2026-10-23 17:05:03 NPdock start 2026-10-23 17:05:03 ver: v1.2-23-gfce5bd3-dirty 2026-10-23 17:05:03 mode: None 2026-10-23 17:05:03 is RNA? True 2026-10-23 17:05:03 Interface: prot: '' na: '' 2026-10-23 17:05:03 Curr dir:/home/rpdock/web/media/jobs/f6f9702c-8193-4f6d-850f-79335bec5b3e/ 2026-10-23 17:05:03 GRAMM in progress... 2026-10-23 17:05:03 timeout 72h python /home/rpdock/run_gramm//run_gramm1.py -d 20000 -p prot.pdb -r na.pdb -pi '' -ri '' -n '1' -pf '*' -rf '*' 2026-10-23 17:44:40 GRAMM done 2026-10-23 17:44:40 DARS scoring in progress... 2026-10-23 17:44:40 timeout 72h /home/rpdock/run_gramm//DARS-RNP_v3//DARS_potential_v3_scoring.py -m 100 -f list.txt -o dars_out.txt 2026-10-23 17:44:41 DARS start [DARS_potential_v3_scoring.py] 2026-10-23 17:44:41 Show log every 100 structures [DARS_potential_v3_scoring.py] 2026-10-23 17:44:41 1/20000 prot-na_1000.pdb -1737040.48 2026-10-23 17:45:38 100/20000 prot-na_94.pdb -2813679.08 2026-10-23 17:46:37 200/20000 prot-na_194.pdb -3346795.49 2026-10-23 17:47:39 300/20000 prot-na_294.pdb -2281878.26 2026-10-23 17:48:40 400/20000 prot-na_394.pdb -1864861.12 2026-10-23 17:49:43 500/20000 prot-na_494.pdb -2262954.81 2026-10-23 17:50:45 600/20000 prot-na_594.pdb -4021061.76 2026-10-23 17:51:48 700/20000 prot-na_694.pdb -2617662.40 2026-10-23 17:52:51 800/20000 prot-na_794.pdb -2951453.93 2026-10-23 17:53:53 900/20000 prot-na_894.pdb -2183995.68 2026-10-23 17:55:03 1000/20000 prot-na_994.pdb -3137223.14 2026-10-23 17:56:10 1100/20000 prot-na_1100.pdb -4208944.62 2026-10-23 17:57:13 1200/20000 prot-na_1200.pdb -1708611.07 2026-10-23 17:58:19 1300/20000 prot-na_1300.pdb -3084718.47 2026-10-23 17:59:23 1400/20000 prot-na_1400.pdb -2492867.18 2026-10-23 18:00:27 1500/20000 prot-na_1500.pdb -2320396.16 2026-10-23 18:01:31 1600/20000 prot-na_1600.pdb -1233240.85 2026-10-23 18:02:35 1700/20000 prot-na_1700.pdb -2477852.60 2026-10-23 18:03:39 1800/20000 prot-na_1800.pdb -2374877.68 2026-10-23 18:04:42 1900/20000 prot-na_1900.pdb -1651397.28 2026-10-23 18:05:45 2000/20000 prot-na_2000.pdb -1875218.38 2026-10-23 18:06:49 2100/20000 prot-na_2100.pdb -3301790.80 2026-10-23 18:07:53 2200/20000 prot-na_2200.pdb -2444202.10 2026-10-23 18:08:57 2300/20000 prot-na_2300.pdb -3190240.84 2026-10-23 18:10:01 2400/20000 prot-na_2400.pdb -1650140.62 2026-10-23 18:11:05 2500/20000 prot-na_2500.pdb -4699808.49 2026-10-23 18:12:09 2600/20000 prot-na_2600.pdb -1496784.91 2026-10-23 18:13:13 2700/20000 prot-na_2700.pdb -2488470.99 2026-10-23 18:14:17 2800/20000 prot-na_2800.pdb -1786737.12 2026-10-23 18:15:32 2900/20000 prot-na_2900.pdb -1685814.78 2026-10-23 18:16:39 3000/20000 prot-na_3000.pdb -2100194.57 2026-10-23 18:17:45 3100/20000 prot-na_3100.pdb -1435539.35 2026-10-23 18:18:50 3200/20000 prot-na_3200.pdb -2297417.06 2026-10-23 18:20:02 3300/20000 prot-na_3300.pdb -2237051.33 2026-10-23 18:21:07 3400/20000 prot-na_3400.pdb -2225232.23 2026-10-23 18:22:12 3500/20000 prot-na_3500.pdb -2262533.50 2026-10-23 18:23:16 3600/20000 prot-na_3600.pdb -2909925.95 2026-10-23 18:24:20 3700/20000 prot-na_3700.pdb -1636960.82 2026-10-23 18:25:25 3800/20000 prot-na_3800.pdb -2173659.02 2026-10-23 18:26:28 3900/20000 prot-na_3900.pdb -1917097.33 2026-10-23 18:27:33 4000/20000 prot-na_4000.pdb -2728185.99 2026-10-23 18:28:37 4100/20000 prot-na_4100.pdb -1525634.17 2026-10-23 18:29:40 4200/20000 prot-na_4200.pdb -2514147.03 2026-10-23 18:30:44 4300/20000 prot-na_4300.pdb -2136348.16 2026-10-23 18:31:48 4400/20000 prot-na_4400.pdb -2531136.51 2026-10-23 18:32:52 4500/20000 prot-na_4500.pdb -2509625.03 2026-10-23 18:34:04 4600/20000 prot-na_4600.pdb -2237059.31 2026-10-23 18:35:18 4700/20000 prot-na_4700.pdb -2748162.81 2026-10-23 18:36:34 4800/20000 prot-na_4800.pdb -2921299.80 2026-10-23 18:37:49 4900/20000 prot-na_4900.pdb -2247545.27 2026-10-23 18:39:05 5000/20000 prot-na_5000.pdb -1891654.44 2026-10-23 18:40:21 5100/20000 prot-na_5100.pdb -2461887.29 2026-10-23 18:41:36 5200/20000 prot-na_5200.pdb -1793057.08 2026-10-23 18:42:51 5300/20000 prot-na_5300.pdb -2550505.27 2026-10-23 18:44:08 5400/20000 prot-na_5400.pdb -1746766.92 2026-10-23 18:45:23 5500/20000 prot-na_5500.pdb -1657432.64 2026-10-23 18:46:39 5600/20000 prot-na_5600.pdb -3590074.85 2026-10-23 18:47:53 5700/20000 prot-na_5700.pdb -2331558.18 2026-10-23 18:49:08 5800/20000 prot-na_5800.pdb -2238324.14 2026-10-23 18:50:24 5900/20000 prot-na_5900.pdb -2117486.51 2026-10-23 18:51:40 6000/20000 prot-na_6000.pdb -1618909.04 2026-10-23 18:52:56 6100/20000 prot-na_6100.pdb -1437872.52 2026-10-23 18:54:13 6200/20000 prot-na_6200.pdb -1811955.87 2026-10-23 18:55:32 6300/20000 prot-na_6300.pdb -2105623.58 2026-10-23 18:56:48 6400/20000 prot-na_6400.pdb -1996459.66 2026-10-23 18:58:03 6500/20000 prot-na_6500.pdb -2670682.71 2026-10-23 18:59:21 6600/20000 prot-na_6600.pdb -1920432.81 2026-10-23 19:00:40 6700/20000 prot-na_6700.pdb -1144635.06 2026-10-23 19:01:57 6800/20000 prot-na_6800.pdb -2460678.88 2026-10-23 19:03:14 6900/20000 prot-na_6900.pdb -1747794.92 2026-10-23 19:04:31 7000/20000 prot-na_7000.pdb -1832398.36 2026-10-23 19:05:48 7100/20000 prot-na_7100.pdb -1501632.42 2026-10-23 19:07:01 7200/20000 prot-na_7200.pdb -1377387.93 2026-10-23 19:08:16 7300/20000 prot-na_7300.pdb -1609457.60 2026-10-23 19:09:33 7400/20000 prot-na_7400.pdb -2197244.63 2026-10-23 19:10:52 7500/20000 prot-na_7500.pdb -2070847.60 2026-10-23 19:12:08 7600/20000 prot-na_7600.pdb -1814267.01 2026-10-23 19:13:23 7700/20000 prot-na_7700.pdb -1521163.06 2026-10-23 19:14:39 7800/20000 prot-na_7800.pdb -2132348.92 2026-10-23 19:15:53 7900/20000 prot-na_7900.pdb -3206916.75 2026-10-23 19:17:07 8000/20000 prot-na_8000.pdb -1725974.81 2026-10-23 19:18:21 8100/20000 prot-na_8100.pdb -787357.96 2026-10-23 19:19:35 8200/20000 prot-na_8200.pdb -1826470.97 2026-10-23 19:21:04 8300/20000 prot-na_8300.pdb -2399498.50 2026-10-23 19:22:23 8400/20000 prot-na_8400.pdb -4287975.62 2026-10-23 19:23:36 8500/20000 prot-na_8500.pdb -2284690.85 2026-10-23 19:24:50 8600/20000 prot-na_8600.pdb -3164351.01 2026-10-23 19:26:04 8700/20000 prot-na_8700.pdb -1842531.04 2026-10-23 19:27:19 8800/20000 prot-na_8800.pdb -1826005.35 2026-10-23 19:28:34 8900/20000 prot-na_8900.pdb -1757071.76 2026-10-23 19:29:50 9000/20000 prot-na_9000.pdb -2110937.06 2026-10-23 19:31:06 9100/20000 prot-na_9100.pdb -2423441.56 2026-10-23 19:32:20 9200/20000 prot-na_9200.pdb -1611781.46 2026-10-23 19:33:37 9300/20000 prot-na_9300.pdb -1143771.08 2026-10-23 19:34:53 9400/20000 prot-na_9400.pdb -2000861.13 2026-10-23 19:36:08 9500/20000 prot-na_9500.pdb -1431134.74 2026-10-23 19:37:22 9600/20000 prot-na_9600.pdb -3038544.06 2026-10-23 19:38:37 9700/20000 prot-na_9700.pdb -1390035.66 2026-10-23 19:39:47 9800/20000 prot-na_9800.pdb -1121411.44 2026-10-23 19:40:58 9900/20000 prot-na_9900.pdb -1708250.34 2026-10-23 19:42:15 10000/20000 prot-na_10000.pdb -2577798.11 2026-10-23 19:43:33 10100/20000 prot-na_10100.pdb -1939443.63 2026-10-23 19:44:40 10200/20000 prot-na_10200.pdb -2434636.40 2026-10-23 19:45:47 10300/20000 prot-na_10300.pdb -2530936.32 2026-10-23 19:46:53 10400/20000 prot-na_10400.pdb -1618818.33 2026-10-23 19:47:59 10500/20000 prot-na_10500.pdb -2664556.81 2026-10-23 19:49:05 10600/20000 prot-na_10600.pdb -1455312.83 2026-10-23 19:50:12 10700/20000 prot-na_10700.pdb -3432257.26 2026-10-23 19:51:18 10800/20000 prot-na_10800.pdb -3334313.93 2026-10-23 19:52:24 10900/20000 prot-na_10900.pdb -1499602.47 2026-10-23 19:53:29 11000/20000 prot-na_11000.pdb -1988264.23 2026-10-23 19:54:35 11100/20000 prot-na_11100.pdb -1669131.06 2026-10-23 19:55:40 11200/20000 prot-na_11200.pdb -1405036.64 2026-10-23 19:56:44 11300/20000 prot-na_11300.pdb -1682703.66 2026-10-23 19:57:50 11400/20000 prot-na_11400.pdb -1663433.01 2026-10-23 19:58:55 11500/20000 prot-na_11500.pdb -3227365.31 2026-10-23 20:00:02 11600/20000 prot-na_11600.pdb -3337940.58 2026-10-23 20:01:10 11700/20000 prot-na_11700.pdb -2438615.12 2026-10-23 20:02:16 11800/20000 prot-na_11800.pdb -3862365.74 2026-10-23 20:03:20 11900/20000 prot-na_11900.pdb -2540138.89 2026-10-23 20:04:25 12000/20000 prot-na_12000.pdb -2199805.32 2026-10-23 20:05:30 12100/20000 prot-na_12100.pdb -959505.88 2026-10-23 20:06:35 12200/20000 prot-na_12200.pdb -2087786.88 2026-10-23 20:07:40 12300/20000 prot-na_12300.pdb -1856262.83 2026-10-23 20:08:46 12400/20000 prot-na_12400.pdb -1949502.88 2026-10-23 20:09:51 12500/20000 prot-na_12500.pdb -3719176.71 2026-10-23 20:11:00 12600/20000 prot-na_12600.pdb -2336381.55 2026-10-23 20:12:06 12700/20000 prot-na_12700.pdb -1670614.01 2026-10-23 20:13:12 12800/20000 prot-na_12800.pdb -2020175.76 2026-10-23 20:14:17 12900/20000 prot-na_12900.pdb -1356949.01 2026-10-23 20:15:23 13000/20000 prot-na_13000.pdb -1715404.22 2026-10-23 20:16:29 13100/20000 prot-na_13100.pdb -2205843.25 2026-10-23 20:17:36 13200/20000 prot-na_13200.pdb -1521778.34 2026-10-23 20:18:42 13300/20000 prot-na_13300.pdb -1405263.43 2026-10-23 20:19:48 13400/20000 prot-na_13400.pdb -1571463.58 2026-10-23 20:20:54 13500/20000 prot-na_13500.pdb -2175271.22 2026-10-23 20:21:59 13600/20000 prot-na_13600.pdb -1821062.21 2026-10-23 20:23:06 13700/20000 prot-na_13700.pdb -1816978.08 2026-10-23 20:24:10 13800/20000 prot-na_13800.pdb -2069135.11 2026-10-23 20:25:15 13900/20000 prot-na_13900.pdb -3221914.07 2026-10-23 20:26:21 14000/20000 prot-na_14000.pdb -2383951.73 2026-10-23 20:27:26 14100/20000 prot-na_14100.pdb -1519002.23 2026-10-23 20:28:31 14200/20000 prot-na_14200.pdb -2236594.85 2026-10-23 20:29:35 14300/20000 prot-na_14300.pdb -2080718.10 2026-10-23 20:30:40 14400/20000 prot-na_14400.pdb -1763041.87 2026-10-23 20:31:50 14500/20000 prot-na_14500.pdb -1445336.83 2026-10-23 20:32:57 14600/20000 prot-na_14600.pdb -1677611.01 2026-10-23 20:34:01 14700/20000 prot-na_14700.pdb -1893145.70 2026-10-23 20:35:06 14800/20000 prot-na_14800.pdb -1439443.67 2026-10-23 20:36:09 14900/20000 prot-na_14900.pdb -1588199.91 2026-10-23 20:37:12 15000/20000 prot-na_15000.pdb -2048173.08 2026-10-23 20:38:16 15100/20000 prot-na_15100.pdb -1533129.63 2026-10-23 20:39:18 15200/20000 prot-na_15200.pdb -1739505.08 2026-10-23 20:40:25 15300/20000 prot-na_15300.pdb -1318316.30 2026-10-23 20:41:28 15400/20000 prot-na_15400.pdb -1217206.92 2026-10-23 20:42:31 15500/20000 prot-na_15500.pdb -2769647.57 2026-10-23 20:43:34 15600/20000 prot-na_15600.pdb -1665169.96 2026-10-23 20:44:36 15700/20000 prot-na_15700.pdb -2394285.47 2026-10-23 20:45:39 15800/20000 prot-na_15800.pdb -2282940.94 2026-10-23 20:46:42 15900/20000 prot-na_15900.pdb -378202.03 2026-10-23 20:47:44 16000/20000 prot-na_16000.pdb -2231343.35 2026-10-23 20:48:47 16100/20000 prot-na_16100.pdb -3227066.36 2026-10-23 20:49:49 16200/20000 prot-na_16200.pdb -2302083.78 2026-10-23 20:50:52 16300/20000 prot-na_16300.pdb -983977.34 2026-10-23 20:51:55 16400/20000 prot-na_16400.pdb -1352090.94 2026-10-23 20:52:57 16500/20000 prot-na_16500.pdb -1666785.15 2026-10-23 20:54:00 16600/20000 prot-na_16600.pdb -1239128.82 2026-10-23 20:55:03 16700/20000 prot-na_16700.pdb -1790042.63 2026-10-23 20:56:06 16800/20000 prot-na_16800.pdb -2679140.38 2026-10-23 20:57:09 16900/20000 prot-na_16900.pdb -2155234.74 2026-10-23 20:58:12 17000/20000 prot-na_17000.pdb -2603130.21 2026-10-23 20:59:16 17100/20000 prot-na_17100.pdb -1590258.83 2026-10-23 21:00:20 17200/20000 prot-na_17200.pdb -1862422.29 2026-10-23 21:01:23 17300/20000 prot-na_17300.pdb -1810663.18 2026-10-23 21:02:27 17400/20000 prot-na_17400.pdb -3063621.41 2026-10-23 21:03:30 17500/20000 prot-na_17500.pdb -2345820.32 2026-10-23 21:04:35 17600/20000 prot-na_17600.pdb -2384714.10 2026-10-23 21:05:39 17700/20000 prot-na_17700.pdb -2034621.41 2026-10-23 21:06:42 17800/20000 prot-na_17800.pdb -1782228.50 2026-10-23 21:07:46 17900/20000 prot-na_17900.pdb -1220228.24 2026-10-23 21:08:50 18000/20000 prot-na_18000.pdb -2082130.76 2026-10-23 21:09:54 18100/20000 prot-na_18100.pdb -1703704.99 2026-10-23 21:10:59 18200/20000 prot-na_18200.pdb -730930.88 2026-10-23 21:12:02 18300/20000 prot-na_18300.pdb -2539978.09 2026-10-23 21:13:05 18400/20000 prot-na_18400.pdb -1827488.68 2026-10-23 21:14:09 18500/20000 prot-na_18500.pdb -1752743.21 2026-10-23 21:15:13 18600/20000 prot-na_18600.pdb -2111993.42 2026-10-23 21:16:16 18700/20000 prot-na_18700.pdb -1948894.44 2026-10-23 21:17:19 18800/20000 prot-na_18800.pdb -2762444.69 2026-10-23 21:18:23 18900/20000 prot-na_18900.pdb -1941890.10 2026-10-23 21:19:33 19000/20000 prot-na_19000.pdb -2453219.79 2026-10-23 21:20:36 19100/20000 prot-na_19100.pdb -2268251.80 2026-10-23 21:21:39 19200/20000 prot-na_19200.pdb -1029712.11 2026-10-23 21:22:42 19300/20000 prot-na_19300.pdb -1407205.73 2026-10-23 21:23:45 19400/20000 prot-na_19400.pdb -1423902.48 2026-10-23 21:24:49 19500/20000 prot-na_19500.pdb -1537565.79 2026-10-23 21:25:52 19600/20000 prot-na_19600.pdb -2263028.54 2026-10-23 21:26:55 19700/20000 prot-na_19700.pdb -2838412.33 2026-10-23 21:27:59 19800/20000 prot-na_19800.pdb -1493699.18 2026-10-23 21:29:02 19900/20000 prot-na_19900.pdb -2239883.01 2026-10-23 21:30:10 20000/20000 prot-na_20000.pdb -2131174.69 2026-10-23 21:30:10 DARS scoring end 2026-10-23 21:30:10 Clustering (cuttoff: 5, nr_clust: 100 ) in progress... 2026-10-23 21:30:10 timeout 72h python /home/rpdock/run_gramm//clustering_v4.py dars_out.txt list.txt 5 100 2026-10-23 21:30:10 100 best scored structures 2026-10-23 21:30:10 1 prot-na_15917.pdb -5666040.01 2026-10-23 21:30:10 2 prot-na_1352.pdb -5616289.58 2026-10-23 21:30:10 3 prot-na_6281.pdb -5536756.01 2026-10-23 21:30:10 4 prot-na_18893.pdb -5492731.64 2026-10-23 21:30:10 5 prot-na_10838.pdb -5471061.86 2026-10-23 21:30:10 6 prot-na_12828.pdb -5420123.69 2026-10-23 21:30:10 7 prot-na_52.pdb -5337531.62 2026-10-23 21:30:10 8 prot-na_180.pdb -5306213.24 2026-10-23 21:30:10 9 prot-na_1521.pdb -5261857.44 2026-10-23 21:30:10 10 prot-na_736.pdb -5261672.71 2026-10-23 21:30:10 11 prot-na_814.pdb -5250739.23 2026-10-23 21:30:10 12 prot-na_18960.pdb -5191023.98 2026-10-23 21:30:10 13 prot-na_12330.pdb -5146547.26 2026-10-23 21:30:10 14 prot-na_16160.pdb -5132847.58 2026-10-23 21:30:10 15 prot-na_5.pdb -5129973.98 2026-10-23 21:30:10 16 prot-na_17762.pdb -5118907.53 2026-10-23 21:30:10 17 prot-na_11332.pdb -5107429.75 2026-10-23 21:30:10 18 prot-na_82.pdb -5087050.72 2026-10-23 21:30:10 19 prot-na_19084.pdb -5081354.85 2026-10-23 21:30:10 20 prot-na_778.pdb -5047812.7 2026-10-23 21:30:10 21 prot-na_3706.pdb -5014360.9 2026-10-23 21:30:10 22 prot-na_11315.pdb -5008736.25 2026-10-23 21:30:10 23 prot-na_2991.pdb -5007678.21 2026-10-23 21:30:10 24 prot-na_13935.pdb -5002702.91 2026-10-23 21:30:10 25 prot-na_12712.pdb -4952454.46 2026-10-23 21:30:10 26 prot-na_911.pdb -4932752.74 2026-10-23 21:30:10 27 prot-na_14380.pdb -4919063.49 2026-10-23 21:30:10 28 prot-na_6907.pdb -4910517.9 2026-10-23 21:30:10 29 prot-na_10530.pdb -4891267.99 2026-10-23 21:30:10 30 prot-na_1913.pdb -4885854.09 2026-10-23 21:30:10 31 prot-na_17280.pdb -4882896.45 2026-10-23 21:30:10 32 prot-na_12.pdb -4861475.33 2026-10-23 21:30:10 33 prot-na_61.pdb -4853706.86 2026-10-23 21:30:10 34 prot-na_5170.pdb -4832760.28 2026-10-23 21:30:10 35 prot-na_5544.pdb -4781102.83 2026-10-23 21:30:10 36 prot-na_6726.pdb -4755366.44 2026-10-23 21:30:10 37 prot-na_3559.pdb -4743092.07 2026-10-23 21:30:10 38 prot-na_10879.pdb -4734681.18 2026-10-23 21:30:10 39 prot-na_10820.pdb -4704184.47 2026-10-23 21:30:10 40 prot-na_2500.pdb -4699808.49 2026-10-23 21:30:10 41 prot-na_8818.pdb -4684219.87 2026-10-23 21:30:10 42 prot-na_1898.pdb -4680052.09 2026-10-23 21:30:10 43 prot-na_12219.pdb -4679934.72 2026-10-23 21:30:10 44 prot-na_14601.pdb -4678704.05 2026-10-23 21:30:10 45 prot-na_1226.pdb -4678396.75 2026-10-23 21:30:10 46 prot-na_18667.pdb -4655285.81 2026-10-23 21:30:10 47 prot-na_13490.pdb -4647293.31 2026-10-23 21:30:10 48 prot-na_5009.pdb -4638678.49 2026-10-23 21:30:10 49 prot-na_14481.pdb -4616564.63 2026-10-23 21:30:10 50 prot-na_10455.pdb -4610467.26 2026-10-23 21:30:10 51 prot-na_19680.pdb -4607617.04 2026-10-23 21:30:10 52 prot-na_2553.pdb -4603683.48 2026-10-23 21:30:10 53 prot-na_10299.pdb -4597301.56 2026-10-23 21:30:10 54 prot-na_432.pdb -4587389.34 2026-10-23 21:30:10 55 prot-na_1154.pdb -4565979.31 2026-10-23 21:30:10 56 prot-na_7909.pdb -4553947.61 2026-10-23 21:30:10 57 prot-na_10127.pdb -4544563.59 2026-10-23 21:30:10 58 prot-na_10521.pdb -4540473.1 2026-10-23 21:30:10 59 prot-na_151.pdb -4539129.6 2026-10-23 21:30:10 60 prot-na_601.pdb -4504693.77 2026-10-23 21:30:10 61 prot-na_7258.pdb -4500588.26 2026-10-23 21:30:10 62 prot-na_5490.pdb -4497366.32 2026-10-23 21:30:10 63 prot-na_7315.pdb -4496321.77 2026-10-23 21:30:10 64 prot-na_302.pdb -4495319.98 2026-10-23 21:30:10 65 prot-na_6566.pdb -4488860.64 2026-10-23 21:30:10 66 prot-na_2410.pdb -4487344.86 2026-10-23 21:30:10 67 prot-na_8521.pdb -4482900.53 2026-10-23 21:30:10 68 prot-na_7634.pdb -4477254.16 2026-10-23 21:30:10 69 prot-na_13312.pdb -4467904.1 2026-10-23 21:30:10 70 prot-na_727.pdb -4456617.53 2026-10-23 21:30:10 71 prot-na_5378.pdb -4450506.28 2026-10-23 21:30:10 72 prot-na_2868.pdb -4449998.22 2026-10-23 21:30:10 73 prot-na_5458.pdb -4448158.97 2026-10-23 21:30:10 74 prot-na_13272.pdb -4447700.11 2026-10-23 21:30:10 75 prot-na_1803.pdb -4447498.58 2026-10-23 21:30:10 76 prot-na_10531.pdb -4435540.93 2026-10-23 21:30:10 77 prot-na_15509.pdb -4427715.33 2026-10-23 21:30:10 78 prot-na_4085.pdb -4423692.01 2026-10-23 21:30:10 79 prot-na_8571.pdb -4419527.29 2026-10-23 21:30:10 80 prot-na_6978.pdb -4402476.8 2026-10-23 21:30:10 81 prot-na_174.pdb -4398398.51 2026-10-23 21:30:10 82 prot-na_1029.pdb -4387827.8 2026-10-23 21:30:10 83 prot-na_6595.pdb -4384076.31 2026-10-23 21:30:10 84 prot-na_10901.pdb -4382141.69 2026-10-23 21:30:10 85 prot-na_225.pdb -4378982.78 2026-10-23 21:30:10 86 prot-na_19.pdb -4377834.38 2026-10-23 21:30:10 87 prot-na_1462.pdb -4373990.03 2026-10-23 21:30:10 88 prot-na_224.pdb -4371633.57 2026-10-23 21:30:10 89 prot-na_17582.pdb -4368433.84 2026-10-23 21:30:10 90 prot-na_11275.pdb -4366125.82 2026-10-23 21:30:10 91 prot-na_1113.pdb -4364974.51 2026-10-23 21:30:10 92 prot-na_2294.pdb -4364733.55 2026-10-23 21:30:10 93 prot-na_6659.pdb -4359526.91 2026-10-23 21:30:10 94 prot-na_16117.pdb -4345397.92 2026-10-23 21:30:10 95 prot-na_5645.pdb -4338042.4 2026-10-23 21:30:10 96 prot-na_7115.pdb -4333551.13 2026-10-23 21:30:10 97 prot-na_3753.pdb -4331528.1 2026-10-23 21:30:10 98 prot-na_3896.pdb -4329964.92 2026-10-23 21:30:10 99 prot-na_17895.pdb -4325505.28 2026-10-23 21:30:10 100 prot-na_3136.pdb -4323355.91 2026-10-23 21:30:10 Chains: B 2026-10-23 21:30:34 100 best scored structures 2026-10-23 21:30:34 GRAMM analysis selected for further analysis: prot-na_25 2026-10-23 21:30:34 Cluster #1 with 6 structures 2026-10-23 21:30:34 1 prot-na_814.pdb -5250739.23 2026-10-23 21:30:34 2 prot-na_18960.pdb -5191023.98 2026-10-23 21:30:34 3 prot-na_19084.pdb -5081354.85 2026-10-23 21:30:34 4 prot-na_778.pdb -5047812.7 2026-10-23 21:30:34 5 prot-na_3706.pdb -5014360.9 2026-10-23 21:30:34 6 prot-na_10521.pdb -4540473.1 2026-10-23 21:30:34 Cluster #2 with 5 structures 2026-10-23 21:30:34 1 prot-na_10838.pdb -5471061.86 2026-10-23 21:30:34 2 prot-na_11332.pdb -5107429.75 2026-10-23 21:30:34 3 prot-na_14380.pdb -4919063.49 2026-10-23 21:30:34 4 prot-na_1913.pdb -4885854.09 2026-10-23 21:30:34 5 prot-na_61.pdb -4853706.86 2026-10-23 21:30:34 Cluster #3 with 5 structures 2026-10-23 21:30:34 1 prot-na_10879.pdb -4734681.18 2026-10-23 21:30:34 2 prot-na_14601.pdb -4678704.05 2026-10-23 21:30:34 3 prot-na_432.pdb -4587389.34 2026-10-23 21:30:34 4 prot-na_1029.pdb -4387827.8 2026-10-23 21:30:34 5 prot-na_6595.pdb -4384076.31 2026-10-23 21:30:34 Cluster #4 with 5 structures 2026-10-23 21:30:34 1 prot-na_7258.pdb -4500588.26 2026-10-23 21:30:34 2 prot-na_2410.pdb -4487344.86 2026-10-23 21:30:34 3 prot-na_13312.pdb -4467904.1 2026-10-23 21:30:34 4 prot-na_1803.pdb -4447498.58 2026-10-23 21:30:34 5 prot-na_16117.pdb -4345397.92 2026-10-23 21:30:34 Sent to refinement: clusters_found|prot-na_814.pdb|prot-na_10838.pdb|prot-na_10879.pdb 2026-10-23 21:30:34 Sent to refinement: clusters_found|prot-na_814.pdb|prot-na_10838.pdb|prot-na_10879.pdb 2026-10-23 21:30:34 DARS clustering end 2026-10-23 21:30:34 MC (refinement) init 2026-10-23 21:30:34 timeout 72h python /home/rpdock/run_gramm//run_mc.py -f dars_to_mc.txt -d /home/rpdock/web/media/jobs/f6f9702c-8193-4f6d-850f-79335bec5b3e/ 2026-10-23 21:30:35 Refinement of #1 /home/rpdock/web/media/jobs/f6f9702c-8193-4f6d-850f-79335bec5b3e/prot-na_814.pdb 2026-10-23 21:30:35 python /home/rpdock/mc/MC.py -s 1000 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/f6f9702c-8193-4f6d-850f-79335bec5b3e//ref_struc/prot-na_814/prot-na_814.pdb 2026-10-23 21:43:35 Refinement of #2 /home/rpdock/web/media/jobs/f6f9702c-8193-4f6d-850f-79335bec5b3e/prot-na_10838.pdb 2026-10-23 21:43:35 python /home/rpdock/mc/MC.py -s 1000 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/f6f9702c-8193-4f6d-850f-79335bec5b3e//ref_struc/prot-na_10838/prot-na_10838.pdb 2026-10-23 21:51:36 run_mc::stderr:Traceback (most recent call last): File "/home/rpdock/mc/MC.py", line 709, in s, datas = write_all_atoms (datas, step_real, cal.split()[0], plik, pars, historyT, historyR, rna) File "/home/rpdock/mc/MC.py", line 360, in write_all_atoms all_at_ch_rna, all_at_ch_prot = all_atom (plik, pars, transl, rotation, rna) File "/home/rpdock/mc/MC.py", line 297, in all_atom pro_ch, rna_ch = check_chains(plik, pars) File "/home/rpdock/mc/MC.py", line 106, in check_chains struc = pars.get_structure('native', plik) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py", line 83, in get_structure self._parse(handle.readlines()) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py", line 109, in _parse self.trailer = self._parse_coordinates(coords_trailer) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py", line 142, in _parse_coordinates global_line_counter = self.line_counter + local_line_counter + 1 MemoryError 2026-10-23 21:51:36 Refinement of #3 /home/rpdock/web/media/jobs/f6f9702c-8193-4f6d-850f-79335bec5b3e/prot-na_10879.pdb 2026-10-23 21:51:36 python /home/rpdock/mc/MC.py -s 1000 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/f6f9702c-8193-4f6d-850f-79335bec5b3e//ref_struc/prot-na_10879/prot-na_10879.pdb 2026-10-23 22:04:37 start - parameters: File name /home/rpdock/web/media/jobs/f6f9702c-8193-4f6d-850f-79335bec5b3e//ref_struc/prot-na_814/prot-na_814.pdb Steps 1000 Temp. start 15000.0 Temp. end 295.0 False msg start - parameters: File name /home/rpdock/web/media/jobs/f6f9702c-8193-4f6d-850f-79335bec5b3e//ref_struc/prot-na_814/prot-na_814.pdb Steps 1000 Temp. start 15000.0 Temp. end 295.0 False Step E Edist Eang Epen Warning, residue G1 in the chain B has not P atom 0 - -2394508.42 -2456339.38 -2238169.04 2300000.00 1 R -2284288.40 -2359868.70 -2124419.70 2200000.00 T= 14985.295 K progress 0.1 2 R -2641942.41 -2321972.78 -2119969.64 1800000.00 T= 14970.59 K progress 0.2 3 R -2644512.47 -2324303.19 -2120209.28 1800000.00 T= 14779.425 K progress 0.3 4 T -2428967.39 -2252182.67 -2076784.72 1900000.00 T= 14661.785 K progress 0.4 5 T -2257227.29 -2333817.36 -2123409.92 2200000.00 T= 14470.62 K progress 0.5 6 R -2479317.29 -2399761.50 -2179555.79 2100000.00 T= 14411.8 K progress 0.6 7 T -2380925.03 -2237128.46 -2043796.57 1900000.00 T= 14352.98 K progress 0.7 8 T -2653979.65 -2396718.07 -2157261.58 1900000.00 T= 14323.57 K progress 0.8 9 T -2620139.53 -2254081.32 -2066058.21 1700000.00 T= 14264.75 K progress 0.9 10 R -2511709.08 -2192573.77 -2019135.31 1700000.00 T= 14205.93 K progress 1.0 11 T -2777543.76 -2228200.44 -2049343.32 1500000.00 T= 14191.225 K progress 1.1 12 R -2798201.09 -2224932.51 -2073268.57 1500000.00 T= 14000.06 K progress 1.2 13 R -2806018.14 -2236202.74 -2069815.40 1500000.00 T= 13941.24 K progress 1.3 14 R -2812406.78 -2241868.99 -2070537.78 1500000.00 T= 13838.305 K progress 1.4 15 R -2812185.37 -2241868.99 -2070316.38 1500000.00 T= 13808.895 K progress 1.5 16 R -2918021.61 -2241630.62 -2076390.99 1400000.00 T= 13794.19 K progress 1.6 17 R -2988307.60 -2227961.90 -2060345.70 1300000.00 T= 13279.515 K progress 1.7 18 R -2955524.76 -2209227.20 -2046297.56 1300000.00 T= 12867.775 K progress 1.8 19 R -2999582.70 -2232724.95 -2066857.76 1300000.00 T= 12853.07 K progress 1.9 20 R -2991075.50 -2228066.42 -2063009.09 1300000.00 T= 12691.315 K progress 2.0 21 T -2966870.09 -2223812.83 -2043057.25 1300000.00 T= 12411.92 K progress 2.1 22 R -2961220.16 -2214799.93 -2046420.23 1300000.00 T= 12294.28 K progress 2.2 23 R -2966595.88 -2221987.38 -2044608.50 1300000.00 T= 12250.165 K progress 2.3 24 R -2960159.10 -2217293.55 -2042865.56 1300000.00 T= 12059.0 K progress 2.4 25 R -2981646.16 -2221324.32 -2060321.85 1300000.00 T= 11720.785 K progress 2.5 26 T -2580958.25 -2114060.68 -1966897.57 1500000.00 T= 11470.8 K progress 2.6 27 T -2650698.27 -2069637.67 -1881060.60 1300000.00 T= 11235.52 K progress 2.7 28 R -2690028.48 -1964136.12 -1825892.36 1100000.00 T= 11206.11 K progress 2.8 29 T -2662274.27 -1994223.83 -1868050.43 1200000.00 T= 10647.32 K progress 2.9 30 R -2648875.21 -1987016.53 -1861858.68 1200000.00 T= 10632.615 K progress 3.0 31 R -2583829.01 -2129120.75 -1954708.26 1500000.00 T= 10514.975 K progress 3.1 32 R -2600161.14 -2150144.90 -1950016.24 1500000.00 T= 10470.86 K progress 3.2 33 R -2530230.16 -2102482.30 -1927747.86 1500000.00 T= 10456.155 K progress 3.3 34 T -2743567.29 -1986148.76 -1857418.53 1100000.00 T= 10441.45 K progress 3.4 35 R -2738814.39 -1974112.37 -1864702.02 1100000.00 T= 10426.745 K progress 3.5 36 R -2635840.75 -1973398.07 -1862442.68 1200000.00 T= 10412.04 K progress 3.6 37 T -3075773.53 -2183077.51 -1992696.02 1100000.00 T= 10397.335 K progress 3.7 38 R -3075229.75 -2198229.99 -1976999.76 1100000.00 T= 10220.875 K progress 3.8 39 R -3099112.80 -2206000.11 -1993112.69 1100000.00 T= 10044.415 K progress 3.9 40 R -3079171.17 -2202711.60 -1976459.57 1100000.00 T= 8720.965 K progress 4.0 41 R -2933227.39 -2172595.28 -1960632.12 1200000.00 T= 8294.52 K progress 4.1 42 R -3079286.57 -2190882.42 -1988404.15 1100000.00 T= 8132.765 K progress 4.2 43 R -3077427.96 -2188528.80 -1988899.16 1100000.00 T= 7559.27 K progress 4.3 44 R -2975402.11 -2192954.64 -1982447.47 1200000.00 T= 7485.745 K progress 4.4 45 R -2969550.11 -2191026.65 -1978523.46 1200000.00 T= 7353.4 K progress 4.5 46 R -3092996.94 -2193249.17 -1999747.77 1100000.00 T= 7338.695 K progress 4.6 47 R -3088722.16 -2191228.25 -1997493.91 1100000.00 T= 7279.875 K progress 4.7 48 R -3058881.14 -2192269.68 -1966611.46 1100000.00 T= 7103.415 K progress 4.8 49 R -3074740.37 -2194233.86 -1980506.51 1100000.00 T= 7044.595 K progress 4.9 50 R -3053176.49 -2190191.03 -1962985.46 1100000.00 T= 6618.15 K progress 5.0 51 R -3068884.58 -2195239.41 -1973645.17 1100000.00 T= 6382.87 K progress 5.1 52 R -3041109.49 -2167544.66 -1973564.83 1100000.00 T= 6206.41 K progress 5.2 53 R -3053176.49 -2190191.03 -1962985.46 1100000.00 T= 5500.57 K progress 5.3 54 R -3054568.41 -2181448.95 -1973119.46 1100000.00 T= 5338.815 K progress 5.4 55 R -3053176.49 -2190191.03 -1962985.46 1100000.00 T= 5118.24 K progress 5.5 56 R -3062708.91 -2192651.94 -1970056.97 1100000.00 T= 5074.125 K progress 5.6 57 R -3075625.72 -2190047.05 -1985578.67 1100000.00 T= 4971.19 K progress 5.7 58 R -3079114.65 -2190778.91 -1988335.74 1100000.00 T= 4780.025 K progress 5.8 59 R -3073464.69 -2191612.50 -1981852.19 1100000.00 T= 3912.43 K progress 5.9 60 R -3048386.64 -2187947.02 -1960439.62 1100000.00 T= 3853.61 K progress 6.0 61 R -3093227.51 -2189267.49 -2003960.02 1100000.00 T= 3338.935 K progress 6.1 62 R -3091509.85 -2200108.10 -1991401.76 1100000.00 T= 2706.62 K progress 6.2 63 R -3094497.33 -2201180.46 -1993316.86 1100000.00 T= 2530.16 K progress 6.3 64 R -3132396.27 -2216544.06 -2015852.21 1100000.00 T= 2133.125 K progress 6.4 65 R -3129857.61 -2209252.13 -2020605.48 1100000.00 T= 1986.075 K progress 6.5 Save no big msg save short traj msg save best.pdb msg save plot e_step.png start - parameters: File name /home/rpdock/web/media/jobs/f6f9702c-8193-4f6d-850f-79335bec5b3e//ref_struc/prot-na_10838/prot-na_10838.pdb Steps 1000 Temp. start 15000.0 Temp. end 295.0 False msg start - parameters: File name /home/rpdock/web/media/jobs/f6f9702c-8193-4f6d-850f-79335bec5b3e//ref_struc/prot-na_10838/prot-na_10838.pdb Steps 1000 Temp. start 15000.0 Temp. end 295.0 False Step E Edist Eang Epen Warning, residue G1 in the chain B has not P atom 0 - -2959120.57 -2536988.27 -2422132.30 2000000.00 1 T -3005661.94 -2436421.14 -2269240.80 1700000.00 T= 15000.0 K progress 0.1 2 R -3183806.35 -2475480.49 -2308325.86 1600000.00 T= 14955.885 K progress 0.2 3 T -3196572.71 -2478322.54 -2318250.18 1600000.00 T= 14911.77 K progress 0.3 4 R -3227049.71 -2498009.19 -2329040.53 1600000.00 T= 14882.36 K progress 0.4 5 T -2886034.91 -2486278.24 -2299756.67 1900000.00 T= 14764.72 K progress 0.5 6 R -2859748.52 -2479828.39 -2279920.13 1900000.00 T= 14750.015 K progress 0.6 7 R -3062537.16 -2510424.03 -2352113.13 1800000.00 T= 14720.605 K progress 0.7 8 R -3261858.82 -2506854.95 -2355003.86 1600000.00 T= 14676.49 K progress 0.8 9 R -3306904.34 -2414714.03 -2292190.31 1400000.00 T= 14617.67 K progress 0.9 10 R -3307190.99 -2414153.39 -2293037.60 1400000.00 T= 14279.455 K progress 1.0 11 T -3416657.31 -2420931.97 -2295725.34 1300000.00 T= 14264.75 K progress 1.1 12 T -3892805.43 -2503851.48 -2388953.95 1000000.00 T= 14250.045 K progress 1.2 13 R -4027511.36 -2511559.31 -2415952.05 900000.00 T= 14235.34 K progress 1.3 14 R -4051734.90 -2527793.62 -2423941.28 900000.00 T= 14088.29 K progress 1.4 15 R -3887031.34 -2512869.64 -2374161.70 1000000.00 T= 13926.535 K progress 1.5 16 R -4033133.47 -2516512.68 -2416620.79 900000.00 T= 13808.895 K progress 1.6 17 R -4019645.61 -2507800.56 -2411845.06 900000.00 T= 13691.255 K progress 1.7 18 R -4016733.11 -2521719.21 -2395013.90 900000.00 T= 13632.435 K progress 1.8 19 R -3933519.87 -2530684.33 -2402835.53 1000000.00 T= 13500.09 K progress 1.9 20 R -3893179.38 -2512053.96 -2381125.42 1000000.00 T= 13250.105 K progress 2.0 21 R -3926372.61 -2526661.80 -2399710.81 1000000.00 T= 13235.4 K progress 2.1 22 R -3862405.32 -2494736.23 -2367669.09 1000000.00 T= 13073.645 K progress 2.2 23 R -3875365.97 -2499160.22 -2376205.75 1000000.00 T= 13014.825 K progress 2.3 24 R -3869486.42 -2484460.80 -2385025.62 1000000.00 T= 12882.48 K progress 2.4 25 T -3846752.67 -2448213.98 -2298538.68 900000.00 T= 12853.07 K progress 2.5 26 R -3915494.83 -2493749.98 -2321744.85 900000.00 T= 12720.725 K progress 2.6 27 R -3939773.25 -2502279.36 -2337493.89 900000.00 T= 12706.02 K progress 2.7 28 R -3824350.36 -2454987.38 -2269362.98 900000.00 T= 12264.87 K progress 2.8 29 R -3847306.07 -2468840.95 -2278465.13 900000.00 T= 12235.46 K progress 2.9 30 R -3774023.02 -2412680.99 -2261342.03 900000.00 T= 11809.015 K progress 3.0 31 R -3778589.20 -2435098.36 -2243490.85 900000.00 T= 11764.9 K progress 3.1 32 T -3762492.57 -2508902.79 -2353589.78 1100000.00 T= 11661.965 K progress 3.2 33 R -3704945.77 -2477570.77 -2327375.00 1100000.00 T= 11617.85 K progress 3.3 34 T -3786091.72 -2399712.07 -2286379.66 900000.00 T= 11603.145 K progress 3.4 35 R -3789091.35 -2403021.67 -2286069.67 900000.00 T= 11411.98 K progress 3.5 36 R -3814523.28 -2406095.35 -2308427.94 900000.00 T= 11367.865 K progress 3.6 37 R -3813339.13 -2434431.98 -2278907.15 900000.00 T= 11353.16 K progress 3.7 38 R -3783356.84 -2404934.99 -2278421.85 900000.00 T= 11338.455 K progress 3.8 39 R -3781411.82 -2403801.81 -2277610.01 900000.00 T= 11161.995 K progress 3.9 40 R -3819066.72 -2402558.13 -2316508.59 900000.00 T= 11117.88 K progress 4.0 41 R -3812638.46 -2398298.48 -2314339.98 900000.00 T= 10941.42 K progress 4.1 42 R -3820785.18 -2433229.31 -2287555.87 900000.00 T= 10794.37 K progress 4.2 43 R -3796308.77 -2415969.97 -2280338.80 900000.00 T= 10632.615 K progress 4.3 44 T -3867568.90 -2394736.15 -2272832.75 800000.00 T= 10456.155 K progress 4.4 45 T -3869368.07 -2498820.26 -2370547.81 1000000.00 T= 10426.745 K progress 4.5 46 R -3880678.83 -2528586.91 -2352091.92 1000000.00 T= 10397.335 K progress 4.6 47 T -3858159.72 -2497915.97 -2360243.75 1000000.00 T= 10382.63 K progress 4.7 48 T -3836367.67 -2505056.95 -2331310.71 1000000.00 T= 10264.99 K progress 4.8 49 R -3848644.24 -2500374.10 -2348270.14 1000000.00 T= 10000.3 K progress 4.9 50 R -4041392.83 -2541837.94 -2399554.89 900000.00 T= 9985.595 K progress 5.0 51 R -4043575.37 -2541837.94 -2401737.43 900000.00 T= 9779.725 K progress 5.1 52 R -4030966.11 -2539964.14 -2391001.97 900000.00 T= 9015.065 K progress 5.2 53 R -4026376.51 -2539714.46 -2386662.05 900000.00 T= 8956.245 K progress 5.3 54 R -3878200.61 -2508857.69 -2369342.92 1000000.00 T= 8750.375 K progress 5.4 55 R -4039861.78 -2546855.78 -2393006.00 900000.00 T= 8735.67 K progress 5.5 56 R -4048695.65 -2549476.41 -2399219.23 900000.00 T= 8647.44 K progress 5.6 57 R -4018240.35 -2522364.44 -2395875.91 900000.00 T= 8632.735 K progress 5.7 58 T -4047056.20 -2536623.52 -2410432.68 900000.00 T= 7912.19 K progress 5.8 59 R -4044365.07 -2532005.20 -2412359.87 900000.00 T= 7809.255 K progress 5.9 60 R -4034977.57 -2527606.92 -2407370.65 900000.00 T= 7603.385 K progress 6.0 61 R -4033805.50 -2526434.85 -2407370.65 900000.00 T= 7588.68 K progress 6.1 62 R -4027029.02 -2522674.73 -2404354.29 900000.00 T= 7235.76 K progress 6.2 63 T -4059076.44 -2544399.32 -2414677.13 900000.00 T= 7221.055 K progress 6.3 64 R -4140292.63 -2594405.59 -2445887.04 900000.00 T= 7191.645 K progress 6.4 65 R -4129934.19 -2588446.22 -2441487.97 900000.00 T= 7147.53 K progress 6.5 66 R -4074367.97 -2552495.14 -2421872.83 900000.00 T= 6794.61 K progress 6.6 67 R -4099077.56 -2563245.45 -2435832.11 900000.00 T= 6721.085 K progress 6.7 68 R -4102287.48 -2569703.31 -2432584.16 900000.00 T= 6662.265 K progress 6.8 69 R -4092626.00 -2561739.82 -2430886.18 900000.00 T= 6397.575 K progress 6.9 70 R -4104155.58 -2570733.40 -2433422.18 900000.00 T= 6162.295 K progress 7.0 71 R -4102128.03 -2557891.11 -2444236.92 900000.00 T= 5912.31 K progress 7.1 72 R -4063321.39 -2538848.24 -2424473.15 900000.00 T= 5779.965 K progress 7.2 73 R -4071145.37 -2545955.25 -2425190.11 900000.00 T= 5765.26 K progress 7.3 74 R -4152802.26 -2593916.11 -2458886.15 900000.00 T= 5735.85 K progress 7.4 75 R -4140229.76 -2584691.21 -2455538.55 900000.00 T= 5030.01 K progress 7.5 Traceback (most recent call last): File "/home/rpdock/mc/MC.py", line 709, in s, datas = write_all_atoms (datas, step_real, cal.split()[0], plik, pars, historyT, historyR, rna) File "/home/rpdock/mc/MC.py", line 360, in write_all_atoms all_at_ch_rna, all_at_ch_prot = all_atom (plik, pars, transl, rotation, rna) File "/home/rpdock/mc/MC.py", line 297, in all_atom pro_ch, rna_ch = check_chains(plik, pars) File "/home/rpdock/mc/MC.py", line 106, in check_chains struc = pars.get_structure('native', plik) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py", line 83, in get_structure self._parse(handle.readlines()) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py", line 109, in _parse self.trailer = self._parse_coordinates(coords_trailer) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py", line 225, in _parse_coordinates fullname, serial_number, element) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/StructureBuilder.py", line 232, in init_atom residue.add(atom) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/Residue.py", line 83, in add Entity.add(self, atom) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/Entity.py", line 89, in add self.child_dict[entity_id]=entity MemoryError Error in run_mc Traceback (most recent call last): File "/home/rpdock/mc/MC.py", line 709, in s, datas = write_all_atoms (datas, step_real, cal.split()[0], plik, pars, historyT, historyR, rna) File "/home/rpdock/mc/MC.py", line 360, in write_all_atoms all_at_ch_rna, all_at_ch_prot = all_atom (plik, pars, transl, rotation, rna) File "/home/rpdock/mc/MC.py", line 297, in all_atom pro_ch, rna_ch = check_chains(plik, pars) File "/home/rpdock/mc/MC.py", line 106, in check_chains struc = pars.get_structure('native', plik) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py", line 83, in get_structure self._parse(handle.readlines()) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py", line 109, in _parse self.trailer = self._parse_coordinates(coords_trailer) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py", line 142, in _parse_coordinates global_line_counter = self.line_counter + local_line_counter + 1 MemoryError start - parameters: File name /home/rpdock/web/media/jobs/f6f9702c-8193-4f6d-850f-79335bec5b3e//ref_struc/prot-na_10879/prot-na_10879.pdb Steps 1000 Temp. start 15000.0 Temp. end 295.0 False msg start - parameters: File name /home/rpdock/web/media/jobs/f6f9702c-8193-4f6d-850f-79335bec5b3e//ref_struc/prot-na_10879/prot-na_10879.pdb Steps 1000 Temp. start 15000.0 Temp. end 295.0 False Step E Edist Eang Epen Warning, residue G1 in the chain B has not P atom 0 - -2264745.00 -2303900.03 -2060844.97 2100000.00 1 R -2274897.40 -2307752.70 -2067144.70 2100000.00 T= 14985.295 K progress 0.1 2 R -1890257.98 -2295178.22 -2095079.76 2500000.00 T= 14911.77 K progress 0.2 3 R -2109549.79 -2240868.81 -2068680.97 2200000.00 T= 14897.065 K progress 0.3 4 R -2449411.14 -2197064.42 -2052346.72 1800000.00 T= 14867.655 K progress 0.4 5 R -2618946.24 -2233285.25 -2085660.99 1700000.00 T= 14852.95 K progress 0.5 6 R -3181295.78 -2228585.21 -2052710.57 1100000.00 T= 14794.13 K progress 0.6 7 R -3192278.57 -2234122.19 -2058156.38 1100000.00 T= 14705.9 K progress 0.7 8 T -3431647.09 -2294581.29 -2137065.79 1000000.00 T= 14661.785 K progress 0.8 9 R -3571630.34 -2318993.18 -2152637.16 900000.00 T= 14308.865 K progress 0.9 10 R -3363772.95 -2259172.64 -2104600.30 1000000.00 T= 14294.16 K progress 1.0 11 R -3256842.26 -2262286.99 -2094555.27 1100000.00 T= 13970.65 K progress 1.1 12 R -3555918.98 -2307665.20 -2148253.79 900000.00 T= 13897.125 K progress 1.2 13 R -3586069.17 -2318799.63 -2167269.54 900000.00 T= 13691.255 K progress 1.3 14 R -3553226.73 -2300893.57 -2152333.15 900000.00 T= 12323.69 K progress 1.4 15 R -3580388.22 -2318036.92 -2162351.30 900000.00 T= 11529.62 K progress 1.5 16 R -3462860.14 -2310326.77 -2152533.37 1000000.00 T= 11176.7 K progress 1.6 17 R -3501886.96 -2277940.74 -2123946.22 900000.00 T= 11117.88 K progress 1.7 18 R -3554009.17 -2303666.09 -2150343.07 900000.00 T= 10970.83 K progress 1.8 19 R -3522488.82 -2286290.48 -2136198.34 900000.00 T= 10809.075 K progress 1.9 20 R -3568720.76 -2316017.82 -2152702.94 900000.00 T= 10470.86 K progress 2.0 21 R -3558971.72 -2309531.04 -2149440.69 900000.00 T= 10294.4 K progress 2.1 22 R -3571359.62 -2315381.75 -2155977.87 900000.00 T= 10103.235 K progress 2.2 23 R -3531402.22 -2296712.33 -2134689.89 900000.00 T= 9750.315 K progress 2.3 24 R -3561887.49 -2309725.35 -2152162.14 900000.00 T= 9617.97 K progress 2.4 25 R -3436084.63 -2296985.08 -2139099.55 1000000.00 T= 9588.56 K progress 2.5 26 R -3431529.75 -2294463.96 -2137065.79 1000000.00 T= 9515.035 K progress 2.6 27 R -3570713.15 -2311728.81 -2158984.34 900000.00 T= 9015.065 K progress 2.7 28 R -3140814.25 -2193723.96 -2047090.29 1100000.00 T= 8735.67 K progress 2.8 29 R -3557832.84 -2306117.81 -2151715.03 900000.00 T= 8720.965 K progress 2.9 30 R -3585700.42 -2323679.13 -2162021.29 900000.00 T= 8441.57 K progress 3.0 31 R -3559589.42 -2306117.81 -2153471.61 900000.00 T= 8147.47 K progress 3.1 32 R -3565070.85 -2313488.18 -2151582.66 900000.00 T= 7294.58 K progress 3.2 33 R -3561038.02 -2313315.47 -2147722.54 900000.00 T= 6897.545 K progress 3.3 34 R -3563420.26 -2316929.60 -2146490.66 900000.00 T= 6735.79 K progress 3.4 35 R -3589927.88 -2322970.36 -2166957.52 900000.00 T= 6368.165 K progress 3.5 36 R -3589167.17 -2327874.97 -2161292.20 900000.00 T= 5103.535 K progress 3.6 37 R -3569222.64 -2316378.86 -2152843.79 900000.00 T= 4824.14 K progress 3.7 38 R -3575657.92 -2318367.17 -2157290.75 900000.00 T= 3971.25 K progress 3.8 39 R -3567907.16 -2314362.39 -2153544.77 900000.00 T= 2721.325 K progress 3.9 40 R -3580503.72 -2319333.47 -2161170.25 900000.00 T= 2662.505 K progress 4.0 41 R -3560414.21 -2311360.75 -2149053.46 900000.00 T= 1618.45 K progress 4.1 42 R -3574119.95 -2317345.35 -2156774.61 900000.00 T= 1574.335 K progress 4.2 43 R -3576786.91 -2315863.41 -2160923.50 900000.00 T= 1383.17 K progress 4.3 44 R -3581606.66 -2319065.90 -2162540.76 900000.00 T= 1089.07 K progress 4.4 Save no big msg save short traj msg save best.pdb msg save plot e_step.png Fri Oct 23 21:30:35 2026 ['prot-na_814.pdb', 'prot-na_10838.pdb', 'prot-na_10879.pdb'] msg Refinement of #1 /home/rpdock/web/media/jobs/f6f9702c-8193-4f6d-850f-79335bec5b3e/prot-na_814.pdb dir: /home/rpdock/web/media/jobs/f6f9702c-8193-4f6d-850f-79335bec5b3e/ file: prot-na_814.pdb find `pwd` -iname prot-na_814.pdb copy /home/rpdock/web/media/jobs/f6f9702c-8193-4f6d-850f-79335bec5b3e/prot-na_25/prot-na_814.pdb to /home/rpdock/web/media/jobs/f6f9702c-8193-4f6d-850f-79335bec5b3e//ref_struc/prot-na_814/prot-na_814.pdb cmd: python /home/rpdock/mc/MC.py -s 1000 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/f6f9702c-8193-4f6d-850f-79335bec5b3e//ref_struc/prot-na_814/prot-na_814.pdb msg python /home/rpdock/mc/MC.py -s 1000 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/f6f9702c-8193-4f6d-850f-79335bec5b3e//ref_struc/prot-na_814/prot-na_814.pdb run_mc::OK! = stderr empty msg Refinement of #2 /home/rpdock/web/media/jobs/f6f9702c-8193-4f6d-850f-79335bec5b3e/prot-na_10838.pdb dir: /home/rpdock/web/media/jobs/f6f9702c-8193-4f6d-850f-79335bec5b3e/ file: prot-na_10838.pdb find `pwd` -iname prot-na_10838.pdb copy /home/rpdock/web/media/jobs/f6f9702c-8193-4f6d-850f-79335bec5b3e/prot-na_25/prot-na_10838.pdb to /home/rpdock/web/media/jobs/f6f9702c-8193-4f6d-850f-79335bec5b3e//ref_struc/prot-na_10838/prot-na_10838.pdb cmd: python /home/rpdock/mc/MC.py -s 1000 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/f6f9702c-8193-4f6d-850f-79335bec5b3e//ref_struc/prot-na_10838/prot-na_10838.pdb msg python /home/rpdock/mc/MC.py -s 1000 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/f6f9702c-8193-4f6d-850f-79335bec5b3e//ref_struc/prot-na_10838/prot-na_10838.pdb msg run_mc::stderr:Traceback (most recent call last): File "/home/rpdock/mc/MC.py", line 709, in s, datas = write_all_atoms (datas, step_real, cal.split()[0], plik, pars, historyT, historyR, rna) File "/home/rpdock/mc/MC.py", line 360, in write_all_atoms all_at_ch_rna, all_at_ch_prot = all_atom (plik, pars, transl, rotation, rna) File "/home/rpdock/mc/MC.py", line 297, in all_atom pro_ch, rna_ch = check_chains(plik, pars) File "/home/rpdock/mc/MC.py", line 106, in check_chains struc = pars.get_structure('native', plik) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py", line 83, in get_structure self._parse(handle.readlines()) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py", line 109, in _parse self.trailer = self._parse_coordinates(coords_trailer) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py", line 142, in _parse_coordinates global_line_counter = self.line_counter + local_line_counter + 1 MemoryError msg Refinement of #3 /home/rpdock/web/media/jobs/f6f9702c-8193-4f6d-850f-79335bec5b3e/prot-na_10879.pdb dir: /home/rpdock/web/media/jobs/f6f9702c-8193-4f6d-850f-79335bec5b3e/ file: prot-na_10879.pdb find `pwd` -iname prot-na_10879.pdb copy /home/rpdock/web/media/jobs/f6f9702c-8193-4f6d-850f-79335bec5b3e/prot-na_25/prot-na_10879.pdb to /home/rpdock/web/media/jobs/f6f9702c-8193-4f6d-850f-79335bec5b3e//ref_struc/prot-na_10879/prot-na_10879.pdb cmd: python /home/rpdock/mc/MC.py -s 1000 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/f6f9702c-8193-4f6d-850f-79335bec5b3e//ref_struc/prot-na_10879/prot-na_10879.pdb msg python /home/rpdock/mc/MC.py -s 1000 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/f6f9702c-8193-4f6d-850f-79335bec5b3e//ref_struc/prot-na_10879/prot-na_10879.pdb run_mc::OK! = stderr empty 2026-10-23 22:04:37 MC (refinement) end 2026-10-23 22:04:37 OK 2026-10-23 22:04:37 Set finished status of f6f9702c-8193-4f6d-850f-79335bec5b3e