2026-09-28 12:48:02 NPdock start 2026-09-28 12:48:02 ver: server 2026-09-28 12:48:02 mode: 11111 2026-09-28 12:48:02 is RNA? 1 2026-09-28 12:48:02 Interface: prot: '' na: '' 2026-09-28 12:48:02 Curr dir:/home/rpdock/web/media/jobs/9af8942e-5c0d-4581-a9a4-b854422d5dfe/ 2026-09-28 12:48:02 GRAMM in progress... 2026-09-28 12:48:02 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 13:27:28 GRAMM done 2026-09-28 13:27:28 DARS scoring in progress... 2026-09-28 13:27:28 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 13:27:29 DARS start [DARS_potential_v3_scoring.py] 2026-09-28 13:27:29 Show log every 100 structures [DARS_potential_v3_scoring.py] 2026-09-28 13:27:29 1/20000 prot-na_1000.pdb -2274049.09 2026-09-28 13:28:08 100/20000 prot-na_94.pdb -2663779.03 2026-09-28 13:28:49 200/20000 prot-na_194.pdb -1750548.15 2026-09-28 13:29:31 300/20000 prot-na_294.pdb -2119260.10 2026-09-28 13:30:14 400/20000 prot-na_394.pdb -1926858.26 2026-09-28 13:30:57 500/20000 prot-na_494.pdb -2024328.13 2026-09-28 13:31:41 600/20000 prot-na_594.pdb -2535872.13 2026-09-28 13:32:25 700/20000 prot-na_694.pdb -2488399.40 2026-09-28 13:33:09 800/20000 prot-na_794.pdb -2221478.34 2026-09-28 13:33:53 900/20000 prot-na_894.pdb -1462096.11 2026-09-28 13:34:37 1000/20000 prot-na_994.pdb -1122838.30 2026-09-28 13:35:20 1100/20000 prot-na_1100.pdb -1587285.43 2026-09-28 13:36:04 1200/20000 prot-na_1200.pdb -1244225.43 2026-09-28 13:36:48 1300/20000 prot-na_1300.pdb -1787921.93 2026-09-28 13:37:33 1400/20000 prot-na_1400.pdb -2414652.70 2026-09-28 13:38:17 1500/20000 prot-na_1500.pdb -1597808.61 2026-09-28 13:39:01 1600/20000 prot-na_1600.pdb -1551013.00 2026-09-28 13:39:45 1700/20000 prot-na_1700.pdb -1451540.43 2026-09-28 13:40:29 1800/20000 prot-na_1800.pdb -2193087.45 2026-09-28 13:41:13 1900/20000 prot-na_1900.pdb -1681790.81 2026-09-28 13:41:56 2000/20000 prot-na_2000.pdb -2333770.57 2026-09-28 13:42:40 2100/20000 prot-na_2100.pdb -2354264.95 2026-09-28 13:43:24 2200/20000 prot-na_2200.pdb -1985934.62 2026-09-28 13:44:07 2300/20000 prot-na_2300.pdb -1706223.86 2026-09-28 13:44:51 2400/20000 prot-na_2400.pdb -1497054.30 2026-09-28 13:45:35 2500/20000 prot-na_2500.pdb -1249593.30 2026-09-28 13:46:19 2600/20000 prot-na_2600.pdb -1644393.73 2026-09-28 13:47:03 2700/20000 prot-na_2700.pdb -2489520.90 2026-09-28 13:47:47 2800/20000 prot-na_2800.pdb -2171287.95 2026-09-28 13:48:31 2900/20000 prot-na_2900.pdb -2505362.87 2026-09-28 13:49:16 3000/20000 prot-na_3000.pdb -2698071.52 2026-09-28 13:50:00 3100/20000 prot-na_3100.pdb -1623232.44 2026-09-28 13:50:44 3200/20000 prot-na_3200.pdb -1998835.30 2026-09-28 13:51:28 3300/20000 prot-na_3300.pdb -2156473.32 2026-09-28 13:52:13 3400/20000 prot-na_3400.pdb -1743094.20 2026-09-28 13:52:57 3500/20000 prot-na_3500.pdb -1678686.31 2026-09-28 13:53:42 3600/20000 prot-na_3600.pdb -1544882.58 2026-09-28 13:54:27 3700/20000 prot-na_3700.pdb -2056012.09 2026-09-28 13:55:12 3800/20000 prot-na_3800.pdb -1153199.23 2026-09-28 13:55:56 3900/20000 prot-na_3900.pdb -1813248.05 2026-09-28 13:56:40 4000/20000 prot-na_4000.pdb -1888783.28 2026-09-28 13:57:25 4100/20000 prot-na_4100.pdb -2158434.15 2026-09-28 13:58:09 4200/20000 prot-na_4200.pdb -1601335.99 2026-09-28 13:58:53 4300/20000 prot-na_4300.pdb -3623924.06 2026-09-28 13:59:37 4400/20000 prot-na_4400.pdb -3777303.60 2026-09-28 14:00:22 4500/20000 prot-na_4500.pdb -1444574.15 2026-09-28 14:01:06 4600/20000 prot-na_4600.pdb -1566952.17 2026-09-28 14:01:50 4700/20000 prot-na_4700.pdb -1902905.46 2026-09-28 14:02:35 4800/20000 prot-na_4800.pdb -2420638.51 2026-09-28 14:03:18 4900/20000 prot-na_4900.pdb -1794048.20 2026-09-28 14:04:03 5000/20000 prot-na_5000.pdb -2119339.81 2026-09-28 14:04:46 5100/20000 prot-na_5100.pdb -1532213.41 2026-09-28 14:05:31 5200/20000 prot-na_5200.pdb -1915422.20 2026-09-28 14:06:14 5300/20000 prot-na_5300.pdb -766132.57 2026-09-28 14:06:58 5400/20000 prot-na_5400.pdb -1099430.14 2026-09-28 14:07:42 5500/20000 prot-na_5500.pdb -1914276.89 2026-09-28 14:08:25 5600/20000 prot-na_5600.pdb -2174855.14 2026-09-28 14:09:09 5700/20000 prot-na_5700.pdb -1360107.65 2026-09-28 14:09:53 5800/20000 prot-na_5800.pdb -2966467.67 2026-09-28 14:10:37 5900/20000 prot-na_5900.pdb -1085547.45 2026-09-28 14:11:21 6000/20000 prot-na_6000.pdb -2944244.08 2026-09-28 14:12:05 6100/20000 prot-na_6100.pdb -1698596.87 2026-09-28 14:12:48 6200/20000 prot-na_6200.pdb -1827756.50 2026-09-28 14:13:32 6300/20000 prot-na_6300.pdb -2176302.09 2026-09-28 14:14:16 6400/20000 prot-na_6400.pdb -855143.59 2026-09-28 14:14:59 6500/20000 prot-na_6500.pdb -1849126.60 2026-09-28 14:15:43 6600/20000 prot-na_6600.pdb -1568107.45 2026-09-28 14:16:27 6700/20000 prot-na_6700.pdb -1910992.00 2026-09-28 14:17:10 6800/20000 prot-na_6800.pdb -1392448.57 2026-09-28 14:17:53 6900/20000 prot-na_6900.pdb -1706887.29 2026-09-28 14:18:37 7000/20000 prot-na_7000.pdb -1473823.29 2026-09-28 14:19:20 7100/20000 prot-na_7100.pdb -1100053.87 2026-09-28 14:20:03 7200/20000 prot-na_7200.pdb -1891505.87 2026-09-28 14:20:46 7300/20000 prot-na_7300.pdb -2126230.36 2026-09-28 14:21:30 7400/20000 prot-na_7400.pdb -2162944.74 2026-09-28 14:22:14 7500/20000 prot-na_7500.pdb -2149358.04 2026-09-28 14:22:57 7600/20000 prot-na_7600.pdb -2636868.87 2026-09-28 14:23:42 7700/20000 prot-na_7700.pdb -1668035.30 2026-09-28 14:24:27 7800/20000 prot-na_7800.pdb -1975361.98 2026-09-28 14:25:12 7900/20000 prot-na_7900.pdb -608246.57 2026-09-28 14:25:56 8000/20000 prot-na_8000.pdb -1399392.69 2026-09-28 14:26:41 8100/20000 prot-na_8100.pdb -770966.82 2026-09-28 14:27:25 8200/20000 prot-na_8200.pdb -1691963.64 2026-09-28 14:28:10 8300/20000 prot-na_8300.pdb -1827121.93 2026-09-28 14:28:54 8400/20000 prot-na_8400.pdb -1402089.93 2026-09-28 14:29:39 8500/20000 prot-na_8500.pdb -1435744.60 2026-09-28 14:30:23 8600/20000 prot-na_8600.pdb -1432791.14 2026-09-28 14:31:08 8700/20000 prot-na_8700.pdb -1087444.97 2026-09-28 14:31:52 8800/20000 prot-na_8800.pdb -2021523.48 2026-09-28 14:32:36 8900/20000 prot-na_8900.pdb -1539113.13 2026-09-28 14:33:20 9000/20000 prot-na_9000.pdb -1664167.68 2026-09-28 14:34:05 9100/20000 prot-na_9100.pdb -1807593.94 2026-09-28 14:34:49 9200/20000 prot-na_9200.pdb -2288891.87 2026-09-28 14:35:33 9300/20000 prot-na_9300.pdb -958983.90 2026-09-28 14:36:17 9400/20000 prot-na_9400.pdb -1624166.10 2026-09-28 14:37:01 9500/20000 prot-na_9500.pdb -2672791.21 2026-09-28 14:37:45 9600/20000 prot-na_9600.pdb -1421469.97 2026-09-28 14:38:29 9700/20000 prot-na_9700.pdb -682163.99 2026-09-28 14:39:13 9800/20000 prot-na_9800.pdb -2708245.73 2026-09-28 14:39:58 9900/20000 prot-na_9900.pdb -1710933.86 2026-09-28 14:40:43 10000/20000 prot-na_10000.pdb -1061596.69 2026-09-28 14:41:28 10100/20000 prot-na_10100.pdb -818973.45 2026-09-28 14:42:11 10200/20000 prot-na_10200.pdb -1407017.10 2026-09-28 14:42:55 10300/20000 prot-na_10300.pdb -1576387.91 2026-09-28 14:43:39 10400/20000 prot-na_10400.pdb -2935993.27 2026-09-28 14:44:23 10500/20000 prot-na_10500.pdb -1935570.18 2026-09-28 14:45:07 10600/20000 prot-na_10600.pdb -1429095.13 2026-09-28 14:45:51 10700/20000 prot-na_10700.pdb -1284368.37 2026-09-28 14:46:35 10800/20000 prot-na_10800.pdb -1345364.82 2026-09-28 14:47:18 10900/20000 prot-na_10900.pdb -1120392.00 2026-09-28 14:48:02 11000/20000 prot-na_11000.pdb -1333752.73 2026-09-28 14:48:46 11100/20000 prot-na_11100.pdb -1729437.07 2026-09-28 14:49:29 11200/20000 prot-na_11200.pdb -1040765.15 2026-09-28 14:50:13 11300/20000 prot-na_11300.pdb -1934988.58 2026-09-28 14:50:57 11400/20000 prot-na_11400.pdb -1346885.34 2026-09-28 14:51:41 11500/20000 prot-na_11500.pdb -2368706.77 2026-09-28 14:52:24 11600/20000 prot-na_11600.pdb -2233100.54 2026-09-28 14:53:07 11700/20000 prot-na_11700.pdb -2455731.70 2026-09-28 14:53:51 11800/20000 prot-na_11800.pdb -1451612.71 2026-09-28 14:54:35 11900/20000 prot-na_11900.pdb -1750289.60 2026-09-28 14:55:18 12000/20000 prot-na_12000.pdb -2664673.97 2026-09-28 14:56:02 12100/20000 prot-na_12100.pdb -1567673.95 2026-09-28 14:56:46 12200/20000 prot-na_12200.pdb -1269922.45 2026-09-28 14:57:29 12300/20000 prot-na_12300.pdb -1689873.09 2026-09-28 14:58:13 12400/20000 prot-na_12400.pdb -1702744.85 2026-09-28 14:58:57 12500/20000 prot-na_12500.pdb -1405186.60 2026-09-28 14:59:40 12600/20000 prot-na_12600.pdb -1901799.79 2026-09-28 15:00:25 12700/20000 prot-na_12700.pdb -1452879.18 2026-09-28 15:01:08 12800/20000 prot-na_12800.pdb -1317863.48 2026-09-28 15:01:52 12900/20000 prot-na_12900.pdb -1504383.43 2026-09-28 15:02:36 13000/20000 prot-na_13000.pdb -1758406.04 2026-09-28 15:03:20 13100/20000 prot-na_13100.pdb -1288646.87 2026-09-28 15:04:04 13200/20000 prot-na_13200.pdb -1744877.03 2026-09-28 15:04:49 13300/20000 prot-na_13300.pdb -1385203.63 2026-09-28 15:05:33 13400/20000 prot-na_13400.pdb -1976427.10 2026-09-28 15:06:17 13500/20000 prot-na_13500.pdb -2088383.89 2026-09-28 15:07:01 13600/20000 prot-na_13600.pdb -2953622.08 2026-09-28 15:07:45 13700/20000 prot-na_13700.pdb -2021548.60 2026-09-28 15:08:28 13800/20000 prot-na_13800.pdb -1316156.73 2026-09-28 15:09:12 13900/20000 prot-na_13900.pdb -1461692.00 2026-09-28 15:09:56 14000/20000 prot-na_14000.pdb -2180467.71 2026-09-28 15:10:44 14100/20000 prot-na_14100.pdb -1382026.35 2026-09-28 15:11:30 14200/20000 prot-na_14200.pdb -1852892.47 2026-09-28 15:12:14 14300/20000 prot-na_14300.pdb -1876712.08 2026-09-28 15:12:59 14400/20000 prot-na_14400.pdb -1955001.89 2026-09-28 15:13:43 14500/20000 prot-na_14500.pdb -1891675.66 2026-09-28 15:14:28 14600/20000 prot-na_14600.pdb -2247773.76 2026-09-28 15:15:12 14700/20000 prot-na_14700.pdb -470858.46 2026-09-28 15:15:55 14800/20000 prot-na_14800.pdb -1761205.99 2026-09-28 15:16:39 14900/20000 prot-na_14900.pdb -1734351.83 2026-09-28 15:17:22 15000/20000 prot-na_15000.pdb -2400938.39 2026-09-28 15:18:06 15100/20000 prot-na_15100.pdb -2273182.04 2026-09-28 15:18:50 15200/20000 prot-na_15200.pdb -952271.66 2026-09-28 15:19:33 15300/20000 prot-na_15300.pdb -1833953.15 2026-09-28 15:20:17 15400/20000 prot-na_15400.pdb -2020026.66 2026-09-28 15:20:59 15500/20000 prot-na_15500.pdb -1955288.10 2026-09-28 15:21:42 15600/20000 prot-na_15600.pdb -1284489.48 2026-09-28 15:22:25 15700/20000 prot-na_15700.pdb -1531129.83 2026-09-28 15:23:07 15800/20000 prot-na_15800.pdb -1977642.10 2026-09-28 15:23:50 15900/20000 prot-na_15900.pdb -1802077.11 2026-09-28 15:24:33 16000/20000 prot-na_16000.pdb -1038643.06 2026-09-28 15:25:15 16100/20000 prot-na_16100.pdb -930174.67 2026-09-28 15:25:58 16200/20000 prot-na_16200.pdb -1733204.88 2026-09-28 15:26:40 16300/20000 prot-na_16300.pdb -1141212.02 2026-09-28 15:27:23 16400/20000 prot-na_16400.pdb -2021340.69 2026-09-28 15:28:06 16500/20000 prot-na_16500.pdb -1249680.85 2026-09-28 15:28:48 16600/20000 prot-na_16600.pdb -1892799.06 2026-09-28 15:29:31 16700/20000 prot-na_16700.pdb -1331721.32 2026-09-28 15:30:14 16800/20000 prot-na_16800.pdb -1256517.00 2026-09-28 15:30:57 16900/20000 prot-na_16900.pdb -1425573.15 2026-09-28 15:31:39 17000/20000 prot-na_17000.pdb -1844843.72 2026-09-28 15:32:22 17100/20000 prot-na_17100.pdb -1505911.92 2026-09-28 15:33:04 17200/20000 prot-na_17200.pdb -1281479.21 2026-09-28 15:33:47 17300/20000 prot-na_17300.pdb -1487223.39 2026-09-28 15:34:30 17400/20000 prot-na_17400.pdb -1053479.95 2026-09-28 15:35:12 17500/20000 prot-na_17500.pdb -1442601.58 2026-09-28 15:35:55 17600/20000 prot-na_17600.pdb -1140487.28 2026-09-28 15:36:37 17700/20000 prot-na_17700.pdb -1487016.72 2026-09-28 15:37:20 17800/20000 prot-na_17800.pdb -1421177.70 2026-09-28 15:38:02 17900/20000 prot-na_17900.pdb -1901743.62 2026-09-28 15:38:45 18000/20000 prot-na_18000.pdb -1558167.80 2026-09-28 15:39:27 18100/20000 prot-na_18100.pdb -1029607.10 2026-09-28 15:40:10 18200/20000 prot-na_18200.pdb -1956054.12 2026-09-28 15:40:52 18300/20000 prot-na_18300.pdb -1554396.60 2026-09-28 15:41:35 18400/20000 prot-na_18400.pdb -1496571.67 2026-09-28 15:42:18 18500/20000 prot-na_18500.pdb -1583452.56 2026-09-28 15:43:01 18600/20000 prot-na_18600.pdb -499217.08 2026-09-28 15:43:43 18700/20000 prot-na_18700.pdb -2460641.71 2026-09-28 15:44:26 18800/20000 prot-na_18800.pdb -771656.12 2026-09-28 15:45:09 18900/20000 prot-na_18900.pdb -2013443.51 2026-09-28 15:45:52 19000/20000 prot-na_19000.pdb -1701114.31 2026-09-28 15:46:34 19100/20000 prot-na_19100.pdb -1278091.11 2026-09-28 15:47:16 19200/20000 prot-na_19200.pdb -1627617.33 2026-09-28 15:47:59 19300/20000 prot-na_19300.pdb -909072.02 2026-09-28 15:48:42 19400/20000 prot-na_19400.pdb -2696334.93 2026-09-28 15:49:24 19500/20000 prot-na_19500.pdb -1029764.58 2026-09-28 15:50:07 19600/20000 prot-na_19600.pdb -1910491.82 2026-09-28 15:50:49 19700/20000 prot-na_19700.pdb -1596814.89 2026-09-28 15:51:32 19800/20000 prot-na_19800.pdb -2065761.48 2026-09-28 15:52:14 19900/20000 prot-na_19900.pdb -970751.65 2026-09-28 15:52:57 20000/20000 prot-na_20000.pdb -1879307.01 2026-09-28 15:52:57 DARS scoring end 2026-09-28 15:52:57 Clustering (cuttoff: 5, nr_clust: 100 ) in progress... 2026-09-28 15:52:57 time python /home/rpdock/run_gramm//clustering_v4.py dars_out.txt list.txt 5 100 2026-09-28 15:52:57 100 best scored structures 2026-09-28 15:52:57 1 prot-na_2977.pdb -4150813.76 2026-09-28 15:52:57 2 prot-na_5555.pdb -4084152.62 2026-09-28 15:52:57 3 prot-na_5328.pdb -4057057.32 2026-09-28 15:52:57 4 prot-na_17256.pdb -4046471.75 2026-09-28 15:52:57 5 prot-na_10718.pdb -4039295.3 2026-09-28 15:52:57 6 prot-na_6027.pdb -3972042.37 2026-09-28 15:52:57 7 prot-na_112.pdb -3959453.05 2026-09-28 15:52:57 8 prot-na_2539.pdb -3916304.01 2026-09-28 15:52:57 9 prot-na_241.pdb -3884670.14 2026-09-28 15:52:57 10 prot-na_17913.pdb -3873288.25 2026-09-28 15:52:57 11 prot-na_17280.pdb -3853505.11 2026-09-28 15:52:57 12 prot-na_13049.pdb -3830813.01 2026-09-28 15:52:57 13 prot-na_4400.pdb -3777303.6 2026-09-28 15:52:57 14 prot-na_11868.pdb -3771556.28 2026-09-28 15:52:57 15 prot-na_8174.pdb -3753614.32 2026-09-28 15:52:57 16 prot-na_19350.pdb -3736186.28 2026-09-28 15:52:57 17 prot-na_70.pdb -3727405.03 2026-09-28 15:52:57 18 prot-na_9.pdb -3720197.53 2026-09-28 15:52:57 19 prot-na_9014.pdb -3710361.3 2026-09-28 15:52:57 20 prot-na_18373.pdb -3667336.35 2026-09-28 15:52:57 21 prot-na_18868.pdb -3663319.44 2026-09-28 15:52:57 22 prot-na_999.pdb -3642491.51 2026-09-28 15:52:57 23 prot-na_4300.pdb -3623924.06 2026-09-28 15:52:57 24 prot-na_56.pdb -3618907.71 2026-09-28 15:52:57 25 prot-na_10331.pdb -3597500.71 2026-09-28 15:52:57 26 prot-na_2160.pdb -3547663.46 2026-09-28 15:52:57 27 prot-na_3939.pdb -3546148.37 2026-09-28 15:52:57 28 prot-na_5075.pdb -3536582.01 2026-09-28 15:52:57 29 prot-na_3106.pdb -3529720.76 2026-09-28 15:52:57 30 prot-na_10201.pdb -3529362.61 2026-09-28 15:52:57 31 prot-na_14.pdb -3502066.92 2026-09-28 15:52:57 32 prot-na_16759.pdb -3492564.15 2026-09-28 15:52:57 33 prot-na_9113.pdb -3491842.67 2026-09-28 15:52:57 34 prot-na_2424.pdb -3478213.14 2026-09-28 15:52:57 35 prot-na_13510.pdb -3476446.91 2026-09-28 15:52:57 36 prot-na_1132.pdb -3473358.66 2026-09-28 15:52:57 37 prot-na_3377.pdb -3469237.89 2026-09-28 15:52:57 38 prot-na_9397.pdb -3463352.42 2026-09-28 15:52:57 39 prot-na_7260.pdb -3461819.09 2026-09-28 15:52:57 40 prot-na_2213.pdb -3459972.12 2026-09-28 15:52:57 41 prot-na_4222.pdb -3442664.45 2026-09-28 15:52:57 42 prot-na_8998.pdb -3440046.76 2026-09-28 15:52:57 43 prot-na_2218.pdb -3436873.18 2026-09-28 15:52:57 44 prot-na_7443.pdb -3434150.92 2026-09-28 15:52:57 45 prot-na_12027.pdb -3429854.85 2026-09-28 15:52:57 46 prot-na_14272.pdb -3428168.22 2026-09-28 15:52:57 47 prot-na_17275.pdb -3426158.65 2026-09-28 15:52:57 48 prot-na_254.pdb -3421682.66 2026-09-28 15:52:57 49 prot-na_6386.pdb -3408089.55 2026-09-28 15:52:57 50 prot-na_8688.pdb -3398339.42 2026-09-28 15:52:57 51 prot-na_55.pdb -3393542.29 2026-09-28 15:52:57 52 prot-na_15208.pdb -3392184.39 2026-09-28 15:52:57 53 prot-na_13992.pdb -3381008.33 2026-09-28 15:52:57 54 prot-na_186.pdb -3379846.92 2026-09-28 15:52:57 55 prot-na_6420.pdb -3379391.35 2026-09-28 15:52:57 56 prot-na_1239.pdb -3373982.96 2026-09-28 15:52:57 57 prot-na_8978.pdb -3356356.32 2026-09-28 15:52:57 58 prot-na_2227.pdb -3355467.13 2026-09-28 15:52:57 59 prot-na_19215.pdb -3354864.12 2026-09-28 15:52:57 60 prot-na_12599.pdb -3351249.49 2026-09-28 15:52:57 61 prot-na_8030.pdb -3350142.26 2026-09-28 15:52:57 62 prot-na_10101.pdb -3349672.0 2026-09-28 15:52:57 63 prot-na_1455.pdb -3341452.45 2026-09-28 15:52:57 64 prot-na_93.pdb -3338255.6 2026-09-28 15:52:57 65 prot-na_4645.pdb -3337602.27 2026-09-28 15:52:57 66 prot-na_9433.pdb -3329796.65 2026-09-28 15:52:57 67 prot-na_346.pdb -3329520.14 2026-09-28 15:52:57 68 prot-na_9276.pdb -3327193.08 2026-09-28 15:52:57 69 prot-na_2827.pdb -3312945.82 2026-09-28 15:52:57 70 prot-na_1846.pdb -3311463.76 2026-09-28 15:52:57 71 prot-na_17326.pdb -3310845.4 2026-09-28 15:52:57 72 prot-na_106.pdb -3307174.36 2026-09-28 15:52:57 73 prot-na_4307.pdb -3298151.17 2026-09-28 15:52:57 74 prot-na_11414.pdb -3297935.56 2026-09-28 15:52:57 75 prot-na_1620.pdb -3290641.78 2026-09-28 15:52:57 76 prot-na_7769.pdb -3288579.71 2026-09-28 15:52:57 77 prot-na_6487.pdb -3288248.31 2026-09-28 15:52:57 78 prot-na_8852.pdb -3282023.86 2026-09-28 15:52:57 79 prot-na_874.pdb -3272250.08 2026-09-28 15:52:57 80 prot-na_6835.pdb -3270553.82 2026-09-28 15:52:57 81 prot-na_6055.pdb -3270302.31 2026-09-28 15:52:57 82 prot-na_5519.pdb -3269022.25 2026-09-28 15:52:57 83 prot-na_13204.pdb -3267058.39 2026-09-28 15:52:57 84 prot-na_6529.pdb -3258633.35 2026-09-28 15:52:57 85 prot-na_467.pdb -3258166.53 2026-09-28 15:52:57 86 prot-na_146.pdb -3256834.15 2026-09-28 15:52:57 87 prot-na_374.pdb -3253954.55 2026-09-28 15:52:57 88 prot-na_493.pdb -3242904.3 2026-09-28 15:52:57 89 prot-na_5097.pdb -3241657.99 2026-09-28 15:52:57 90 prot-na_6050.pdb -3239735.66 2026-09-28 15:52:57 91 prot-na_1066.pdb -3239314.52 2026-09-28 15:52:57 92 prot-na_18393.pdb -3238558.38 2026-09-28 15:52:57 93 prot-na_11937.pdb -3236367.57 2026-09-28 15:52:57 94 prot-na_2301.pdb -3234950.57 2026-09-28 15:52:57 95 prot-na_18854.pdb -3233441.56 2026-09-28 15:52:57 96 prot-na_13654.pdb -3229621.66 2026-09-28 15:52:57 97 prot-na_6425.pdb -3228254.85 2026-09-28 15:52:57 98 prot-na_9820.pdb -3222358.42 2026-09-28 15:52:57 99 prot-na_397.pdb -3218019.31 2026-09-28 15:52:57 100 prot-na_6603.pdb -3215613.87 2026-09-28 15:52:57 Chains: B 2026-09-28 15:53:14 100 best scored structures 2026-09-28 15:53:14 GRAMM analysis selected for further analysis: prot-na_25 2026-09-28 15:53:14 Sent to refinement: clusters_not_found|prot-na_2977.pdb|prot-na_5555.pdb|prot-na_5328.pdb 2026-09-28 15:53:14 Sent to refinement: clusters_not_found|prot-na_2977.pdb|prot-na_5555.pdb|prot-na_5328.pdb 2026-09-28 15:53:14 DARS clustering end 2026-09-28 15:53:14 MC (refinement) init 2026-09-28 15:53:14 python /home/rpdock/run_gramm//run_mc.py -f dars_to_mc.txt -d /home/rpdock/web/media/jobs/9af8942e-5c0d-4581-a9a4-b854422d5dfe/ 2026-09-28 15:53:15 Refinement of #1 /home/rpdock/web/media/jobs/9af8942e-5c0d-4581-a9a4-b854422d5dfe/prot-na_2977.pdb 2026-09-28 15:53:15 python /home/rpdock/mc/MC.py -s 295 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/9af8942e-5c0d-4581-a9a4-b854422d5dfe//ref_struc/prot-na_2977/prot-na_2977.pdb 2026-09-28 15:55:45 Refinement of #2 /home/rpdock/web/media/jobs/9af8942e-5c0d-4581-a9a4-b854422d5dfe/prot-na_5555.pdb 2026-09-28 15:55:45 python /home/rpdock/mc/MC.py -s 295 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/9af8942e-5c0d-4581-a9a4-b854422d5dfe//ref_struc/prot-na_5555/prot-na_5555.pdb 2026-09-28 15:58:11 Refinement of #3 /home/rpdock/web/media/jobs/9af8942e-5c0d-4581-a9a4-b854422d5dfe/prot-na_5328.pdb 2026-09-28 15:58:11 python /home/rpdock/mc/MC.py -s 295 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/9af8942e-5c0d-4581-a9a4-b854422d5dfe//ref_struc/prot-na_5328/prot-na_5328.pdb 2026-09-28 16:00:45 start - parameters: File name /home/rpdock/web/media/jobs/9af8942e-5c0d-4581-a9a4-b854422d5dfe//ref_struc/prot-na_2977/prot-na_2977.pdb Steps 295 Temp. start 15000.0 Temp. end 295.0 False msg start - parameters: File name /home/rpdock/web/media/jobs/9af8942e-5c0d-4581-a9a4-b854422d5dfe//ref_struc/prot-na_2977/prot-na_2977.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 - -2586297.08 -1828725.25 -1557571.83 800000.00 1 R -2746240.81 -1773222.85 -1473017.96 500000.00 T= 14950.1525424 K progress 0.338983050847 2 T -2873484.68 -1769306.98 -1504177.69 400000.00 T= 14900.3050847 K progress 0.677966101695 3 R -2870267.32 -1765227.32 -1505040.00 400000.00 T= 14700.9152542 K progress 1.01694915254 4 R -2971479.13 -1807327.94 -1464151.19 300000.00 T= 14651.0677966 K progress 1.35593220339 5 R -2980499.52 -1807098.02 -1473401.50 300000.00 T= 14202.440678 K progress 1.69491525424 6 R -2957481.70 -1731513.30 -1425968.40 200000.00 T= 14152.5932203 K progress 2.03389830508 7 R -2870733.52 -1746463.48 -1424270.05 300000.00 T= 14052.8983051 K progress 2.37288135593 8 T -2907071.31 -1748139.47 -1558931.84 400000.00 T= 13853.5084746 K progress 2.71186440678 9 R -3089647.45 -1836323.46 -1553323.99 300000.00 T= 13753.8135593 K progress 3.05084745763 10 R -2946735.02 -1777401.75 -1569333.27 400000.00 T= 12358.0847458 K progress 3.38983050847 11 T -2899330.60 -1765361.57 -1433969.04 300000.00 T= 12258.3898305 K progress 3.72881355932 12 R -2911736.76 -1764096.68 -1447640.07 300000.00 T= 12208.5423729 K progress 4.06779661017 13 R -2881521.98 -1739812.13 -1441709.85 300000.00 T= 12108.8474576 K progress 4.40677966102 14 T -3300001.14 -1838076.26 -1561924.87 100000.00 T= 12059.0 K progress 4.74576271186 15 R -3112442.25 -1742056.98 -1570385.26 200000.00 T= 9666.3220339 K progress 5.08474576271 16 T -2871923.65 -1684725.47 -1487198.19 300000.00 T= 9516.77966102 K progress 5.42372881356 17 R -2847918.11 -1674525.23 -1473392.88 300000.00 T= 9317.38983051 K progress 5.76271186441 18 T -2556789.03 -1789110.11 -1567678.92 800000.00 T= 9267.54237288 K progress 6.10169491525 19 T -2660383.71 -1768553.73 -1591829.98 700000.00 T= 9217.69491525 K progress 6.4406779661 20 R -2724301.84 -1798803.30 -1625498.55 700000.00 T= 9118.0 K progress 6.77966101695 21 T -3130202.72 -1801907.22 -1628295.50 300000.00 T= 8769.06779661 K progress 7.1186440678 22 T -3023257.62 -1793957.42 -1629300.20 400000.00 T= 8669.37288136 K progress 7.45762711864 23 T -3083707.84 -1854092.66 -1529615.18 300000.00 T= 8420.13559322 K progress 7.79661016949 24 R -3060546.61 -1906761.15 -1553785.46 400000.00 T= 7971.50847458 K progress 8.13559322034 25 R -3183046.60 -1922465.57 -1560581.03 300000.00 T= 7821.96610169 K progress 8.47457627119 26 R -3119736.10 -1865286.37 -1554449.74 300000.00 T= 7373.33898305 K progress 8.81355932203 27 R -3237967.76 -1880964.15 -1657003.61 300000.00 T= 7273.6440678 K progress 9.15254237288 28 R -3443734.28 -1981444.26 -1662290.02 200000.00 T= 6974.55932203 K progress 9.49152542373 29 R -3449961.90 -1981444.26 -1668517.64 200000.00 T= 5130.20338983 K progress 9.83050847458 30 R -3455088.71 -1985037.51 -1670051.21 200000.00 T= 4482.18644068 K progress 10.1694915254 31 R -3452526.25 -1988157.78 -1664368.47 200000.00 T= 4282.79661017 K progress 10.5084745763 32 R -3448626.09 -1982346.19 -1666279.90 200000.00 T= 3535.08474576 K progress 10.8474576271 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/9af8942e-5c0d-4581-a9a4-b854422d5dfe//ref_struc/prot-na_5555/prot-na_5555.pdb Steps 295 Temp. start 15000.0 Temp. end 295.0 False msg start - parameters: File name /home/rpdock/web/media/jobs/9af8942e-5c0d-4581-a9a4-b854422d5dfe//ref_struc/prot-na_5555/prot-na_5555.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 - -916052.40 -1935897.27 -1680155.12 2700000.00 1 R -1218694.37 -1954858.36 -1663836.01 2400000.00 T= 15000.0 K progress 0.338983050847 2 T -1326666.03 -1836921.72 -1589744.30 2100000.00 T= 14900.3050847 K progress 0.677966101695 3 R -1327505.31 -1837926.88 -1589578.43 2100000.00 T= 14750.7627119 K progress 1.01694915254 4 T -1405800.57 -1775891.52 -1529909.05 1900000.00 T= 14700.9152542 K progress 1.35593220339 5 R -1405750.40 -1775891.52 -1529858.88 1900000.00 T= 14401.8305085 K progress 1.69491525424 6 T -1394829.44 -1799104.09 -1595725.35 2000000.00 T= 14152.5932203 K progress 2.03389830508 7 T -1448740.18 -1665821.44 -1482918.74 1700000.00 T= 14052.8983051 K progress 2.37288135593 8 T -1460108.03 -1670369.08 -1489738.95 1700000.00 T= 13953.2033898 K progress 2.71186440678 9 R -1579614.02 -1703317.32 -1476296.70 1600000.00 T= 13853.5084746 K progress 3.05084745763 10 R -1633315.19 -1712223.86 -1521091.33 1600000.00 T= 13753.8135593 K progress 3.38983050847 11 R -1531645.84 -1699496.30 -1532149.54 1700000.00 T= 13554.4237288 K progress 3.72881355932 12 R -1490065.03 -1673696.52 -1516368.51 1700000.00 T= 13454.7288136 K progress 4.06779661017 13 T -1246246.90 -1597449.95 -1448796.95 1800000.00 T= 13404.8813559 K progress 4.40677966102 14 R -1722419.81 -1635997.23 -1486422.58 1400000.00 T= 13305.1864407 K progress 4.74576271186 15 R -1704389.49 -1618799.89 -1485589.60 1400000.00 T= 13105.7966102 K progress 5.08474576271 16 R -1716728.57 -1642677.21 -1474051.36 1400000.00 T= 12407.9322034 K progress 5.42372881356 17 R -1708369.87 -1644236.77 -1464133.11 1400000.00 T= 12308.2372881 K progress 5.76271186441 18 R -1740919.51 -1653172.30 -1487747.21 1400000.00 T= 12059.0 K progress 6.10169491525 19 R -1726375.80 -1651917.88 -1474457.92 1400000.00 T= 11610.3728814 K progress 6.4406779661 20 R -1667496.55 -1614720.91 -1452775.64 1400000.00 T= 11361.1355932 K progress 6.77966101695 21 T -1691826.70 -1695058.89 -1496767.81 1500000.00 T= 11211.5932203 K progress 7.1186440678 22 T -1768855.31 -1680793.71 -1488061.59 1400000.00 T= 10563.5762712 K progress 7.45762711864 23 T -1522873.22 -1827138.74 -1595734.47 1900000.00 T= 9965.40677966 K progress 7.79661016949 24 R -1479396.68 -1822854.83 -1556541.85 1900000.00 T= 9716.16949153 K progress 8.13559322034 25 T -1607047.73 -1883091.17 -1623956.56 1900000.00 T= 9666.3220339 K progress 8.47457627119 26 T -1777959.16 -1999688.22 -1678270.94 1900000.00 T= 9367.23728814 K progress 8.81355932203 27 R -2012279.71 -1955059.54 -1657220.17 1600000.00 T= 9217.69491525 K progress 9.15254237288 28 R -2073773.59 -1903607.28 -1670166.31 1500000.00 T= 9018.30508475 K progress 9.49152542373 29 R -2169112.23 -1894243.29 -1674868.94 1400000.00 T= 8968.45762712 K progress 9.83050847458 30 R -2060310.69 -1890231.80 -1670078.90 1500000.00 T= 8918.61016949 K progress 10.1694915254 31 R -2187585.39 -1900794.38 -1686791.00 1400000.00 T= 8769.06779661 K progress 10.5084745763 32 R -2181687.56 -1899050.79 -1682636.77 1400000.00 T= 8569.6779661 K progress 10.8474576271 33 R -2181687.56 -1899050.79 -1682636.77 1400000.00 T= 8370.28813559 K progress 11.186440678 34 T -2369685.43 -1961861.10 -1707824.33 1300000.00 T= 8220.74576271 K progress 11.5254237288 35 R -2523428.30 -1871892.63 -1651535.67 1000000.00 T= 8071.20338983 K progress 11.8644067797 36 R -2499641.52 -1856642.81 -1642998.71 1000000.00 T= 7522.88135593 K progress 12.2033898305 37 R -2536462.05 -1871112.40 -1665349.65 1000000.00 T= 6027.45762712 K progress 12.5423728814 38 R -2536462.05 -1871112.40 -1665349.65 1000000.00 T= 5429.28813559 K progress 12.8813559322 39 R -2548601.54 -1876097.83 -1672503.71 1000000.00 T= 5130.20338983 K progress 13.2203389831 40 R -2537464.72 -1875414.81 -1662049.91 1000000.00 T= 4781.27118644 K progress 13.5593220339 41 R -2534050.96 -1875714.31 -1658336.65 1000000.00 T= 4332.6440678 K progress 13.8983050847 42 T -2541796.43 -2204528.05 -1937268.38 1600000.00 T= 3983.71186441 K progress 14.2372881356 43 R -2678811.12 -2307476.70 -1971334.43 1600000.00 T= 2986.76271186 K progress 14.5762711864 44 R -2678920.39 -2313004.96 -1965915.43 1600000.00 T= 344.847457627 K progress 14.9152542373 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/9af8942e-5c0d-4581-a9a4-b854422d5dfe//ref_struc/prot-na_5328/prot-na_5328.pdb Steps 295 Temp. start 15000.0 Temp. end 295.0 False msg start - parameters: File name /home/rpdock/web/media/jobs/9af8942e-5c0d-4581-a9a4-b854422d5dfe//ref_struc/prot-na_5328/prot-na_5328.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 - -2431637.27 -1799461.11 -1532176.16 900000.00 1 T -2619960.75 -1926921.88 -1693038.87 1000000.00 T= 15000.0 K progress 0.338983050847 2 T -2732853.49 -1907843.05 -1625010.44 800000.00 T= 14651.0677966 K progress 0.677966101695 3 R -2487526.74 -1820062.61 -1567464.13 900000.00 T= 14601.220339 K progress 1.01694915254 4 R -2689792.03 -1856033.83 -1733758.20 900000.00 T= 14501.5254237 K progress 1.35593220339 5 R -2740456.66 -1857690.26 -1682766.40 800000.00 T= 14451.6779661 K progress 1.69491525424 6 T -2579595.53 -1774986.37 -1604609.15 800000.00 T= 14351.9830508 K progress 2.03389830508 7 T -2632048.33 -1811691.11 -1620357.23 800000.00 T= 14302.1355932 K progress 2.37288135593 8 T -3276975.95 -1845764.65 -1631211.29 200000.00 T= 14252.2881356 K progress 2.71186440678 9 T -3191546.25 -1799516.03 -1592030.22 200000.00 T= 13803.6610169 K progress 3.05084745763 10 R -3391204.68 -1890126.51 -1601078.17 100000.00 T= 13703.9661017 K progress 3.38983050847 11 R -3366327.99 -1876957.93 -1589370.06 100000.00 T= 13205.4915254 K progress 3.72881355932 12 R -3370359.72 -1864189.30 -1606170.41 100000.00 T= 13155.6440678 K progress 4.06779661017 13 R -3393252.37 -1878082.74 -1615169.63 100000.00 T= 13105.7966102 K progress 4.40677966102 14 R -3368333.95 -1878944.79 -1589389.16 100000.00 T= 12059.0 K progress 4.74576271186 15 R -3385422.52 -1888700.04 -1596722.48 100000.00 T= 11161.7457627 K progress 5.08474576271 16 R -3385785.01 -1874651.13 -1611133.88 100000.00 T= 10812.8135593 K progress 5.42372881356 17 R -3346318.20 -1856808.63 -1589509.57 100000.00 T= 10563.5762712 K progress 5.76271186441 18 R -3361497.59 -1875976.45 -1585521.14 100000.00 T= 10414.0338983 K progress 6.10169491525 19 R -3334905.45 -1839620.37 -1595285.08 100000.00 T= 9716.16949153 K progress 6.4406779661 20 R -3348607.36 -1853964.85 -1594642.52 100000.00 T= 9317.38983051 K progress 6.77966101695 21 R -3348962.20 -1860609.66 -1588352.54 100000.00 T= 9068.15254237 K progress 7.1186440678 22 R -3348534.91 -1847667.55 -1600867.37 100000.00 T= 8818.91525424 K progress 7.45762711864 23 R -3366549.35 -1883328.50 -1583220.85 100000.00 T= 7821.96610169 K progress 7.79661016949 24 R -3364394.02 -1856859.23 -1607534.79 100000.00 T= 7622.57627119 K progress 8.13559322034 25 R -3181635.48 -1821127.18 -1560508.31 200000.00 T= 7423.18644068 K progress 8.47457627119 26 T -3110840.98 -1833733.62 -1577107.35 300000.00 T= 7273.6440678 K progress 8.81355932203 27 T -3158240.01 -1808070.79 -1550169.22 200000.00 T= 6825.01694915 K progress 9.15254237288 28 R -3322493.99 -1840187.17 -1582306.83 100000.00 T= 6725.3220339 K progress 9.49152542373 29 T -3292998.06 -1817080.25 -1575917.81 100000.00 T= 6525.93220339 K progress 9.83050847458 30 T -3334518.85 -1880188.81 -1654330.03 200000.00 T= 5977.61016949 K progress 10.1694915254 31 R -3352840.96 -1888428.35 -1664412.61 200000.00 T= 4183.10169492 K progress 10.5084745763 32 R -3325585.44 -1875019.73 -1650565.71 200000.00 T= 1740.57627119 K progress 10.8474576271 33 R -3332198.65 -1891412.89 -1640785.76 200000.00 T= 1541.18644068 K progress 11.186440678 Save no big msg save short traj msg save best.pdb msg save plot e_step.png Mon Sep 28 15:53:15 2026 ['prot-na_2977.pdb', 'prot-na_5555.pdb', 'prot-na_5328.pdb'] msg Refinement of #1 /home/rpdock/web/media/jobs/9af8942e-5c0d-4581-a9a4-b854422d5dfe/prot-na_2977.pdb dir: /home/rpdock/web/media/jobs/9af8942e-5c0d-4581-a9a4-b854422d5dfe/ file: prot-na_2977.pdb find `pwd` -iname prot-na_2977.pdb copy /home/rpdock/web/media/jobs/9af8942e-5c0d-4581-a9a4-b854422d5dfe/prot-na_25/prot-na_2977.pdb to /home/rpdock/web/media/jobs/9af8942e-5c0d-4581-a9a4-b854422d5dfe//ref_struc/prot-na_2977/prot-na_2977.pdb cmd: python /home/rpdock/mc/MC.py -s 295 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/9af8942e-5c0d-4581-a9a4-b854422d5dfe//ref_struc/prot-na_2977/prot-na_2977.pdb msg python /home/rpdock/mc/MC.py -s 295 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/9af8942e-5c0d-4581-a9a4-b854422d5dfe//ref_struc/prot-na_2977/prot-na_2977.pdb run_mc::OK! = stderr empty msg Refinement of #2 /home/rpdock/web/media/jobs/9af8942e-5c0d-4581-a9a4-b854422d5dfe/prot-na_5555.pdb dir: /home/rpdock/web/media/jobs/9af8942e-5c0d-4581-a9a4-b854422d5dfe/ file: prot-na_5555.pdb find `pwd` -iname prot-na_5555.pdb copy /home/rpdock/web/media/jobs/9af8942e-5c0d-4581-a9a4-b854422d5dfe/prot-na_25/prot-na_5555.pdb to /home/rpdock/web/media/jobs/9af8942e-5c0d-4581-a9a4-b854422d5dfe//ref_struc/prot-na_5555/prot-na_5555.pdb cmd: python /home/rpdock/mc/MC.py -s 295 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/9af8942e-5c0d-4581-a9a4-b854422d5dfe//ref_struc/prot-na_5555/prot-na_5555.pdb msg python /home/rpdock/mc/MC.py -s 295 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/9af8942e-5c0d-4581-a9a4-b854422d5dfe//ref_struc/prot-na_5555/prot-na_5555.pdb run_mc::OK! = stderr empty msg Refinement of #3 /home/rpdock/web/media/jobs/9af8942e-5c0d-4581-a9a4-b854422d5dfe/prot-na_5328.pdb dir: /home/rpdock/web/media/jobs/9af8942e-5c0d-4581-a9a4-b854422d5dfe/ file: prot-na_5328.pdb find `pwd` -iname prot-na_5328.pdb copy /home/rpdock/web/media/jobs/9af8942e-5c0d-4581-a9a4-b854422d5dfe/prot-na_25/prot-na_5328.pdb to /home/rpdock/web/media/jobs/9af8942e-5c0d-4581-a9a4-b854422d5dfe//ref_struc/prot-na_5328/prot-na_5328.pdb cmd: python /home/rpdock/mc/MC.py -s 295 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/9af8942e-5c0d-4581-a9a4-b854422d5dfe//ref_struc/prot-na_5328/prot-na_5328.pdb msg python /home/rpdock/mc/MC.py -s 295 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/9af8942e-5c0d-4581-a9a4-b854422d5dfe//ref_struc/prot-na_5328/prot-na_5328.pdb run_mc::OK! = stderr empty 2026-09-28 16:00:45 npdock::MC (refinement) end 2026-09-28 16:00:45 npdock::OK 2026-09-28 16:00:45 Set finished status of 9af8942e-5c0d-4581-a9a4-b854422d5dfe