2026-10-23 12:16:02 NPdock start 2026-10-23 12:16:02 ver: v1.2-23-gfce5bd3-dirty 2026-10-23 12:16:02 mode: None 2026-10-23 12:16:02 is RNA? True 2026-10-23 12:16:02 Interface: prot: '' na: '' 2026-10-23 12:16:02 Curr dir:/home/rpdock/web/media/jobs/d0c280cb-2ab6-427b-a7a4-b709e96386b0/ 2026-10-23 12:16:02 GRAMM in progress... 2026-10-23 12:16:02 timeout 72h python /home/rpdock/run_gramm//run_gramm1.py -d 20000 -p prot.pdb -r na.pdb -pi '' -ri '' -n '1' -pf 'B,C' -rf 'R' 2026-10-23 13:07:08 GRAMM done 2026-10-23 13:07:08 DARS scoring in progress... 2026-10-23 13:07:08 timeout 72h /home/rpdock/run_gramm//DARS-RNP_v3//DARS_potential_v3_scoring.py -m 100 -f list.txt -o dars_out.txt 2026-10-23 13:07:08 DARS start [DARS_potential_v3_scoring.py] 2026-10-23 13:07:08 Show log every 100 structures [DARS_potential_v3_scoring.py] 2026-10-23 13:07:09 1/20000 prot-na_1000.pdb -3248206.77 2026-10-23 13:07:44 100/20000 prot-na_94.pdb -2442275.59 2026-10-23 13:08:20 200/20000 prot-na_194.pdb -4011256.67 2026-10-23 13:08:57 300/20000 prot-na_294.pdb -3538334.29 2026-10-23 13:09:34 400/20000 prot-na_394.pdb -1218454.60 2026-10-23 13:10:12 500/20000 prot-na_494.pdb -1788432.52 2026-10-23 13:10:51 600/20000 prot-na_594.pdb -1977637.94 2026-10-23 13:11:29 700/20000 prot-na_694.pdb -2267144.59 2026-10-23 13:12:07 800/20000 prot-na_794.pdb -2423227.31 2026-10-23 13:12:46 900/20000 prot-na_894.pdb -1755540.86 2026-10-23 13:13:26 1000/20000 prot-na_994.pdb -2234338.73 2026-10-23 13:14:04 1100/20000 prot-na_1100.pdb -1525400.75 2026-10-23 13:14:43 1200/20000 prot-na_1200.pdb -2078693.19 2026-10-23 13:15:21 1300/20000 prot-na_1300.pdb -2297359.96 2026-10-23 13:16:00 1400/20000 prot-na_1400.pdb -1357062.14 2026-10-23 13:16:39 1500/20000 prot-na_1500.pdb -3264938.80 2026-10-23 13:17:17 1600/20000 prot-na_1600.pdb -2345534.79 2026-10-23 13:17:56 1700/20000 prot-na_1700.pdb -2180057.14 2026-10-23 13:18:35 1800/20000 prot-na_1800.pdb -2677468.17 2026-10-23 13:19:14 1900/20000 prot-na_1900.pdb -1817226.66 2026-10-23 13:19:54 2000/20000 prot-na_2000.pdb -1635819.00 2026-10-23 13:20:33 2100/20000 prot-na_2100.pdb -2151497.75 2026-10-23 13:21:12 2200/20000 prot-na_2200.pdb -1217563.03 2026-10-23 13:21:51 2300/20000 prot-na_2300.pdb -3166763.45 2026-10-23 13:22:30 2400/20000 prot-na_2400.pdb -3158459.58 2026-10-23 13:23:09 2500/20000 prot-na_2500.pdb -1190531.83 2026-10-23 13:23:49 2600/20000 prot-na_2600.pdb -1872452.75 2026-10-23 13:24:32 2700/20000 prot-na_2700.pdb -3342151.72 2026-10-23 13:25:13 2800/20000 prot-na_2800.pdb -2348478.87 2026-10-23 13:25:54 2900/20000 prot-na_2900.pdb -2150297.54 2026-10-23 13:26:37 3000/20000 prot-na_3000.pdb -1556017.41 2026-10-23 13:27:17 3100/20000 prot-na_3100.pdb -1412600.53 2026-10-23 13:27:57 3200/20000 prot-na_3200.pdb -2338242.62 2026-10-23 13:28:36 3300/20000 prot-na_3300.pdb -1406915.40 2026-10-23 13:29:16 3400/20000 prot-na_3400.pdb -2455296.66 2026-10-23 13:30:00 3500/20000 prot-na_3500.pdb -1232924.83 2026-10-23 13:30:41 3600/20000 prot-na_3600.pdb -1422395.24 2026-10-23 13:31:22 3700/20000 prot-na_3700.pdb -2043052.49 2026-10-23 13:32:01 3800/20000 prot-na_3800.pdb -1093708.62 2026-10-23 13:32:41 3900/20000 prot-na_3900.pdb -2715888.34 2026-10-23 13:33:21 4000/20000 prot-na_4000.pdb -1671252.03 2026-10-23 13:34:00 4100/20000 prot-na_4100.pdb -1750521.45 2026-10-23 13:34:40 4200/20000 prot-na_4200.pdb -1500325.85 2026-10-23 13:35:19 4300/20000 prot-na_4300.pdb -1117544.68 2026-10-23 13:35:58 4400/20000 prot-na_4400.pdb -1605333.02 2026-10-23 13:36:37 4500/20000 prot-na_4500.pdb -1522706.88 2026-10-23 13:37:16 4600/20000 prot-na_4600.pdb -1662758.29 2026-10-23 13:37:55 4700/20000 prot-na_4700.pdb -1250711.62 2026-10-23 13:38:35 4800/20000 prot-na_4800.pdb -2835718.31 2026-10-23 13:39:14 4900/20000 prot-na_4900.pdb -1598931.88 2026-10-23 13:39:54 5000/20000 prot-na_5000.pdb -1512571.04 2026-10-23 13:40:34 5100/20000 prot-na_5100.pdb -2271888.46 2026-10-23 13:41:13 5200/20000 prot-na_5200.pdb -1714932.25 2026-10-23 13:41:53 5300/20000 prot-na_5300.pdb -1470529.88 2026-10-23 13:42:33 5400/20000 prot-na_5400.pdb -2466701.12 2026-10-23 13:43:12 5500/20000 prot-na_5500.pdb -1691725.66 2026-10-23 13:43:52 5600/20000 prot-na_5600.pdb -2866388.32 2026-10-23 13:44:30 5700/20000 prot-na_5700.pdb -3045321.52 2026-10-23 13:45:09 5800/20000 prot-na_5800.pdb -1957282.16 2026-10-23 13:45:49 5900/20000 prot-na_5900.pdb -1673287.23 2026-10-23 13:46:28 6000/20000 prot-na_6000.pdb -1575626.49 2026-10-23 13:47:07 6100/20000 prot-na_6100.pdb -4505701.03 2026-10-23 13:47:45 6200/20000 prot-na_6200.pdb -2240543.86 2026-10-23 13:48:24 6300/20000 prot-na_6300.pdb -1642084.35 2026-10-23 13:49:04 6400/20000 prot-na_6400.pdb -1984102.84 2026-10-23 13:49:42 6500/20000 prot-na_6500.pdb -1998836.23 2026-10-23 13:50:21 6600/20000 prot-na_6600.pdb -2378629.98 2026-10-23 13:51:00 6700/20000 prot-na_6700.pdb -1614680.84 2026-10-23 13:51:39 6800/20000 prot-na_6800.pdb -2132516.43 2026-10-23 13:52:18 6900/20000 prot-na_6900.pdb -1162993.22 2026-10-23 13:52:56 7000/20000 prot-na_7000.pdb -2348593.17 2026-10-23 13:53:35 7100/20000 prot-na_7100.pdb -2070196.78 2026-10-23 13:54:14 7200/20000 prot-na_7200.pdb -1142226.36 2026-10-23 13:54:52 7300/20000 prot-na_7300.pdb -1490534.15 2026-10-23 13:55:31 7400/20000 prot-na_7400.pdb -2045843.11 2026-10-23 13:56:10 7500/20000 prot-na_7500.pdb -1573326.25 2026-10-23 13:56:48 7600/20000 prot-na_7600.pdb -1943161.32 2026-10-23 13:57:27 7700/20000 prot-na_7700.pdb -1737338.96 2026-10-23 13:58:06 7800/20000 prot-na_7800.pdb -1163182.66 2026-10-23 13:58:45 7900/20000 prot-na_7900.pdb -1969813.46 2026-10-23 13:59:24 8000/20000 prot-na_8000.pdb -1494066.18 2026-10-23 14:00:02 8100/20000 prot-na_8100.pdb -1729946.10 2026-10-23 14:00:41 8200/20000 prot-na_8200.pdb -1162563.95 2026-10-23 14:01:20 8300/20000 prot-na_8300.pdb -746684.01 2026-10-23 14:01:58 8400/20000 prot-na_8400.pdb -2010173.44 2026-10-23 14:02:37 8500/20000 prot-na_8500.pdb -1967953.55 2026-10-23 14:03:16 8600/20000 prot-na_8600.pdb -1638929.43 2026-10-23 14:03:55 8700/20000 prot-na_8700.pdb -3105268.81 2026-10-23 14:04:34 8800/20000 prot-na_8800.pdb -1851197.76 2026-10-23 14:05:13 8900/20000 prot-na_8900.pdb -1527829.84 2026-10-23 14:05:51 9000/20000 prot-na_9000.pdb -2165551.89 2026-10-23 14:06:30 9100/20000 prot-na_9100.pdb -1429359.58 2026-10-23 14:07:09 9200/20000 prot-na_9200.pdb -1464083.81 2026-10-23 14:07:48 9300/20000 prot-na_9300.pdb -2189364.15 2026-10-23 14:08:27 9400/20000 prot-na_9400.pdb -1332883.08 2026-10-23 14:09:05 9500/20000 prot-na_9500.pdb -1277743.05 2026-10-23 14:09:44 9600/20000 prot-na_9600.pdb -2026639.38 2026-10-23 14:10:24 9700/20000 prot-na_9700.pdb -2542653.06 2026-10-23 14:11:05 9800/20000 prot-na_9800.pdb -1585055.09 2026-10-23 14:11:44 9900/20000 prot-na_9900.pdb -2076606.07 2026-10-23 14:12:23 10000/20000 prot-na_10000.pdb -1624045.12 2026-10-23 14:13:02 10100/20000 prot-na_10100.pdb -2044332.62 2026-10-23 14:13:41 10200/20000 prot-na_10200.pdb -2335897.56 2026-10-23 14:14:20 10300/20000 prot-na_10300.pdb -1892023.53 2026-10-23 14:14:58 10400/20000 prot-na_10400.pdb -1215564.28 2026-10-23 14:15:37 10500/20000 prot-na_10500.pdb -1505261.14 2026-10-23 14:16:16 10600/20000 prot-na_10600.pdb -2736312.10 2026-10-23 14:16:55 10700/20000 prot-na_10700.pdb -770104.10 2026-10-23 14:17:35 10800/20000 prot-na_10800.pdb -1776167.70 2026-10-23 14:18:15 10900/20000 prot-na_10900.pdb -1493774.63 2026-10-23 14:18:54 11000/20000 prot-na_11000.pdb -1031904.62 2026-10-23 14:19:33 11100/20000 prot-na_11100.pdb -2075133.90 2026-10-23 14:20:12 11200/20000 prot-na_11200.pdb -1391228.77 2026-10-23 14:20:52 11300/20000 prot-na_11300.pdb -2296796.80 2026-10-23 14:21:31 11400/20000 prot-na_11400.pdb -2682290.02 2026-10-23 14:22:11 11500/20000 prot-na_11500.pdb -991086.67 2026-10-23 14:22:50 11600/20000 prot-na_11600.pdb -501366.31 2026-10-23 14:23:30 11700/20000 prot-na_11700.pdb -1254342.54 2026-10-23 14:24:10 11800/20000 prot-na_11800.pdb -2613843.83 2026-10-23 14:24:49 11900/20000 prot-na_11900.pdb -2957156.24 2026-10-23 14:25:28 12000/20000 prot-na_12000.pdb -1802673.08 2026-10-23 14:26:07 12100/20000 prot-na_12100.pdb -935318.67 2026-10-23 14:26:46 12200/20000 prot-na_12200.pdb -2441798.40 2026-10-23 14:27:31 12300/20000 prot-na_12300.pdb -1093257.26 2026-10-23 14:28:11 12400/20000 prot-na_12400.pdb -1995540.51 2026-10-23 14:28:50 12500/20000 prot-na_12500.pdb -785393.93 2026-10-23 14:29:29 12600/20000 prot-na_12600.pdb -1912260.68 2026-10-23 14:30:08 12700/20000 prot-na_12700.pdb -1026904.91 2026-10-23 14:30:47 12800/20000 prot-na_12800.pdb -1483992.21 2026-10-23 14:31:26 12900/20000 prot-na_12900.pdb -1575029.95 2026-10-23 14:32:06 13000/20000 prot-na_13000.pdb -1837199.04 2026-10-23 14:32:44 13100/20000 prot-na_13100.pdb -1400507.64 2026-10-23 14:33:24 13200/20000 prot-na_13200.pdb -1528776.09 2026-10-23 14:34:03 13300/20000 prot-na_13300.pdb -1388603.58 2026-10-23 14:34:41 13400/20000 prot-na_13400.pdb -1234895.62 2026-10-23 14:35:20 13500/20000 prot-na_13500.pdb -1502158.16 2026-10-23 14:36:00 13600/20000 prot-na_13600.pdb -2377152.53 2026-10-23 14:36:38 13700/20000 prot-na_13700.pdb -1226171.41 2026-10-23 14:37:17 13800/20000 prot-na_13800.pdb -1885851.16 2026-10-23 14:37:57 13900/20000 prot-na_13900.pdb -780448.38 2026-10-23 14:38:36 14000/20000 prot-na_14000.pdb -2423188.67 2026-10-23 14:39:15 14100/20000 prot-na_14100.pdb -915749.99 2026-10-23 14:39:55 14200/20000 prot-na_14200.pdb -1375979.69 2026-10-23 14:40:34 14300/20000 prot-na_14300.pdb -2557048.35 2026-10-23 14:41:13 14400/20000 prot-na_14400.pdb -1634205.44 2026-10-23 14:41:53 14500/20000 prot-na_14500.pdb -2107597.21 2026-10-23 14:42:31 14600/20000 prot-na_14600.pdb -1352321.10 2026-10-23 14:43:15 14700/20000 prot-na_14700.pdb -1315029.61 2026-10-23 14:43:54 14800/20000 prot-na_14800.pdb -1036185.03 2026-10-23 14:44:33 14900/20000 prot-na_14900.pdb -1114179.79 2026-10-23 14:45:13 15000/20000 prot-na_15000.pdb -3343729.96 2026-10-23 14:45:52 15100/20000 prot-na_15100.pdb -1168286.61 2026-10-23 14:46:31 15200/20000 prot-na_15200.pdb -1925864.99 2026-10-23 14:47:11 15300/20000 prot-na_15300.pdb -1087225.02 2026-10-23 14:47:50 15400/20000 prot-na_15400.pdb -2362298.76 2026-10-23 14:48:29 15500/20000 prot-na_15500.pdb -2205783.26 2026-10-23 14:49:09 15600/20000 prot-na_15600.pdb -2059225.87 2026-10-23 14:49:49 15700/20000 prot-na_15700.pdb -1412037.95 2026-10-23 14:50:29 15800/20000 prot-na_15800.pdb -2383710.91 2026-10-23 14:51:09 15900/20000 prot-na_15900.pdb -2576983.63 2026-10-23 14:51:48 16000/20000 prot-na_16000.pdb -2229698.75 2026-10-23 14:52:28 16100/20000 prot-na_16100.pdb -1622849.75 2026-10-23 14:53:07 16200/20000 prot-na_16200.pdb -2198675.82 2026-10-23 14:53:47 16300/20000 prot-na_16300.pdb -1769901.66 2026-10-23 14:54:27 16400/20000 prot-na_16400.pdb -1724817.38 2026-10-23 14:55:07 16500/20000 prot-na_16500.pdb -849133.89 2026-10-23 14:55:46 16600/20000 prot-na_16600.pdb -2066101.01 2026-10-23 14:56:26 16700/20000 prot-na_16700.pdb -1250919.87 2026-10-23 14:57:06 16800/20000 prot-na_16800.pdb -2198465.06 2026-10-23 14:57:46 16900/20000 prot-na_16900.pdb -727340.38 2026-10-23 14:58:25 17000/20000 prot-na_17000.pdb -1635138.80 2026-10-23 14:59:05 17100/20000 prot-na_17100.pdb -2183186.79 2026-10-23 14:59:45 17200/20000 prot-na_17200.pdb -1456599.95 2026-10-23 15:00:24 17300/20000 prot-na_17300.pdb -2054967.12 2026-10-23 15:01:05 17400/20000 prot-na_17400.pdb -1017317.42 2026-10-23 15:01:44 17500/20000 prot-na_17500.pdb -3394981.81 2026-10-23 15:02:24 17600/20000 prot-na_17600.pdb -1599014.15 2026-10-23 15:03:04 17700/20000 prot-na_17700.pdb -1855425.30 2026-10-23 15:03:43 17800/20000 prot-na_17800.pdb -2062747.13 2026-10-23 15:04:23 17900/20000 prot-na_17900.pdb -1838437.73 2026-10-23 15:05:03 18000/20000 prot-na_18000.pdb -1188832.55 2026-10-23 15:05:42 18100/20000 prot-na_18100.pdb -2039757.88 2026-10-23 15:06:22 18200/20000 prot-na_18200.pdb -2348794.27 2026-10-23 15:07:01 18300/20000 prot-na_18300.pdb -2225835.56 2026-10-23 15:07:41 18400/20000 prot-na_18400.pdb -824713.58 2026-10-23 15:08:20 18500/20000 prot-na_18500.pdb -1622346.83 2026-10-23 15:08:59 18600/20000 prot-na_18600.pdb -1920224.75 2026-10-23 15:09:39 18700/20000 prot-na_18700.pdb -1413071.85 2026-10-23 15:10:19 18800/20000 prot-na_18800.pdb -1294960.16 2026-10-23 15:10:59 18900/20000 prot-na_18900.pdb -1766439.34 2026-10-23 15:11:40 19000/20000 prot-na_19000.pdb -1027860.08 2026-10-23 15:12:20 19100/20000 prot-na_19100.pdb -1701516.59 2026-10-23 15:13:00 19200/20000 prot-na_19200.pdb -1587934.25 2026-10-23 15:13:40 19300/20000 prot-na_19300.pdb -1962108.32 2026-10-23 15:14:20 19400/20000 prot-na_19400.pdb -1064088.01 2026-10-23 15:14:59 19500/20000 prot-na_19500.pdb -1035410.17 2026-10-23 15:15:39 19600/20000 prot-na_19600.pdb -1517795.46 2026-10-23 15:16:18 19700/20000 prot-na_19700.pdb -1824000.80 2026-10-23 15:16:58 19800/20000 prot-na_19800.pdb -1358675.76 2026-10-23 15:17:37 19900/20000 prot-na_19900.pdb -1181434.43 2026-10-23 15:18:17 20000/20000 prot-na_20000.pdb -1177160.14 2026-10-23 15:18:17 DARS scoring end 2026-10-23 15:18:17 Clustering (cuttoff: 5, nr_clust: 100 ) in progress... 2026-10-23 15:18:17 timeout 72h python /home/rpdock/run_gramm//clustering_v4.py dars_out.txt list.txt 5 100 2026-10-23 15:18:17 100 best scored structures 2026-10-23 15:18:17 1 prot-na_1.pdb -8769133.06 2026-10-23 15:18:17 2 prot-na_2.pdb -8236888.64 2026-10-23 15:18:17 3 prot-na_382.pdb -7319782.82 2026-10-23 15:18:17 4 prot-na_1567.pdb -6051754.66 2026-10-23 15:18:17 5 prot-na_15512.pdb -5912864.72 2026-10-23 15:18:17 6 prot-na_34.pdb -5789449.49 2026-10-23 15:18:17 7 prot-na_5207.pdb -5501471.69 2026-10-23 15:18:17 8 prot-na_19571.pdb -5187861.68 2026-10-23 15:18:17 9 prot-na_3728.pdb -5134391.15 2026-10-23 15:18:17 10 prot-na_8395.pdb -5067959.97 2026-10-23 15:18:17 11 prot-na_4979.pdb -5031965.05 2026-10-23 15:18:17 12 prot-na_6622.pdb -5016503.43 2026-10-23 15:18:17 13 prot-na_312.pdb -5011242.91 2026-10-23 15:18:17 14 prot-na_21.pdb -4892442.23 2026-10-23 15:18:17 15 prot-na_1118.pdb -4871800.77 2026-10-23 15:18:17 16 prot-na_13894.pdb -4836540.35 2026-10-23 15:18:17 17 prot-na_4192.pdb -4831526.48 2026-10-23 15:18:17 18 prot-na_13829.pdb -4798669.55 2026-10-23 15:18:17 19 prot-na_2670.pdb -4796325.92 2026-10-23 15:18:17 20 prot-na_2550.pdb -4791775.85 2026-10-23 15:18:17 21 prot-na_5051.pdb -4791699.32 2026-10-23 15:18:17 22 prot-na_13504.pdb -4788707.85 2026-10-23 15:18:17 23 prot-na_552.pdb -4769927.94 2026-10-23 15:18:17 24 prot-na_315.pdb -4766755.92 2026-10-23 15:18:17 25 prot-na_3468.pdb -4737520.12 2026-10-23 15:18:17 26 prot-na_17255.pdb -4736937.96 2026-10-23 15:18:17 27 prot-na_8247.pdb -4663872.48 2026-10-23 15:18:17 28 prot-na_4005.pdb -4653576.1 2026-10-23 15:18:17 29 prot-na_346.pdb -4652796.42 2026-10-23 15:18:17 30 prot-na_2378.pdb -4629542.66 2026-10-23 15:18:17 31 prot-na_673.pdb -4613465.02 2026-10-23 15:18:17 32 prot-na_12167.pdb -4608158.19 2026-10-23 15:18:17 33 prot-na_8770.pdb -4570899.19 2026-10-23 15:18:17 34 prot-na_19205.pdb -4568869.99 2026-10-23 15:18:17 35 prot-na_39.pdb -4533661.28 2026-10-23 15:18:17 36 prot-na_5929.pdb -4522636.7 2026-10-23 15:18:17 37 prot-na_6100.pdb -4505701.03 2026-10-23 15:18:17 38 prot-na_2201.pdb -4497669.54 2026-10-23 15:18:17 39 prot-na_6621.pdb -4485599.34 2026-10-23 15:18:17 40 prot-na_106.pdb -4475154.01 2026-10-23 15:18:17 41 prot-na_344.pdb -4467370.25 2026-10-23 15:18:17 42 prot-na_6623.pdb -4460771.43 2026-10-23 15:18:17 43 prot-na_12589.pdb -4439363.63 2026-10-23 15:18:17 44 prot-na_10947.pdb -4437581.72 2026-10-23 15:18:17 45 prot-na_6865.pdb -4431521.82 2026-10-23 15:18:17 46 prot-na_17587.pdb -4427756.54 2026-10-23 15:18:17 47 prot-na_2736.pdb -4407413.48 2026-10-23 15:18:17 48 prot-na_14879.pdb -4406616.99 2026-10-23 15:18:17 49 prot-na_16173.pdb -4403953.42 2026-10-23 15:18:17 50 prot-na_2667.pdb -4386759.12 2026-10-23 15:18:17 51 prot-na_9805.pdb -4380226.88 2026-10-23 15:18:17 52 prot-na_18449.pdb -4373060.94 2026-10-23 15:18:17 53 prot-na_9198.pdb -4363575.59 2026-10-23 15:18:17 54 prot-na_14332.pdb -4348309.93 2026-10-23 15:18:17 55 prot-na_2185.pdb -4336587.54 2026-10-23 15:18:17 56 prot-na_12529.pdb -4327206.9 2026-10-23 15:18:17 57 prot-na_154.pdb -4326923.23 2026-10-23 15:18:17 58 prot-na_19012.pdb -4321127.84 2026-10-23 15:18:17 59 prot-na_18590.pdb -4320826.0 2026-10-23 15:18:17 60 prot-na_8084.pdb -4319994.21 2026-10-23 15:18:17 61 prot-na_123.pdb -4313671.24 2026-10-23 15:18:17 62 prot-na_15744.pdb -4313616.65 2026-10-23 15:18:17 63 prot-na_8903.pdb -4309726.95 2026-10-23 15:18:17 64 prot-na_8239.pdb -4308921.56 2026-10-23 15:18:17 65 prot-na_2416.pdb -4307658.04 2026-10-23 15:18:17 66 prot-na_567.pdb -4291624.98 2026-10-23 15:18:17 67 prot-na_18292.pdb -4277776.57 2026-10-23 15:18:17 68 prot-na_2768.pdb -4273527.78 2026-10-23 15:18:17 69 prot-na_478.pdb -4266489.74 2026-10-23 15:18:17 70 prot-na_8727.pdb -4262336.12 2026-10-23 15:18:17 71 prot-na_17659.pdb -4252894.99 2026-10-23 15:18:17 72 prot-na_13073.pdb -4237874.54 2026-10-23 15:18:17 73 prot-na_1506.pdb -4228032.4 2026-10-23 15:18:17 74 prot-na_10667.pdb -4224619.43 2026-10-23 15:18:17 75 prot-na_2842.pdb -4224380.33 2026-10-23 15:18:17 76 prot-na_11377.pdb -4220875.07 2026-10-23 15:18:17 77 prot-na_18410.pdb -4201754.82 2026-10-23 15:18:17 78 prot-na_2682.pdb -4200922.9 2026-10-23 15:18:17 79 prot-na_966.pdb -4200789.66 2026-10-23 15:18:17 80 prot-na_9579.pdb -4197245.65 2026-10-23 15:18:17 81 prot-na_4757.pdb -4191218.11 2026-10-23 15:18:17 82 prot-na_11878.pdb -4183514.82 2026-10-23 15:18:17 83 prot-na_5732.pdb -4181755.23 2026-10-23 15:18:17 84 prot-na_17446.pdb -4176819.35 2026-10-23 15:18:17 85 prot-na_18221.pdb -4164018.4 2026-10-23 15:18:17 86 prot-na_3579.pdb -4161531.79 2026-10-23 15:18:17 87 prot-na_1022.pdb -4157601.22 2026-10-23 15:18:17 88 prot-na_286.pdb -4155191.81 2026-10-23 15:18:17 89 prot-na_5167.pdb -4150724.24 2026-10-23 15:18:17 90 prot-na_15750.pdb -4148393.85 2026-10-23 15:18:17 91 prot-na_2535.pdb -4144436.48 2026-10-23 15:18:17 92 prot-na_5936.pdb -4141127.21 2026-10-23 15:18:17 93 prot-na_3021.pdb -4127733.64 2026-10-23 15:18:17 94 prot-na_1838.pdb -4125199.62 2026-10-23 15:18:17 95 prot-na_5218.pdb -4119313.51 2026-10-23 15:18:17 96 prot-na_1546.pdb -4118377.51 2026-10-23 15:18:17 97 prot-na_7471.pdb -4109456.66 2026-10-23 15:18:17 98 prot-na_13242.pdb -4100613.46 2026-10-23 15:18:17 99 prot-na_15923.pdb -4097472.08 2026-10-23 15:18:17 100 prot-na_12798.pdb -4081525.41 2026-10-23 15:18:17 Chains: C 2026-10-23 15:18:45 100 best scored structures 2026-10-23 15:18:45 GRAMM analysis selected for further analysis: prot-na_30 2026-10-23 15:18:45 Cluster #1 with 5 structures 2026-10-23 15:18:45 1 prot-na_312.pdb -5011242.91 2026-10-23 15:18:45 2 prot-na_13829.pdb -4798669.55 2026-10-23 15:18:45 3 prot-na_2550.pdb -4791775.85 2026-10-23 15:18:45 4 prot-na_5929.pdb -4522636.7 2026-10-23 15:18:45 5 prot-na_5218.pdb -4119313.51 2026-10-23 15:18:45 Sent to refinement: clusters_found|prot-na_312.pdb 2026-10-23 15:18:45 Sent to refinement: clusters_found|prot-na_312.pdb 2026-10-23 15:18:45 DARS clustering end 2026-10-23 15:18:45 MC (refinement) init 2026-10-23 15:18:45 timeout 72h python /home/rpdock/run_gramm//run_mc.py -f dars_to_mc.txt -d /home/rpdock/web/media/jobs/d0c280cb-2ab6-427b-a7a4-b709e96386b0/ 2026-10-23 15:18:45 Refinement of #1 /home/rpdock/web/media/jobs/d0c280cb-2ab6-427b-a7a4-b709e96386b0/prot-na_312.pdb 2026-10-23 15:18:45 python /home/rpdock/mc/MC.py -s 1000 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/d0c280cb-2ab6-427b-a7a4-b709e96386b0//ref_struc/prot-na_312/prot-na_312.pdb 2026-10-23 15:28:37 start - parameters: File name /home/rpdock/web/media/jobs/d0c280cb-2ab6-427b-a7a4-b709e96386b0//ref_struc/prot-na_312/prot-na_312.pdb Steps 1000 Temp. start 15000.0 Temp. end 295.0 False msg start - parameters: File name /home/rpdock/web/media/jobs/d0c280cb-2ab6-427b-a7a4-b709e96386b0//ref_struc/prot-na_312/prot-na_312.pdb Steps 1000 Temp. start 15000.0 Temp. end 295.0 False Step E Edist Eang Epen 0 - -3465156.79 -2101451.42 -1963705.37 600000.00 1 R -3234420.64 -2133284.17 -2001136.47 900000.00 T= 14808.835 K progress 0.1 2 R -3249740.50 -2140636.03 -2009104.47 900000.00 T= 14794.13 K progress 0.2 3 R -3280448.59 -2164984.38 -2015464.21 900000.00 T= 14779.425 K progress 0.3 4 T -3101799.29 -2069263.52 -1932535.77 900000.00 T= 14735.31 K progress 0.4 5 R -2852461.57 -1929561.91 -1822899.66 900000.00 T= 14661.785 K progress 0.5 6 R -3032570.26 -2054614.12 -1877956.14 900000.00 T= 14632.375 K progress 0.6 7 T -3315900.35 -2177793.98 -2038106.37 900000.00 T= 14617.67 K progress 0.7 8 T -3771945.96 -2210345.51 -2061600.45 500000.00 T= 14529.44 K progress 0.8 9 R -3787383.23 -2226432.92 -2060950.30 500000.00 T= 14470.62 K progress 0.9 10 R -3814949.02 -2237511.45 -2077437.58 500000.00 T= 14220.635 K progress 1.0 11 R -3821215.26 -2240220.64 -2080994.62 500000.00 T= 14073.585 K progress 1.1 12 R -3773740.24 -2207675.49 -2066064.75 500000.00 T= 13867.715 K progress 1.2 13 R -3792871.87 -2231346.28 -2061525.59 500000.00 T= 13573.615 K progress 1.3 14 T -3774880.48 -2220492.25 -2054388.23 500000.00 T= 13514.795 K progress 1.4 15 R -3670492.36 -2222049.52 -2048442.84 600000.00 T= 13426.565 K progress 1.5 16 R -3638122.71 -2140098.23 -1998024.48 500000.00 T= 13382.45 K progress 1.6 17 R -3732302.03 -2201145.06 -2031156.97 500000.00 T= 13367.745 K progress 1.7 18 R -3654866.15 -2150175.36 -2004690.79 500000.00 T= 13308.925 K progress 1.8 19 R -3655584.10 -2157158.23 -1998425.86 500000.00 T= 13279.515 K progress 1.9 20 T -3569876.18 -2184370.44 -1985505.74 600000.00 T= 13073.645 K progress 2.0 21 R -3691460.52 -2180758.70 -2010701.82 500000.00 T= 13058.94 K progress 2.1 22 R -3706754.79 -2193944.51 -2012810.29 500000.00 T= 13029.53 K progress 2.2 23 T -3572720.95 -2157174.77 -2015546.19 600000.00 T= 13014.825 K progress 2.3 24 R -3576585.28 -2160655.22 -2015930.05 600000.00 T= 12911.89 K progress 2.4 25 R -3689092.66 -2234564.02 -2054528.64 600000.00 T= 12853.07 K progress 2.5 26 R -3729653.29 -2182922.34 -2046730.94 500000.00 T= 12808.955 K progress 2.6 27 T -3623959.69 -2182406.16 -2041553.53 600000.00 T= 12764.84 K progress 2.7 28 R -3665338.02 -2195769.05 -2069568.97 600000.00 T= 12676.61 K progress 2.8 29 T -3608843.26 -2245828.22 -2063015.05 700000.00 T= 12617.79 K progress 2.9 30 R -3543566.72 -2233797.62 -2009769.11 700000.00 T= 12514.855 K progress 3.0 31 T -3428058.67 -2159191.98 -1968866.69 700000.00 T= 12485.445 K progress 3.1 32 R -3494389.56 -2203087.35 -1991302.22 700000.00 T= 12456.035 K progress 3.2 33 R -3501458.67 -2206629.63 -1994829.04 700000.00 T= 12353.1 K progress 3.3 34 T -3850033.52 -2352554.27 -2097479.25 600000.00 T= 12323.69 K progress 3.4 35 R -3883777.97 -2336718.59 -2147059.37 600000.00 T= 12191.345 K progress 3.5 36 R -3861193.90 -2327777.55 -2133416.36 600000.00 T= 11823.72 K progress 3.6 37 R -3860894.36 -2360742.21 -2100152.16 600000.00 T= 11750.195 K progress 3.7 38 R -3865972.66 -2330322.73 -2135649.93 600000.00 T= 11691.375 K progress 3.8 39 R -3986937.78 -2339610.81 -2147326.98 500000.00 T= 11206.11 K progress 3.9 40 R -3890678.30 -2334649.44 -2156028.86 600000.00 T= 10853.19 K progress 4.0 41 R -3594728.83 -2244018.51 -2050710.33 700000.00 T= 9779.725 K progress 4.1 42 R -3730202.51 -2265762.11 -2064440.40 600000.00 T= 9735.61 K progress 4.2 43 R -3910377.27 -2337748.91 -2172628.36 600000.00 T= 9617.97 K progress 4.3 44 R -3776450.69 -2287355.08 -2089095.61 600000.00 T= 8897.425 K progress 4.4 45 R -3797033.27 -2293287.26 -2103746.01 600000.00 T= 8838.605 K progress 4.5 46 R -3900386.06 -2337903.22 -2162482.84 600000.00 T= 8573.915 K progress 4.6 47 R -3893718.20 -2335150.77 -2158567.44 600000.00 T= 7691.615 K progress 4.7 48 R -3866338.13 -2323120.43 -2143217.71 600000.00 T= 7544.565 K progress 4.8 49 T -3919987.45 -2303094.36 -2116893.10 500000.00 T= 7088.71 K progress 4.9 50 R -3933590.28 -2305451.90 -2128138.38 500000.00 T= 6662.265 K progress 5.0 51 R -3903255.12 -2293726.09 -2109529.02 500000.00 T= 5529.98 K progress 5.1 52 R -3915659.50 -2303851.40 -2111808.10 500000.00 T= 5500.57 K progress 5.2 53 R -3912395.10 -2300587.00 -2111808.10 500000.00 T= 4912.37 K progress 5.3 54 R -3910515.86 -2300461.03 -2110054.82 500000.00 T= 4809.435 K progress 5.4 55 R -3896518.50 -2289526.04 -2106992.46 500000.00 T= 4662.385 K progress 5.5 56 R -3932542.06 -2307137.71 -2125404.35 500000.00 T= 4103.595 K progress 5.6 57 R -3932516.27 -2307137.71 -2125378.57 500000.00 T= 692.035 K progress 5.7 Save no big msg save short traj msg save best.pdb msg save plot e_step.png Fri Oct 23 15:18:45 2026 ['prot-na_312.pdb'] msg Refinement of #1 /home/rpdock/web/media/jobs/d0c280cb-2ab6-427b-a7a4-b709e96386b0/prot-na_312.pdb dir: /home/rpdock/web/media/jobs/d0c280cb-2ab6-427b-a7a4-b709e96386b0/ file: prot-na_312.pdb find `pwd` -iname prot-na_312.pdb copy /home/rpdock/web/media/jobs/d0c280cb-2ab6-427b-a7a4-b709e96386b0/prot-na_30/prot-na_312.pdb to /home/rpdock/web/media/jobs/d0c280cb-2ab6-427b-a7a4-b709e96386b0//ref_struc/prot-na_312/prot-na_312.pdb cmd: python /home/rpdock/mc/MC.py -s 1000 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/d0c280cb-2ab6-427b-a7a4-b709e96386b0//ref_struc/prot-na_312/prot-na_312.pdb msg python /home/rpdock/mc/MC.py -s 1000 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/d0c280cb-2ab6-427b-a7a4-b709e96386b0//ref_struc/prot-na_312/prot-na_312.pdb run_mc::OK! = stderr empty 2026-10-23 15:28:37 MC (refinement) end 2026-10-23 15:28:37 OK 2026-10-23 15:28:37 Set finished status of d0c280cb-2ab6-427b-a7a4-b709e96386b0