20:44:50 10 na-prot_15433.pdb -2873223.82 2026-04-26 20:44:50 11 na-prot_3240.pdb -2851124.01 2026-04-26 20:44:50 12 na-prot_14244.pdb -2846002.49 2026-04-26 20:44:50 13 na-prot_10529.pdb -2838245.28 2026-04-26 20:44:50 14 na-prot_1916.pdb -2794454.13 2026-04-26 20:44:50 15 na-prot_943.pdb -2783834.23 2026-04-26 20:44:50 16 na-prot_15237.pdb -2753391.03 2026-04-26 20:44:50 17 na-prot_6664.pdb -2735105.66 2026-04-26 20:44:50 18 na-prot_14670.pdb -2715745.75 2026-04-26 20:44:50 19 na-prot_5725.pdb -2702277.16 2026-04-26 20:44:50 20 na-prot_19996.pdb -2692637.68 2026-04-26 20:44:50 21 na-prot_3014.pdb -2682943.14 2026-04-26 20:44:50 22 na-prot_18954.pdb -2668010.49 2026-04-26 20:44:50 23 na-prot_10020.pdb -2658446.85 2026-04-26 20:44:50 24 na-prot_5824.pdb -2616549.0 2026-04-26 20:44:50 25 na-prot_5058.pdb -2597537.59 2026-04-26 20:44:50 26 na-prot_401.pdb -2584937.37 2026-04-26 20:44:50 27 na-prot_6848.pdb -2584590.92 2026-04-26 20:44:50 28 na-prot_418.pdb -2557167.63 2026-04-26 20:44:50 29 na-prot_2437.pdb -2526327.12 2026-04-26 20:44:50 30 na-prot_4235.pdb -2517702.18 2026-04-26 20:44:50 31 na-prot_19395.pdb -2512250.12 2026-04-26 20:44:50 32 na-prot_4244.pdb -2504788.63 2026-04-26 20:44:50 33 na-prot_19481.pdb -2502178.9 2026-04-26 20:44:50 34 na-prot_1709.pdb -2501042.65 2026-04-26 20:44:50 35 na-prot_14712.pdb -2493477.92 2026-04-26 20:44:50 36 na-prot_12731.pdb -2479168.92 2026-04-26 20:44:50 37 na-prot_5029.pdb -2472548.5 2026-04-26 20:44:50 38 na-prot_8371.pdb -2448068.75 2026-04-26 20:44:50 39 na-prot_2868.pdb -2444104.87 2026-04-26 20:44:50 40 na-prot_7011.pdb -2439332.31 2026-04-26 20:44:50 41 na-prot_2768.pdb -2438539.13 2026-04-26 20:44:50 42 na-prot_16151.pdb -2430072.83 2026-04-26 20:44:50 43 na-prot_1107.pdb -2425659.25 2026-04-26 20:44:50 44 na-prot_15970.pdb -2425177.86 2026-04-26 20:44:50 45 na-prot_1393.pdb -2400155.29 2026-04-26 20:44:50 46 na-prot_2394.pdb -2399429.59 2026-04-26 20:44:50 47 na-prot_3770.pdb -2393572.47 2026-04-26 20:44:50 48 na-prot_2751.pdb -2393509.7 2026-04-26 20:44:50 49 na-prot_2379.pdb -2392522.47 2026-04-26 20:44:50 50 na-prot_214.pdb -2389371.49 2026-04-26 20:44:50 51 na-prot_12036.pdb -2373781.23 2026-04-26 20:44:50 52 na-prot_13381.pdb -2368268.63 2026-04-26 20:44:50 53 na-prot_2852.pdb -2360083.3 2026-04-26 20:44:50 54 na-prot_12768.pdb -2345121.41 2026-04-26 20:44:50 55 na-prot_1914.pdb -2343708.33 2026-04-26 20:44:50 56 na-prot_1908.pdb -2337916.07 2026-04-26 20:44:50 57 na-prot_2713.pdb -2323810.27 2026-04-26 20:44:50 58 na-prot_3679.pdb -2313549.58 2026-04-26 20:44:50 59 na-prot_19172.pdb -2304641.61 2026-04-26 20:44:50 60 na-prot_9285.pdb -2290653.41 2026-04-26 20:44:50 61 na-prot_3146.pdb -2286349.59 2026-04-26 20:44:50 62 na-prot_1479.pdb -2282508.07 2026-04-26 20:44:50 63 na-prot_18634.pdb -2281780.47 2026-04-26 20:44:50 64 na-prot_2762.pdb -2263566.56 2026-04-26 20:44:50 65 na-prot_16554.pdb -2261218.73 2026-04-26 20:44:50 66 na-prot_9604.pdb -2255708.13 2026-04-26 20:44:50 67 na-prot_5938.pdb -2213635.84 2026-04-26 20:44:50 68 na-prot_8124.pdb -2210598.22 2026-04-26 20:44:50 69 na-prot_7108.pdb -2205434.99 2026-04-26 20:44:50 70 na-prot_8470.pdb -2201440.24 2026-04-26 20:44:50 71 na-prot_11098.pdb -2197974.22 2026-04-26 20:44:50 72 na-prot_11831.pdb -2162204.36 2026-04-26 20:44:50 73 na-prot_16720.pdb -2143016.78 2026-04-26 20:44:50 74 na-prot_14973.pdb -2142086.83 2026-04-26 20:44:50 75 na-prot_11556.pdb -2136225.9 2026-04-26 20:44:50 76 na-prot_3261.pdb -2121853.9 2026-04-26 20:44:50 77 na-prot_1745.pdb -2104043.09 2026-04-26 20:44:50 78 na-prot_6925.pdb -2102423.47 2026-04-26 20:44:50 79 na-prot_1793.pdb -2102335.65 2026-04-26 20:44:50 80 na-prot_3644.pdb -2100313.33 2026-04-26 20:44:50 81 na-prot_1331.pdb -2100140.68 2026-04-26 20:44:50 82 na-prot_7950.pdb -2085224.69 2026-04-26 20:44:50 83 na-prot_2841.pdb -2083251.25 2026-04-26 20:44:50 84 na-prot_14404.pdb -2082387.72 2026-04-26 20:44:50 85 na-prot_16678.pdb -2081823.57 2026-04-26 20:44:50 86 na-prot_2673.pdb -2061662.63 2026-04-26 20:44:50 87 na-prot_16592.pdb -2053652.32 2026-04-26 20:44:50 88 na-prot_4959.pdb -2036263.19 2026-04-26 20:44:50 89 na-prot_3840.pdb -2017743.7 2026-04-26 20:44:50 90 na-prot_12516.pdb -2010640.22 2026-04-26 20:44:50 91 na-prot_13852.pdb -2002133.56 2026-04-26 20:44:50 92 na-prot_6172.pdb -1992521.35 2026-04-26 20:44:50 93 na-prot_1758.pdb -1989248.91 2026-04-26 20:44:50 94 na-prot_16762.pdb -1977935.86 2026-04-26 20:44:50 95 na-prot_5943.pdb -1966006.06 2026-04-26 20:44:50 96 na-prot_11551.pdb -1965324.38 2026-04-26 20:44:50 97 na-prot_17069.pdb -1951815.69 2026-04-26 20:44:50 98 na-prot_10371.pdb -1943110.14 2026-04-26 20:44:50 99 na-prot_2632.pdb -1938923.47 2026-04-26 20:44:50 100 na-prot_11267.pdb -1935180.64 2026-04-26 20:44:50 Chains: B 2026-04-26 20:45:11 100 best scored structures 2026-04-26 20:45:11 GRAMM analysis selected for further analysis: prot-na_30 2026-04-26 20:45:11 Cluster #1 with 5 structures 2026-04-26 20:45:11 1 na-prot_5029.pdb -2472548.5 2026-04-26 20:45:11 2 na-prot_16151.pdb -2430072.83 2026-04-26 20:45:11 3 na-prot_15970.pdb -2425177.86 2026-04-26 20:45:11 4 na-prot_3146.pdb -2286349.59 2026-04-26 20:45:11 5 na-prot_16678.pdb -2081823.57 2026-04-26 20:45:11 Sent to refinement: clusters_found|na-prot_5029.pdb 2026-04-26 20:45:11 Sent to refinement: clusters_found|na-prot_5029.pdb 2026-04-26 20:45:11 DARS clustering end 2026-04-26 20:45:11 MC (refinement) init 2026-04-26 20:45:11 python /home/rpdock/run_gramm//run_mc.py -f dars_to_mc.txt -d /home/rpdock/web/media/jobs/e928101a-6fc1-4ee9-b29a-f0fc85335d1c/ 2026-04-26 20:45:11 Refinement of #1 /home/rpdock/web/media/jobs/e928101a-6fc1-4ee9-b29a-f0fc85335d1c/na-prot_5029.pdb 2026-04-26 20:45:11 python /home/rpdock/mc/MC.py -s 1000 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/e928101a-6fc1-4ee9-b29a-f0fc85335d1c//ref_struc/na-prot_5029/na-prot_5029.pdb 2026-04-26 20:49:56 run_mc::stderr:/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom N defined twice in residue at line 1689. Exception ignored. Some atoms or residues may be missing in the data structure. % message, PDBConstructionWarning) /usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CA defined twice in residue at line 1691. Exception ignored. Some atoms or residues may be missing in the data structure. % message, PDBConstructionWarning) /usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C defined twice in residue at line 1693. Exception ignored. Some atoms or residues may be missing in the data structure. % message, PDBConstructionWarning) /usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom O defined twice in residue at line 1695. Exception ignored. Some atoms or residues may be missing in the data structure. % message, PDBConstructionWarning) /usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CB defined twice in residue at line 1697. Exception ignored. Some atoms or residues may be missing in the data structure. % message, PDBConstructionWarning) /usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom OG defined twice in residue at line 1699. Exception ignored. Some atoms or residues may be missing in the data structure. % message, PDBConstructionWarning) /usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom N defined twice in residue at line 2540. Exception ignored. Some atoms or residues may be missing in the data structure. % message, PDBConstructionWarning) /usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CA defined twice in residue at line 2542. Exception ignored. Some atoms or residues may be missing in the data structure. % message, PDBConstructionWarning) /usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C defined twice in residue at line 2544. Exception ignored. Some atoms or residues may be missing in the data structure. % message, PDBConstructionWarning) /usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom O defined twice in residue at line 2546. Exception ignored. Some atoms or residues may be missing in the data structure. % message, PDBConstructionWarning) /usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CB defined twice in residue at line 2548. Exception ignored. Some atoms or residues may be missing in the data structure. % message, PDBConstructionWarning) /usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CG defined twice in residue at line 2550. Exception ignored. Some atoms or residues may be missing in the data structure. % message, PDBConstructionWarning) /usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CD defined twice in residue at line 2552. Exception ignored. Some atoms or residues may be missing in the data structure. % message, PDBConstructionWarning) /usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom NE defined twice in residue at line 2554. Exception ignored. Some atoms or residues may be missing in the data structure. % message, PDBConstructionWarning) /usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CZ defined twice in residue at line 2556. Exception ignored. Some atoms or residues may be missing in the data structure. % message, PDBConstructionWarning) /usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom NH2 defined twice in residue at line 2559. Exception ignored. Some atoms or residues may be missing in the data structure. % message, PDBConstructionWarning) 2026-04-26 20:49:56 /usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom N defined twice in residue at line 1689. Exception ignored. Some atoms or residues may be missing in the data structure. % message, PDBConstructionWarning) /usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CA defined twice in residue at line 1691. Exception ignored. Some atoms or residues may be missing in the data structure. % message, PDBConstructionWarning) /usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C defined twice in residue at line 1693. Exception ignored. Some atoms or residues may be missing in the data structure. % message, PDBConstructionWarning) /usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom O defined twice in residue at line 1695. Exception ignored. Some atoms or residues may be missing in the data structure. % message, PDBConstructionWarning) /usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CB defined twice in residue at line 1697. Exception ignored. Some atoms or residues may be missing in the data structure. % message, PDBConstructionWarning) /usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom OG defined twice in residue at line 1699. Exception ignored. Some atoms or residues may be missing in the data structure. % message, PDBConstructionWarning) /usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom N defined twice in residue at line 2540. Exception ignored. Some atoms or residues may be missing in the data structure. % message, PDBConstructionWarning) /usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CA defined twice in residue at line 2542. Exception ignored. Some atoms or residues may be missing in the data structure. % message, PDBConstructionWarning) /usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C defined twice in residue at line 2544. Exception ignored. Some atoms or residues may be missing in the data structure. % message, PDBConstructionWarning) /usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom O defined twice in residue at line 2546. Exception ignored. Some atoms or residues may be missing in the data structure. % message, PDBConstructionWarning) /usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CB defined twice in residue at line 2548. Exception ignored. Some atoms or residues may be missing in the data structure. % message, PDBConstructionWarning) /usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CG defined twice in residue at line 2550. Exception ignored. Some atoms or residues may be missing in the data structure. % message, PDBConstructionWarning) /usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CD defined twice in residue at line 2552. Exception ignored. Some atoms or residues may be missing in the data structure. % message, PDBConstructionWarning) /usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom NE defined twice in residue at line 2554. Exception ignored. Some atoms or residues may be missing in the data structure. % message, PDBConstructionWarning) /usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CZ defined twice in residue at line 2556. Exception ignored. Some atoms or residues may be missing in the data structure. % message, PDBConstructionWarning) /usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom NH2 defined twice in residue at line 2559. Exception ignored. Some atoms or residues may be missing in the data structure. % message, PDBConstructionWarning) start - parameters: File name /home/rpdock/web/media/jobs/e928101a-6fc1-4ee9-b29a-f0fc85335d1c//ref_struc/na-prot_5029/na-prot_5029.pdb Steps 1000 Temp. start 15000.0 Temp. end 295.0 False msg start - parameters: File name /home/rpdock/web/media/jobs/e928101a-6fc1-4ee9-b29a-f0fc85335d1c//ref_struc/na-prot_5029/na-prot_5029.pdb Steps 1000 Temp. start 15000.0 Temp. end 295.0 False Step E Edist Eang Epen Warning, residue G1 in the chain A has not P atom Missed atom OD2 in the ASP 34 Missed atom CZ in the ARG 37 Missed atom NH1 in the ARG 37 Missed atom NH2 in the ARG 37 Missed atom CE in the LYS 50 Missed atom NZ in the LYS 50 Missed atom CG in the LYS 55 Missed atom CD in the LYS 55 Missed atom CE in the LYS 55 Missed atom NZ in the LYS 55 Missed atom CG in the LYS 72 Missed atom CD in the LYS 72 Missed atom CE in the LYS 72 Missed atom NZ in the LYS 72 Missed atom CG in the ARG 85 Missed atom CD in the ARG 85 Missed atom NE in the ARG 85 Missed atom CZ in the ARG 85 Missed atom NH1 in the ARG 85 Missed atom NH2 in the ARG 85 Missed atom OG in the SER 88 Missed atom CE in the LYS 120 Missed atom NZ in the LYS 120 Missed atom CD1 in the ILE 152 0 - -567211.01 -1229538.74 -1137672.27 1800000.00 1 T -920215.26 -1101381.69 -1018833.57 1200000.00 T= 14985.295 K progress 0.1 2 R -894777.68 -1092707.11 -1002070.57 1200000.00 T= 14970.59 K progress 0.2 3 R -834610.38 -990129.82 -944480.55 1100000.00 T= 14911.77 K progress 0.3 4 R -789646.19 -1085387.06 -1004259.13 1300000.00 T= 14882.36 K progress 0.4 5 R -934761.26 -1112626.94 -1022134.32 1200000.00 T= 14867.655 K progress 0.5 6 T -918605.15 -1036797.61 -981807.54 1100000.00 T= 14852.95 K progress 0.6 7 R -729054.89 -1113585.16 -1015469.73 1400000.00 T= 14764.72 K progress 0.7 8 T -719752.22 -1000024.87 -919727.35 1200000.00 T= 14750.015 K progress 0.8 9 T -631182.41 -946574.14 -884608.26 1200000.00 T= 14720.605 K progress 0.9 10 T -919795.51 -821551.10 -798244.41 700000.00 T= 14705.9 K progress 1.0 11 T -939999.76 -826924.67 -813075.09 700000.00 T= 14691.195 K progress 1.1 12 R -872969.32 -1076223.85 -996745.47 1200000.00 T= 14661.785 K progress 1.2 13 T -1034332.81 -1211061.63 -1123271.18 1300000.00 T= 14588.26 K progress 1.3 14 T -1372798.23 -1137107.88 -1035690.34 800000.00 T= 14544.145 K progress 1.4 15 T -1383878.70 -1138905.27 -1044973.43 800000.00 T= 14470.62 K progress 1.5 16 T -1748628.18 -1168530.60 -1080097.58 500000.00 T= 14426.505 K progress 1.6 17 R -1748628.18 -1168530.60 -1080097.58 500000.00 T= 13911.83 K progress 1.7 18 T -1764680.54 -1174892.81 -1089787.72 500000.00 T= 12823.66 K progress 1.8 19 T -1351288.41 -1116155.56 -1035132.85 800000.00 T= 11147.29 K progress 1.9 20 T -1357202.92 -1064839.36 -992363.56 700000.00 T= 11132.585 K progress 2.0 21 R -1443480.18 -1059108.07 -984372.11 600000.00 T= 10970.83 K progress 2.1 22 T -1273042.39 -910444.83 -862597.56 500000.00 T= 10397.335 K progress 2.2 23 T -1203528.34 -1031680.95 -971847.39 800000.00 T= 9941.48 K progress 2.3 24 R -1418368.24 -1160137.40 -1058230.84 800000.00 T= 9926.775 K progress 2.4 25 R -1391899.21 -1201080.05 -1090819.16 900000.00 T= 9794.43 K progress 2.5 26 R -1381076.52 -1189490.99 -1091585.52 900000.00 T= 9529.74 K progress 2.6 27 T -1396596.54 -1033801.72 -962794.83 600000.00 T= 9044.475 K progress 2.7 28 T -1358132.16 -1177190.15 -1080942.01 900000.00 T= 8662.145 K progress 2.8 29 T -1363002.17 -1113857.49 -1049144.68 800000.00 T= 8573.915 K progress 2.9 30 R -1568124.86 -1155196.48 -1112928.38 700000.00 T= 8397.455 K progress 3.0 31 R -1578203.62 -1161189.59 -1117014.03 700000.00 T= 7882.78 K progress 3.1 32 R -1568124.86 -1155196.48 -1112928.38 700000.00 T= 7691.615 K progress 3.2 33 R -1561917.72 -1152856.40 -1109061.32 700000.00 T= 7662.205 K progress 3.3 34 R -1563442.77 -1153739.24 -1109703.53 700000.00 T= 6074.065 K progress 3.4 35 R -1546689.06 -1144215.94 -1102473.11 700000.00 T= 5427.045 K progress 3.5 36 R -1667105.61 -1217544.98 -1149560.63 700000.00 T= 5368.225 K progress 3.6 37 R -1634439.11 -1199877.64 -1134561.48 700000.00 T= 3838.905 K progress 3.7 38 R -1634985.15 -1199877.64 -1135107.51 700000.00 T= 3133.065 K progress 3.8 39 R -1637974.96 -1202484.22 -1135490.74 700000.00 T= 2647.8 K progress 3.9 40 R -1645628.64 -1207727.77 -1137900.87 700000.00 T= 1147.89 K progress 4.0 41 R -1672254.62 -1224592.50 -1147662.12 700000.00 T= 1044.955 K progress 4.1 Save no big msg save short traj msg save best.pdb msg save plot e_step.png Sun Apr 26 20:45:11 2026 ['na-prot_5029.pdb'] msg Refinement of #1 /home/rpdock/web/media/jobs/e928101a-6fc1-4ee9-b29a-f0fc85335d1c/na-prot_5029.pdb dir: /home/rpdock/web/media/jobs/e928101a-6fc1-4ee9-b29a-f0fc85335d1c/ file: na-prot_5029.pdb find `pwd` -iname na-prot_5029.pdb copy /home/rpdock/web/media/jobs/e928101a-6fc1-4ee9-b29a-f0fc85335d1c/prot-na_30/na-prot_5029.pdb to /home/rpdock/web/media/jobs/e928101a-6fc1-4ee9-b29a-f0fc85335d1c//ref_struc/na-prot_5029/na-prot_5029.pdb cmd: python /home/rpdock/mc/MC.py -s 1000 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/e928101a-6fc1-4ee9-b29a-f0fc85335d1c//ref_struc/na-prot_5029/na-prot_5029.pdb msg python /home/rpdock/mc/MC.py -s 1000 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/e928101a-6fc1-4ee9-b29a-f0fc85335d1c//ref_struc/na-prot_5029/na-prot_5029.pdb msg run_mc::stderr:/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom N defined twice in residue at line 1689. Exception ignored. Some atoms or residues may be missing in the data structure. % message, PDBConstructionWarning) /usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CA defined twice in residue at line 1691. Exception ignored. Some atoms or residues may be missing in the data structure. % message, PDBConstructionWarning) /usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C defined twice in residue at line 1693. Exception ignored. Some atoms or residues may be missing in the data structure. % message, PDBConstructionWarning) /usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom O defined twice in residue at line 1695. Exception ignored. Some atoms or residues may be missing in the data structure. % message, PDBConstructionWarning) /usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CB defined twice in residue at line 1697. Exception ignored. Some atoms or residues may be missing in the data structure. % message, PDBConstructionWarning) /usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom OG defined twice in residue at line 1699. Exception ignored. Some atoms or residues may be missing in the data structure. % message, PDBConstructionWarning) /usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom N defined twice in residue at line 2540. Exception ignored. Some atoms or residues may be missing in the data structure. % message, PDBConstructionWarning) /usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CA defined twice in residue at line 2542. Exception ignored. Some atoms or residues may be missing in the data structure. % message, PDBConstructionWarning) /usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C defined twice in residue at line 2544. Exception ignored. Some atoms or residues may be missing in the data structure. % message, PDBConstructionWarning) /usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom O defined twice in residue at line 2546. Exception ignored. Some atoms or residues may be missing in the data structure. % message, PDBConstructionWarning) /usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: Error in run_mc /usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom N defined twice in residue at line 1689. Exception ignored. Some atoms or residues may be missing in the data structure. % message, PDBConstructionWarning) /usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CA defined twice in residue at line 1691. Exception ignored. Some atoms or residues may be missing in the data structure. % message, PDBConstructionWarning) /usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C defined twice in residue at line 1693. Exception ignored. Some atoms or residues may be missing in the data structure. % message, PDBConstructionWarning) /usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom O defined twice in residue at line 1695. Exception ignored. Some atoms or residues may be missing in the data structure. % message, PDBConstructionWarning) /usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CB defined twice in residue at line 1697. Exception ignored. Some atoms or residues may be missing in the data structure. % message, PDBConstructionWarning) /usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom OG defined twice in residue at line 1699. Exception ignored. Some atoms or residues may be missing in the data structure. % message, PDBConstructionWarning) /usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom N defined twice in residue at line 2540. Exception ignored. Some atoms or residues may be missing in the data structure. % message, PDBConstructionWarning) /usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CA defined twice in residue at line 2542. Exception ignored. Some atoms or residues may be missing in the data structure. % message, PDBConstructionWarning) /usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C defined twice in residue at line 2544. Exception ignored. Some atoms or residues may be missing in the data structure. % message, PDBConstructionWarning) /usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom O defined twice in residue at line 2546. Exception ignored. Some atoms or residues may be missing in the data structure. % message, PDBConstructionWarning) /usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CB defined twice in residue at line 2548. Exception ignored. Some atoms or residues may be missing in the data structure. % message, PDBConstructionWarning) /usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CG defined twice in residue at line 2550. Exception ignored. Some atoms or residues may be missing in the data structure. % message, PDBConstructionWarning) /usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CD defined twice in residue at line 2552. Exception ignored. Some atoms or residues may be missing in the data structure. % message, PDBConstructionWarning) /usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom NE defined twice in residue at line 2554. Exception ignored. Some atoms or residues may be missing in the data structure. % message, PDBConstructionWarning) /usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CZ defined twice in residue at line 2556. Exception ignored. Some atoms or residues may be missing in the data structure. % message, PDBConstructionWarning) /usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom NH2 defined twice in residue at line 2559. Exception ignored. Some atoms or residues may be missing in the data structure. % message, PDBConstructionWarning) PDBConstructionException: Atom CB defined twice in residue at line 2548. Exception ignored. Some atoms or residues may be missing in the data structure. % message, PDBConstructionWarning) /usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CG defined twice in residue at line 2550. Exception ignored. Some atoms or residues may be missing in the data structure. % message, PDBConstructionWarning) /usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CD defined twice in residue at line 2552. Exception ignored. Some atoms or residues may be missing in the data structure. % message, PDBConstructionWarning) /usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom NE defined twice in residue at line 2554. Exception ignored. Some atoms or residues may be missing in the data structure. % message, PDBConstructionWarning) /usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CZ defined twice in residue at line 2556. Exception ignored. Some atoms or residues may be missing in the data structure. % message, PDBConstructionWarning) /usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom NH2 defined twice in residue at line 2559. Exception ignored. Some atoms or residues may be missing in the data structure. % message, PDBConstructionWarning) 2026-04-26 20:49:56 npdock::MC (refinement) end 2026-04-26 20:49:56 npdock::OK 2026-04-26 20:49:56 Set finished status of e928101a-6fc1-4ee9-b29a-f0fc85335d1c