2026-07-26 18:05:02 NPdock start 2026-07-26 18:05:02 ver: server 2026-07-26 18:05:02 mode: 11111 2026-07-26 18:05:02 is RNA? 1 2026-07-26 18:05:02 Interface: prot: '' na: '' 2026-07-26 18:05:02 Curr dir:/home/rpdock/web/media/jobs/22d2d6a7-5d68-4e34-b967-3f99034261e4/ 2026-07-26 18:05:02 GRAMM in progress... 2026-07-26 18:05:02 python /home/rpdock/run_gramm//run_gramm1.py -d 20000 -p prot.pdb -r na.pdb -pi '' -ri '' -n 1 -pf '*' -rf '*' 2026-07-26 18:40:46 GRAMM done 2026-07-26 18:40:46 DARS scoring in progress... 2026-07-26 18:40:46 time python /home/rpdock/run_gramm//DARS-RNP_v3//DARS_potential_v3_scoring.py -m 100 -f list.txt -o dars_out.txt 2026-07-26 18:40:47 DARS start [DARS_potential_v3_scoring.py] 2026-07-26 18:40:47 Show log every 100 structures [DARS_potential_v3_scoring.py] 2026-07-26 18:40:47 1/20000 na-prot_1000.pdb -739978.73 2026-07-26 18:41:00 100/20000 na-prot_94.pdb -2868398.08 2026-07-26 18:41:14 200/20000 na-prot_194.pdb -1583547.43 2026-07-26 18:41:29 300/20000 na-prot_294.pdb -1522648.11 2026-07-26 18:41:43 400/20000 na-prot_394.pdb -1447608.55 2026-07-26 18:41:57 500/20000 na-prot_494.pdb -1251133.28 2026-07-26 18:42:11 600/20000 na-prot_594.pdb -1399742.38 2026-07-26 18:42:25 700/20000 na-prot_694.pdb -1479073.88 2026-07-26 18:42:39 800/20000 na-prot_794.pdb -1608627.52 2026-07-26 18:42:53 900/20000 na-prot_894.pdb -556194.52 2026-07-26 18:43:07 1000/20000 na-prot_994.pdb -2410828.31 2026-07-26 18:43:21 1100/20000 na-prot_1100.pdb -1434147.78 2026-07-26 18:43:35 1200/20000 na-prot_1200.pdb -1318836.87 2026-07-26 18:43:50 1300/20000 na-prot_1300.pdb -2020496.82 2026-07-26 18:44:04 1400/20000 na-prot_1400.pdb -2389839.58 2026-07-26 18:44:19 1500/20000 na-prot_1500.pdb -571573.01 2026-07-26 18:44:33 1600/20000 na-prot_1600.pdb -2132153.40 2026-07-26 18:44:46 1700/20000 na-prot_1700.pdb -1255522.04 2026-07-26 18:45:00 1800/20000 na-prot_1800.pdb -3188642.99 2026-07-26 18:45:15 1900/20000 na-prot_1900.pdb -959368.06 2026-07-26 18:45:28 2000/20000 na-prot_2000.pdb -1789681.88 2026-07-26 18:45:42 2100/20000 na-prot_2100.pdb -734626.05 2026-07-26 18:45:56 2200/20000 na-prot_2200.pdb -1681123.20 2026-07-26 18:46:11 2300/20000 na-prot_2300.pdb -1190598.89 2026-07-26 18:46:24 2400/20000 na-prot_2400.pdb -1046103.46 2026-07-26 18:46:38 2500/20000 na-prot_2500.pdb -1539671.30 2026-07-26 18:46:52 2600/20000 na-prot_2600.pdb -1367665.56 2026-07-26 18:47:06 2700/20000 na-prot_2700.pdb -877630.20 2026-07-26 18:47:21 2800/20000 na-prot_2800.pdb -1980651.02 2026-07-26 18:47:36 2900/20000 na-prot_2900.pdb -2679945.07 2026-07-26 18:47:50 3000/20000 na-prot_3000.pdb -2410596.20 2026-07-26 18:48:05 3100/20000 na-prot_3100.pdb -986263.28 2026-07-26 18:48:19 3200/20000 na-prot_3200.pdb -1313031.55 2026-07-26 18:48:33 3300/20000 na-prot_3300.pdb -1396079.42 2026-07-26 18:48:46 3400/20000 na-prot_3400.pdb -1522189.99 2026-07-26 18:49:00 3500/20000 na-prot_3500.pdb -1205816.20 2026-07-26 18:49:14 3600/20000 na-prot_3600.pdb -735584.01 2026-07-26 18:49:28 3700/20000 na-prot_3700.pdb -951155.34 2026-07-26 18:49:42 3800/20000 na-prot_3800.pdb -1127417.65 2026-07-26 18:49:56 3900/20000 na-prot_3900.pdb -1953007.79 2026-07-26 18:50:10 4000/20000 na-prot_4000.pdb -1162513.64 2026-07-26 18:50:23 4100/20000 na-prot_4100.pdb -661632.74 2026-07-26 18:50:37 4200/20000 na-prot_4200.pdb -1985368.07 2026-07-26 18:50:51 4300/20000 na-prot_4300.pdb -2255513.77 2026-07-26 18:51:04 4400/20000 na-prot_4400.pdb -1431122.19 2026-07-26 18:51:18 4500/20000 na-prot_4500.pdb -2015391.15 2026-07-26 18:51:32 4600/20000 na-prot_4600.pdb -1544541.81 2026-07-26 18:51:45 4700/20000 na-prot_4700.pdb -1839401.89 2026-07-26 18:51:58 4800/20000 na-prot_4800.pdb -2590881.09 2026-07-26 18:52:12 4900/20000 na-prot_4900.pdb -1649804.46 2026-07-26 18:52:26 5000/20000 na-prot_5000.pdb -594139.17 2026-07-26 18:52:39 5100/20000 na-prot_5100.pdb -1530597.98 2026-07-26 18:52:53 5200/20000 na-prot_5200.pdb -2262226.54 2026-07-26 18:53:06 5300/20000 na-prot_5300.pdb -1892501.35 2026-07-26 18:53:20 5400/20000 na-prot_5400.pdb -1325496.52 2026-07-26 18:53:33 5500/20000 na-prot_5500.pdb -1934654.01 2026-07-26 18:53:47 5600/20000 na-prot_5600.pdb -1627922.36 2026-07-26 18:54:00 5700/20000 na-prot_5700.pdb -1084516.04 2026-07-26 18:54:14 5800/20000 na-prot_5800.pdb -1527658.84 2026-07-26 18:54:28 5900/20000 na-prot_5900.pdb -1268197.69 2026-07-26 18:54:41 6000/20000 na-prot_6000.pdb -2488390.46 2026-07-26 18:54:54 6100/20000 na-prot_6100.pdb -1109614.16 2026-07-26 18:55:08 6200/20000 na-prot_6200.pdb -1737148.10 2026-07-26 18:55:21 6300/20000 na-prot_6300.pdb -2577978.74 2026-07-26 18:55:35 6400/20000 na-prot_6400.pdb -1575583.95 2026-07-26 18:55:48 6500/20000 na-prot_6500.pdb -1405849.24 2026-07-26 18:56:02 6600/20000 na-prot_6600.pdb -922488.68 2026-07-26 18:56:15 6700/20000 na-prot_6700.pdb -1321736.55 2026-07-26 18:56:29 6800/20000 na-prot_6800.pdb -728949.92 2026-07-26 18:56:42 6900/20000 na-prot_6900.pdb -2319742.64 2026-07-26 18:56:55 7000/20000 na-prot_7000.pdb -1428011.08 2026-07-26 18:57:09 7100/20000 na-prot_7100.pdb -1324287.71 2026-07-26 18:57:22 7200/20000 na-prot_7200.pdb -1462026.88 2026-07-26 18:57:36 7300/20000 na-prot_7300.pdb -3481470.17 2026-07-26 18:57:49 7400/20000 na-prot_7400.pdb -1282967.91 2026-07-26 18:58:02 7500/20000 na-prot_7500.pdb -2438923.32 2026-07-26 18:58:16 7600/20000 na-prot_7600.pdb -1775648.75 2026-07-26 18:58:29 7700/20000 na-prot_7700.pdb -1076415.53 2026-07-26 18:58:42 7800/20000 na-prot_7800.pdb -1539070.52 2026-07-26 18:58:55 7900/20000 na-prot_7900.pdb -2450275.56 2026-07-26 18:59:09 8000/20000 na-prot_8000.pdb -837343.33 2026-07-26 18:59:22 8100/20000 na-prot_8100.pdb -1237173.32 2026-07-26 18:59:36 8200/20000 na-prot_8200.pdb -510214.91 2026-07-26 18:59:49 8300/20000 na-prot_8300.pdb -2223735.46 2026-07-26 19:00:02 8400/20000 na-prot_8400.pdb -1161082.87 2026-07-26 19:00:16 8500/20000 na-prot_8500.pdb -1929558.11 2026-07-26 19:00:29 8600/20000 na-prot_8600.pdb -658261.38 2026-07-26 19:00:42 8700/20000 na-prot_8700.pdb -1471778.16 2026-07-26 19:00:56 8800/20000 na-prot_8800.pdb -1608039.36 2026-07-26 19:01:09 8900/20000 na-prot_8900.pdb -1665911.10 2026-07-26 19:01:22 9000/20000 na-prot_9000.pdb -1569164.95 2026-07-26 19:01:36 9100/20000 na-prot_9100.pdb -1412779.91 2026-07-26 19:01:50 9200/20000 na-prot_9200.pdb -899544.40 2026-07-26 19:02:03 9300/20000 na-prot_9300.pdb -1239680.07 2026-07-26 19:02:16 9400/20000 na-prot_9400.pdb -798325.44 2026-07-26 19:02:29 9500/20000 na-prot_9500.pdb -1050463.35 2026-07-26 19:02:43 9600/20000 na-prot_9600.pdb -1825807.43 2026-07-26 19:02:56 9700/20000 na-prot_9700.pdb -873429.89 2026-07-26 19:03:10 9800/20000 na-prot_9800.pdb -978560.46 2026-07-26 19:03:23 9900/20000 na-prot_9900.pdb -1513591.06 2026-07-26 19:03:36 10000/20000 na-prot_10000.pdb -2163685.48 2026-07-26 19:03:50 10100/20000 na-prot_10100.pdb -1231246.93 2026-07-26 19:04:03 10200/20000 na-prot_10200.pdb -807224.62 2026-07-26 19:04:16 10300/20000 na-prot_10300.pdb -1377944.73 2026-07-26 19:04:30 10400/20000 na-prot_10400.pdb -2082188.95 2026-07-26 19:04:43 10500/20000 na-prot_10500.pdb -2784695.21 2026-07-26 19:04:56 10600/20000 na-prot_10600.pdb -614209.60 2026-07-26 19:05:10 10700/20000 na-prot_10700.pdb -1299608.28 2026-07-26 19:05:23 10800/20000 na-prot_10800.pdb -1222035.97 2026-07-26 19:05:37 10900/20000 na-prot_10900.pdb -1049615.52 2026-07-26 19:05:50 11000/20000 na-prot_11000.pdb -1547572.00 2026-07-26 19:06:03 11100/20000 na-prot_11100.pdb -1245519.13 2026-07-26 19:06:17 11200/20000 na-prot_11200.pdb -1388380.50 2026-07-26 19:06:30 11300/20000 na-prot_11300.pdb -1543531.73 2026-07-26 19:06:43 11400/20000 na-prot_11400.pdb -928306.07 2026-07-26 19:06:56 11500/20000 na-prot_11500.pdb -1380037.10 2026-07-26 19:07:10 11600/20000 na-prot_11600.pdb -2726876.27 2026-07-26 19:07:23 11700/20000 na-prot_11700.pdb -1548648.51 2026-07-26 19:07:36 11800/20000 na-prot_11800.pdb -1289160.49 2026-07-26 19:07:50 11900/20000 na-prot_11900.pdb -2461778.40 2026-07-26 19:08:03 12000/20000 na-prot_12000.pdb -1655984.57 2026-07-26 19:08:17 12100/20000 na-prot_12100.pdb -1528420.55 2026-07-26 19:08:30 12200/20000 na-prot_12200.pdb -1632491.92 2026-07-26 19:08:43 12300/20000 na-prot_12300.pdb -629253.91 2026-07-26 19:08:56 12400/20000 na-prot_12400.pdb -1185565.81 2026-07-26 19:09:09 12500/20000 na-prot_12500.pdb -1947852.06 2026-07-26 19:09:23 12600/20000 na-prot_12600.pdb -426238.37 2026-07-26 19:09:36 12700/20000 na-prot_12700.pdb -1139568.45 2026-07-26 19:09:49 12800/20000 na-prot_12800.pdb -1060231.79 2026-07-26 19:10:03 12900/20000 na-prot_12900.pdb -1034090.80 2026-07-26 19:10:16 13000/20000 na-prot_13000.pdb -2063923.95 2026-07-26 19:10:30 13100/20000 na-prot_13100.pdb -2207074.74 2026-07-26 19:10:43 13200/20000 na-prot_13200.pdb -1808994.46 2026-07-26 19:10:56 13300/20000 na-prot_13300.pdb -1374130.44 2026-07-26 19:11:10 13400/20000 na-prot_13400.pdb -1074321.23 2026-07-26 19:11:23 13500/20000 na-prot_13500.pdb -795938.79 2026-07-26 19:11:37 13600/20000 na-prot_13600.pdb -653015.52 2026-07-26 19:11:50 13700/20000 na-prot_13700.pdb -1071397.09 2026-07-26 19:12:04 13800/20000 na-prot_13800.pdb -1405749.59 2026-07-26 19:12:17 13900/20000 na-prot_13900.pdb -1111681.73 2026-07-26 19:12:30 14000/20000 na-prot_14000.pdb -822697.18 2026-07-26 19:12:44 14100/20000 na-prot_14100.pdb -1581810.32 2026-07-26 19:12:57 14200/20000 na-prot_14200.pdb -1831373.31 2026-07-26 19:13:11 14300/20000 na-prot_14300.pdb -2742727.76 2026-07-26 19:13:24 14400/20000 na-prot_14400.pdb -1467223.18 2026-07-26 19:13:37 14500/20000 na-prot_14500.pdb -2663217.37 2026-07-26 19:13:50 14600/20000 na-prot_14600.pdb -2351568.74 2026-07-26 19:14:04 14700/20000 na-prot_14700.pdb -1508048.16 2026-07-26 19:14:17 14800/20000 na-prot_14800.pdb -1705174.56 2026-07-26 19:14:31 14900/20000 na-prot_14900.pdb -999609.82 2026-07-26 19:14:44 15000/20000 na-prot_15000.pdb -1514426.84 2026-07-26 19:14:57 15100/20000 na-prot_15100.pdb -1428477.95 2026-07-26 19:15:10 15200/20000 na-prot_15200.pdb -1529764.96 2026-07-26 19:15:24 15300/20000 na-prot_15300.pdb -1736018.64 2026-07-26 19:15:37 15400/20000 na-prot_15400.pdb -1395822.33 2026-07-26 19:15:50 15500/20000 na-prot_15500.pdb -1959918.86 2026-07-26 19:16:03 15600/20000 na-prot_15600.pdb -1580189.02 2026-07-26 19:16:17 15700/20000 na-prot_15700.pdb -2000185.26 2026-07-26 19:16:30 15800/20000 na-prot_15800.pdb -2324095.96 2026-07-26 19:16:43 15900/20000 na-prot_15900.pdb -2145351.95 2026-07-26 19:16:56 16000/20000 na-prot_16000.pdb -1987976.37 2026-07-26 19:17:10 16100/20000 na-prot_16100.pdb -1449876.82 2026-07-26 19:17:23 16200/20000 na-prot_16200.pdb -613341.43 2026-07-26 19:17:36 16300/20000 na-prot_16300.pdb -1240795.70 2026-07-26 19:17:50 16400/20000 na-prot_16400.pdb -2075906.51 2026-07-26 19:18:03 16500/20000 na-prot_16500.pdb -1959551.24 2026-07-26 19:18:16 16600/20000 na-prot_16600.pdb -957221.08 2026-07-26 19:18:30 16700/20000 na-prot_16700.pdb -1067573.02 2026-07-26 19:18:43 16800/20000 na-prot_16800.pdb -855083.21 2026-07-26 19:18:56 16900/20000 na-prot_16900.pdb -1247759.36 2026-07-26 19:19:09 17000/20000 na-prot_17000.pdb -1106316.05 2026-07-26 19:19:23 17100/20000 na-prot_17100.pdb -1138910.58 2026-07-26 19:19:36 17200/20000 na-prot_17200.pdb -2193900.21 2026-07-26 19:19:49 17300/20000 na-prot_17300.pdb -1712806.93 2026-07-26 19:20:03 17400/20000 na-prot_17400.pdb -1806335.03 2026-07-26 19:20:16 17500/20000 na-prot_17500.pdb -1411303.48 2026-07-26 19:20:29 17600/20000 na-prot_17600.pdb -657883.76 2026-07-26 19:20:43 17700/20000 na-prot_17700.pdb -2014290.24 2026-07-26 19:20:56 17800/20000 na-prot_17800.pdb -1424569.17 2026-07-26 19:21:09 17900/20000 na-prot_17900.pdb -2480721.13 2026-07-26 19:21:22 18000/20000 na-prot_18000.pdb -1793449.63 2026-07-26 19:21:36 18100/20000 na-prot_18100.pdb -1781976.27 2026-07-26 19:21:50 18200/20000 na-prot_18200.pdb -911727.41 2026-07-26 19:22:03 18300/20000 na-prot_18300.pdb -1374401.64 2026-07-26 19:22:16 18400/20000 na-prot_18400.pdb -1831744.92 2026-07-26 19:22:30 18500/20000 na-prot_18500.pdb -1288561.14 2026-07-26 19:22:43 18600/20000 na-prot_18600.pdb -1014199.78 2026-07-26 19:22:56 18700/20000 na-prot_18700.pdb -2091041.88 2026-07-26 19:23:09 18800/20000 na-prot_18800.pdb -955219.21 2026-07-26 19:23:23 18900/20000 na-prot_18900.pdb -1060811.20 2026-07-26 19:23:36 19000/20000 na-prot_19000.pdb -1089481.71 2026-07-26 19:23:49 19100/20000 na-prot_19100.pdb -972082.57 2026-07-26 19:24:03 19200/20000 na-prot_19200.pdb -3735039.08 2026-07-26 19:24:16 19300/20000 na-prot_19300.pdb -2097359.91 2026-07-26 19:24:29 19400/20000 na-prot_19400.pdb -1221723.49 2026-07-26 19:24:43 19500/20000 na-prot_19500.pdb -791723.81 2026-07-26 19:24:56 19600/20000 na-prot_19600.pdb -1311384.47 2026-07-26 19:25:10 19700/20000 na-prot_19700.pdb -1807817.76 2026-07-26 19:25:23 19800/20000 na-prot_19800.pdb -2584081.53 2026-07-26 19:25:36 19900/20000 na-prot_19900.pdb -1762387.22 2026-07-26 19:25:49 20000/20000 na-prot_20000.pdb -947084.07 2026-07-26 19:25:49 DARS scoring end 2026-07-26 19:25:49 Clustering (cuttoff: 5, nr_clust: 100 ) in progress... 2026-07-26 19:25:49 time python /home/rpdock/run_gramm//clustering_v4.py dars_out.txt list.txt 5 100 2026-07-26 19:25:49 100 best scored structures 2026-07-26 19:25:49 1 na-prot_673.pdb -5069724.9 2026-07-26 19:25:49 2 na-prot_18401.pdb -4814934.26 2026-07-26 19:25:49 3 na-prot_1201.pdb -4507167.74 2026-07-26 19:25:49 4 na-prot_16109.pdb -4466009.15 2026-07-26 19:25:49 5 na-prot_13759.pdb -4294756.2 2026-07-26 19:25:49 6 na-prot_1490.pdb -4177157.98 2026-07-26 19:25:49 7 na-prot_10492.pdb -4156508.92 2026-07-26 19:25:49 8 na-prot_87.pdb -4115476.22 2026-07-26 19:25:49 9 na-prot_40.pdb -4108278.76 2026-07-26 19:25:49 10 na-prot_2964.pdb -4092380.86 2026-07-26 19:25:49 11 na-prot_4832.pdb -4012062.14 2026-07-26 19:25:49 12 na-prot_17630.pdb -3990872.53 2026-07-26 19:25:49 13 na-prot_713.pdb -3968106.66 2026-07-26 19:25:49 14 na-prot_8555.pdb -3965756.32 2026-07-26 19:25:49 15 na-prot_1335.pdb -3962385.71 2026-07-26 19:25:49 16 na-prot_8759.pdb -3954672.7 2026-07-26 19:25:49 17 na-prot_9889.pdb -3904389.41 2026-07-26 19:25:49 18 na-prot_6562.pdb -3879850.65 2026-07-26 19:25:49 19 na-prot_943.pdb -3869301.25 2026-07-26 19:25:49 20 na-prot_106.pdb -3865553.57 2026-07-26 19:25:49 21 na-prot_13301.pdb -3855316.37 2026-07-26 19:25:49 22 na-prot_278.pdb -3782559.53 2026-07-26 19:25:49 23 na-prot_3897.pdb -3779383.42 2026-07-26 19:25:49 24 na-prot_3622.pdb -3750594.78 2026-07-26 19:25:49 25 na-prot_7908.pdb -3742656.4 2026-07-26 19:25:49 26 na-prot_3639.pdb -3741690.31 2026-07-26 19:25:49 27 na-prot_19200.pdb -3735039.08 2026-07-26 19:25:49 28 na-prot_4742.pdb -3691866.31 2026-07-26 19:25:49 29 na-prot_8211.pdb -3668751.45 2026-07-26 19:25:49 30 na-prot_17797.pdb -3646706.8 2026-07-26 19:25:49 31 na-prot_1437.pdb -3629651.91 2026-07-26 19:25:49 32 na-prot_7995.pdb -3627201.95 2026-07-26 19:25:49 33 na-prot_5881.pdb -3600230.7 2026-07-26 19:25:49 34 na-prot_10622.pdb -3594881.09 2026-07-26 19:25:49 35 na-prot_15497.pdb -3588960.88 2026-07-26 19:25:49 36 na-prot_611.pdb -3588638.76 2026-07-26 19:25:49 37 na-prot_529.pdb -3588583.49 2026-07-26 19:25:49 38 na-prot_2234.pdb -3584209.75 2026-07-26 19:25:49 39 na-prot_7834.pdb -3582300.95 2026-07-26 19:25:49 40 na-prot_12437.pdb -3575851.9 2026-07-26 19:25:49 41 na-prot_114.pdb -3566321.66 2026-07-26 19:25:49 42 na-prot_6902.pdb -3535157.1 2026-07-26 19:25:49 43 na-prot_5982.pdb -3533605.8 2026-07-26 19:25:49 44 na-prot_12317.pdb -3526410.26 2026-07-26 19:25:49 45 na-prot_17489.pdb -3526074.68 2026-07-26 19:25:49 46 na-prot_5664.pdb -3520351.43 2026-07-26 19:25:49 47 na-prot_292.pdb -3515482.98 2026-07-26 19:25:49 48 na-prot_4681.pdb -3503442.71 2026-07-26 19:25:49 49 na-prot_17663.pdb -3496373.97 2026-07-26 19:25:49 50 na-prot_2078.pdb -3495271.06 2026-07-26 19:25:49 51 na-prot_6503.pdb -3494552.11 2026-07-26 19:25:49 52 na-prot_1032.pdb -3485605.47 2026-07-26 19:25:49 53 na-prot_19690.pdb -3483702.1 2026-07-26 19:25:49 54 na-prot_5379.pdb -3482324.87 2026-07-26 19:25:49 55 na-prot_7300.pdb -3481470.17 2026-07-26 19:25:49 56 na-prot_3087.pdb -3480284.84 2026-07-26 19:25:49 57 na-prot_75.pdb -3470664.52 2026-07-26 19:25:49 58 na-prot_5325.pdb -3467626.84 2026-07-26 19:25:49 59 na-prot_8935.pdb -3465989.59 2026-07-26 19:25:49 60 na-prot_14818.pdb -3464450.57 2026-07-26 19:25:49 61 na-prot_11511.pdb -3462973.82 2026-07-26 19:25:49 62 na-prot_11889.pdb -3455851.04 2026-07-26 19:25:49 63 na-prot_1283.pdb -3453188.08 2026-07-26 19:25:49 64 na-prot_480.pdb -3450763.78 2026-07-26 19:25:49 65 na-prot_7838.pdb -3438670.66 2026-07-26 19:25:49 66 na-prot_1486.pdb -3429909.12 2026-07-26 19:25:49 67 na-prot_12679.pdb -3428291.35 2026-07-26 19:25:49 68 na-prot_3354.pdb -3421947.55 2026-07-26 19:25:49 69 na-prot_18981.pdb -3416556.58 2026-07-26 19:25:49 70 na-prot_12735.pdb -3413100.82 2026-07-26 19:25:49 71 na-prot_13555.pdb -3397727.54 2026-07-26 19:25:49 72 na-prot_1327.pdb -3377437.17 2026-07-26 19:25:49 73 na-prot_346.pdb -3377302.86 2026-07-26 19:25:49 74 na-prot_3129.pdb -3375456.8 2026-07-26 19:25:49 75 na-prot_19687.pdb -3373832.98 2026-07-26 19:25:49 76 na-prot_4201.pdb -3370425.9 2026-07-26 19:25:49 77 na-prot_11642.pdb -3366714.56 2026-07-26 19:25:49 78 na-prot_3680.pdb -3360884.61 2026-07-26 19:25:49 79 na-prot_15270.pdb -3358729.0 2026-07-26 19:25:49 80 na-prot_7304.pdb -3340072.94 2026-07-26 19:25:49 81 na-prot_9240.pdb -3339092.32 2026-07-26 19:25:49 82 na-prot_15566.pdb -3333898.83 2026-07-26 19:25:49 83 na-prot_12863.pdb -3319706.71 2026-07-26 19:25:49 84 na-prot_4204.pdb -3316180.61 2026-07-26 19:25:49 85 na-prot_18764.pdb -3313827.02 2026-07-26 19:25:49 86 na-prot_1817.pdb -3309301.77 2026-07-26 19:25:49 87 na-prot_1697.pdb -3308836.62 2026-07-26 19:25:49 88 na-prot_577.pdb -3307865.21 2026-07-26 19:25:49 89 na-prot_1759.pdb -3294322.12 2026-07-26 19:25:49 90 na-prot_173.pdb -3293850.78 2026-07-26 19:25:49 91 na-prot_19469.pdb -3293592.08 2026-07-26 19:25:49 92 na-prot_522.pdb -3291872.18 2026-07-26 19:25:49 93 na-prot_5226.pdb -3289191.82 2026-07-26 19:25:49 94 na-prot_15132.pdb -3287621.41 2026-07-26 19:25:49 95 na-prot_15763.pdb -3280446.76 2026-07-26 19:25:49 96 na-prot_17520.pdb -3279421.35 2026-07-26 19:25:49 97 na-prot_312.pdb -3278924.66 2026-07-26 19:25:49 98 na-prot_14280.pdb -3278846.9 2026-07-26 19:25:49 99 na-prot_147.pdb -3278822.67 2026-07-26 19:25:49 100 na-prot_9260.pdb -3272274.23 2026-07-26 19:25:49 Chains: B 2026-07-26 19:26:01 100 best scored structures 2026-07-26 19:26:01 GRAMM analysis selected for further analysis: prot-na_25 2026-07-26 19:26:01 Cluster #1 with 12 structures 2026-07-26 19:26:01 1 na-prot_1490.pdb -4177157.98 2026-07-26 19:26:01 2 na-prot_87.pdb -4115476.22 2026-07-26 19:26:01 3 na-prot_40.pdb -4108278.76 2026-07-26 19:26:01 4 na-prot_713.pdb -3968106.66 2026-07-26 19:26:01 5 na-prot_9889.pdb -3904389.41 2026-07-26 19:26:01 6 na-prot_1437.pdb -3629651.91 2026-07-26 19:26:01 7 na-prot_15497.pdb -3588960.88 2026-07-26 19:26:01 8 na-prot_529.pdb -3588583.49 2026-07-26 19:26:01 9 na-prot_2234.pdb -3584209.75 2026-07-26 19:26:01 10 na-prot_7834.pdb -3582300.95 2026-07-26 19:26:01 11 na-prot_5982.pdb -3533605.8 2026-07-26 19:26:01 12 na-prot_5226.pdb -3289191.82 2026-07-26 19:26:01 Sent to refinement: clusters_found|na-prot_1490.pdb 2026-07-26 19:26:01 Sent to refinement: clusters_found|na-prot_1490.pdb 2026-07-26 19:26:01 DARS clustering end 2026-07-26 19:26:01 MC (refinement) init 2026-07-26 19:26:01 python /home/rpdock/run_gramm//run_mc.py -f dars_to_mc.txt -d /home/rpdock/web/media/jobs/22d2d6a7-5d68-4e34-b967-3f99034261e4/ 2026-07-26 19:26:01 Refinement of #1 /home/rpdock/web/media/jobs/22d2d6a7-5d68-4e34-b967-3f99034261e4/na-prot_1490.pdb 2026-07-26 19:26:01 python /home/rpdock/mc/MC.py -s 1000 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/22d2d6a7-5d68-4e34-b967-3f99034261e4//ref_struc/na-prot_1490/na-prot_1490.pdb 2026-07-26 19:29:20 start - parameters: File name /home/rpdock/web/media/jobs/22d2d6a7-5d68-4e34-b967-3f99034261e4//ref_struc/na-prot_1490/na-prot_1490.pdb Steps 1000 Temp. start 15000.0 Temp. end 295.0 False msg start - parameters: File name /home/rpdock/web/media/jobs/22d2d6a7-5d68-4e34-b967-3f99034261e4//ref_struc/na-prot_1490/na-prot_1490.pdb Steps 1000 Temp. start 15000.0 Temp. end 295.0 False Step E Edist Eang Epen Warning, residue A1 in the chain A has not P atom 0 - -1892403.07 -1927714.84 -1764688.23 1800000.00 1 T -2536456.59 -1891755.72 -1744700.87 1100000.00 T= 14985.295 K progress 0.1 2 T -2687002.40 -1759054.20 -1627948.20 700000.00 T= 14911.77 K progress 0.2 3 T -2703702.85 -1725717.97 -1577984.88 600000.00 T= 14882.36 K progress 0.3 4 T -2734007.78 -1765848.03 -1668159.75 700000.00 T= 14764.72 K progress 0.4 5 R -3006541.24 -1946849.76 -1759691.48 700000.00 T= 14750.015 K progress 0.5 6 R -3010077.85 -1942589.21 -1767488.64 700000.00 T= 14720.605 K progress 0.6 7 R -3017337.12 -2110379.03 -1906958.09 1000000.00 T= 14691.195 K progress 0.7 8 R -2804131.17 -2012317.49 -1791813.68 1000000.00 T= 14588.26 K progress 0.8 9 R -2750526.14 -2023462.71 -1827063.43 1100000.00 T= 14573.555 K progress 0.9 10 R -2788372.92 -2042891.16 -1845481.76 1100000.00 T= 14544.145 K progress 1.0 11 R -2687815.50 -1735420.00 -1652395.50 700000.00 T= 14514.735 K progress 1.1 12 T -2682060.13 -1994083.77 -1787976.36 1100000.00 T= 14500.03 K progress 1.2 13 T -2557196.94 -1808490.85 -1648706.09 900000.00 T= 14294.16 K progress 1.3 14 R -2524816.79 -1914594.56 -1710222.22 1100000.00 T= 14279.455 K progress 1.4 15 T -2351518.66 -1872781.50 -1678737.16 1200000.00 T= 14205.93 K progress 1.5 16 T -2439890.61 -1915286.62 -1724603.98 1200000.00 T= 14191.225 K progress 1.6 17 R -2485881.22 -1942014.39 -1743866.83 1200000.00 T= 14073.585 K progress 1.7 18 T -2618519.19 -1975446.38 -1843072.81 1200000.00 T= 14029.47 K progress 1.8 19 R -2519999.86 -1952366.69 -1867633.17 1300000.00 T= 13985.355 K progress 1.9 20 R -2597797.39 -1990279.19 -1907518.20 1300000.00 T= 13955.945 K progress 2.0 21 T -2607283.06 -1996866.28 -1910416.78 1300000.00 T= 13764.78 K progress 2.1 22 R -2605815.49 -1994888.62 -1910926.87 1300000.00 T= 13750.075 K progress 2.2 23 R -2579680.32 -1949577.91 -1830102.40 1200000.00 T= 13735.37 K progress 2.3 24 T -2527687.68 -1928531.39 -1799156.28 1200000.00 T= 13691.255 K progress 2.4 25 R -2581402.74 -2039629.19 -1941773.55 1400000.00 T= 13661.845 K progress 2.5 26 R -2542617.26 -2024349.47 -1918267.79 1400000.00 T= 13632.435 K progress 2.6 27 R -2553297.22 -2024269.45 -1929027.78 1400000.00 T= 13617.73 K progress 2.7 28 R -2555362.20 -1908566.15 -1846796.06 1200000.00 T= 13500.09 K progress 2.8 29 R -2561573.67 -1918874.15 -1842699.51 1200000.00 T= 13485.385 K progress 2.9 30 R -2508401.99 -1926111.02 -1882290.97 1300000.00 T= 13367.745 K progress 3.0 31 R -2574572.59 -1913381.16 -1861191.43 1200000.00 T= 13279.515 K progress 3.1 32 T -2586658.55 -2065056.01 -1921602.54 1400000.00 T= 13250.105 K progress 3.2 33 T -2315310.62 -2080669.74 -1934640.88 1700000.00 T= 13176.58 K progress 3.3 34 R -2542765.66 -2037454.55 -1905311.11 1400000.00 T= 13161.875 K progress 3.4 35 T -2499351.04 -2019494.65 -1879856.39 1400000.00 T= 13103.055 K progress 3.5 36 T -2437785.88 -2068899.65 -1868886.23 1500000.00 T= 13088.35 K progress 3.6 37 R -2589454.08 -2091225.58 -1898228.50 1400000.00 T= 13000.12 K progress 3.7 38 T -2657886.07 -2177328.33 -1980557.74 1500000.00 T= 12897.185 K progress 3.8 39 T -2635428.06 -2181663.58 -1953764.48 1500000.00 T= 12882.48 K progress 3.9 40 T -2770771.40 -2237638.73 -2033132.67 1500000.00 T= 12853.07 K progress 4.0 41 T -2821451.13 -2096432.14 -1925018.99 1200000.00 T= 12808.955 K progress 4.1 42 R -2924480.54 -2060097.72 -1864382.82 1000000.00 T= 12764.84 K progress 4.2 43 T -2985815.82 -2003089.48 -1782726.33 800000.00 T= 12706.02 K progress 4.3 44 R -2674165.74 -1803886.38 -1670279.36 800000.00 T= 12617.79 K progress 4.4 45 R -2391001.75 -1813480.46 -1677521.28 1100000.00 T= 12573.675 K progress 4.5 46 R -3054815.57 -1916946.45 -1737869.12 600000.00 T= 12500.15 K progress 4.6 47 R -3064810.59 -1980224.50 -1784586.10 700000.00 T= 12441.33 K progress 4.7 48 R -3132740.31 -1967002.22 -1765738.09 600000.00 T= 12220.755 K progress 4.8 49 R -3112465.13 -1939642.24 -1772822.89 600000.00 T= 12147.23 K progress 4.9 50 R -3068763.96 -1993434.84 -1775329.11 700000.00 T= 12029.59 K progress 5.0 51 R -2956723.48 -1996324.06 -1760399.42 800000.00 T= 12000.18 K progress 5.1 52 R -2988840.14 -1942718.57 -1746121.57 700000.00 T= 11941.36 K progress 5.2 53 R -2779550.45 -1812627.22 -1666923.23 700000.00 T= 11779.605 K progress 5.3 54 R -2854197.50 -1800525.15 -1653672.36 600000.00 T= 11691.375 K progress 5.4 55 T -2668178.26 -1983734.82 -1784443.44 1100000.00 T= 11617.85 K progress 5.5 56 T -2562367.76 -2028900.53 -1833467.22 1300000.00 T= 11544.325 K progress 5.6 57 T -2892701.75 -2250633.03 -2042068.72 1400000.00 T= 11529.62 K progress 5.7 58 R -2892841.55 -2255744.80 -2037096.74 1400000.00 T= 11500.21 K progress 5.8 59 T -2817635.77 -2307963.25 -2109672.52 1600000.00 T= 11456.095 K progress 5.9 60 R -2845528.61 -2165419.88 -1980108.73 1300000.00 T= 11367.865 K progress 6.0 61 T -2512645.97 -2147038.74 -1965607.23 1600000.00 T= 11161.995 K progress 6.1 62 R -3069507.00 -2226284.76 -2043222.24 1200000.00 T= 11059.06 K progress 6.2 63 R -3215929.35 -2245979.06 -2069950.29 1100000.00 T= 10838.485 K progress 6.3 64 T -3175565.63 -2234623.00 -2040942.63 1100000.00 T= 10514.975 K progress 6.4 65 R -3149389.14 -2262784.28 -2086604.87 1200000.00 T= 10470.86 K progress 6.5 66 R -3148536.87 -2263594.08 -2084942.79 1200000.00 T= 10279.695 K progress 6.6 67 R -3131777.54 -2270277.43 -2061500.12 1200000.00 T= 10235.58 K progress 6.7 68 R -2743327.51 -2143845.60 -1999481.91 1400000.00 T= 10088.53 K progress 6.8 69 R -2616968.97 -2217300.00 -1999668.97 1600000.00 T= 9897.365 K progress 6.9 70 T -2744525.97 -2070720.50 -1873805.47 1200000.00 T= 9882.66 K progress 7.0 71 T -2680738.79 -1984771.29 -1795967.50 1100000.00 T= 9853.25 K progress 7.1 72 R -2603893.15 -1945549.34 -1758343.81 1100000.00 T= 9779.725 K progress 7.2 73 R -2667812.91 -1980307.85 -1787505.06 1100000.00 T= 9706.2 K progress 7.3 74 T -2394749.81 -1661185.16 -1533564.66 800000.00 T= 9647.38 K progress 7.4 75 R -2426632.26 -1689205.65 -1537426.61 800000.00 T= 9515.035 K progress 7.5 76 T -2566349.72 -1696868.07 -1569481.65 700000.00 T= 9456.215 K progress 7.6 77 R -2551739.03 -1750942.88 -1600796.15 800000.00 T= 9206.23 K progress 7.7 78 T -2513591.17 -1844888.04 -1668703.14 1000000.00 T= 9059.18 K progress 7.8 79 T -2691518.97 -1775795.51 -1615723.46 700000.00 T= 8985.655 K progress 7.9 80 T -2811731.13 -1809829.59 -1701901.54 700000.00 T= 8838.605 K progress 8.0 81 R -2768673.19 -1746515.19 -1622158.00 600000.00 T= 8720.965 K progress 8.1 82 T -2705744.88 -1861565.90 -1744178.98 900000.00 T= 8691.555 K progress 8.2 83 T -2776797.60 -1717561.25 -1559236.35 500000.00 T= 8662.145 K progress 8.3 84 R -2680852.95 -1712136.95 -1568716.00 600000.00 T= 8647.44 K progress 8.4 85 R -2697652.18 -1720961.64 -1576690.53 600000.00 T= 8603.325 K progress 8.5 86 R -2731029.55 -1781730.59 -1649298.96 700000.00 T= 8588.62 K progress 8.6 87 T -3082459.18 -1924662.21 -1857796.96 700000.00 T= 8338.635 K progress 8.7 88 R -3061575.22 -1921099.12 -1840476.10 700000.00 T= 8250.405 K progress 8.8 89 R -3062249.96 -1921773.86 -1840476.10 700000.00 T= 7853.37 K progress 8.9 90 R -3079125.16 -1923497.25 -1855627.92 700000.00 T= 7412.22 K progress 9.0 91 R -3079125.16 -1923497.25 -1855627.92 700000.00 T= 7382.81 K progress 9.1 92 R -3092989.27 -1928650.43 -1864338.84 700000.00 T= 5485.865 K progress 9.2 93 R -3089641.41 -1925302.56 -1864338.84 700000.00 T= 5177.06 K progress 9.3 94 R -3089129.23 -1931830.14 -1857299.10 700000.00 T= 4927.075 K progress 9.4 95 R -3066564.69 -1920437.39 -1846127.31 700000.00 T= 4824.14 K progress 9.5 96 R -3070819.58 -1917610.62 -1853208.96 700000.00 T= 4456.515 K progress 9.6 97 R -3076133.73 -1920373.88 -1855759.85 700000.00 T= 4103.595 K progress 9.7 98 R -3095243.22 -1933333.50 -1861909.72 700000.00 T= 2177.24 K progress 9.8 99 R -3083657.89 -1926872.34 -1856785.55 700000.00 T= 1618.45 K progress 9.9 100 R -3070340.32 -1920210.63 -1850129.70 700000.00 T= 1412.58 K progress 10.0 101 R -3071548.39 -1921251.06 -1850297.33 700000.00 T= 589.1 K progress 10.1 Save no big msg save short traj msg save best.pdb msg save plot e_step.png Sun Jul 26 19:26:01 2026 ['na-prot_1490.pdb'] msg Refinement of #1 /home/rpdock/web/media/jobs/22d2d6a7-5d68-4e34-b967-3f99034261e4/na-prot_1490.pdb dir: /home/rpdock/web/media/jobs/22d2d6a7-5d68-4e34-b967-3f99034261e4/ file: na-prot_1490.pdb find `pwd` -iname na-prot_1490.pdb copy /home/rpdock/web/media/jobs/22d2d6a7-5d68-4e34-b967-3f99034261e4/prot-na_25/na-prot_1490.pdb to /home/rpdock/web/media/jobs/22d2d6a7-5d68-4e34-b967-3f99034261e4//ref_struc/na-prot_1490/na-prot_1490.pdb cmd: python /home/rpdock/mc/MC.py -s 1000 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/22d2d6a7-5d68-4e34-b967-3f99034261e4//ref_struc/na-prot_1490/na-prot_1490.pdb msg python /home/rpdock/mc/MC.py -s 1000 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/22d2d6a7-5d68-4e34-b967-3f99034261e4//ref_struc/na-prot_1490/na-prot_1490.pdb run_mc::OK! = stderr empty 2026-07-26 19:29:20 npdock::MC (refinement) end 2026-07-26 19:29:20 npdock::OK 2026-07-26 19:29:20 Set finished status of 22d2d6a7-5d68-4e34-b967-3f99034261e4