2026-09-28 09:38:01 NPdock start 2026-09-28 09:38:01 ver: server 2026-09-28 09:38:01 mode: 11111 2026-09-28 09:38:01 is RNA? 1 2026-09-28 09:38:01 Interface: prot: '' na: '' 2026-09-28 09:38:01 Curr dir:/home/rpdock/web/media/jobs/f7013d68-6b34-49b0-8df9-a432b0fb0c11/ 2026-09-28 09:38:01 GRAMM in progress... 2026-09-28 09:38:01 python /home/rpdock/run_gramm//run_gramm1.py -d 20000 -p prot.pdb -r na.pdb -pi '' -ri '' -n 1 -pf '*' -rf '*' 2026-09-28 10:17:31 GRAMM done 2026-09-28 10:17:31 DARS scoring in progress... 2026-09-28 10:17:31 time python /home/rpdock/run_gramm//DARS-RNP_v3//DARS_potential_v3_scoring.py -m 100 -f list.txt -o dars_out.txt 2026-09-28 10:17:32 DARS start [DARS_potential_v3_scoring.py] 2026-09-28 10:17:32 Show log every 100 structures [DARS_potential_v3_scoring.py] 2026-09-28 10:17:33 1/20000 prot-na_1000.pdb -2109475.82 2026-09-28 10:18:12 100/20000 prot-na_94.pdb -2158163.27 2026-09-28 10:18:52 200/20000 prot-na_194.pdb -1745667.34 2026-09-28 10:19:34 300/20000 prot-na_294.pdb -2212184.51 2026-09-28 10:20:17 400/20000 prot-na_394.pdb -2318551.35 2026-09-28 10:21:01 500/20000 prot-na_494.pdb -1683904.36 2026-09-28 10:21:45 600/20000 prot-na_594.pdb -2782338.84 2026-09-28 10:22:29 700/20000 prot-na_694.pdb -1524112.11 2026-09-28 10:23:14 800/20000 prot-na_794.pdb -2077334.50 2026-09-28 10:23:57 900/20000 prot-na_894.pdb -1642561.63 2026-09-28 10:24:41 1000/20000 prot-na_994.pdb -2371307.17 2026-09-28 10:25:26 1100/20000 prot-na_1100.pdb -2502133.16 2026-09-28 10:26:10 1200/20000 prot-na_1200.pdb -1545678.63 2026-09-28 10:26:55 1300/20000 prot-na_1300.pdb -2176494.30 2026-09-28 10:27:40 1400/20000 prot-na_1400.pdb -1267970.53 2026-09-28 10:28:24 1500/20000 prot-na_1500.pdb -1503040.62 2026-09-28 10:29:09 1600/20000 prot-na_1600.pdb -1878478.49 2026-09-28 10:29:54 1700/20000 prot-na_1700.pdb -1575814.98 2026-09-28 10:30:38 1800/20000 prot-na_1800.pdb -1205428.44 2026-09-28 10:31:23 1900/20000 prot-na_1900.pdb -2026351.36 2026-09-28 10:32:08 2000/20000 prot-na_2000.pdb -1555751.44 2026-09-28 10:32:52 2100/20000 prot-na_2100.pdb -2292211.21 2026-09-28 10:33:40 2200/20000 prot-na_2200.pdb -1806124.39 2026-09-28 10:34:25 2300/20000 prot-na_2300.pdb -650477.44 2026-09-28 10:35:10 2400/20000 prot-na_2400.pdb -1629956.35 2026-09-28 10:35:55 2500/20000 prot-na_2500.pdb -2846573.54 2026-09-28 10:36:40 2600/20000 prot-na_2600.pdb -729376.55 2026-09-28 10:37:25 2700/20000 prot-na_2700.pdb -1095639.77 2026-09-28 10:38:09 2800/20000 prot-na_2800.pdb -1337377.09 2026-09-28 10:38:53 2900/20000 prot-na_2900.pdb -2307564.99 2026-09-28 10:39:38 3000/20000 prot-na_3000.pdb -2013229.26 2026-09-28 10:40:23 3100/20000 prot-na_3100.pdb -2584564.34 2026-09-28 10:41:07 3200/20000 prot-na_3200.pdb -1466429.10 2026-09-28 10:41:52 3300/20000 prot-na_3300.pdb -1364245.49 2026-09-28 10:42:36 3400/20000 prot-na_3400.pdb -904979.83 2026-09-28 10:43:20 3500/20000 prot-na_3500.pdb -1488340.33 2026-09-28 10:44:05 3600/20000 prot-na_3600.pdb -1793680.68 2026-09-28 10:44:50 3700/20000 prot-na_3700.pdb -1534478.65 2026-09-28 10:45:34 3800/20000 prot-na_3800.pdb -1604685.88 2026-09-28 10:46:19 3900/20000 prot-na_3900.pdb -2782428.77 2026-09-28 10:47:03 4000/20000 prot-na_4000.pdb -1834556.27 2026-09-28 10:47:47 4100/20000 prot-na_4100.pdb -1923517.92 2026-09-28 10:48:32 4200/20000 prot-na_4200.pdb -1444804.82 2026-09-28 10:49:15 4300/20000 prot-na_4300.pdb -1985379.09 2026-09-28 10:49:59 4400/20000 prot-na_4400.pdb -1635008.47 2026-09-28 10:50:43 4500/20000 prot-na_4500.pdb -1569292.01 2026-09-28 10:51:27 4600/20000 prot-na_4600.pdb -1902687.11 2026-09-28 10:52:10 4700/20000 prot-na_4700.pdb -1244317.83 2026-09-28 10:52:54 4800/20000 prot-na_4800.pdb -1850677.01 2026-09-28 10:53:38 4900/20000 prot-na_4900.pdb -1720313.49 2026-09-28 10:54:22 5000/20000 prot-na_5000.pdb -2271800.75 2026-09-28 10:55:05 5100/20000 prot-na_5100.pdb -1664542.77 2026-09-28 10:55:49 5200/20000 prot-na_5200.pdb -1566548.97 2026-09-28 10:56:32 5300/20000 prot-na_5300.pdb -1683347.23 2026-09-28 10:57:16 5400/20000 prot-na_5400.pdb -1395810.38 2026-09-28 10:58:00 5500/20000 prot-na_5500.pdb -1937676.87 2026-09-28 10:58:43 5600/20000 prot-na_5600.pdb -1868597.99 2026-09-28 10:59:26 5700/20000 prot-na_5700.pdb -2270493.87 2026-09-28 11:00:09 5800/20000 prot-na_5800.pdb -1944598.68 2026-09-28 11:00:52 5900/20000 prot-na_5900.pdb -1663985.88 2026-09-28 11:01:36 6000/20000 prot-na_6000.pdb -1518933.23 2026-09-28 11:02:19 6100/20000 prot-na_6100.pdb -2458998.53 2026-09-28 11:03:03 6200/20000 prot-na_6200.pdb -1348909.35 2026-09-28 11:03:48 6300/20000 prot-na_6300.pdb -1641977.87 2026-09-28 11:04:37 6400/20000 prot-na_6400.pdb -1853179.03 2026-09-28 11:05:21 6500/20000 prot-na_6500.pdb -2158796.67 2026-09-28 11:06:06 6600/20000 prot-na_6600.pdb -1676144.79 2026-09-28 11:06:50 6700/20000 prot-na_6700.pdb -1308859.70 2026-09-28 11:07:34 6800/20000 prot-na_6800.pdb -1204977.29 2026-09-28 11:08:18 6900/20000 prot-na_6900.pdb -1432103.31 2026-09-28 11:09:02 7000/20000 prot-na_7000.pdb -1321366.71 2026-09-28 11:09:46 7100/20000 prot-na_7100.pdb -2409499.12 2026-09-28 11:10:29 7200/20000 prot-na_7200.pdb -2294891.60 2026-09-28 11:11:13 7300/20000 prot-na_7300.pdb -1523616.33 2026-09-28 11:11:57 7400/20000 prot-na_7400.pdb -3008983.36 2026-09-28 11:12:40 7500/20000 prot-na_7500.pdb -1625564.57 2026-09-28 11:13:24 7600/20000 prot-na_7600.pdb -1542260.26 2026-09-28 11:14:08 7700/20000 prot-na_7700.pdb -1850626.38 2026-09-28 11:14:52 7800/20000 prot-na_7800.pdb -1411619.11 2026-09-28 11:15:36 7900/20000 prot-na_7900.pdb -1569871.97 2026-09-28 11:16:20 8000/20000 prot-na_8000.pdb -670406.45 2026-09-28 11:17:04 8100/20000 prot-na_8100.pdb -1967447.01 2026-09-28 11:17:47 8200/20000 prot-na_8200.pdb -1308519.85 2026-09-28 11:18:31 8300/20000 prot-na_8300.pdb -1274295.41 2026-09-28 11:19:15 8400/20000 prot-na_8400.pdb -1484434.40 2026-09-28 11:19:59 8500/20000 prot-na_8500.pdb -1622375.11 2026-09-28 11:20:42 8600/20000 prot-na_8600.pdb -1163707.62 2026-09-28 11:21:26 8700/20000 prot-na_8700.pdb -1802378.59 2026-09-28 11:22:10 8800/20000 prot-na_8800.pdb -1929613.94 2026-09-28 11:22:54 8900/20000 prot-na_8900.pdb -1898736.11 2026-09-28 11:23:38 9000/20000 prot-na_9000.pdb -1041775.85 2026-09-28 11:24:21 9100/20000 prot-na_9100.pdb -1489716.81 2026-09-28 11:25:05 9200/20000 prot-na_9200.pdb -1835698.46 2026-09-28 11:25:48 9300/20000 prot-na_9300.pdb -1729707.76 2026-09-28 11:26:32 9400/20000 prot-na_9400.pdb -1812385.40 2026-09-28 11:27:16 9500/20000 prot-na_9500.pdb -1533446.02 2026-09-28 11:28:00 9600/20000 prot-na_9600.pdb -1037594.70 2026-09-28 11:28:43 9700/20000 prot-na_9700.pdb -1179375.94 2026-09-28 11:29:27 9800/20000 prot-na_9800.pdb -1379174.59 2026-09-28 11:30:11 9900/20000 prot-na_9900.pdb -1396998.23 2026-09-28 11:30:54 10000/20000 prot-na_10000.pdb -816436.72 2026-09-28 11:31:38 10100/20000 prot-na_10100.pdb -4071039.30 2026-09-28 11:32:22 10200/20000 prot-na_10200.pdb -1820916.13 2026-09-28 11:33:05 10300/20000 prot-na_10300.pdb -525979.93 2026-09-28 11:33:49 10400/20000 prot-na_10400.pdb -2391006.87 2026-09-28 11:34:33 10500/20000 prot-na_10500.pdb -703417.80 2026-09-28 11:35:16 10600/20000 prot-na_10600.pdb -1560692.54 2026-09-28 11:36:00 10700/20000 prot-na_10700.pdb -1657033.43 2026-09-28 11:36:43 10800/20000 prot-na_10800.pdb -1039303.60 2026-09-28 11:37:27 10900/20000 prot-na_10900.pdb -1425011.95 2026-09-28 11:38:11 11000/20000 prot-na_11000.pdb -1201018.56 2026-09-28 11:38:54 11100/20000 prot-na_11100.pdb -1986383.60 2026-09-28 11:39:38 11200/20000 prot-na_11200.pdb -1596955.29 2026-09-28 11:40:22 11300/20000 prot-na_11300.pdb -2574492.11 2026-09-28 11:41:06 11400/20000 prot-na_11400.pdb -1419954.44 2026-09-28 11:41:55 11500/20000 prot-na_11500.pdb -1042420.53 2026-09-28 11:42:40 11600/20000 prot-na_11600.pdb -2330586.38 2026-09-28 11:43:23 11700/20000 prot-na_11700.pdb -2242312.07 2026-09-28 11:44:07 11800/20000 prot-na_11800.pdb -949123.94 2026-09-28 11:44:50 11900/20000 prot-na_11900.pdb -2327229.83 2026-09-28 11:45:34 12000/20000 prot-na_12000.pdb -1337372.64 2026-09-28 11:46:18 12100/20000 prot-na_12100.pdb -1790727.60 2026-09-28 11:47:01 12200/20000 prot-na_12200.pdb -2920130.49 2026-09-28 11:47:45 12300/20000 prot-na_12300.pdb -2224495.58 2026-09-28 11:48:32 12400/20000 prot-na_12400.pdb -1293430.98 2026-09-28 11:49:16 12500/20000 prot-na_12500.pdb -1073975.60 2026-09-28 11:50:01 12600/20000 prot-na_12600.pdb -1906626.67 2026-09-28 11:50:45 12700/20000 prot-na_12700.pdb -2311654.52 2026-09-28 11:51:29 12800/20000 prot-na_12800.pdb -2025408.90 2026-09-28 11:52:12 12900/20000 prot-na_12900.pdb -2101276.54 2026-09-28 11:52:56 13000/20000 prot-na_13000.pdb -1163680.49 2026-09-28 11:53:40 13100/20000 prot-na_13100.pdb -2390267.36 2026-09-28 11:54:23 13200/20000 prot-na_13200.pdb -1859187.28 2026-09-28 11:55:07 13300/20000 prot-na_13300.pdb -2080069.28 2026-09-28 11:55:51 13400/20000 prot-na_13400.pdb -1259678.01 2026-09-28 11:56:34 13500/20000 prot-na_13500.pdb -1818600.08 2026-09-28 11:57:18 13600/20000 prot-na_13600.pdb -1559404.81 2026-09-28 11:58:02 13700/20000 prot-na_13700.pdb -1110153.07 2026-09-28 11:58:45 13800/20000 prot-na_13800.pdb -2144094.53 2026-09-28 11:59:29 13900/20000 prot-na_13900.pdb -1608252.16 2026-09-28 12:00:12 14000/20000 prot-na_14000.pdb -953773.45 2026-09-28 12:00:55 14100/20000 prot-na_14100.pdb -1509132.58 2026-09-28 12:01:38 14200/20000 prot-na_14200.pdb -2039934.20 2026-09-28 12:02:21 14300/20000 prot-na_14300.pdb -2317417.32 2026-09-28 12:03:04 14400/20000 prot-na_14400.pdb -1722479.34 2026-09-28 12:03:47 14500/20000 prot-na_14500.pdb -775658.72 2026-09-28 12:04:30 14600/20000 prot-na_14600.pdb -1095361.20 2026-09-28 12:05:13 14700/20000 prot-na_14700.pdb -1716539.96 2026-09-28 12:05:56 14800/20000 prot-na_14800.pdb -1197000.40 2026-09-28 12:06:39 14900/20000 prot-na_14900.pdb -1653727.16 2026-09-28 12:07:23 15000/20000 prot-na_15000.pdb -865426.85 2026-09-28 12:08:06 15100/20000 prot-na_15100.pdb -2607108.09 2026-09-28 12:08:49 15200/20000 prot-na_15200.pdb -1222182.63 2026-09-28 12:09:32 15300/20000 prot-na_15300.pdb -1406635.31 2026-09-28 12:10:16 15400/20000 prot-na_15400.pdb -1649056.16 2026-09-28 12:10:59 15500/20000 prot-na_15500.pdb -1486996.40 2026-09-28 12:11:41 15600/20000 prot-na_15600.pdb -1468024.08 2026-09-28 12:12:24 15700/20000 prot-na_15700.pdb -2109912.91 2026-09-28 12:13:07 15800/20000 prot-na_15800.pdb -2501282.04 2026-09-28 12:13:49 15900/20000 prot-na_15900.pdb -2484401.62 2026-09-28 12:14:32 16000/20000 prot-na_16000.pdb -1890629.73 2026-09-28 12:15:15 16100/20000 prot-na_16100.pdb -1569819.34 2026-09-28 12:15:57 16200/20000 prot-na_16200.pdb -1235602.53 2026-09-28 12:16:39 16300/20000 prot-na_16300.pdb -1715571.02 2026-09-28 12:17:22 16400/20000 prot-na_16400.pdb -1465903.70 2026-09-28 12:18:05 16500/20000 prot-na_16500.pdb -1422415.34 2026-09-28 12:18:47 16600/20000 prot-na_16600.pdb -2132306.59 2026-09-28 12:19:29 16700/20000 prot-na_16700.pdb -1557147.42 2026-09-28 12:20:12 16800/20000 prot-na_16800.pdb -2095061.00 2026-09-28 12:20:54 16900/20000 prot-na_16900.pdb -1669160.96 2026-09-28 12:21:36 17000/20000 prot-na_17000.pdb -1918555.93 2026-09-28 12:22:19 17100/20000 prot-na_17100.pdb -978443.48 2026-09-28 12:23:01 17200/20000 prot-na_17200.pdb -931678.54 2026-09-28 12:23:43 17300/20000 prot-na_17300.pdb -2270646.81 2026-09-28 12:24:26 17400/20000 prot-na_17400.pdb -2551326.24 2026-09-28 12:25:08 17500/20000 prot-na_17500.pdb -1255444.25 2026-09-28 12:25:50 17600/20000 prot-na_17600.pdb -1919446.02 2026-09-28 12:26:32 17700/20000 prot-na_17700.pdb -1445197.48 2026-09-28 12:27:14 17800/20000 prot-na_17800.pdb -1493593.99 2026-09-28 12:27:57 17900/20000 prot-na_17900.pdb -1779576.04 2026-09-28 12:28:39 18000/20000 prot-na_18000.pdb -1384298.14 2026-09-28 12:29:21 18100/20000 prot-na_18100.pdb -1767787.37 2026-09-28 12:30:04 18200/20000 prot-na_18200.pdb -1623753.39 2026-09-28 12:30:46 18300/20000 prot-na_18300.pdb -1431377.85 2026-09-28 12:31:28 18400/20000 prot-na_18400.pdb -2192433.93 2026-09-28 12:32:10 18500/20000 prot-na_18500.pdb -1387078.48 2026-09-28 12:32:53 18600/20000 prot-na_18600.pdb -1278910.46 2026-09-28 12:33:35 18700/20000 prot-na_18700.pdb -1201424.91 2026-09-28 12:34:18 18800/20000 prot-na_18800.pdb -2503005.98 2026-09-28 12:35:00 18900/20000 prot-na_18900.pdb -802685.02 2026-09-28 12:35:42 19000/20000 prot-na_19000.pdb -1675056.93 2026-09-28 12:36:25 19100/20000 prot-na_19100.pdb -1043664.73 2026-09-28 12:37:07 19200/20000 prot-na_19200.pdb -908357.71 2026-09-28 12:37:50 19300/20000 prot-na_19300.pdb -2000263.32 2026-09-28 12:38:32 19400/20000 prot-na_19400.pdb -1748820.96 2026-09-28 12:39:15 19500/20000 prot-na_19500.pdb -2072786.71 2026-09-28 12:39:58 19600/20000 prot-na_19600.pdb -1496430.11 2026-09-28 12:40:46 19700/20000 prot-na_19700.pdb -850454.27 2026-09-28 12:41:29 19800/20000 prot-na_19800.pdb -1142295.59 2026-09-28 12:42:11 19900/20000 prot-na_19900.pdb -1761196.84 2026-09-28 12:42:54 20000/20000 prot-na_20000.pdb -1558302.11 2026-09-28 12:42:54 DARS scoring end 2026-09-28 12:42:54 Clustering (cuttoff: 5, nr_clust: 100 ) in progress... 2026-09-28 12:42:54 time python /home/rpdock/run_gramm//clustering_v4.py dars_out.txt list.txt 5 100 2026-09-28 12:42:54 100 best scored structures 2026-09-28 12:42:54 1 prot-na_14273.pdb -5261829.95 2026-09-28 12:42:54 2 prot-na_9761.pdb -5047985.99 2026-09-28 12:42:54 3 prot-na_1392.pdb -4642753.76 2026-09-28 12:42:54 4 prot-na_3526.pdb -4612408.21 2026-09-28 12:42:54 5 prot-na_9834.pdb -4510248.08 2026-09-28 12:42:54 6 prot-na_12347.pdb -4365919.24 2026-09-28 12:42:54 7 prot-na_13969.pdb -4324712.47 2026-09-28 12:42:54 8 prot-na_6649.pdb -4254951.95 2026-09-28 12:42:54 9 prot-na_18377.pdb -4252714.55 2026-09-28 12:42:54 10 prot-na_857.pdb -4188374.88 2026-09-28 12:42:54 11 prot-na_575.pdb -4167513.46 2026-09-28 12:42:54 12 prot-na_8413.pdb -4122289.13 2026-09-28 12:42:54 13 prot-na_42.pdb -4090102.5 2026-09-28 12:42:54 14 prot-na_10100.pdb -4071039.3 2026-09-28 12:42:54 15 prot-na_7762.pdb -4057446.18 2026-09-28 12:42:54 16 prot-na_5113.pdb -4056198.77 2026-09-28 12:42:54 17 prot-na_2395.pdb -4048980.9 2026-09-28 12:42:54 18 prot-na_535.pdb -4020616.08 2026-09-28 12:42:54 19 prot-na_1054.pdb -4009761.33 2026-09-28 12:42:54 20 prot-na_7606.pdb -4008550.35 2026-09-28 12:42:54 21 prot-na_2886.pdb -3968249.16 2026-09-28 12:42:54 22 prot-na_709.pdb -3953067.8 2026-09-28 12:42:54 23 prot-na_3422.pdb -3936683.34 2026-09-28 12:42:54 24 prot-na_3908.pdb -3907530.93 2026-09-28 12:42:54 25 prot-na_8272.pdb -3907355.94 2026-09-28 12:42:54 26 prot-na_2332.pdb -3899668.27 2026-09-28 12:42:54 27 prot-na_2447.pdb -3857162.14 2026-09-28 12:42:54 28 prot-na_807.pdb -3826383.63 2026-09-28 12:42:54 29 prot-na_6246.pdb -3795833.96 2026-09-28 12:42:54 30 prot-na_4573.pdb -3786476.67 2026-09-28 12:42:54 31 prot-na_1596.pdb -3782411.34 2026-09-28 12:42:54 32 prot-na_601.pdb -3779136.83 2026-09-28 12:42:54 33 prot-na_9894.pdb -3774943.08 2026-09-28 12:42:54 34 prot-na_1303.pdb -3769051.78 2026-09-28 12:42:54 35 prot-na_19244.pdb -3760646.37 2026-09-28 12:42:54 36 prot-na_810.pdb -3760078.48 2026-09-28 12:42:54 37 prot-na_793.pdb -3754378.1 2026-09-28 12:42:54 38 prot-na_168.pdb -3751100.76 2026-09-28 12:42:54 39 prot-na_43.pdb -3749235.73 2026-09-28 12:42:54 40 prot-na_16006.pdb -3745764.9 2026-09-28 12:42:54 41 prot-na_5065.pdb -3744479.87 2026-09-28 12:42:54 42 prot-na_13565.pdb -3744342.94 2026-09-28 12:42:54 43 prot-na_16442.pdb -3740396.44 2026-09-28 12:42:54 44 prot-na_3676.pdb -3733166.35 2026-09-28 12:42:54 45 prot-na_7868.pdb -3732885.49 2026-09-28 12:42:54 46 prot-na_16050.pdb -3732749.97 2026-09-28 12:42:54 47 prot-na_4427.pdb -3707465.96 2026-09-28 12:42:54 48 prot-na_57.pdb -3687851.89 2026-09-28 12:42:54 49 prot-na_14256.pdb -3683099.47 2026-09-28 12:42:54 50 prot-na_9896.pdb -3678569.14 2026-09-28 12:42:54 51 prot-na_12148.pdb -3677114.26 2026-09-28 12:42:54 52 prot-na_6890.pdb -3671643.16 2026-09-28 12:42:54 53 prot-na_14679.pdb -3662977.0 2026-09-28 12:42:54 54 prot-na_4560.pdb -3655334.09 2026-09-28 12:42:54 55 prot-na_1489.pdb -3647949.72 2026-09-28 12:42:54 56 prot-na_250.pdb -3643035.21 2026-09-28 12:42:54 57 prot-na_9645.pdb -3631874.34 2026-09-28 12:42:54 58 prot-na_10142.pdb -3620515.92 2026-09-28 12:42:54 59 prot-na_2140.pdb -3617050.67 2026-09-28 12:42:54 60 prot-na_2566.pdb -3610505.26 2026-09-28 12:42:54 61 prot-na_3876.pdb -3601453.99 2026-09-28 12:42:54 62 prot-na_4824.pdb -3599199.37 2026-09-28 12:42:54 63 prot-na_137.pdb -3586970.88 2026-09-28 12:42:54 64 prot-na_5989.pdb -3582224.79 2026-09-28 12:42:54 65 prot-na_1507.pdb -3581111.31 2026-09-28 12:42:54 66 prot-na_12920.pdb -3575975.22 2026-09-28 12:42:54 67 prot-na_4272.pdb -3572501.37 2026-09-28 12:42:54 68 prot-na_4271.pdb -3572074.14 2026-09-28 12:42:54 69 prot-na_8089.pdb -3563389.69 2026-09-28 12:42:54 70 prot-na_15525.pdb -3558510.54 2026-09-28 12:42:54 71 prot-na_5147.pdb -3556662.76 2026-09-28 12:42:54 72 prot-na_17318.pdb -3521607.94 2026-09-28 12:42:54 73 prot-na_543.pdb -3518856.17 2026-09-28 12:42:54 74 prot-na_2565.pdb -3517856.84 2026-09-28 12:42:54 75 prot-na_4388.pdb -3515713.58 2026-09-28 12:42:54 76 prot-na_13968.pdb -3510339.64 2026-09-28 12:42:54 77 prot-na_12941.pdb -3506564.81 2026-09-28 12:42:54 78 prot-na_959.pdb -3489449.35 2026-09-28 12:42:54 79 prot-na_605.pdb -3478113.28 2026-09-28 12:42:54 80 prot-na_532.pdb -3472298.75 2026-09-28 12:42:54 81 prot-na_3951.pdb -3472060.36 2026-09-28 12:42:54 82 prot-na_6592.pdb -3471815.96 2026-09-28 12:42:54 83 prot-na_503.pdb -3463109.32 2026-09-28 12:42:54 84 prot-na_1678.pdb -3461178.23 2026-09-28 12:42:54 85 prot-na_8060.pdb -3459927.09 2026-09-28 12:42:54 86 prot-na_2984.pdb -3456752.57 2026-09-28 12:42:54 87 prot-na_479.pdb -3454419.09 2026-09-28 12:42:54 88 prot-na_90.pdb -3449398.52 2026-09-28 12:42:54 89 prot-na_16730.pdb -3448807.41 2026-09-28 12:42:54 90 prot-na_4852.pdb -3448167.29 2026-09-28 12:42:54 91 prot-na_3830.pdb -3444625.51 2026-09-28 12:42:54 92 prot-na_1536.pdb -3443205.15 2026-09-28 12:42:54 93 prot-na_1952.pdb -3441974.26 2026-09-28 12:42:54 94 prot-na_8802.pdb -3437270.15 2026-09-28 12:42:54 95 prot-na_2859.pdb -3436088.22 2026-09-28 12:42:54 96 prot-na_1644.pdb -3435561.99 2026-09-28 12:42:54 97 prot-na_20.pdb -3432372.76 2026-09-28 12:42:54 98 prot-na_5667.pdb -3430129.59 2026-09-28 12:42:54 99 prot-na_2510.pdb -3429338.8 2026-09-28 12:42:54 100 prot-na_617.pdb -3428955.36 2026-09-28 12:42:54 Chains: B 2026-09-28 12:43:12 100 best scored structures 2026-09-28 12:43:12 GRAMM analysis selected for further analysis: prot-na_25 2026-09-28 12:43:12 Cluster #1 with 8 structures 2026-09-28 12:43:12 1 prot-na_575.pdb -4167513.46 2026-09-28 12:43:12 2 prot-na_535.pdb -4020616.08 2026-09-28 12:43:12 3 prot-na_3422.pdb -3936683.34 2026-09-28 12:43:12 4 prot-na_4824.pdb -3599199.37 2026-09-28 12:43:12 5 prot-na_479.pdb -3454419.09 2026-09-28 12:43:12 6 prot-na_90.pdb -3449398.52 2026-09-28 12:43:12 7 prot-na_1644.pdb -3435561.99 2026-09-28 12:43:12 8 prot-na_20.pdb -3432372.76 2026-09-28 12:43:12 Cluster #2 with 5 structures 2026-09-28 12:43:12 1 prot-na_2447.pdb -3857162.14 2026-09-28 12:43:12 2 prot-na_16006.pdb -3745764.9 2026-09-28 12:43:12 3 prot-na_13565.pdb -3744342.94 2026-09-28 12:43:12 4 prot-na_250.pdb -3643035.21 2026-09-28 12:43:12 5 prot-na_2510.pdb -3429338.8 2026-09-28 12:43:12 Sent to refinement: clusters_found|prot-na_575.pdb|prot-na_2447.pdb 2026-09-28 12:43:12 Sent to refinement: clusters_found|prot-na_575.pdb|prot-na_2447.pdb 2026-09-28 12:43:12 DARS clustering end 2026-09-28 12:43:12 MC (refinement) init 2026-09-28 12:43:12 python /home/rpdock/run_gramm//run_mc.py -f dars_to_mc.txt -d /home/rpdock/web/media/jobs/f7013d68-6b34-49b0-8df9-a432b0fb0c11/ 2026-09-28 12:43:12 Refinement of #1 /home/rpdock/web/media/jobs/f7013d68-6b34-49b0-8df9-a432b0fb0c11/prot-na_575.pdb 2026-09-28 12:43:12 python /home/rpdock/mc/MC.py -s 295 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/f7013d68-6b34-49b0-8df9-a432b0fb0c11//ref_struc/prot-na_575/prot-na_575.pdb 2026-09-28 12:45:36 Refinement of #2 /home/rpdock/web/media/jobs/f7013d68-6b34-49b0-8df9-a432b0fb0c11/prot-na_2447.pdb 2026-09-28 12:45:36 python /home/rpdock/mc/MC.py -s 295 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/f7013d68-6b34-49b0-8df9-a432b0fb0c11//ref_struc/prot-na_2447/prot-na_2447.pdb 2026-09-28 12:47:59 start - parameters: File name /home/rpdock/web/media/jobs/f7013d68-6b34-49b0-8df9-a432b0fb0c11//ref_struc/prot-na_575/prot-na_575.pdb Steps 295 Temp. start 15000.0 Temp. end 295.0 False msg start - parameters: File name /home/rpdock/web/media/jobs/f7013d68-6b34-49b0-8df9-a432b0fb0c11//ref_struc/prot-na_575/prot-na_575.pdb Steps 295 Temp. start 15000.0 Temp. end 295.0 False Step E Edist Eang Epen Warning, residue A1 in the chain B has not P atom 0 - -1063012.69 -1938019.97 -1724992.71 2600000.00 1 T -963957.21 -1986667.11 -1777290.10 2800000.00 T= 15000.0 K progress 0.338983050847 2 T -1599868.42 -1960444.50 -1739423.91 2100000.00 T= 14950.1525424 K progress 0.677966101695 3 T -1843833.05 -2018078.01 -1825755.03 2000000.00 T= 14900.3050847 K progress 1.01694915254 4 T -2067566.28 -2082538.99 -1885027.29 1900000.00 T= 14850.4576271 K progress 1.35593220339 5 R -2038220.38 -2070776.85 -1867443.53 1900000.00 T= 14750.7627119 K progress 1.69491525424 6 R -2021794.80 -2059946.25 -1861848.55 1900000.00 T= 14003.0508475 K progress 2.03389830508 7 R -1998520.30 -2058523.30 -1839997.00 1900000.00 T= 13903.3559322 K progress 2.37288135593 8 R -2044244.51 -2073949.02 -1870295.49 1900000.00 T= 13703.9661017 K progress 2.71186440678 9 R -2032155.93 -2073853.59 -1858302.34 1900000.00 T= 12707.0169492 K progress 3.05084745763 10 R -2042871.54 -2078416.18 -1864455.36 1900000.00 T= 12607.3220339 K progress 3.38983050847 11 R -2046215.41 -2076861.83 -1869353.58 1900000.00 T= 11809.7627119 K progress 3.72881355932 12 R -2007209.33 -2059286.41 -1847922.92 1900000.00 T= 11560.5254237 K progress 4.06779661017 13 R -1965061.72 -2040081.94 -1824979.79 1900000.00 T= 11510.6779661 K progress 4.40677966102 14 T -1922350.57 -2073346.29 -1849004.28 2000000.00 T= 11410.9830508 K progress 4.74576271186 15 R -2006428.86 -2113504.12 -1892924.74 2000000.00 T= 11361.1355932 K progress 5.08474576271 16 R -1942913.29 -2092150.59 -1850762.70 2000000.00 T= 11311.2881356 K progress 5.42372881356 17 R -2327325.29 -2072368.64 -1854956.65 1600000.00 T= 11062.0508475 K progress 5.76271186441 18 R -2319267.69 -2068601.46 -1850666.23 1600000.00 T= 9217.69491525 K progress 6.10169491525 19 R -2304220.81 -2053728.91 -1850491.90 1600000.00 T= 8968.45762712 K progress 6.4406779661 20 R -2307106.39 -2059990.03 -1847116.36 1600000.00 T= 8469.98305085 K progress 6.77966101695 21 R -2307106.39 -2059990.03 -1847116.36 1600000.00 T= 8270.59322034 K progress 7.1186440678 22 R -2317949.83 -2067046.13 -1850903.71 1600000.00 T= 7522.88135593 K progress 7.45762711864 23 R -2302263.97 -2064524.47 -1837739.50 1600000.00 T= 6775.16949153 K progress 7.79661016949 24 R -2309556.87 -2060926.45 -1848630.42 1600000.00 T= 6575.77966102 K progress 8.13559322034 25 R -2317647.67 -2066928.05 -1850719.62 1600000.00 T= 5229.89830508 K progress 8.47457627119 26 R -2322204.99 -2075213.32 -1846991.66 1600000.00 T= 3136.30508475 K progress 8.81355932203 27 R -2303036.36 -2064057.61 -1838978.75 1600000.00 T= 2787.37288136 K progress 9.15254237288 28 R -2317501.96 -2066790.70 -1850711.27 1600000.00 T= 2438.44067797 K progress 9.49152542373 29 R -2317647.67 -2066928.05 -1850719.62 1600000.00 T= 344.847457627 K progress 9.83050847458 Save no big msg save short traj msg save best.pdb msg save plot e_step.png start - parameters: File name /home/rpdock/web/media/jobs/f7013d68-6b34-49b0-8df9-a432b0fb0c11//ref_struc/prot-na_2447/prot-na_2447.pdb Steps 295 Temp. start 15000.0 Temp. end 295.0 False msg start - parameters: File name /home/rpdock/web/media/jobs/f7013d68-6b34-49b0-8df9-a432b0fb0c11//ref_struc/prot-na_2447/prot-na_2447.pdb Steps 295 Temp. start 15000.0 Temp. end 295.0 False Step E Edist Eang Epen Warning, residue A1 in the chain B has not P atom 0 - -1587809.47 -1791511.98 -1796297.49 2000000.00 1 R -1583497.83 -1789511.11 -1793986.72 2000000.00 T= 14750.7627119 K progress 0.338983050847 2 R -1582189.60 -1789511.11 -1792678.49 2000000.00 T= 14651.0677966 K progress 0.677966101695 3 R -1221898.21 -1809436.48 -1812461.73 2400000.00 T= 14351.9830508 K progress 1.01694915254 4 T -1649746.86 -1897431.61 -1852315.25 2100000.00 T= 14102.7457627 K progress 1.35593220339 5 R -1701131.39 -1924130.47 -1877000.92 2100000.00 T= 13953.2033898 K progress 1.69491525424 6 R -1690093.75 -1807248.78 -1782844.96 1900000.00 T= 13903.3559322 K progress 2.03389830508 7 R -1347664.86 -1843086.35 -1804578.50 2300000.00 T= 13803.6610169 K progress 2.37288135593 8 T -1470674.66 -1823764.55 -1746910.11 2100000.00 T= 13753.8135593 K progress 2.71186440678 9 R -1743609.15 -2019125.55 -1924483.60 2200000.00 T= 13654.1186441 K progress 3.05084745763 10 R -1743610.20 -2019126.60 -1924483.60 2200000.00 T= 13155.6440678 K progress 3.38983050847 11 R -1754878.72 -2024925.55 -1929953.17 2200000.00 T= 12906.4067797 K progress 3.72881355932 12 T -1771974.05 -1931775.98 -1840198.06 2000000.00 T= 12507.6271186 K progress 4.06779661017 13 T -1523694.09 -1990467.96 -1933226.12 2400000.00 T= 12308.2372881 K progress 4.40677966102 14 R -1535573.32 -1995523.78 -1940049.54 2400000.00 T= 11959.3050847 K progress 4.74576271186 15 T -1485728.75 -1843176.05 -1742552.71 2100000.00 T= 11361.1355932 K progress 5.08474576271 16 T -1846873.64 -1868219.35 -1778654.29 1800000.00 T= 11311.2881356 K progress 5.42372881356 17 T -1777264.12 -1839194.22 -1738069.90 1800000.00 T= 11012.2033898 K progress 5.76271186441 18 R -1777223.03 -1840606.36 -1736616.67 1800000.00 T= 10962.3559322 K progress 6.10169491525 19 T -1789129.87 -1878052.83 -1811077.04 1900000.00 T= 10364.1864407 K progress 6.4406779661 20 T -1762232.33 -1813214.40 -1749017.94 1800000.00 T= 10264.4915254 K progress 6.77966101695 21 T -1799363.58 -1738194.79 -1661168.80 1600000.00 T= 10015.2542373 K progress 7.1186440678 22 R -1795268.97 -1737580.60 -1657688.37 1600000.00 T= 9666.3220339 K progress 7.45762711864 23 R -1917829.63 -1749429.40 -1668400.23 1500000.00 T= 9367.23728814 K progress 7.79661016949 24 T -2077013.29 -1864379.86 -1812633.43 1600000.00 T= 9267.54237288 K progress 8.13559322034 25 T -2205684.27 -1792879.12 -1712805.14 1300000.00 T= 8170.89830508 K progress 8.47457627119 26 R -2220322.22 -1797612.55 -1722709.67 1300000.00 T= 7223.79661017 K progress 8.81355932203 27 R -2233795.60 -1793988.66 -1739806.94 1300000.00 T= 6974.55932203 K progress 9.15254237288 28 R -2225347.92 -1788373.48 -1736974.44 1300000.00 T= 6426.23728814 K progress 9.49152542373 29 R -2197989.74 -1789797.55 -1708192.19 1300000.00 T= 5528.98305085 K progress 9.83050847458 30 R -2216705.47 -1800175.99 -1716529.48 1300000.00 T= 5429.28813559 K progress 10.1694915254 31 R -2207224.78 -1797146.50 -1710078.29 1300000.00 T= 4980.66101695 K progress 10.5084745763 32 R -2224150.66 -1801893.73 -1722256.93 1300000.00 T= 4033.55932203 K progress 10.8474576271 33 R -2203817.51 -1798629.64 -1705187.87 1300000.00 T= 3933.86440678 K progress 11.186440678 34 R -2215840.88 -1802926.12 -1712914.75 1300000.00 T= 3634.77966102 K progress 11.5254237288 35 R -2209132.29 -1800046.18 -1709086.11 1300000.00 T= 2538.13559322 K progress 11.8644067797 36 T -2626358.31 -1747160.07 -1679198.25 800000.00 T= 2039.66101695 K progress 12.2033898305 37 R -2626812.11 -1751846.06 -1674966.06 800000.00 T= 1840.27118644 K progress 12.5423728814 38 R -2613593.80 -1745292.29 -1668301.51 800000.00 T= 1092.55932203 K progress 12.8813559322 Save no big msg save short traj msg save best.pdb msg save plot e_step.png Mon Sep 28 12:43:12 2026 ['prot-na_575.pdb', 'prot-na_2447.pdb'] msg Refinement of #1 /home/rpdock/web/media/jobs/f7013d68-6b34-49b0-8df9-a432b0fb0c11/prot-na_575.pdb dir: /home/rpdock/web/media/jobs/f7013d68-6b34-49b0-8df9-a432b0fb0c11/ file: prot-na_575.pdb find `pwd` -iname prot-na_575.pdb copy /home/rpdock/web/media/jobs/f7013d68-6b34-49b0-8df9-a432b0fb0c11/prot-na_25/prot-na_575.pdb to /home/rpdock/web/media/jobs/f7013d68-6b34-49b0-8df9-a432b0fb0c11//ref_struc/prot-na_575/prot-na_575.pdb cmd: python /home/rpdock/mc/MC.py -s 295 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/f7013d68-6b34-49b0-8df9-a432b0fb0c11//ref_struc/prot-na_575/prot-na_575.pdb msg python /home/rpdock/mc/MC.py -s 295 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/f7013d68-6b34-49b0-8df9-a432b0fb0c11//ref_struc/prot-na_575/prot-na_575.pdb run_mc::OK! = stderr empty msg Refinement of #2 /home/rpdock/web/media/jobs/f7013d68-6b34-49b0-8df9-a432b0fb0c11/prot-na_2447.pdb dir: /home/rpdock/web/media/jobs/f7013d68-6b34-49b0-8df9-a432b0fb0c11/ file: prot-na_2447.pdb find `pwd` -iname prot-na_2447.pdb copy /home/rpdock/web/media/jobs/f7013d68-6b34-49b0-8df9-a432b0fb0c11/prot-na_25/prot-na_2447.pdb to /home/rpdock/web/media/jobs/f7013d68-6b34-49b0-8df9-a432b0fb0c11//ref_struc/prot-na_2447/prot-na_2447.pdb cmd: python /home/rpdock/mc/MC.py -s 295 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/f7013d68-6b34-49b0-8df9-a432b0fb0c11//ref_struc/prot-na_2447/prot-na_2447.pdb msg python /home/rpdock/mc/MC.py -s 295 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/f7013d68-6b34-49b0-8df9-a432b0fb0c11//ref_struc/prot-na_2447/prot-na_2447.pdb run_mc::OK! = stderr empty 2026-09-28 12:47:59 npdock::MC (refinement) end 2026-09-28 12:47:59 npdock::OK 2026-09-28 12:47:59 Set finished status of f7013d68-6b34-49b0-8df9-a432b0fb0c11