2026-04-28 15:32:04 NPdock start 2026-04-28 15:32:04 ver: server 2026-04-28 15:32:04 mode: 11111 2026-04-28 15:32:04 is RNA? 1 2026-04-28 15:32:04 Interface: prot: '' na: '' 2026-04-28 15:32:04 Curr dir:/home/rpdock/web/media/jobs/12967bbf-65b9-49e9-b7a4-7793b1f8a860/ 2026-04-28 15:32:04 GRAMM in progress... 2026-04-28 15:32:04 python /home/rpdock/run_gramm//run_gramm1.py -d 20000 -p prot.pdb -r na.pdb -pi '' -ri '' -n 1 -pf '*' -rf '*' 2026-04-28 16:41:05 GRAMM done 2026-04-28 16:41:05 DARS scoring in progress... 2026-04-28 16:41:05 time python /home/rpdock/run_gramm//DARS-RNP_v3//DARS_potential_v3_scoring.py -m 100 -f list.txt -o dars_out.txt 2026-04-28 16:41:05 DARS start [DARS_potential_v3_scoring.py] 2026-04-28 16:41:05 Show log every 100 structures [DARS_potential_v3_scoring.py] 2026-04-28 16:41:05 1/20000 na-prot_1000.pdb -2318273.74 2026-04-28 16:41:26 100/20000 na-prot_94.pdb -2512178.24 2026-04-28 16:41:47 200/20000 na-prot_194.pdb -2912479.07 2026-04-28 16:42:08 300/20000 na-prot_294.pdb -2508144.39 2026-04-28 16:42:29 400/20000 na-prot_394.pdb -1766883.92 2026-04-28 16:42:50 500/20000 na-prot_494.pdb -1666037.54 2026-04-28 16:43:11 600/20000 na-prot_594.pdb -2352186.31 2026-04-28 16:43:33 700/20000 na-prot_694.pdb -1824107.09 2026-04-28 16:43:54 800/20000 na-prot_794.pdb -2094033.06 2026-04-28 16:44:16 900/20000 na-prot_894.pdb -1472721.79 2026-04-28 16:44:37 1000/20000 na-prot_994.pdb -1896422.80 2026-04-28 16:44:59 1100/20000 na-prot_1100.pdb -1858008.56 2026-04-28 16:45:21 1200/20000 na-prot_1200.pdb -1834374.87 2026-04-28 16:45:43 1300/20000 na-prot_1300.pdb -2124906.26 2026-04-28 16:46:05 1400/20000 na-prot_1400.pdb -2025712.00 2026-04-28 16:46:27 1500/20000 na-prot_1500.pdb -2107464.03 2026-04-28 16:46:49 1600/20000 na-prot_1600.pdb -1139902.50 2026-04-28 16:47:11 1700/20000 na-prot_1700.pdb -1987138.72 2026-04-28 16:47:32 1800/20000 na-prot_1800.pdb -2743995.35 2026-04-28 16:47:53 1900/20000 na-prot_1900.pdb -2353162.71 2026-04-28 16:48:15 2000/20000 na-prot_2000.pdb -1655838.57 2026-04-28 16:48:37 2100/20000 na-prot_2100.pdb -1687608.66 2026-04-28 16:48:59 2200/20000 na-prot_2200.pdb -1589352.38 2026-04-28 16:49:21 2300/20000 na-prot_2300.pdb -1590235.53 2026-04-28 16:49:43 2400/20000 na-prot_2400.pdb -1725948.34 2026-04-28 16:50:06 2500/20000 na-prot_2500.pdb -1682795.86 2026-04-28 16:50:28 2600/20000 na-prot_2600.pdb -2011094.11 2026-04-28 16:50:50 2700/20000 na-prot_2700.pdb -1573983.02 2026-04-28 16:51:12 2800/20000 na-prot_2800.pdb -2112458.84 2026-04-28 16:51:34 2900/20000 na-prot_2900.pdb -2420978.75 2026-04-28 16:51:56 3000/20000 na-prot_3000.pdb -2343629.34 2026-04-28 16:52:19 3100/20000 na-prot_3100.pdb -1396694.34 2026-04-28 16:52:42 3200/20000 na-prot_3200.pdb -1807807.54 2026-04-28 16:53:04 3300/20000 na-prot_3300.pdb -2819150.01 2026-04-28 16:53:26 3400/20000 na-prot_3400.pdb -1933517.23 2026-04-28 16:53:50 3500/20000 na-prot_3500.pdb -1901868.05 2026-04-28 16:54:14 3600/20000 na-prot_3600.pdb -2582869.07 2026-04-28 16:54:38 3700/20000 na-prot_3700.pdb -1650087.83 2026-04-28 16:55:00 3800/20000 na-prot_3800.pdb -2429967.39 2026-04-28 16:55:23 3900/20000 na-prot_3900.pdb -1719168.10 2026-04-28 16:55:45 4000/20000 na-prot_4000.pdb -2072014.27 2026-04-28 16:56:07 4100/20000 na-prot_4100.pdb -2167498.29 2026-04-28 16:56:30 4200/20000 na-prot_4200.pdb -2388199.59 2026-04-28 16:56:52 4300/20000 na-prot_4300.pdb -1835898.32 2026-04-28 16:57:14 4400/20000 na-prot_4400.pdb -1555510.80 2026-04-28 16:57:36 4500/20000 na-prot_4500.pdb -1576880.04 2026-04-28 16:57:57 4600/20000 na-prot_4600.pdb -1460241.83 2026-04-28 16:58:19 4700/20000 na-prot_4700.pdb -1650638.48 2026-04-28 16:58:41 4800/20000 na-prot_4800.pdb -1650275.08 2026-04-28 16:59:03 4900/20000 na-prot_4900.pdb -2758382.55 2026-04-28 16:59:25 5000/20000 na-prot_5000.pdb -1927159.69 2026-04-28 16:59:48 5100/20000 na-prot_5100.pdb -1365795.50 2026-04-28 17:00:10 5200/20000 na-prot_5200.pdb -2233742.61 2026-04-28 17:00:32 5300/20000 na-prot_5300.pdb -1315829.63 2026-04-28 17:00:55 5400/20000 na-prot_5400.pdb -1914058.89 2026-04-28 17:01:17 5500/20000 na-prot_5500.pdb -2175533.43 2026-04-28 17:01:39 5600/20000 na-prot_5600.pdb -1690272.53 2026-04-28 17:02:01 5700/20000 na-prot_5700.pdb -2257289.28 2026-04-28 17:02:23 5800/20000 na-prot_5800.pdb -1669220.41 2026-04-28 17:02:46 5900/20000 na-prot_5900.pdb -1546243.52 2026-04-28 17:03:08 6000/20000 na-prot_6000.pdb -2030406.87 2026-04-28 17:03:30 6100/20000 na-prot_6100.pdb -2781177.94 2026-04-28 17:03:52 6200/20000 na-prot_6200.pdb -1111281.88 2026-04-28 17:04:14 6300/20000 na-prot_6300.pdb -1702569.89 2026-04-28 17:04:37 6400/20000 na-prot_6400.pdb -1764932.63 2026-04-28 17:04:59 6500/20000 na-prot_6500.pdb -1921567.21 2026-04-28 17:05:21 6600/20000 na-prot_6600.pdb -2095728.87 2026-04-28 17:05:43 6700/20000 na-prot_6700.pdb -3127067.11 2026-04-28 17:06:05 6800/20000 na-prot_6800.pdb -2264036.54 2026-04-28 17:06:27 6900/20000 na-prot_6900.pdb -1503011.03 2026-04-28 17:06:49 7000/20000 na-prot_7000.pdb -1928332.05 2026-04-28 17:07:12 7100/20000 na-prot_7100.pdb -2040739.13 2026-04-28 17:07:34 7200/20000 na-prot_7200.pdb -1711118.92 2026-04-28 17:07:56 7300/20000 na-prot_7300.pdb -1606300.48 2026-04-28 17:08:18 7400/20000 na-prot_7400.pdb -1981428.30 2026-04-28 17:08:40 7500/20000 na-prot_7500.pdb -1490573.25 2026-04-28 17:09:02 7600/20000 na-prot_7600.pdb -1752546.68 2026-04-28 17:09:25 7700/20000 na-prot_7700.pdb -1573184.09 2026-04-28 17:09:47 7800/20000 na-prot_7800.pdb -1894761.67 2026-04-28 17:10:09 7900/20000 na-prot_7900.pdb -1766717.70 2026-04-28 17:10:31 8000/20000 na-prot_8000.pdb -2446185.33 2026-04-28 17:10:54 8100/20000 na-prot_8100.pdb -2312897.10 2026-04-28 17:11:16 8200/20000 na-prot_8200.pdb -1685053.91 2026-04-28 17:11:38 8300/20000 na-prot_8300.pdb -1588990.62 2026-04-28 17:12:00 8400/20000 na-prot_8400.pdb -2290616.17 2026-04-28 17:12:23 8500/20000 na-prot_8500.pdb -1965907.80 2026-04-28 17:12:45 8600/20000 na-prot_8600.pdb -1457000.29 2026-04-28 17:13:07 8700/20000 na-prot_8700.pdb -1991796.88 2026-04-28 17:13:29 8800/20000 na-prot_8800.pdb -2239413.89 2026-04-28 17:13:51 8900/20000 na-prot_8900.pdb -1287686.77 2026-04-28 17:14:14 9000/20000 na-prot_9000.pdb -1994265.58 2026-04-28 17:14:36 9100/20000 na-prot_9100.pdb -1834606.43 2026-04-28 17:14:58 9200/20000 na-prot_9200.pdb -1785626.85 2026-04-28 17:15:20 9300/20000 na-prot_9300.pdb -1740176.62 2026-04-28 17:15:42 9400/20000 na-prot_9400.pdb -1794147.74 2026-04-28 17:16:03 9500/20000 na-prot_9500.pdb -2254060.41 2026-04-28 17:16:25 9600/20000 na-prot_9600.pdb -1895200.87 2026-04-28 17:16:47 9700/20000 na-prot_9700.pdb -2620392.66 2026-04-28 17:17:10 9800/20000 na-prot_9800.pdb -2285479.68 2026-04-28 17:17:32 9900/20000 na-prot_9900.pdb -1716316.57 2026-04-28 17:17:54 10000/20000 na-prot_10000.pdb -2341613.23 2026-04-28 17:18:16 10100/20000 na-prot_10100.pdb -1258265.31 2026-04-28 17:18:38 10200/20000 na-prot_10200.pdb -1908591.10 2026-04-28 17:19:00 10300/20000 na-prot_10300.pdb -1641602.54 2026-04-28 17:19:23 10400/20000 na-prot_10400.pdb -1655540.28 2026-04-28 17:19:44 10500/20000 na-prot_10500.pdb -1924475.09 2026-04-28 17:20:07 10600/20000 na-prot_10600.pdb -2039805.70 2026-04-28 17:20:29 10700/20000 na-prot_10700.pdb -2189805.22 2026-04-28 17:20:51 10800/20000 na-prot_10800.pdb -1857523.48 2026-04-28 17:21:13 10900/20000 na-prot_10900.pdb -1832867.27 2026-04-28 17:21:36 11000/20000 na-prot_11000.pdb -1874682.62 2026-04-28 17:21:57 11100/20000 na-prot_11100.pdb -1773440.90 2026-04-28 17:22:20 11200/20000 na-prot_11200.pdb -2119405.19 2026-04-28 17:22:42 11300/20000 na-prot_11300.pdb -1868169.74 2026-04-28 17:23:04 11400/20000 na-prot_11400.pdb -1402880.91 2026-04-28 17:23:26 11500/20000 na-prot_11500.pdb -1808420.63 2026-04-28 17:23:49 11600/20000 na-prot_11600.pdb -1814616.21 2026-04-28 17:24:11 11700/20000 na-prot_11700.pdb -1997228.96 2026-04-28 17:24:33 11800/20000 na-prot_11800.pdb -2262546.81 2026-04-28 17:24:56 11900/20000 na-prot_11900.pdb -1837596.25 2026-04-28 17:25:18 12000/20000 na-prot_12000.pdb -2016078.00 2026-04-28 17:25:40 12100/20000 na-prot_12100.pdb -2323779.35 2026-04-28 17:26:02 12200/20000 na-prot_12200.pdb -1048437.11 2026-04-28 17:26:25 12300/20000 na-prot_12300.pdb -2226894.64 2026-04-28 17:26:47 12400/20000 na-prot_12400.pdb -2215658.59 2026-04-28 17:27:09 12500/20000 na-prot_12500.pdb -1246046.53 2026-04-28 17:27:31 12600/20000 na-prot_12600.pdb -2035320.30 2026-04-28 17:27:53 12700/20000 na-prot_12700.pdb -1993451.64 2026-04-28 17:28:15 12800/20000 na-prot_12800.pdb -2041437.68 2026-04-28 17:28:37 12900/20000 na-prot_12900.pdb -1872205.55 2026-04-28 17:28:59 13000/20000 na-prot_13000.pdb -2224019.22 2026-04-28 17:29:22 13100/20000 na-prot_13100.pdb -1242959.12 2026-04-28 17:29:44 13200/20000 na-prot_13200.pdb -1737100.61 2026-04-28 17:30:06 13300/20000 na-prot_13300.pdb -2345850.98 2026-04-28 17:30:28 13400/20000 na-prot_13400.pdb -1939968.50 2026-04-28 17:30:50 13500/20000 na-prot_13500.pdb -1405284.02 2026-04-28 17:31:12 13600/20000 na-prot_13600.pdb -1267022.24 2026-04-28 17:31:34 13700/20000 na-prot_13700.pdb -1345779.19 2026-04-28 17:31:57 13800/20000 na-prot_13800.pdb -1363329.74 2026-04-28 17:32:19 13900/20000 na-prot_13900.pdb -2168709.05 2026-04-28 17:32:41 14000/20000 na-prot_14000.pdb -1613039.46 2026-04-28 17:33:03 14100/20000 na-prot_14100.pdb -1435737.64 2026-04-28 17:33:25 14200/20000 na-prot_14200.pdb -1497723.16 2026-04-28 17:33:47 14300/20000 na-prot_14300.pdb -1826586.09 2026-04-28 17:34:10 14400/20000 na-prot_14400.pdb -1532863.56 2026-04-28 17:34:32 14500/20000 na-prot_14500.pdb -2250059.65 2026-04-28 17:34:54 14600/20000 na-prot_14600.pdb -2209140.79 2026-04-28 17:35:17 14700/20000 na-prot_14700.pdb -1742752.28 2026-04-28 17:35:39 14800/20000 na-prot_14800.pdb -2005409.98 2026-04-28 17:36:01 14900/20000 na-prot_14900.pdb -1708982.30 2026-04-28 17:36:23 15000/20000 na-prot_15000.pdb -1187922.96 2026-04-28 17:36:45 15100/20000 na-prot_15100.pdb -1378202.64 2026-04-28 17:37:08 15200/20000 na-prot_15200.pdb -1685969.50 2026-04-28 17:37:30 15300/20000 na-prot_15300.pdb -2026871.76 2026-04-28 17:37:52 15400/20000 na-prot_15400.pdb -1686133.58 2026-04-28 17:38:14 15500/20000 na-prot_15500.pdb -2400056.91 2026-04-28 17:38:36 15600/20000 na-prot_15600.pdb -2126342.38 2026-04-28 17:38:59 15700/20000 na-prot_15700.pdb -1915847.25 2026-04-28 17:39:21 15800/20000 na-prot_15800.pdb -1538112.27 2026-04-28 17:39:43 15900/20000 na-prot_15900.pdb -1615389.80 2026-04-28 17:40:06 16000/20000 na-prot_16000.pdb -1333122.24 2026-04-28 17:40:28 16100/20000 na-prot_16100.pdb -2210539.38 2026-04-28 17:40:50 16200/20000 na-prot_16200.pdb -1830285.59 2026-04-28 17:41:12 16300/20000 na-prot_16300.pdb -1521403.19 2026-04-28 17:41:35 16400/20000 na-prot_16400.pdb -2041987.82 2026-04-28 17:41:59 16500/20000 na-prot_16500.pdb -1821887.17 2026-04-28 17:42:22 16600/20000 na-prot_16600.pdb -2979049.74 2026-04-28 17:42:48 16700/20000 na-prot_16700.pdb -1632389.88 2026-04-28 17:43:12 16800/20000 na-prot_16800.pdb -2179119.13 2026-04-28 17:43:35 16900/20000 na-prot_16900.pdb -2202292.55 2026-04-28 17:43:57 17000/20000 na-prot_17000.pdb -1381261.23 2026-04-28 17:44:19 17100/20000 na-prot_17100.pdb -2079130.97 2026-04-28 17:44:41 17200/20000 na-prot_17200.pdb -1683379.67 2026-04-28 17:45:04 17300/20000 na-prot_17300.pdb -1858866.37 2026-04-28 17:45:26 17400/20000 na-prot_17400.pdb -2051736.91 2026-04-28 17:45:48 17500/20000 na-prot_17500.pdb -1323424.42 2026-04-28 17:46:11 17600/20000 na-prot_17600.pdb -1724278.50 2026-04-28 17:46:33 17700/20000 na-prot_17700.pdb -1466243.97 2026-04-28 17:46:55 17800/20000 na-prot_17800.pdb -1758073.73 2026-04-28 17:47:18 17900/20000 na-prot_17900.pdb -1628672.28 2026-04-28 17:47:40 18000/20000 na-prot_18000.pdb -1832474.88 2026-04-28 17:48:02 18100/20000 na-prot_18100.pdb -2568476.53 2026-04-28 17:48:25 18200/20000 na-prot_18200.pdb -1911197.82 2026-04-28 17:48:47 18300/20000 na-prot_18300.pdb -1430848.15 2026-04-28 17:49:09 18400/20000 na-prot_18400.pdb -2164806.80 2026-04-28 17:49:31 18500/20000 na-prot_18500.pdb -1878837.67 2026-04-28 17:49:55 18600/20000 na-prot_18600.pdb -1287463.16 2026-04-28 17:50:18 18700/20000 na-prot_18700.pdb -1801531.58 2026-04-28 17:50:40 18800/20000 na-prot_18800.pdb -1837326.79 2026-04-28 17:51:03 18900/20000 na-prot_18900.pdb -1286131.93 2026-04-28 17:51:26 19000/20000 na-prot_19000.pdb -1955005.40 2026-04-28 17:51:48 19100/20000 na-prot_19100.pdb -1920113.66 2026-04-28 17:52:11 19200/20000 na-prot_19200.pdb -1533867.09 2026-04-28 17:52:33 19300/20000 na-prot_19300.pdb -1355669.80 2026-04-28 17:52:55 19400/20000 na-prot_19400.pdb -1527288.82 2026-04-28 17:53:17 19500/20000 na-prot_19500.pdb -1553021.98 2026-04-28 17:53:40 19600/20000 na-prot_19600.pdb -1866105.19 2026-04-28 17:54:04 19700/20000 na-prot_19700.pdb -2226498.67 2026-04-28 17:54:26 19800/20000 na-prot_19800.pdb -1989728.71 2026-04-28 17:54:48 19900/20000 na-prot_19900.pdb -1234392.47 2026-04-28 17:55:11 20000/20000 na-prot_20000.pdb -1987756.51 2026-04-28 17:55:11 DARS scoring end 2026-04-28 17:55:11 Clustering (cuttoff: 5, nr_clust: 100 ) in progress... 2026-04-28 17:55:11 time python /home/rpdock/run_gramm//clustering_v4.py dars_out.txt list.txt 5 100 2026-04-28 17:55:11 100 best scored structures 2026-04-28 17:55:11 1 na-prot_11.pdb -4236848.31 2026-04-28 17:55:11 2 na-prot_17346.pdb -4116278.45 2026-04-28 17:55:11 3 na-prot_4017.pdb -4092479.73 2026-04-28 17:55:11 4 na-prot_326.pdb -4011735.35 2026-04-28 17:55:11 5 na-prot_798.pdb -4005272.74 2026-04-28 17:55:11 6 na-prot_11781.pdb -4001650.99 2026-04-28 17:55:11 7 na-prot_4908.pdb -3985167.78 2026-04-28 17:55:11 8 na-prot_14380.pdb -3962850.63 2026-04-28 17:55:11 9 na-prot_3187.pdb -3960961.9 2026-04-28 17:55:11 10 na-prot_13917.pdb -3938894.29 2026-04-28 17:55:11 11 na-prot_13658.pdb -3858659.89 2026-04-28 17:55:11 12 na-prot_11009.pdb -3855787.15 2026-04-28 17:55:11 13 na-prot_55.pdb -3808550.81 2026-04-28 17:55:11 14 na-prot_9989.pdb -3737544.8 2026-04-28 17:55:11 15 na-prot_2236.pdb -3735487.28 2026-04-28 17:55:11 16 na-prot_8631.pdb -3709666.86 2026-04-28 17:55:11 17 na-prot_1598.pdb -3704618.42 2026-04-28 17:55:11 18 na-prot_15772.pdb -3703858.36 2026-04-28 17:55:11 19 na-prot_18535.pdb -3698837.01 2026-04-28 17:55:11 20 na-prot_3.pdb -3698524.44 2026-04-28 17:55:11 21 na-prot_7889.pdb -3698156.32 2026-04-28 17:55:11 22 na-prot_11017.pdb -3662127.33 2026-04-28 17:55:11 23 na-prot_8879.pdb -3652354.73 2026-04-28 17:55:11 24 na-prot_627.pdb -3650396.53 2026-04-28 17:55:11 25 na-prot_8812.pdb -3636744.08 2026-04-28 17:55:11 26 na-prot_11850.pdb -3635812.04 2026-04-28 17:55:11 27 na-prot_14476.pdb -3624647.87 2026-04-28 17:55:11 28 na-prot_7931.pdb -3614513.14 2026-04-28 17:55:11 29 na-prot_13992.pdb -3611259.14 2026-04-28 17:55:11 30 na-prot_565.pdb -3607982.57 2026-04-28 17:55:11 31 na-prot_101.pdb -3601324.95 2026-04-28 17:55:11 32 na-prot_15266.pdb -3596088.49 2026-04-28 17:55:11 33 na-prot_959.pdb -3578227.79 2026-04-28 17:55:11 34 na-prot_1094.pdb -3569688.25 2026-04-28 17:55:11 35 na-prot_2496.pdb -3567892.31 2026-04-28 17:55:11 36 na-prot_4905.pdb -3558239.29 2026-04-28 17:55:11 37 na-prot_16140.pdb -3547828.0 2026-04-28 17:55:11 38 na-prot_5612.pdb -3546215.1 2026-04-28 17:55:11 39 na-prot_12905.pdb -3544607.8 2026-04-28 17:55:11 40 na-prot_3360.pdb -3543079.5 2026-04-28 17:55:11 41 na-prot_8923.pdb -3537387.82 2026-04-28 17:55:11 42 na-prot_3661.pdb -3527573.46 2026-04-28 17:55:11 43 na-prot_17177.pdb -3514866.88 2026-04-28 17:55:11 44 na-prot_29.pdb -3509173.28 2026-04-28 17:55:11 45 na-prot_1267.pdb -3507721.83 2026-04-28 17:55:11 46 na-prot_4111.pdb -3502182.08 2026-04-28 17:55:11 47 na-prot_8511.pdb -3491754.11 2026-04-28 17:55:11 48 na-prot_7932.pdb -3488642.25 2026-04-28 17:55:11 49 na-prot_3744.pdb -3481406.52 2026-04-28 17:55:11 50 na-prot_15371.pdb -3473854.33 2026-04-28 17:55:11 51 na-prot_14885.pdb -3456436.03 2026-04-28 17:55:11 52 na-prot_671.pdb -3447746.66 2026-04-28 17:55:11 53 na-prot_46.pdb -3443498.29 2026-04-28 17:55:11 54 na-prot_61.pdb -3441726.76 2026-04-28 17:55:11 55 na-prot_902.pdb -3441579.9 2026-04-28 17:55:11 56 na-prot_9139.pdb -3436498.06 2026-04-28 17:55:11 57 na-prot_537.pdb -3436384.97 2026-04-28 17:55:11 58 na-prot_6179.pdb -3434313.94 2026-04-28 17:55:11 59 na-prot_18186.pdb -3431528.21 2026-04-28 17:55:11 60 na-prot_7177.pdb -3429911.18 2026-04-28 17:55:11 61 na-prot_19631.pdb -3427431.57 2026-04-28 17:55:11 62 na-prot_8345.pdb -3423689.96 2026-04-28 17:55:11 63 na-prot_3463.pdb -3412503.9 2026-04-28 17:55:11 64 na-prot_16903.pdb -3405029.03 2026-04-28 17:55:11 65 na-prot_9253.pdb -3397486.11 2026-04-28 17:55:11 66 na-prot_19494.pdb -3389524.08 2026-04-28 17:55:11 67 na-prot_2821.pdb -3384238.06 2026-04-28 17:55:11 68 na-prot_2134.pdb -3383248.63 2026-04-28 17:55:11 69 na-prot_105.pdb -3382321.89 2026-04-28 17:55:11 70 na-prot_5344.pdb -3376982.07 2026-04-28 17:55:11 71 na-prot_8974.pdb -3376513.22 2026-04-28 17:55:11 72 na-prot_185.pdb -3367234.98 2026-04-28 17:55:11 73 na-prot_107.pdb -3358251.47 2026-04-28 17:55:11 74 na-prot_237.pdb -3347763.99 2026-04-28 17:55:11 75 na-prot_215.pdb -3340773.53 2026-04-28 17:55:11 76 na-prot_548.pdb -3332857.64 2026-04-28 17:55:11 77 na-prot_524.pdb -3331531.85 2026-04-28 17:55:11 78 na-prot_1443.pdb -3331499.59 2026-04-28 17:55:11 79 na-prot_18338.pdb -3331006.9 2026-04-28 17:55:11 80 na-prot_11046.pdb -3328775.93 2026-04-28 17:55:11 81 na-prot_18356.pdb -3325273.29 2026-04-28 17:55:11 82 na-prot_842.pdb -3324691.43 2026-04-28 17:55:11 83 na-prot_6067.pdb -3323150.52 2026-04-28 17:55:11 84 na-prot_3412.pdb -3322938.7 2026-04-28 17:55:11 85 na-prot_2502.pdb -3320620.16 2026-04-28 17:55:11 86 na-prot_7936.pdb -3320366.11 2026-04-28 17:55:11 87 na-prot_13821.pdb -3315323.98 2026-04-28 17:55:11 88 na-prot_12937.pdb -3310502.24 2026-04-28 17:55:11 89 na-prot_343.pdb -3305239.75 2026-04-28 17:55:11 90 na-prot_14217.pdb -3304020.23 2026-04-28 17:55:11 91 na-prot_317.pdb -3303846.31 2026-04-28 17:55:11 92 na-prot_287.pdb -3292457.31 2026-04-28 17:55:11 93 na-prot_2647.pdb -3291382.35 2026-04-28 17:55:11 94 na-prot_743.pdb -3286378.46 2026-04-28 17:55:11 95 na-prot_4517.pdb -3284827.97 2026-04-28 17:55:11 96 na-prot_30.pdb -3282427.24 2026-04-28 17:55:11 97 na-prot_7593.pdb -3279733.91 2026-04-28 17:55:11 98 na-prot_156.pdb -3275984.87 2026-04-28 17:55:11 99 na-prot_17218.pdb -3275592.64 2026-04-28 17:55:11 100 na-prot_12058.pdb -3270876.04 2026-04-28 17:55:11 Chains: B 2026-04-28 17:55:32 100 best scored structures 2026-04-28 17:55:32 GRAMM analysis selected for further analysis: prot-na_10 2026-04-28 17:55:32 Cluster #1 with 10 structures 2026-04-28 17:55:32 1 na-prot_11.pdb -4236848.31 2026-04-28 17:55:32 2 na-prot_55.pdb -3808550.81 2026-04-28 17:55:32 3 na-prot_1598.pdb -3704618.42 2026-04-28 17:55:32 4 na-prot_3.pdb -3698524.44 2026-04-28 17:55:32 5 na-prot_8812.pdb -3636744.08 2026-04-28 17:55:32 6 na-prot_2496.pdb -3567892.31 2026-04-28 17:55:32 7 na-prot_46.pdb -3443498.29 2026-04-28 17:55:32 8 na-prot_7177.pdb -3429911.18 2026-04-28 17:55:32 9 na-prot_215.pdb -3340773.53 2026-04-28 17:55:32 10 na-prot_1443.pdb -3331499.59 2026-04-28 17:55:32 Cluster #2 with 8 structures 2026-04-28 17:55:32 1 na-prot_9989.pdb -3737544.8 2026-04-28 17:55:32 2 na-prot_2236.pdb -3735487.28 2026-04-28 17:55:32 3 na-prot_565.pdb -3607982.57 2026-04-28 17:55:32 4 na-prot_101.pdb -3601324.95 2026-04-28 17:55:32 5 na-prot_15266.pdb -3596088.49 2026-04-28 17:55:32 6 na-prot_5612.pdb -3546215.1 2026-04-28 17:55:32 7 na-prot_2134.pdb -3383248.63 2026-04-28 17:55:32 8 na-prot_317.pdb -3303846.31 2026-04-28 17:55:32 Cluster #3 with 5 structures 2026-04-28 17:55:32 1 na-prot_798.pdb -4005272.74 2026-04-28 17:55:32 2 na-prot_7889.pdb -3698156.32 2026-04-28 17:55:32 3 na-prot_6179.pdb -3434313.94 2026-04-28 17:55:32 4 na-prot_5344.pdb -3376982.07 2026-04-28 17:55:32 5 na-prot_842.pdb -3324691.43 2026-04-28 17:55:32 Sent to refinement: clusters_found|na-prot_11.pdb|na-prot_9989.pdb|na-prot_798.pdb 2026-04-28 17:55:32 Sent to refinement: clusters_found|na-prot_11.pdb|na-prot_9989.pdb|na-prot_798.pdb 2026-04-28 17:55:32 DARS clustering end 2026-04-28 17:55:32 MC (refinement) init 2026-04-28 17:55:32 python /home/rpdock/run_gramm//run_mc.py -f dars_to_mc.txt -d /home/rpdock/web/media/jobs/12967bbf-65b9-49e9-b7a4-7793b1f8a860/ 2026-04-28 17:55:32 Refinement of #1 /home/rpdock/web/media/jobs/12967bbf-65b9-49e9-b7a4-7793b1f8a860/na-prot_11.pdb 2026-04-28 17:55:32 python /home/rpdock/mc/MC.py -s 1000 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/12967bbf-65b9-49e9-b7a4-7793b1f8a860//ref_struc/na-prot_11/na-prot_11.pdb 2026-04-28 18:00:56 run_mc::stderr:/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CA defined twice in residue at line 1776. 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 1780. 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 1782. 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 1784. 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 1786. 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 1788. 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 NH1 defined twice in residue at line 1790. 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 1792. 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 1885. 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 1889. 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 1891. 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 1893. 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 OE1 defined twice in residue at line 1895. 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 OE2 defined twice in residue at line 1897. 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 2285. 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 2289. 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 2291. 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 SD defined twice in residue at line 2293. 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 CE defined twice in residue at line 2295. 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 2406. 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 2410. 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 2412. 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 2414. 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 CE defined twice in residue at line 2416. 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 NZ defined twice in residue at line 2418. 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 2505. 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 2509. 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 2511. 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 OD1 defined twice in residue at line 2513. 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 OD2 defined twice in residue at line 2515. 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 2536. 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 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 OG defined twice in residue at line 2542. Exception ignored. Some atoms or residues may be missing in the data structure. % message, PDBConstructionWarning) 2026-04-28 18:00:56 Refinement of #2 /home/rpdock/web/media/jobs/12967bbf-65b9-49e9-b7a4-7793b1f8a860/na-prot_9989.pdb 2026-04-28 18:00:56 python /home/rpdock/mc/MC.py -s 1000 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/12967bbf-65b9-49e9-b7a4-7793b1f8a860//ref_struc/na-prot_9989/na-prot_9989.pdb 2026-04-28 18:06:13 run_mc::stderr:/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CA defined twice in residue at line 1776. 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 1780. 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 1782. 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 1784. 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 1786. 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 1788. 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 NH1 defined twice in residue at line 1790. 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 1792. 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 1885. 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 1889. 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 1891. 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 1893. 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 OE1 defined twice in residue at line 1895. 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 OE2 defined twice in residue at line 1897. 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 2285. 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 2289. 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 2291. 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 SD defined twice in residue at line 2293. 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 CE defined twice in residue at line 2295. 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 2406. 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 2410. 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 2412. 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 2414. 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 CE defined twice in residue at line 2416. 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 NZ defined twice in residue at line 2418. 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 2505. 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 2509. 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 2511. 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 OD1 defined twice in residue at line 2513. 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 OD2 defined twice in residue at line 2515. 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 2536. 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 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 OG defined twice in residue at line 2542. Exception ignored. Some atoms or residues may be missing in the data structure. % message, PDBConstructionWarning) 2026-04-28 18:06:13 Refinement of #3 /home/rpdock/web/media/jobs/12967bbf-65b9-49e9-b7a4-7793b1f8a860/na-prot_798.pdb 2026-04-28 18:06:13 python /home/rpdock/mc/MC.py -s 1000 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/12967bbf-65b9-49e9-b7a4-7793b1f8a860//ref_struc/na-prot_798/na-prot_798.pdb 2026-04-28 18:11:40 run_mc::stderr:/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CA defined twice in residue at line 1776. 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 1780. 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 1782. 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 1784. 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 1786. 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 1788. 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 NH1 defined twice in residue at line 1790. 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 1792. 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 1885. 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 1889. 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 1891. 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 1893. 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 OE1 defined twice in residue at line 1895. 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 OE2 defined twice in residue at line 1897. 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 2285. 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 2289. 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 2291. 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 SD defined twice in residue at line 2293. 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 CE defined twice in residue at line 2295. 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 2406. 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 2410. 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 2412. 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 2414. 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 CE defined twice in residue at line 2416. 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 NZ defined twice in residue at line 2418. 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 2505. 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 2509. 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 2511. 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 OD1 defined twice in residue at line 2513. 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 OD2 defined twice in residue at line 2515. 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 2536. 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 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 OG defined twice in residue at line 2542. Exception ignored. Some atoms or residues may be missing in the data structure. % message, PDBConstructionWarning) 2026-04-28 18:11:41 /usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CA defined twice in residue at line 1776. 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 1780. 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 1782. 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 1784. 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 1786. 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 1788. 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 NH1 defined twice in residue at line 1790. 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 1792. 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 1885. 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 1889. 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 1891. 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 1893. 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 OE1 defined twice in residue at line 1895. 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 OE2 defined twice in residue at line 1897. 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 2285. 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 2289. 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 2291. 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 SD defined twice in residue at line 2293. 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 CE defined twice in residue at line 2295. 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 2406. 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 2410. 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 2412. 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 2414. 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 CE defined twice in residue at line 2416. 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 NZ defined twice in residue at line 2418. 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 2505. 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 2509. 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 2511. 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 OD1 defined twice in residue at line 2513. 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 OD2 defined twice in residue at line 2515. 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 2536. 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 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 OG defined twice in residue at line 2542. Exception ignored. Some atoms or residues may be missing in the data structure. % message, PDBConstructionWarning) start - parameters: File name /home/rpdock/web/media/jobs/12967bbf-65b9-49e9-b7a4-7793b1f8a860//ref_struc/na-prot_11/na-prot_11.pdb Steps 1000 Temp. start 15000.0 Temp. end 295.0 False msg start - parameters: File name /home/rpdock/web/media/jobs/12967bbf-65b9-49e9-b7a4-7793b1f8a860//ref_struc/na-prot_11/na-prot_11.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 0 - -2152608.97 -1940116.23 -1912492.74 1700000.00 1 R -2170579.18 -1604635.32 -1565943.86 1000000.00 T= 15000.0 K progress 0.1 2 R -2117247.23 -1877086.87 -1840160.36 1600000.00 T= 14941.18 K progress 0.2 3 T -2508167.27 -1693633.52 -1614533.75 800000.00 T= 14911.77 K progress 0.3 4 T -2520893.90 -1732751.08 -1688142.82 900000.00 T= 14852.95 K progress 0.4 5 T -2396269.91 -1363323.78 -1332946.14 300000.00 T= 14838.245 K progress 0.5 6 R -2413352.74 -1321548.39 -1291804.35 200000.00 T= 14823.54 K progress 0.6 7 R -2425932.30 -1326979.08 -1298953.22 200000.00 T= 14735.31 K progress 0.7 8 R -2328143.24 -1377359.39 -1350783.85 400000.00 T= 14720.605 K progress 0.8 9 R -2378189.94 -1399089.54 -1379100.39 400000.00 T= 14705.9 K progress 0.9 10 R -2471876.18 -1353100.73 -1318775.46 200000.00 T= 14676.49 K progress 1.0 11 T -2496992.27 -1680606.91 -1616385.35 800000.00 T= 14573.555 K progress 1.1 12 R -2549835.03 -1794176.53 -1755658.50 1000000.00 T= 14544.145 K progress 1.2 13 T -2941609.71 -1780287.18 -1761322.53 600000.00 T= 14397.095 K progress 1.3 14 R -3050589.88 -1740588.84 -1710001.05 400000.00 T= 14382.39 K progress 1.4 15 R -3047033.96 -1737073.43 -1709960.52 400000.00 T= 14235.34 K progress 1.5 16 R -2944222.83 -1701365.54 -1642857.29 400000.00 T= 14205.93 K progress 1.6 17 T -2986805.87 -1814579.54 -1772226.33 600000.00 T= 14161.815 K progress 1.7 18 R -3152945.72 -1847313.51 -1805632.21 500000.00 T= 14117.7 K progress 1.8 19 R -3163686.52 -1850347.90 -1813338.62 500000.00 T= 13220.695 K progress 1.9 20 R -3077724.67 -1804859.90 -1772864.78 500000.00 T= 13132.465 K progress 2.0 21 T -3040676.84 -1785966.92 -1754709.93 500000.00 T= 13103.055 K progress 2.1 22 T -2945237.15 -1692716.95 -1652520.20 400000.00 T= 13088.35 K progress 2.2 23 T -2922879.26 -1768241.59 -1754637.67 600000.00 T= 13014.825 K progress 2.3 24 T -3063872.27 -1643082.31 -1620789.96 200000.00 T= 13000.12 K progress 2.4 25 R -3093369.30 -1655131.17 -1638238.13 200000.00 T= 12926.595 K progress 2.5 26 T -2795913.69 -1673730.93 -1622182.76 500000.00 T= 12853.07 K progress 2.6 27 T -2941524.54 -1795077.95 -1746446.59 600000.00 T= 12808.955 K progress 2.7 28 R -2919053.19 -1872199.56 -1846853.63 800000.00 T= 12647.2 K progress 2.8 29 R -2938021.23 -1786045.09 -1751976.15 600000.00 T= 12588.38 K progress 2.9 30 R -2938021.23 -1786045.09 -1751976.15 600000.00 T= 12514.855 K progress 3.0 31 R -2990896.58 -1900584.55 -1890312.04 800000.00 T= 12456.035 K progress 3.1 32 R -3062024.42 -1808745.47 -1753278.95 500000.00 T= 12279.575 K progress 3.2 33 T -3269278.93 -1912816.69 -1856462.25 500000.00 T= 12250.165 K progress 3.3 34 R -3267106.11 -1911271.89 -1855834.22 500000.00 T= 12117.82 K progress 3.4 35 R -3191091.21 -1877036.40 -1814054.80 500000.00 T= 11661.965 K progress 3.5 36 R -2898691.58 -1874223.63 -1824467.95 800000.00 T= 11514.915 K progress 3.6 37 R -2434842.96 -1705115.03 -1629727.93 900000.00 T= 11470.8 K progress 3.7 38 R -2281854.90 -1647007.24 -1634847.67 1000000.00 T= 11411.98 K progress 3.8 39 R -2314786.57 -1747615.80 -1667170.77 1100000.00 T= 11309.045 K progress 3.9 40 R -2551352.86 -1893775.22 -1857577.64 1200000.00 T= 11294.34 K progress 4.0 41 T -2697889.81 -1670495.22 -1627394.60 600000.00 T= 11235.52 K progress 4.1 42 R -2882764.80 -1707409.99 -1675354.80 500000.00 T= 11191.405 K progress 4.2 43 T -3090028.48 -1818597.73 -1771430.75 500000.00 T= 11161.995 K progress 4.3 44 R -3104156.75 -1825447.19 -1778709.56 500000.00 T= 10867.895 K progress 4.4 45 T -3115904.44 -1821822.38 -1794082.05 500000.00 T= 10720.845 K progress 4.5 46 R -3093052.98 -1808281.26 -1784771.72 500000.00 T= 10676.73 K progress 4.6 47 R -3110751.24 -1817249.28 -1793501.96 500000.00 T= 10353.22 K progress 4.7 48 R -3074738.91 -1803124.76 -1771614.15 500000.00 T= 9985.595 K progress 4.8 49 R -2750805.22 -1638504.76 -1612300.46 500000.00 T= 9882.66 K progress 4.9 50 T -2784580.46 -1522564.31 -1462016.15 200000.00 T= 9662.085 K progress 5.0 51 R -2827908.99 -1582384.58 -1545524.41 300000.00 T= 9617.97 K progress 5.1 52 R -3017247.13 -1561776.74 -1555470.40 100000.00 T= 9588.56 K progress 5.2 53 T -3026052.01 -1798689.63 -1727362.38 500000.00 T= 9412.1 K progress 5.3 54 R -3160319.85 -1843514.63 -1816805.22 500000.00 T= 9132.705 K progress 5.4 55 R -3164806.09 -1864661.56 -1800144.53 500000.00 T= 8970.95 K progress 5.5 56 R -3166043.60 -1864908.40 -1801135.20 500000.00 T= 8897.425 K progress 5.6 57 R -3186542.24 -1877973.02 -1808569.22 500000.00 T= 8588.62 K progress 5.7 58 R -3182470.49 -1871377.19 -1811093.30 500000.00 T= 8235.7 K progress 5.8 59 R -3187285.35 -1812898.46 -1774386.90 400000.00 T= 8118.06 K progress 5.9 60 R -3122584.25 -1835050.18 -1787534.07 500000.00 T= 7971.01 K progress 6.0 61 T -3133171.07 -1786587.70 -1746583.37 400000.00 T= 7897.485 K progress 6.1 62 R -3113073.11 -1824738.65 -1788334.46 500000.00 T= 7765.14 K progress 6.2 63 R -3043149.38 -1791806.73 -1751342.65 500000.00 T= 7632.795 K progress 6.3 64 R -3054154.53 -1690205.80 -1663948.73 300000.00 T= 7588.68 K progress 6.4 65 R -3101792.49 -1768335.64 -1733456.84 400000.00 T= 7515.155 K progress 6.5 66 R -3077133.14 -1700276.44 -1676856.70 300000.00 T= 6750.495 K progress 6.6 67 R -2697866.26 -1557929.47 -1539936.79 400000.00 T= 6706.38 K progress 6.7 68 R -2838117.92 -1689301.22 -1648816.70 500000.00 T= 6691.675 K progress 6.8 69 T -2933163.13 -1676661.43 -1656501.70 400000.00 T= 6676.97 K progress 6.9 70 T -2893326.76 -1510955.59 -1482371.17 100000.00 T= 6588.74 K progress 7.0 71 T -3057332.97 -1586591.28 -1570741.69 100000.00 T= 6574.035 K progress 7.1 72 R -2994399.19 -1556392.65 -1538006.54 100000.00 T= 6471.1 K progress 7.2 73 R -2880434.40 -1803047.39 -1777387.01 700000.00 T= 6397.575 K progress 7.3 74 T -2895005.50 -1862675.80 -1832329.70 800000.00 T= 6353.46 K progress 7.4 75 R -3071161.85 -1807460.64 -1763701.21 500000.00 T= 6265.23 K progress 7.5 76 R -2959728.31 -1838315.25 -1821413.06 700000.00 T= 6147.59 K progress 7.6 77 R -3001229.08 -1864640.45 -1836588.63 700000.00 T= 6044.655 K progress 7.7 78 R -2998563.83 -1863474.67 -1835089.16 700000.00 T= 5809.375 K progress 7.8 79 R -3097851.96 -1775093.78 -1722758.18 400000.00 T= 5750.555 K progress 7.9 80 R -3159169.10 -1796283.50 -1762885.60 400000.00 T= 5647.62 K progress 8.0 81 T -3113021.85 -1767815.50 -1745206.35 400000.00 T= 5588.8 K progress 8.1 82 T -3061387.08 -1602472.27 -1558914.81 100000.00 T= 5559.39 K progress 8.2 83 R -3037279.76 -1587078.33 -1550201.43 100000.00 T= 5485.865 K progress 8.3 84 R -3076501.99 -1604836.46 -1571665.53 100000.00 T= 5412.34 K progress 8.4 85 T -3074895.53 -1808786.00 -1766109.53 500000.00 T= 5368.225 K progress 8.5 86 R -3003065.17 -1619913.50 -1583151.67 200000.00 T= 5324.11 K progress 8.6 87 R -3040583.59 -1641318.26 -1599265.33 200000.00 T= 5221.175 K progress 8.7 88 T -3127803.64 -1668515.12 -1659288.52 200000.00 T= 5177.06 K progress 8.8 89 R -3152607.35 -1680080.61 -1672526.74 200000.00 T= 5118.24 K progress 8.9 90 R -3077436.65 -1761902.26 -1715534.39 400000.00 T= 4662.385 K progress 9.0 91 T -3142834.92 -1851626.97 -1791207.95 500000.00 T= 4647.68 K progress 9.1 92 R -3187641.22 -1868573.99 -1819067.23 500000.00 T= 4632.975 K progress 9.2 93 R -3144715.46 -1791949.33 -1752766.13 400000.00 T= 4441.81 K progress 9.3 94 R -3222990.52 -1883945.86 -1839044.66 500000.00 T= 4412.4 K progress 9.4 95 R -3338611.07 -1728962.04 -1709649.02 100000.00 T= 4191.825 K progress 9.5 96 R -3289844.55 -1750970.06 -1738874.49 200000.00 T= 3735.97 K progress 9.6 97 R -3285003.95 -1708860.85 -1676143.11 100000.00 T= 3633.035 K progress 9.7 98 R -3323095.00 -1777341.61 -1745753.39 200000.00 T= 3544.805 K progress 9.8 99 R -3357581.77 -1903232.53 -1854349.24 400000.00 T= 3338.935 K progress 9.9 100 T -3384304.29 -1958710.62 -1925593.67 500000.00 T= 3059.54 K progress 10.0 101 T -3328792.36 -1917975.38 -1910816.98 500000.00 T= 2441.93 K progress 10.1 102 R -3335290.06 -1923094.83 -1912195.23 500000.00 T= 2044.895 K progress 10.2 103 R -3350680.58 -1926438.95 -1924241.63 500000.00 T= 1044.955 K progress 10.3 104 R -3353164.85 -1937796.78 -1915368.08 500000.00 T= 603.805 K progress 10.4 105 R -3361348.31 -1934963.67 -1926384.64 500000.00 T= 324.41 K progress 10.5 Save no big msg save short traj msg save best.pdb msg save plot e_step.png Tue Apr 28 17:55:32 2026 ['na-prot_11.pdb', 'na-prot_9989.pdb', 'na-prot_798.pdb'] msg Refinement of #1 /home/rpdock/web/media/jobs/12967bbf-65b9-49e9-b7a4-7793b1f8a860/na-prot_11.pdb dir: /home/rpdock/web/media/jobs/12967bbf-65b9-49e9-b7a4-7793b1f8a860/ file: na-prot_11.pdb find `pwd` -iname na-prot_11.pdb copy /home/rpdock/web/media/jobs/12967bbf-65b9-49e9-b7a4-7793b1f8a860/prot-na_10/na-prot_11.pdb to /home/rpdock/web/media/jobs/12967bbf-65b9-49e9-b7a4-7793b1f8a860//ref_struc/na-prot_11/na-prot_11.pdb cmd: python /home/rpdock/mc/MC.py -s 1000 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/12967bbf-65b9-49e9-b7a4-7793b1f8a860//ref_struc/na-prot_11/na-prot_11.pdb msg python /home/rpdock/mc/MC.py -s 1000 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/12967bbf-65b9-49e9-b7a4-7793b1f8a860//ref_struc/na-prot_11/na-prot_11.pdb msg run_mc::stderr:/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CA defined twice in residue at line 1776. 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 1780. 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 1782. 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 1784. 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 1786. 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 1788. 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 NH1 defined twice in residue at line 1790. 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 1792. 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 1885. 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 1889. 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 1891. 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 1893. 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 OE1 defined twice in residue at line 1895. 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 OE2 defined twice in residue at line 1897. 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 2285. 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 2289. 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 2291. 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 SD defined twice in residue at line 2293. 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 CE defined twice in residue at line 2295. 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 2406. 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 2410. 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 2412. 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 2414. Exception ignored. Some atoms or residues may be missing in the data structure. % message, PDBConstructionWarning) /usr/local/lib/python2.7/dist-packages/BiError in run_mc /usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CA defined twice in residue at line 1776. 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 1780. 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 1782. 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 1784. 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 1786. 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 1788. 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 NH1 defined twice in residue at line 1790. 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 1792. 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 1885. 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 1889. 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 1891. 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 1893. 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 OE1 defined twice in residue at line 1895. 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 OE2 defined twice in residue at line 1897. 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 2285. 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 2289. 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 2291. 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 SD defined twice in residue at line 2293. 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 CE defined twice in residue at line 2295. 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 2406. 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 2410. 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 2412. 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 2414. 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 CE defined twice in residue at line 2416. 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 NZ defined twice in residue at line 2418. 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 2505. 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 2509. 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 2511. 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 OD1 defined twice in residue at line 2513. 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 OD2 defined twice in residue at line 2515. 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 2536. 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 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 OG 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 CA defined twice in residue at line 1776. 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 1780. 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 1782. 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 1784. 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 1786. 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 1788. 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 NH1 defined twice in residue at line 1790. 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 1792. 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 1885. 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 1889. 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 1891. 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 1893. 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 OE1 defined twice in residue at line 1895. 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 OE2 defined twice in residue at line 1897. 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 2285. 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 2289. 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 2291. 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 SD defined twice in residue at line 2293. 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 CE defined twice in residue at line 2295. 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 2406. 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 2410. 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 2412. 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 2414. 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 CE defined twice in residue at line 2416. 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 NZ defined twice in residue at line 2418. 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 2505. 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 2509. 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 2511. 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 OD1 defined twice in residue at line 2513. 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 OD2 defined twice in residue at line 2515. 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 2536. 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 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 OG defined twice in residue at line 2542. Exception ignored. Some atoms or residues may be missing in the data structure. % message, PDBConstructionWarning) start - parameters: File name /home/rpdock/web/media/jobs/12967bbf-65b9-49e9-b7a4-7793b1f8a860//ref_struc/na-prot_9989/na-prot_9989.pdb Steps 1000 Temp. start 15000.0 Temp. end 295.0 False msg start - parameters: File name /home/rpdock/web/media/jobs/12967bbf-65b9-49e9-b7a4-7793b1f8a860//ref_struc/na-prot_9989/na-prot_9989.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 0 - -1966371.31 -1753099.13 -1713272.18 1500000.00 1 T -2348216.48 -1957182.22 -1891034.26 1500000.00 T= 15000.0 K progress 0.1 2 T -2638458.78 -2289134.72 -2149324.06 1800000.00 T= 14985.295 K progress 0.2 3 T -2579047.83 -2378945.25 -2300102.57 2100000.00 T= 14808.835 K progress 0.3 4 T -2539531.64 -2122658.96 -2016872.68 1600000.00 T= 14720.605 K progress 0.4 5 T -2550205.77 -2136034.38 -2014171.38 1600000.00 T= 14676.49 K progress 0.5 6 T -2806926.29 -2152607.18 -2054319.11 1400000.00 T= 14632.375 K progress 0.6 7 R -2598383.32 -2124842.44 -2073540.89 1600000.00 T= 14191.225 K progress 0.7 8 R -2450985.36 -2053000.77 -1997984.59 1600000.00 T= 14176.52 K progress 0.8 9 R -2545894.62 -1675295.32 -1670599.30 800000.00 T= 14147.11 K progress 0.9 10 R -2368867.44 -1688713.22 -1680154.22 1000000.00 T= 14132.405 K progress 1.0 11 R -2420354.07 -1707666.19 -1712687.88 1000000.00 T= 14088.29 K progress 1.1 12 T -2718352.98 -1709759.54 -1708593.43 700000.00 T= 14058.88 K progress 1.2 13 R -2931938.15 -1720131.17 -1711806.98 500000.00 T= 14014.765 K progress 1.3 14 T -2931875.16 -1562689.01 -1569186.15 200000.00 T= 14000.06 K progress 1.4 15 R -3228993.70 -1666726.64 -1662267.05 100000.00 T= 13661.845 K progress 1.5 16 R -2899573.47 -1634595.60 -1664977.86 400000.00 T= 12603.085 K progress 1.6 17 R -2910814.68 -1640653.02 -1670161.66 400000.00 T= 12588.38 K progress 1.7 18 T -2652897.81 -1420699.09 -1432198.72 200000.00 T= 12426.625 K progress 1.8 19 R -2717138.49 -1408865.37 -1408273.12 100000.00 T= 12382.51 K progress 1.9 20 T -2675592.64 -1377085.53 -1398507.11 100000.00 T= 12367.805 K progress 2.0 21 T -2717260.58 -1413596.59 -1403663.99 100000.00 T= 12235.46 K progress 2.1 22 T -2621048.51 -1364495.15 -1356553.36 100000.00 T= 12220.755 K progress 2.2 23 R -2590487.42 -1400806.44 -1389680.98 200000.00 T= 12176.64 K progress 2.3 24 R -2595970.13 -1353725.87 -1342244.26 100000.00 T= 12147.23 K progress 2.4 25 T -2573388.98 -1395183.73 -1378205.25 200000.00 T= 12117.82 K progress 2.5 26 T -2555231.75 -1324913.60 -1330318.15 100000.00 T= 12059.0 K progress 2.6 27 T -2282169.89 -1226355.93 -1255813.96 200000.00 T= 11970.77 K progress 2.7 28 T -2399615.21 -1354080.69 -1345534.52 300000.00 T= 11956.065 K progress 2.8 29 R -2635522.65 -1509548.54 -1525974.11 400000.00 T= 11941.36 K progress 2.9 30 R -2641764.35 -1566457.37 -1575306.98 500000.00 T= 11926.655 K progress 3.0 31 T -2600193.46 -1707387.93 -1692805.53 800000.00 T= 11911.95 K progress 3.1 32 T -2695126.53 -1564655.28 -1530471.25 400000.00 T= 11867.835 K progress 3.2 33 R -2766016.94 -1647517.70 -1618499.23 500000.00 T= 11823.72 K progress 3.3 34 R -2650898.71 -1708117.20 -1642781.51 700000.00 T= 11809.015 K progress 3.4 35 R -2848632.81 -1698850.59 -1649782.22 500000.00 T= 11750.195 K progress 3.5 36 R -2848632.81 -1698850.59 -1649782.22 500000.00 T= 11470.8 K progress 3.6 37 T -2306443.51 -1506006.05 -1500437.45 700000.00 T= 11367.865 K progress 3.7 38 T -2456109.22 -1716462.09 -1639647.13 900000.00 T= 11294.34 K progress 3.8 39 T -2461350.64 -1817147.72 -1744202.92 1100000.00 T= 11264.93 K progress 3.9 40 T -2576427.54 -1999297.07 -1877130.47 1300000.00 T= 11250.225 K progress 4.0 41 R -2433121.12 -1756840.99 -1676280.13 1000000.00 T= 11206.11 K progress 4.1 42 R -2278959.10 -1758095.54 -1720863.56 1200000.00 T= 11161.995 K progress 4.2 43 R -2252467.33 -1795113.31 -1757354.02 1300000.00 T= 11147.29 K progress 4.3 44 T -2775646.50 -1706474.41 -1669172.09 600000.00 T= 11132.585 K progress 4.4 45 T -2957006.82 -1793865.85 -1763140.97 600000.00 T= 11059.06 K progress 4.5 46 T -2939161.05 -1844517.91 -1794643.13 700000.00 T= 11029.65 K progress 4.6 47 T -3034014.47 -1886992.71 -1847021.76 700000.00 T= 10985.535 K progress 4.7 48 R -3001105.10 -1871514.64 -1829590.47 700000.00 T= 10441.45 K progress 4.8 49 T -2786589.17 -1666546.99 -1620042.17 500000.00 T= 10220.875 K progress 4.9 50 T -2742977.57 -1707636.52 -1735341.06 700000.00 T= 10176.76 K progress 5.0 51 R -2805354.32 -1689682.83 -1715671.49 600000.00 T= 10147.35 K progress 5.1 52 T -2863120.60 -1746483.95 -1716636.65 600000.00 T= 10029.71 K progress 5.2 53 T -2718168.36 -1503531.70 -1514636.66 300000.00 T= 9941.48 K progress 5.3 54 T -2780820.00 -1646323.15 -1634496.85 500000.00 T= 9882.66 K progress 5.4 55 R -2730608.82 -1620506.26 -1610102.56 500000.00 T= 9838.545 K progress 5.5 56 T -2900633.98 -1549221.61 -1551412.37 200000.00 T= 9691.495 K progress 5.6 57 R -2900562.40 -1550043.40 -1550519.00 200000.00 T= 9662.085 K progress 5.7 58 R -2901584.09 -1548772.71 -1552811.39 200000.00 T= 9573.855 K progress 5.8 59 R -2884465.57 -1539150.67 -1545314.90 200000.00 T= 8603.325 K progress 5.9 60 R -2889945.25 -1543431.75 -1546513.50 200000.00 T= 8588.62 K progress 6.0 61 R -2867245.01 -1531680.80 -1535564.20 200000.00 T= 8500.39 K progress 6.1 62 T -2962893.32 -1686397.11 -1676496.21 400000.00 T= 8382.75 K progress 6.2 63 R -2966894.27 -1629303.52 -1637590.75 300000.00 T= 7485.745 K progress 6.3 64 R -2853549.03 -1620619.97 -1632929.06 400000.00 T= 7176.94 K progress 6.4 65 R -2855296.97 -1626405.32 -1628891.65 400000.00 T= 6868.135 K progress 6.5 66 T -2918064.65 -1547512.47 -1570552.17 200000.00 T= 6838.725 K progress 6.6 67 R -2930806.21 -1558463.42 -1572342.79 200000.00 T= 6809.315 K progress 6.7 68 R -2928240.81 -1555656.05 -1572584.77 200000.00 T= 6691.675 K progress 6.8 69 R -2915425.48 -1558449.54 -1556975.94 200000.00 T= 6368.165 K progress 6.9 70 R -2922791.66 -1560606.71 -1562184.95 200000.00 T= 6088.77 K progress 7.0 71 R -3045295.59 -1605428.59 -1639866.99 200000.00 T= 5985.835 K progress 7.1 72 R -3031327.60 -1597638.34 -1633689.26 200000.00 T= 1839.025 K progress 7.2 73 R -3031551.70 -1598245.07 -1633306.63 200000.00 T= 1221.415 K progress 7.3 74 R -3031934.32 -1598245.07 -1633689.26 200000.00 T= 780.265 K progress 7.4 Save no big msg save short traj msg save best.pdb msg save plot e_step.png o/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CE defined twice in residue at line 2416. 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 NZ defined twice in residue at line 2418. 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 2505. 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 2509. 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 2511. 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 OD1 defined twice in residue at line 2513. 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 OD2 defined twice in residue at line 2515. 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 2536. 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 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 OG defined twice in residue at line 2542. Exception ignored. Some atoms or residues may be missing in the data structure. % message, PDBConstructionWarning) msg Refinement of #2 /home/rpdock/web/media/jobs/12967bbf-65b9-49e9-b7a4-7793b1f8a860/na-prot_9989.pdb dir: /home/rpdock/web/media/jobs/12967bbf-65b9-49e9-b7a4-7793b1f8a860/ file: na-prot_9989.pdb find `pwd` -iname na-prot_9989.pdb copy /home/rpdock/web/media/jobs/12967bbf-65b9-49e9-b7a4-7793b1f8a860/prot-na_10/na-prot_9989.pdb to /home/rpdock/web/media/jobs/12967bbf-65b9-49e9-b7a4-7793b1f8a860//ref_struc/na-prot_9989/na-prot_9989.pdb cmd: python /home/rpdock/mc/MC.py -s 1000 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/12967bbf-65b9-49e9-b7a4-7793b1f8a860//ref_struc/na-prot_9989/na-prot_9989.pdb msg python /home/rpdock/mc/MC.py -s 1000 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/12967bbf-65b9-49e9-b7a4-7793b1f8a860//ref_struc/na-prot_9989/na-prot_9989.pdb msg run_mc::stderr:/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CA defined twice in residue at line 1776. 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 1780. 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 1782. 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 1784. 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 1786. 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 1788. 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 NH1 defined twice in residue at line 1790. 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 1792. 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 1885. 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 1889. 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 1891. 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 1893. 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 OE1 defined twice in residue at line 1895. 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 OE2 defined twice in residue at line 1897. 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 2285. 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 2289. 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 2291. 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 SD defined twice in residue at line 2293. 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 CE defined twice in residue at line 2295. 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 2406. 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 2410. 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 2412. 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 2414. 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 CE defined twice in residue at line 2416. 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 NZ defined twice in residue at line 2418. 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 2505. 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: PDBConstructionExcepError in run_mc /usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CA defined twice in residue at line 1776. 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 1780. 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 1782. 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 1784. 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 1786. 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 1788. 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 NH1 defined twice in residue at line 1790. 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 1792. 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 1885. 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 1889. 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 1891. 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 1893. 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 OE1 defined twice in residue at line 1895. 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 OE2 defined twice in residue at line 1897. 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 2285. 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 2289. 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 2291. 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 SD defined twice in residue at line 2293. 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 CE defined twice in residue at line 2295. 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 2406. 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 2410. 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 2412. 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 2414. 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 CE defined twice in residue at line 2416. 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 NZ defined twice in residue at line 2418. 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 2505. 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 2509. 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 2511. 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 OD1 defined twice in residue at line 2513. 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 OD2 defined twice in residue at line 2515. 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 2536. 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 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 OG 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 CA defined twice in residue at line 1776. 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 1780. 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 1782. 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 1784. 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 1786. 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 1788. 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 NH1 defined twice in residue at line 1790. 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 1792. 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 1885. 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 1889. 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 1891. 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 1893. 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 OE1 defined twice in residue at line 1895. 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 OE2 defined twice in residue at line 1897. 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 2285. 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 2289. 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 2291. 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 SD defined twice in residue at line 2293. 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 CE defined twice in residue at line 2295. 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 2406. 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 2410. 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 2412. 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 2414. 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 CE defined twice in residue at line 2416. 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 NZ defined twice in residue at line 2418. 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 2505. 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 2509. 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 2511. 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 OD1 defined twice in residue at line 2513. 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 OD2 defined twice in residue at line 2515. 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 2536. 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 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 OG defined twice in residue at line 2542. Exception ignored. Some atoms or residues may be missing in the data structure. % message, PDBConstructionWarning) start - parameters: File name /home/rpdock/web/media/jobs/12967bbf-65b9-49e9-b7a4-7793b1f8a860//ref_struc/na-prot_798/na-prot_798.pdb Steps 1000 Temp. start 15000.0 Temp. end 295.0 False msg start - parameters: File name /home/rpdock/web/media/jobs/12967bbf-65b9-49e9-b7a4-7793b1f8a860//ref_struc/na-prot_798/na-prot_798.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 0 - -1190116.84 -1859371.07 -1830745.77 2500000.00 1 R -2702958.60 -2184585.75 -2118372.85 1600000.00 T= 15000.0 K progress 0.1 2 R -2692543.41 -2185746.35 -2106797.07 1600000.00 T= 14970.59 K progress 0.2 3 R -2764307.93 -2353628.86 -2310679.07 1900000.00 T= 14911.77 K progress 0.3 4 R -2837622.85 -2386435.94 -2351186.91 1900000.00 T= 14750.015 K progress 0.4 5 R -2920201.81 -2281072.25 -2239129.57 1600000.00 T= 14720.605 K progress 0.5 6 R -2909203.15 -2280644.91 -2228558.25 1600000.00 T= 14691.195 K progress 0.6 7 R -3099989.53 -2143950.48 -2056039.05 1100000.00 T= 14617.67 K progress 0.7 8 R -3001074.39 -2321077.43 -2279996.96 1600000.00 T= 13897.125 K progress 0.8 9 R -3036535.42 -2345205.38 -2291330.05 1600000.00 T= 13867.715 K progress 0.9 10 R -3036535.42 -2345205.38 -2291330.05 1600000.00 T= 13853.01 K progress 1.0 11 R -3032692.13 -2299428.05 -2233264.08 1500000.00 T= 13794.19 K progress 1.1 12 R -3002633.49 -2284256.60 -2218376.89 1500000.00 T= 13647.14 K progress 1.2 13 R -3027502.91 -2341572.64 -2285930.27 1600000.00 T= 13558.91 K progress 1.3 14 R -3013434.16 -2334919.94 -2278514.21 1600000.00 T= 13544.205 K progress 1.4 15 R -3025389.24 -2339458.97 -2285930.27 1600000.00 T= 13323.63 K progress 1.5 16 R -3023926.42 -2343927.07 -2279999.35 1600000.00 T= 13308.925 K progress 1.6 17 R -2983776.93 -2371697.83 -2312079.11 1700000.00 T= 12970.71 K progress 1.7 18 R -3018893.42 -2282625.96 -2236267.46 1500000.00 T= 12794.25 K progress 1.8 19 R -3041356.70 -2297220.23 -2244136.47 1500000.00 T= 12500.15 K progress 1.9 20 R -3046575.16 -2303104.79 -2243470.37 1500000.00 T= 12426.625 K progress 2.0 21 T -3026591.70 -2300774.35 -2225817.35 1500000.00 T= 12220.755 K progress 2.1 22 T -3110624.46 -2398904.40 -2311720.07 1600000.00 T= 11897.245 K progress 2.2 23 R -3053687.88 -2366029.60 -2287658.28 1600000.00 T= 11691.375 K progress 2.3 24 R -3274787.12 -2428580.19 -2346206.93 1500000.00 T= 11470.8 K progress 2.4 25 R -3242856.58 -2416043.63 -2326812.95 1500000.00 T= 8309.225 K progress 2.5 26 R -3249925.24 -2424573.91 -2325351.33 1500000.00 T= 5721.145 K progress 2.6 27 R -3269029.19 -2424577.26 -2344451.93 1500000.00 T= 5368.225 K progress 2.7 28 R -3266750.92 -2424770.24 -2341980.68 1500000.00 T= 4853.55 K progress 2.8 29 R -3273456.82 -2435661.05 -2337795.77 1500000.00 T= 4647.68 K progress 2.9 30 R -3273456.82 -2435661.05 -2337795.77 1500000.00 T= 3853.61 K progress 3.0 31 R -3270653.50 -2431979.28 -2338674.21 1500000.00 T= 2191.945 K progress 3.1 32 R -3273134.71 -2427040.78 -2346093.93 1500000.00 T= 1927.255 K progress 3.2 33 R -3273456.82 -2435661.05 -2337795.77 1500000.00 T= 1530.22 K progress 3.3 34 R -3276746.50 -2428937.77 -2347808.73 1500000.00 T= 1368.465 K progress 3.4 Save no big msg save short traj msg save best.pdb msg save plot e_step.png tion: Atom CB defined twice in residue at line 2509. 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 2511. 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 OD1 defined twice in residue at line 2513. 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 OD2 defined twice in residue at line 2515. 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 2536. 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 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 OG defined twice in residue at line 2542. Exception ignored. Some atoms or residues may be missing in the data structure. % message, PDBConstructionWarning) msg Refinement of #3 /home/rpdock/web/media/jobs/12967bbf-65b9-49e9-b7a4-7793b1f8a860/na-prot_798.pdb dir: /home/rpdock/web/media/jobs/12967bbf-65b9-49e9-b7a4-7793b1f8a860/ file: na-prot_798.pdb find `pwd` -iname na-prot_798.pdb copy /home/rpdock/web/media/jobs/12967bbf-65b9-49e9-b7a4-7793b1f8a860/prot-na_10/na-prot_798.pdb to /home/rpdock/web/media/jobs/12967bbf-65b9-49e9-b7a4-7793b1f8a860//ref_struc/na-prot_798/na-prot_798.pdb cmd: python /home/rpdock/mc/MC.py -s 1000 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/12967bbf-65b9-49e9-b7a4-7793b1f8a860//ref_struc/na-prot_798/na-prot_798.pdb msg python /home/rpdock/mc/MC.py -s 1000 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/12967bbf-65b9-49e9-b7a4-7793b1f8a860//ref_struc/na-prot_798/na-prot_798.pdb msg run_mc::stderr:/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CA defined twice in residue at line 1776. 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 1780. 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 1782. 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 1784. 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 1786. 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 1788. 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 NH1 defined twice in residue at line 1790. 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 1792. 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 1885. 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 1889. 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 1891. 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 1893. 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 OE1 defined twice in residue at line 1895. 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 OE2 defined twice in residue at line 1897. 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 2285. 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 2289. 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 2291. 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 SD defined twice in residue at line 2293. 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 CE defined twice in residue at line 2295. 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 2406. 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 2410. 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 2412. 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 2414. 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 CE defined twice in residue at line 2416. 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 NZ defined twice in residue at line 2418. 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 2505. 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 2509. 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 2511. 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 OD1 defined twice in residue at line 2513. 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 OD2 defined twice in residue at line 1776. 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 1780. 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 1782. 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 1784. 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 1786. 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 1788. 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 NH1 defined twice in residue at line 1790. 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 1792. 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 1885. 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 1889. 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 1891. 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 1893. 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 OE1 defined twice in residue at line 1895. 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 OE2 defined twice in residue at line 1897. 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 2285. 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 2289. 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 2291. 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 SD defined twice in residue at line 2293. 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 CE defined twice in residue at line 2295. 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 2406. 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 2410. 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 2412. 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 2414. 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 CE defined twice in residue at line 2416. 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 NZ defined twice in residue at line 2418. 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 2505. 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 2509. 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 2511. 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 OD1 defined twice in residue at line 2513. 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 OD2 defined twice in residue at line 2515. 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 2536. 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 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 OG defined twice in residue at line 2542. Exception ignored. Some atoms or residues may be missing in the data structure. % message, PDBConstructionWarning) = > at line 2515. 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 2536. 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 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 OG defined twice in residue at line 2542. Exception ignored. Some atoms or residues may be missing in the data structure. % message, PDBConstructionWarning) 2026-04-28 18:11:41 npdock::MC (refinement) end 2026-04-28 18:11:41 npdock::OK 2026-04-28 18:11:41 Set finished status of 12967bbf-65b9-49e9-b7a4-7793b1f8a860