2026-04-28 18:36:04 NPdock start 2026-04-28 18:36:04 ver: server 2026-04-28 18:36:04 mode: 11111 2026-04-28 18:36:04 is RNA? 1 2026-04-28 18:36:04 Interface: prot: '' na: '' 2026-04-28 18:36:04 Curr dir:/home/rpdock/web/media/jobs/629e21dd-2962-42b3-94ab-0391bc554550/ 2026-04-28 18:36:04 GRAMM in progress... 2026-04-28 18:36:04 python /home/rpdock/run_gramm//run_gramm1.py -d 20000 -p prot.pdb -r na.pdb -pi '' -ri '' -n 1 -pf '*' -rf '*' 2026-04-28 19:12:51 GRAMM done 2026-04-28 19:12:51 DARS scoring in progress... 2026-04-28 19:12:51 time python /home/rpdock/run_gramm//DARS-RNP_v3//DARS_potential_v3_scoring.py -m 100 -f list.txt -o dars_out.txt 2026-04-28 19:12:51 DARS start [DARS_potential_v3_scoring.py] 2026-04-28 19:12:51 Show log every 100 structures [DARS_potential_v3_scoring.py] 2026-04-28 19:12:51 1/20000 prot-na_1000.pdb -1091542.60 2026-04-28 19:13:05 100/20000 prot-na_94.pdb -1547493.27 2026-04-28 19:13:19 200/20000 prot-na_194.pdb -2245062.92 2026-04-28 19:13:33 300/20000 prot-na_294.pdb -2586227.72 2026-04-28 19:13:48 400/20000 prot-na_394.pdb -1845439.82 2026-04-28 19:14:02 500/20000 prot-na_494.pdb -1279439.25 2026-04-28 19:14:16 600/20000 prot-na_594.pdb -1507777.00 2026-04-28 19:14:30 700/20000 prot-na_694.pdb -1099339.76 2026-04-28 19:14:44 800/20000 prot-na_794.pdb -1913285.74 2026-04-28 19:14:58 900/20000 prot-na_894.pdb -1524459.65 2026-04-28 19:15:12 1000/20000 prot-na_994.pdb -1247307.97 2026-04-28 19:15:26 1100/20000 prot-na_1100.pdb -1589802.74 2026-04-28 19:15:41 1200/20000 prot-na_1200.pdb -1622843.66 2026-04-28 19:15:55 1300/20000 prot-na_1300.pdb -1644673.10 2026-04-28 19:16:10 1400/20000 prot-na_1400.pdb -863243.80 2026-04-28 19:16:25 1500/20000 prot-na_1500.pdb -1755261.43 2026-04-28 19:16:39 1600/20000 prot-na_1600.pdb -1745318.63 2026-04-28 19:16:53 1700/20000 prot-na_1700.pdb -1041045.95 2026-04-28 19:17:08 1800/20000 prot-na_1800.pdb -1381769.76 2026-04-28 19:17:23 1900/20000 prot-na_1900.pdb -2337701.45 2026-04-28 19:17:37 2000/20000 prot-na_2000.pdb -1034884.39 2026-04-28 19:17:52 2100/20000 prot-na_2100.pdb -2042462.14 2026-04-28 19:18:07 2200/20000 prot-na_2200.pdb -1565391.51 2026-04-28 19:18:21 2300/20000 prot-na_2300.pdb -1626963.54 2026-04-28 19:18:36 2400/20000 prot-na_2400.pdb -2197870.88 2026-04-28 19:18:51 2500/20000 prot-na_2500.pdb -2097350.46 2026-04-28 19:19:06 2600/20000 prot-na_2600.pdb -874553.03 2026-04-28 19:19:20 2700/20000 prot-na_2700.pdb -1259856.53 2026-04-28 19:19:35 2800/20000 prot-na_2800.pdb -926917.75 2026-04-28 19:19:49 2900/20000 prot-na_2900.pdb -1820302.54 2026-04-28 19:20:03 3000/20000 prot-na_3000.pdb -518292.69 2026-04-28 19:20:18 3100/20000 prot-na_3100.pdb -2078946.88 2026-04-28 19:20:32 3200/20000 prot-na_3200.pdb -1882361.38 2026-04-28 19:20:47 3300/20000 prot-na_3300.pdb -1506894.03 2026-04-28 19:21:01 3400/20000 prot-na_3400.pdb -1992857.12 2026-04-28 19:21:16 3500/20000 prot-na_3500.pdb -1817414.31 2026-04-28 19:21:31 3600/20000 prot-na_3600.pdb -1906921.73 2026-04-28 19:21:45 3700/20000 prot-na_3700.pdb -1180672.98 2026-04-28 19:22:00 3800/20000 prot-na_3800.pdb -1989880.42 2026-04-28 19:22:15 3900/20000 prot-na_3900.pdb -1299723.35 2026-04-28 19:22:30 4000/20000 prot-na_4000.pdb -1744661.04 2026-04-28 19:22:44 4100/20000 prot-na_4100.pdb -796859.34 2026-04-28 19:22:59 4200/20000 prot-na_4200.pdb -1024846.75 2026-04-28 19:23:14 4300/20000 prot-na_4300.pdb -1906199.29 2026-04-28 19:23:28 4400/20000 prot-na_4400.pdb -2120170.25 2026-04-28 19:23:43 4500/20000 prot-na_4500.pdb -1076871.94 2026-04-28 19:23:57 4600/20000 prot-na_4600.pdb -1661559.50 2026-04-28 19:24:12 4700/20000 prot-na_4700.pdb -1150140.61 2026-04-28 19:24:26 4800/20000 prot-na_4800.pdb -1461194.62 2026-04-28 19:24:41 4900/20000 prot-na_4900.pdb -1646331.69 2026-04-28 19:24:56 5000/20000 prot-na_5000.pdb -918775.19 2026-04-28 19:25:11 5100/20000 prot-na_5100.pdb -971535.06 2026-04-28 19:25:25 5200/20000 prot-na_5200.pdb -1252783.34 2026-04-28 19:25:40 5300/20000 prot-na_5300.pdb -1345401.50 2026-04-28 19:25:55 5400/20000 prot-na_5400.pdb -712321.14 2026-04-28 19:26:10 5500/20000 prot-na_5500.pdb -1040186.86 2026-04-28 19:26:25 5600/20000 prot-na_5600.pdb -1245540.44 2026-04-28 19:26:39 5700/20000 prot-na_5700.pdb -2311197.30 2026-04-28 19:26:54 5800/20000 prot-na_5800.pdb -1709505.93 2026-04-28 19:27:08 5900/20000 prot-na_5900.pdb -935255.81 2026-04-28 19:27:22 6000/20000 prot-na_6000.pdb -1855572.71 2026-04-28 19:27:37 6100/20000 prot-na_6100.pdb -1648266.78 2026-04-28 19:27:53 6200/20000 prot-na_6200.pdb -1599032.28 2026-04-28 19:28:08 6300/20000 prot-na_6300.pdb -1466338.59 2026-04-28 19:28:22 6400/20000 prot-na_6400.pdb -1887950.52 2026-04-28 19:28:37 6500/20000 prot-na_6500.pdb -892118.73 2026-04-28 19:28:51 6600/20000 prot-na_6600.pdb -1045005.75 2026-04-28 19:29:05 6700/20000 prot-na_6700.pdb -2015136.39 2026-04-28 19:29:20 6800/20000 prot-na_6800.pdb -2213340.59 2026-04-28 19:29:35 6900/20000 prot-na_6900.pdb -879534.30 2026-04-28 19:29:49 7000/20000 prot-na_7000.pdb -1079646.71 2026-04-28 19:30:04 7100/20000 prot-na_7100.pdb -1036319.07 2026-04-28 19:30:18 7200/20000 prot-na_7200.pdb -2111153.76 2026-04-28 19:30:33 7300/20000 prot-na_7300.pdb -1249136.46 2026-04-28 19:30:47 7400/20000 prot-na_7400.pdb -621937.51 2026-04-28 19:31:02 7500/20000 prot-na_7500.pdb -1553258.16 2026-04-28 19:31:17 7600/20000 prot-na_7600.pdb -551233.50 2026-04-28 19:31:32 7700/20000 prot-na_7700.pdb -900284.51 2026-04-28 19:31:47 7800/20000 prot-na_7800.pdb -1147160.97 2026-04-28 19:32:01 7900/20000 prot-na_7900.pdb -972789.19 2026-04-28 19:32:16 8000/20000 prot-na_8000.pdb -1642303.10 2026-04-28 19:32:30 8100/20000 prot-na_8100.pdb -665793.51 2026-04-28 19:32:46 8200/20000 prot-na_8200.pdb -844911.03 2026-04-28 19:33:01 8300/20000 prot-na_8300.pdb -1017134.75 2026-04-28 19:33:15 8400/20000 prot-na_8400.pdb -1310702.82 2026-04-28 19:33:30 8500/20000 prot-na_8500.pdb -1605148.12 2026-04-28 19:33:45 8600/20000 prot-na_8600.pdb -1778011.24 2026-04-28 19:33:59 8700/20000 prot-na_8700.pdb -1533123.92 2026-04-28 19:34:14 8800/20000 prot-na_8800.pdb -1459123.22 2026-04-28 19:34:29 8900/20000 prot-na_8900.pdb -1449998.93 2026-04-28 19:34:44 9000/20000 prot-na_9000.pdb -1612531.41 2026-04-28 19:34:58 9100/20000 prot-na_9100.pdb -1243972.93 2026-04-28 19:35:15 9200/20000 prot-na_9200.pdb -1208346.32 2026-04-28 19:35:31 9300/20000 prot-na_9300.pdb -2030617.81 2026-04-28 19:35:45 9400/20000 prot-na_9400.pdb -1123943.73 2026-04-28 19:36:00 9500/20000 prot-na_9500.pdb -913984.80 2026-04-28 19:36:15 9600/20000 prot-na_9600.pdb -770050.77 2026-04-28 19:36:29 9700/20000 prot-na_9700.pdb -1389976.34 2026-04-28 19:36:44 9800/20000 prot-na_9800.pdb -797265.72 2026-04-28 19:36:59 9900/20000 prot-na_9900.pdb -1155122.52 2026-04-28 19:37:14 10000/20000 prot-na_10000.pdb -1082820.42 2026-04-28 19:37:29 10100/20000 prot-na_10100.pdb -945221.41 2026-04-28 19:37:44 10200/20000 prot-na_10200.pdb -1539618.62 2026-04-28 19:37:59 10300/20000 prot-na_10300.pdb -884834.56 2026-04-28 19:38:14 10400/20000 prot-na_10400.pdb -1626632.29 2026-04-28 19:38:29 10500/20000 prot-na_10500.pdb -915700.16 2026-04-28 19:38:43 10600/20000 prot-na_10600.pdb -1758157.19 2026-04-28 19:38:59 10700/20000 prot-na_10700.pdb -596453.74 2026-04-28 19:39:14 10800/20000 prot-na_10800.pdb -1913621.99 2026-04-28 19:39:28 10900/20000 prot-na_10900.pdb -1138966.78 2026-04-28 19:39:43 11000/20000 prot-na_11000.pdb -1837390.95 2026-04-28 19:39:58 11100/20000 prot-na_11100.pdb -1208732.78 2026-04-28 19:40:13 11200/20000 prot-na_11200.pdb -598003.24 2026-04-28 19:40:28 11300/20000 prot-na_11300.pdb -500711.30 2026-04-28 19:40:43 11400/20000 prot-na_11400.pdb -1278793.73 2026-04-28 19:40:58 11500/20000 prot-na_11500.pdb -2176752.47 2026-04-28 19:41:12 11600/20000 prot-na_11600.pdb -1629476.20 2026-04-28 19:41:27 11700/20000 prot-na_11700.pdb -1121707.85 2026-04-28 19:41:42 11800/20000 prot-na_11800.pdb -1241281.37 2026-04-28 19:41:57 11900/20000 prot-na_11900.pdb -1092008.16 2026-04-28 19:42:11 12000/20000 prot-na_12000.pdb -1412591.32 2026-04-28 19:42:26 12100/20000 prot-na_12100.pdb -806969.89 2026-04-28 19:42:41 12200/20000 prot-na_12200.pdb -1363599.66 2026-04-28 19:42:56 12300/20000 prot-na_12300.pdb -1687186.53 2026-04-28 19:43:11 12400/20000 prot-na_12400.pdb -1261665.24 2026-04-28 19:43:26 12500/20000 prot-na_12500.pdb -1934847.62 2026-04-28 19:43:41 12600/20000 prot-na_12600.pdb -1470230.19 2026-04-28 19:43:56 12700/20000 prot-na_12700.pdb -1388337.01 2026-04-28 19:44:11 12800/20000 prot-na_12800.pdb -1121534.09 2026-04-28 19:44:26 12900/20000 prot-na_12900.pdb -1678342.04 2026-04-28 19:44:41 13000/20000 prot-na_13000.pdb -1713128.51 2026-04-28 19:44:56 13100/20000 prot-na_13100.pdb -1258768.65 2026-04-28 19:45:10 13200/20000 prot-na_13200.pdb -1736521.59 2026-04-28 19:45:25 13300/20000 prot-na_13300.pdb -1361335.37 2026-04-28 19:45:40 13400/20000 prot-na_13400.pdb -1192581.77 2026-04-28 19:45:55 13500/20000 prot-na_13500.pdb -1012399.89 2026-04-28 19:46:10 13600/20000 prot-na_13600.pdb -880901.50 2026-04-28 19:46:25 13700/20000 prot-na_13700.pdb -1446017.29 2026-04-28 19:46:41 13800/20000 prot-na_13800.pdb -1852493.14 2026-04-28 19:46:55 13900/20000 prot-na_13900.pdb -1694292.45 2026-04-28 19:47:10 14000/20000 prot-na_14000.pdb -925255.83 2026-04-28 19:47:25 14100/20000 prot-na_14100.pdb -1226872.54 2026-04-28 19:47:40 14200/20000 prot-na_14200.pdb -931468.83 2026-04-28 19:47:55 14300/20000 prot-na_14300.pdb -968087.68 2026-04-28 19:48:10 14400/20000 prot-na_14400.pdb -972440.45 2026-04-28 19:48:25 14500/20000 prot-na_14500.pdb -1029426.61 2026-04-28 19:48:40 14600/20000 prot-na_14600.pdb -1290973.80 2026-04-28 19:48:55 14700/20000 prot-na_14700.pdb -876113.02 2026-04-28 19:49:10 14800/20000 prot-na_14800.pdb -415376.85 2026-04-28 19:49:25 14900/20000 prot-na_14900.pdb -1371286.40 2026-04-28 19:49:40 15000/20000 prot-na_15000.pdb -1489397.44 2026-04-28 19:49:55 15100/20000 prot-na_15100.pdb -1785079.02 2026-04-28 19:50:10 15200/20000 prot-na_15200.pdb -778833.82 2026-04-28 19:50:25 15300/20000 prot-na_15300.pdb -2142737.36 2026-04-28 19:50:40 15400/20000 prot-na_15400.pdb -1318643.25 2026-04-28 19:50:55 15500/20000 prot-na_15500.pdb -852133.19 2026-04-28 19:51:10 15600/20000 prot-na_15600.pdb -918456.81 2026-04-28 19:51:25 15700/20000 prot-na_15700.pdb -1739474.70 2026-04-28 19:51:41 15800/20000 prot-na_15800.pdb -1511135.06 2026-04-28 19:51:58 15900/20000 prot-na_15900.pdb -1712463.33 2026-04-28 19:52:17 16000/20000 prot-na_16000.pdb -1125919.65 2026-04-28 19:52:32 16100/20000 prot-na_16100.pdb -837376.55 2026-04-28 19:52:48 16200/20000 prot-na_16200.pdb -578475.51 2026-04-28 19:53:03 16300/20000 prot-na_16300.pdb -1655842.72 2026-04-28 19:53:18 16400/20000 prot-na_16400.pdb -1577039.45 2026-04-28 19:53:33 16500/20000 prot-na_16500.pdb -2178076.77 2026-04-28 19:53:49 16600/20000 prot-na_16600.pdb -2074204.69 2026-04-28 19:54:04 16700/20000 prot-na_16700.pdb -950913.58 2026-04-28 19:54:19 16800/20000 prot-na_16800.pdb -1197581.10 2026-04-28 19:54:34 16900/20000 prot-na_16900.pdb -1571876.89 2026-04-28 19:54:49 17000/20000 prot-na_17000.pdb -2359892.99 2026-04-28 19:55:04 17100/20000 prot-na_17100.pdb -1284817.81 2026-04-28 19:55:20 17200/20000 prot-na_17200.pdb -1558231.38 2026-04-28 19:55:35 17300/20000 prot-na_17300.pdb -895741.86 2026-04-28 19:55:50 17400/20000 prot-na_17400.pdb -808617.16 2026-04-28 19:56:06 17500/20000 prot-na_17500.pdb -1256279.79 2026-04-28 19:56:21 17600/20000 prot-na_17600.pdb -2133513.00 2026-04-28 19:56:37 17700/20000 prot-na_17700.pdb -860147.94 2026-04-28 19:56:52 17800/20000 prot-na_17800.pdb -1421878.13 2026-04-28 19:57:07 17900/20000 prot-na_17900.pdb -1037771.83 2026-04-28 19:57:23 18000/20000 prot-na_18000.pdb -1808091.05 2026-04-28 19:57:38 18100/20000 prot-na_18100.pdb -1100141.39 2026-04-28 19:57:53 18200/20000 prot-na_18200.pdb -1129702.53 2026-04-28 19:58:08 18300/20000 prot-na_18300.pdb -981509.07 2026-04-28 19:58:24 18400/20000 prot-na_18400.pdb -1523293.41 2026-04-28 19:58:39 18500/20000 prot-na_18500.pdb -948350.57 2026-04-28 19:58:55 18600/20000 prot-na_18600.pdb -583241.41 2026-04-28 19:59:10 18700/20000 prot-na_18700.pdb -1249454.68 2026-04-28 19:59:25 18800/20000 prot-na_18800.pdb -834033.59 2026-04-28 19:59:40 18900/20000 prot-na_18900.pdb -1467549.19 2026-04-28 19:59:55 19000/20000 prot-na_19000.pdb -1461896.38 2026-04-28 20:00:11 19100/20000 prot-na_19100.pdb -1575674.95 2026-04-28 20:00:26 19200/20000 prot-na_19200.pdb -2078314.03 2026-04-28 20:00:41 19300/20000 prot-na_19300.pdb -2045684.90 2026-04-28 20:00:56 19400/20000 prot-na_19400.pdb -2036325.77 2026-04-28 20:01:11 19500/20000 prot-na_19500.pdb -684182.24 2026-04-28 20:01:26 19600/20000 prot-na_19600.pdb -923079.59 2026-04-28 20:01:42 19700/20000 prot-na_19700.pdb -590293.50 2026-04-28 20:01:59 19800/20000 prot-na_19800.pdb -1321529.71 2026-04-28 20:02:18 19900/20000 prot-na_19900.pdb -1789229.58 2026-04-28 20:02:37 20000/20000 prot-na_20000.pdb -1525165.15 2026-04-28 20:02:37 DARS scoring end 2026-04-28 20:02:37 Clustering (cuttoff: 5, nr_clust: 100 ) in progress... 2026-04-28 20:02:37 time python /home/rpdock/run_gramm//clustering_v4.py dars_out.txt list.txt 5 100 2026-04-28 20:02:37 100 best scored structures 2026-04-28 20:02:37 1 prot-na_19602.pdb -3334600.54 2026-04-28 20:02:37 2 prot-na_10707.pdb -3264166.2 2026-04-28 20:02:37 3 prot-na_3945.pdb -3249800.72 2026-04-28 20:02:37 4 prot-na_11802.pdb -3246704.9 2026-04-28 20:02:37 5 prot-na_12762.pdb -3206779.51 2026-04-28 20:02:37 6 prot-na_6780.pdb -3141808.99 2026-04-28 20:02:37 7 prot-na_6067.pdb -3130627.44 2026-04-28 20:02:37 8 prot-na_4871.pdb -3124233.97 2026-04-28 20:02:37 9 prot-na_5345.pdb -3106588.44 2026-04-28 20:02:37 10 prot-na_15.pdb -3083015.32 2026-04-28 20:02:37 11 prot-na_8724.pdb -3080354.22 2026-04-28 20:02:37 12 prot-na_347.pdb -3059243.64 2026-04-28 20:02:37 13 prot-na_19873.pdb -3054044.55 2026-04-28 20:02:37 14 prot-na_2494.pdb -3049510.83 2026-04-28 20:02:37 15 prot-na_6.pdb -3004826.06 2026-04-28 20:02:37 16 prot-na_19539.pdb -2996295.02 2026-04-28 20:02:37 17 prot-na_219.pdb -2990160.92 2026-04-28 20:02:37 18 prot-na_2334.pdb -2988398.38 2026-04-28 20:02:37 19 prot-na_440.pdb -2983044.91 2026-04-28 20:02:37 20 prot-na_10884.pdb -2978308.67 2026-04-28 20:02:37 21 prot-na_161.pdb -2977359.85 2026-04-28 20:02:37 22 prot-na_6174.pdb -2973428.52 2026-04-28 20:02:37 23 prot-na_1262.pdb -2971154.75 2026-04-28 20:02:37 24 prot-na_5450.pdb -2969601.52 2026-04-28 20:02:37 25 prot-na_1398.pdb -2965170.93 2026-04-28 20:02:37 26 prot-na_6171.pdb -2964708.31 2026-04-28 20:02:37 27 prot-na_118.pdb -2956104.62 2026-04-28 20:02:37 28 prot-na_6782.pdb -2951890.06 2026-04-28 20:02:37 29 prot-na_6747.pdb -2947140.57 2026-04-28 20:02:37 30 prot-na_15445.pdb -2944810.02 2026-04-28 20:02:37 31 prot-na_1247.pdb -2926736.18 2026-04-28 20:02:37 32 prot-na_9256.pdb -2925018.77 2026-04-28 20:02:37 33 prot-na_2750.pdb -2921382.54 2026-04-28 20:02:37 34 prot-na_374.pdb -2919539.79 2026-04-28 20:02:37 35 prot-na_7477.pdb -2915815.2 2026-04-28 20:02:37 36 prot-na_5571.pdb -2915142.42 2026-04-28 20:02:37 37 prot-na_10.pdb -2913695.52 2026-04-28 20:02:37 38 prot-na_19234.pdb -2912163.75 2026-04-28 20:02:37 39 prot-na_123.pdb -2911421.58 2026-04-28 20:02:37 40 prot-na_4044.pdb -2906767.28 2026-04-28 20:02:37 41 prot-na_1.pdb -2905884.85 2026-04-28 20:02:37 42 prot-na_16690.pdb -2904183.35 2026-04-28 20:02:37 43 prot-na_1738.pdb -2903277.06 2026-04-28 20:02:37 44 prot-na_5035.pdb -2901457.3 2026-04-28 20:02:37 45 prot-na_9539.pdb -2893898.55 2026-04-28 20:02:37 46 prot-na_128.pdb -2891004.17 2026-04-28 20:02:37 47 prot-na_281.pdb -2884002.76 2026-04-28 20:02:37 48 prot-na_15017.pdb -2869911.67 2026-04-28 20:02:37 49 prot-na_13217.pdb -2868468.84 2026-04-28 20:02:37 50 prot-na_3910.pdb -2866402.56 2026-04-28 20:02:37 51 prot-na_5078.pdb -2859532.11 2026-04-28 20:02:37 52 prot-na_1155.pdb -2853140.01 2026-04-28 20:02:37 53 prot-na_4730.pdb -2841512.15 2026-04-28 20:02:37 54 prot-na_1084.pdb -2839950.04 2026-04-28 20:02:37 55 prot-na_965.pdb -2839448.17 2026-04-28 20:02:37 56 prot-na_2699.pdb -2837019.54 2026-04-28 20:02:37 57 prot-na_7975.pdb -2833071.0 2026-04-28 20:02:37 58 prot-na_1795.pdb -2831499.0 2026-04-28 20:02:37 59 prot-na_17088.pdb -2831009.4 2026-04-28 20:02:37 60 prot-na_13211.pdb -2829532.58 2026-04-28 20:02:37 61 prot-na_6124.pdb -2823659.91 2026-04-28 20:02:37 62 prot-na_11.pdb -2820883.63 2026-04-28 20:02:37 63 prot-na_18663.pdb -2818423.99 2026-04-28 20:02:37 64 prot-na_1215.pdb -2817915.57 2026-04-28 20:02:37 65 prot-na_10635.pdb -2817740.91 2026-04-28 20:02:37 66 prot-na_18326.pdb -2817230.28 2026-04-28 20:02:37 67 prot-na_5829.pdb -2816188.48 2026-04-28 20:02:37 68 prot-na_1451.pdb -2815355.57 2026-04-28 20:02:37 69 prot-na_213.pdb -2815336.9 2026-04-28 20:02:37 70 prot-na_470.pdb -2811987.37 2026-04-28 20:02:37 71 prot-na_4078.pdb -2811274.02 2026-04-28 20:02:37 72 prot-na_5355.pdb -2810194.36 2026-04-28 20:02:37 73 prot-na_10602.pdb -2805603.44 2026-04-28 20:02:37 74 prot-na_18561.pdb -2802877.32 2026-04-28 20:02:37 75 prot-na_19154.pdb -2801410.58 2026-04-28 20:02:37 76 prot-na_284.pdb -2801048.01 2026-04-28 20:02:37 77 prot-na_3985.pdb -2799728.69 2026-04-28 20:02:37 78 prot-na_18151.pdb -2799498.37 2026-04-28 20:02:37 79 prot-na_17004.pdb -2797171.41 2026-04-28 20:02:37 80 prot-na_5460.pdb -2794918.8 2026-04-28 20:02:37 81 prot-na_1413.pdb -2790734.17 2026-04-28 20:02:37 82 prot-na_5061.pdb -2788579.41 2026-04-28 20:02:37 83 prot-na_1692.pdb -2783579.3 2026-04-28 20:02:37 84 prot-na_11262.pdb -2779209.76 2026-04-28 20:02:37 85 prot-na_7118.pdb -2775785.26 2026-04-28 20:02:37 86 prot-na_8368.pdb -2775411.3 2026-04-28 20:02:37 87 prot-na_1878.pdb -2773037.03 2026-04-28 20:02:37 88 prot-na_1955.pdb -2771664.76 2026-04-28 20:02:37 89 prot-na_7639.pdb -2770961.07 2026-04-28 20:02:37 90 prot-na_19978.pdb -2767865.98 2026-04-28 20:02:37 91 prot-na_465.pdb -2765974.81 2026-04-28 20:02:37 92 prot-na_11643.pdb -2760102.96 2026-04-28 20:02:37 93 prot-na_9829.pdb -2759960.08 2026-04-28 20:02:37 94 prot-na_1984.pdb -2757604.56 2026-04-28 20:02:37 95 prot-na_9726.pdb -2756187.82 2026-04-28 20:02:37 96 prot-na_563.pdb -2756076.36 2026-04-28 20:02:37 97 prot-na_7208.pdb -2754793.21 2026-04-28 20:02:37 98 prot-na_2.pdb -2753707.13 2026-04-28 20:02:37 99 prot-na_13318.pdb -2750489.2 2026-04-28 20:02:37 100 prot-na_137.pdb -2746434.03 2026-04-28 20:02:37 Chains: B 2026-04-28 20:02:47 100 best scored structures 2026-04-28 20:02:47 GRAMM analysis selected for further analysis: prot-na_15 2026-04-28 20:02:47 Cluster #1 with 16 structures 2026-04-28 20:02:47 1 prot-na_10707.pdb -3264166.2 2026-04-28 20:02:47 2 prot-na_6.pdb -3004826.06 2026-04-28 20:02:47 3 prot-na_19539.pdb -2996295.02 2026-04-28 20:02:47 4 prot-na_9256.pdb -2925018.77 2026-04-28 20:02:47 5 prot-na_2750.pdb -2921382.54 2026-04-28 20:02:47 6 prot-na_5035.pdb -2901457.3 2026-04-28 20:02:47 7 prot-na_3910.pdb -2866402.56 2026-04-28 20:02:47 8 prot-na_5078.pdb -2859532.11 2026-04-28 20:02:47 9 prot-na_4730.pdb -2841512.15 2026-04-28 20:02:47 10 prot-na_17088.pdb -2831009.4 2026-04-28 20:02:47 11 prot-na_19154.pdb -2801410.58 2026-04-28 20:02:47 12 prot-na_284.pdb -2801048.01 2026-04-28 20:02:47 13 prot-na_8368.pdb -2775411.3 2026-04-28 20:02:47 14 prot-na_1984.pdb -2757604.56 2026-04-28 20:02:47 15 prot-na_2.pdb -2753707.13 2026-04-28 20:02:47 16 prot-na_137.pdb -2746434.03 2026-04-28 20:02:47 Cluster #2 with 16 structures 2026-04-28 20:02:47 1 prot-na_5450.pdb -2969601.52 2026-04-28 20:02:47 2 prot-na_6171.pdb -2964708.31 2026-04-28 20:02:47 3 prot-na_1247.pdb -2926736.18 2026-04-28 20:02:47 4 prot-na_374.pdb -2919539.79 2026-04-28 20:02:47 5 prot-na_123.pdb -2911421.58 2026-04-28 20:02:47 6 prot-na_16690.pdb -2904183.35 2026-04-28 20:02:47 7 prot-na_128.pdb -2891004.17 2026-04-28 20:02:47 8 prot-na_281.pdb -2884002.76 2026-04-28 20:02:47 9 prot-na_2699.pdb -2837019.54 2026-04-28 20:02:47 10 prot-na_1795.pdb -2831499.0 2026-04-28 20:02:47 11 prot-na_6124.pdb -2823659.91 2026-04-28 20:02:47 12 prot-na_11.pdb -2820883.63 2026-04-28 20:02:47 13 prot-na_1215.pdb -2817915.57 2026-04-28 20:02:47 14 prot-na_213.pdb -2815336.9 2026-04-28 20:02:47 15 prot-na_4078.pdb -2811274.02 2026-04-28 20:02:47 16 prot-na_18151.pdb -2799498.37 2026-04-28 20:02:47 Cluster #3 with 15 structures 2026-04-28 20:02:47 1 prot-na_11802.pdb -3246704.9 2026-04-28 20:02:47 2 prot-na_15.pdb -3083015.32 2026-04-28 20:02:47 3 prot-na_219.pdb -2990160.92 2026-04-28 20:02:47 4 prot-na_6174.pdb -2973428.52 2026-04-28 20:02:47 5 prot-na_118.pdb -2956104.62 2026-04-28 20:02:47 6 prot-na_13217.pdb -2868468.84 2026-04-28 20:02:47 7 prot-na_1084.pdb -2839950.04 2026-04-28 20:02:47 8 prot-na_13211.pdb -2829532.58 2026-04-28 20:02:47 9 prot-na_18663.pdb -2818423.99 2026-04-28 20:02:47 10 prot-na_5829.pdb -2816188.48 2026-04-28 20:02:47 11 prot-na_5355.pdb -2810194.36 2026-04-28 20:02:47 12 prot-na_3985.pdb -2799728.69 2026-04-28 20:02:47 13 prot-na_5061.pdb -2788579.41 2026-04-28 20:02:47 14 prot-na_1955.pdb -2771664.76 2026-04-28 20:02:47 15 prot-na_7639.pdb -2770961.07 2026-04-28 20:02:47 Cluster #4 with 10 structures 2026-04-28 20:02:47 1 prot-na_6780.pdb -3141808.99 2026-04-28 20:02:47 2 prot-na_4871.pdb -3124233.97 2026-04-28 20:02:47 3 prot-na_8724.pdb -3080354.22 2026-04-28 20:02:47 4 prot-na_347.pdb -3059243.64 2026-04-28 20:02:47 5 prot-na_1398.pdb -2965170.93 2026-04-28 20:02:47 6 prot-na_5571.pdb -2915142.42 2026-04-28 20:02:47 7 prot-na_1155.pdb -2853140.01 2026-04-28 20:02:47 8 prot-na_1451.pdb -2815355.57 2026-04-28 20:02:47 9 prot-na_11643.pdb -2760102.96 2026-04-28 20:02:47 10 prot-na_9726.pdb -2756187.82 2026-04-28 20:02:47 Cluster #5 with 8 structures 2026-04-28 20:02:47 1 prot-na_19602.pdb -3334600.54 2026-04-28 20:02:47 2 prot-na_440.pdb -2983044.91 2026-04-28 20:02:47 3 prot-na_4044.pdb -2906767.28 2026-04-28 20:02:47 4 prot-na_1.pdb -2905884.85 2026-04-28 20:02:47 5 prot-na_7975.pdb -2833071.0 2026-04-28 20:02:47 6 prot-na_470.pdb -2811987.37 2026-04-28 20:02:47 7 prot-na_1413.pdb -2790734.17 2026-04-28 20:02:47 8 prot-na_465.pdb -2765974.81 2026-04-28 20:02:47 Cluster #6 with 6 structures 2026-04-28 20:02:47 1 prot-na_10635.pdb -2817740.91 2026-04-28 20:02:47 2 prot-na_10602.pdb -2805603.44 2026-04-28 20:02:47 3 prot-na_1878.pdb -2773037.03 2026-04-28 20:02:47 4 prot-na_9829.pdb -2759960.08 2026-04-28 20:02:47 5 prot-na_563.pdb -2756076.36 2026-04-28 20:02:47 6 prot-na_7208.pdb -2754793.21 2026-04-28 20:02:47 Cluster #7 with 5 structures 2026-04-28 20:02:47 1 prot-na_6067.pdb -3130627.44 2026-04-28 20:02:47 2 prot-na_5345.pdb -3106588.44 2026-04-28 20:02:47 3 prot-na_161.pdb -2977359.85 2026-04-28 20:02:47 4 prot-na_1262.pdb -2971154.75 2026-04-28 20:02:47 5 prot-na_6782.pdb -2951890.06 2026-04-28 20:02:47 Cluster #8 with 5 structures 2026-04-28 20:02:47 1 prot-na_3945.pdb -3249800.72 2026-04-28 20:02:47 2 prot-na_2494.pdb -3049510.83 2026-04-28 20:02:47 3 prot-na_19234.pdb -2912163.75 2026-04-28 20:02:47 4 prot-na_9539.pdb -2893898.55 2026-04-28 20:02:47 5 prot-na_17004.pdb -2797171.41 2026-04-28 20:02:47 Sent to refinement: clusters_found|prot-na_10707.pdb|prot-na_5450.pdb|prot-na_11802.pdb 2026-04-28 20:02:47 Sent to refinement: clusters_found|prot-na_10707.pdb|prot-na_5450.pdb|prot-na_11802.pdb 2026-04-28 20:02:47 DARS clustering end 2026-04-28 20:02:47 MC (refinement) init 2026-04-28 20:02:47 python /home/rpdock/run_gramm//run_mc.py -f dars_to_mc.txt -d /home/rpdock/web/media/jobs/629e21dd-2962-42b3-94ab-0391bc554550/ 2026-04-28 20:02:47 Refinement of #1 /home/rpdock/web/media/jobs/629e21dd-2962-42b3-94ab-0391bc554550/prot-na_10707.pdb 2026-04-28 20:02:47 python /home/rpdock/mc/MC.py -s 295 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/629e21dd-2962-42b3-94ab-0391bc554550//ref_struc/prot-na_10707/prot-na_10707.pdb 2026-04-28 20:03:33 Refinement of #2 /home/rpdock/web/media/jobs/629e21dd-2962-42b3-94ab-0391bc554550/prot-na_5450.pdb 2026-04-28 20:03:33 python /home/rpdock/mc/MC.py -s 295 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/629e21dd-2962-42b3-94ab-0391bc554550//ref_struc/prot-na_5450/prot-na_5450.pdb 2026-04-28 20:04:22 Refinement of #3 /home/rpdock/web/media/jobs/629e21dd-2962-42b3-94ab-0391bc554550/prot-na_11802.pdb 2026-04-28 20:04:22 python /home/rpdock/mc/MC.py -s 295 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/629e21dd-2962-42b3-94ab-0391bc554550//ref_struc/prot-na_11802/prot-na_11802.pdb 2026-04-28 20:05:19 start - parameters: File name /home/rpdock/web/media/jobs/629e21dd-2962-42b3-94ab-0391bc554550//ref_struc/prot-na_10707/prot-na_10707.pdb Steps 295 Temp. start 15000.0 Temp. end 295.0 False msg start - parameters: File name /home/rpdock/web/media/jobs/629e21dd-2962-42b3-94ab-0391bc554550//ref_struc/prot-na_10707/prot-na_10707.pdb Steps 295 Temp. start 15000.0 Temp. end 295.0 False Step E Edist Eang Epen Warning, residue A400 in the chain B is not compleet Warning, residue A400 in the chain B has not P atom Missed atom C4' in the A 400 Missed atom C3' in the A 400 Missed atom C1' in the A 400 Missed atom C2' in the A 400 Missed atom O4' in the A 400 Missed atom N9 in the A 400 Missed atom C8 in the A 400 Missed atom N7 in the A 400 Missed atom C5 in the A 400 Missed atom C4 in the A 400 Missed atom N1 in the A 400 Missed atom C2 in the A 400 Missed atom N3 in the A 400 Missed atom C4 in the A 400 Missed atom C6 in the A 400 Missed atom C5 in the A 400 Missed atom CA in the ILE 275 Missed atom CB in the ILE 275 Missed atom CG1 in the ILE 275 Missed atom CG2 in the ILE 275 Missed atom CD1 in the ILE 275 0 - -2347655.68 -1400792.22 -1246863.46 300000.00 1 R -2377956.47 -1410942.48 -1267013.98 300000.00 T= 15000.0 K progress 0.338983050847 2 T -2413452.17 -1452206.02 -1261246.15 300000.00 T= 14202.440678 K progress 0.677966101695 3 R -2651104.05 -1506129.56 -1344974.49 200000.00 T= 14102.7457627 K progress 1.01694915254 4 R -2643403.14 -1501463.43 -1341939.72 200000.00 T= 12657.1694915 K progress 1.35593220339 5 R -2396011.26 -1435912.12 -1260099.14 300000.00 T= 12557.4745763 K progress 1.69491525424 6 T -2308068.11 -1452588.13 -1255479.99 400000.00 T= 12358.0847458 K progress 2.03389830508 7 R -2322329.70 -1463890.16 -1258439.55 400000.00 T= 12258.3898305 K progress 2.37288135593 8 R -2305965.29 -1454997.65 -1250967.64 400000.00 T= 12108.8474576 K progress 2.71186440678 9 R -2308951.81 -1461027.21 -1247924.60 400000.00 T= 12009.1525424 K progress 3.05084745763 10 T -2437626.93 -1446500.33 -1291126.61 300000.00 T= 11909.4576271 K progress 3.38983050847 11 R -2476981.63 -1476368.88 -1300612.75 300000.00 T= 11859.6101695 K progress 3.72881355932 12 R -2651912.89 -1509095.04 -1342817.85 200000.00 T= 11660.220339 K progress 4.06779661017 13 R -2501564.51 -1488757.53 -1312806.98 300000.00 T= 11261.440678 K progress 4.40677966102 14 R -2668687.26 -1523297.73 -1345389.52 200000.00 T= 10812.8135593 K progress 4.74576271186 15 R -2595781.97 -1478964.81 -1316817.15 200000.00 T= 10214.6440678 K progress 5.08474576271 16 R -2626343.11 -1501209.42 -1325133.69 200000.00 T= 9616.47457627 K progress 5.42372881356 17 R -2607132.92 -1490717.00 -1316415.92 200000.00 T= 9317.38983051 K progress 5.76271186441 18 R -2629445.89 -1505604.82 -1323841.06 200000.00 T= 9118.0 K progress 6.10169491525 19 R -2620210.70 -1499196.79 -1321013.91 200000.00 T= 8818.91525424 K progress 6.4406779661 20 R -2573935.66 -1475042.23 -1298893.42 200000.00 T= 8719.22033898 K progress 6.77966101695 21 T -2657644.52 -1525754.54 -1331889.99 200000.00 T= 8619.52542373 K progress 7.1186440678 22 R -2652213.90 -1530180.61 -1322033.29 200000.00 T= 8569.6779661 K progress 7.45762711864 23 R -2650166.58 -1526630.86 -1323535.72 200000.00 T= 8469.98305085 K progress 7.79661016949 24 R -2650162.66 -1527187.66 -1322975.00 200000.00 T= 8420.13559322 K progress 8.13559322034 25 R -2645661.98 -1522639.31 -1323022.67 200000.00 T= 8320.44067797 K progress 8.47457627119 26 R -2661027.63 -1527474.88 -1333552.75 200000.00 T= 8170.89830508 K progress 8.81355932203 27 R -2683094.05 -1524997.07 -1358096.98 200000.00 T= 8071.20338983 K progress 9.15254237288 28 R -2673671.31 -1522010.87 -1351660.45 200000.00 T= 8021.3559322 K progress 9.49152542373 29 R -2653412.68 -1514676.88 -1338735.81 200000.00 T= 7871.81355932 K progress 9.83050847458 30 R -2616949.47 -1493941.97 -1323007.50 200000.00 T= 7821.96610169 K progress 10.1694915254 31 R -2622908.16 -1494434.62 -1328473.55 200000.00 T= 7522.88135593 K progress 10.5084745763 32 R -2658181.78 -1532179.20 -1326002.57 200000.00 T= 7323.49152542 K progress 10.8474576271 33 R -2677276.02 -1530695.85 -1346580.17 200000.00 T= 7124.10169492 K progress 11.186440678 34 R -2669633.71 -1531904.89 -1337728.82 200000.00 T= 6825.01694915 K progress 11.5254237288 35 R -2633353.76 -1516056.89 -1317296.87 200000.00 T= 6725.3220339 K progress 11.8644067797 36 R -2652877.74 -1518451.74 -1334426.00 200000.00 T= 6376.38983051 K progress 12.2033898305 37 R -2669709.27 -1513825.56 -1355883.71 200000.00 T= 5828.06779661 K progress 12.5423728814 38 R -2676784.07 -1536439.85 -1340344.22 200000.00 T= 5628.6779661 K progress 12.8813559322 39 R -2653264.68 -1528157.57 -1325107.11 200000.00 T= 5528.98305085 K progress 13.2203389831 40 R -2660473.31 -1532292.58 -1328180.73 200000.00 T= 5180.05084746 K progress 13.5593220339 41 R -2656201.08 -1530509.87 -1325691.21 200000.00 T= 5130.20338983 K progress 13.8983050847 42 R -2659387.37 -1523593.65 -1335793.72 200000.00 T= 4930.81355932 K progress 14.2372881356 43 R -2672293.86 -1520337.61 -1351956.25 200000.00 T= 4532.03389831 K progress 14.5762711864 44 R -2615061.29 -1493381.88 -1321679.40 200000.00 T= 4232.94915254 K progress 14.9152542373 45 R -2683619.88 -1527489.45 -1356130.42 200000.00 T= 4183.10169492 K progress 15.2542372881 46 T -2645729.68 -1513619.60 -1332110.07 200000.00 T= 3933.86440678 K progress 15.593220339 47 R -2679462.62 -1521425.45 -1358037.17 200000.00 T= 3435.38983051 K progress 15.9322033898 48 R -2662983.39 -1516299.12 -1346684.27 200000.00 T= 2488.28813559 K progress 16.2711864407 49 R -2675804.40 -1516682.92 -1359121.48 200000.00 T= 2139.3559322 K progress 16.6101694915 50 R -2653802.98 -1508497.93 -1345305.05 200000.00 T= 1690.72881356 K progress 16.9491525424 51 R -2633018.01 -1499878.06 -1333139.95 200000.00 T= 1591.03389831 K progress 17.2881355932 52 R -2645308.06 -1506901.48 -1338406.58 200000.00 T= 943.016949153 K progress 17.6271186441 53 R -2699198.40 -1545789.18 -1353409.22 200000.00 T= 793.474576271 K progress 17.9661016949 54 R -2711779.38 -1550278.69 -1361500.69 200000.00 T= 643.93220339 K progress 18.3050847458 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/629e21dd-2962-42b3-94ab-0391bc554550//ref_struc/prot-na_5450/prot-na_5450.pdb Steps 295 Temp. start 15000.0 Temp. end 295.0 False msg start - parameters: File name /home/rpdock/web/media/jobs/629e21dd-2962-42b3-94ab-0391bc554550//ref_struc/prot-na_5450/prot-na_5450.pdb Steps 295 Temp. start 15000.0 Temp. end 295.0 False Step E Edist Eang Epen Warning, residue A400 in the chain B is not compleet Warning, residue A400 in the chain B has not P atom Missed atom C4' in the A 400 Missed atom C3' in the A 400 Missed atom C1' in the A 400 Missed atom C2' in the A 400 Missed atom O4' in the A 400 Missed atom N9 in the A 400 Missed atom C8 in the A 400 Missed atom N7 in the A 400 Missed atom C5 in the A 400 Missed atom C4 in the A 400 Missed atom N1 in the A 400 Missed atom C2 in the A 400 Missed atom N3 in the A 400 Missed atom C4 in the A 400 Missed atom C6 in the A 400 Missed atom C5 in the A 400 Missed atom CA in the ILE 275 Missed atom CB in the ILE 275 Missed atom CG1 in the ILE 275 Missed atom CG2 in the ILE 275 Missed atom CD1 in the ILE 275 0 - -1541472.57 -1302400.00 -1139072.57 900000.00 1 R -1547737.82 -1306596.19 -1141141.63 900000.00 T= 14900.3050847 K progress 0.338983050847 2 R -1905683.45 -1281327.96 -1124355.50 500000.00 T= 14850.4576271 K progress 0.677966101695 3 R -1913463.41 -1283444.23 -1130019.18 500000.00 T= 14700.9152542 K progress 1.01694915254 4 R -1796128.16 -1211199.05 -1084929.11 500000.00 T= 14302.1355932 K progress 1.35593220339 5 R -1811899.68 -1232472.09 -1079427.59 500000.00 T= 14102.7457627 K progress 1.69491525424 6 R -1495630.10 -1281306.90 -1114323.19 900000.00 T= 14052.8983051 K progress 2.03389830508 7 T -1503666.44 -1275246.63 -1128419.81 900000.00 T= 14003.0508475 K progress 2.37288135593 8 T -1465281.74 -1250888.66 -1114393.08 900000.00 T= 13903.3559322 K progress 2.71186440678 9 R -1428444.59 -1240338.02 -1088106.57 900000.00 T= 13853.5084746 K progress 3.05084745763 10 R -1458675.31 -1254418.48 -1104256.83 900000.00 T= 13753.8135593 K progress 3.38983050847 11 R -1446661.13 -1255492.21 -1091168.92 900000.00 T= 13703.9661017 K progress 3.72881355932 12 R -1470536.92 -1255330.50 -1115206.42 900000.00 T= 13604.2711864 K progress 4.06779661017 13 R -1464549.84 -1265836.07 -1098713.77 900000.00 T= 13554.4237288 K progress 4.40677966102 14 T -1737012.73 -1172264.48 -1064748.25 500000.00 T= 13454.7288136 K progress 4.74576271186 15 R -1840858.61 -1233599.15 -1107259.46 500000.00 T= 13355.0338983 K progress 5.08474576271 16 R -1850386.99 -1236220.45 -1114166.54 500000.00 T= 12806.7118644 K progress 5.42372881356 17 R -1837599.67 -1228171.81 -1109427.86 500000.00 T= 12657.1694915 K progress 5.76271186441 18 R -1862450.34 -1242830.52 -1119619.82 500000.00 T= 12507.6271186 K progress 6.10169491525 19 R -1723205.03 -1166333.82 -1056871.21 500000.00 T= 11610.3728814 K progress 6.4406779661 20 T -1790213.75 -1238697.65 -1051516.11 500000.00 T= 11261.440678 K progress 6.77966101695 21 T -1834353.65 -1262904.60 -1071449.05 500000.00 T= 11211.5932203 K progress 7.1186440678 22 R -1844760.98 -1271397.09 -1073363.89 500000.00 T= 10812.8135593 K progress 7.45762711864 23 R -1845420.42 -1275304.36 -1070116.06 500000.00 T= 10513.7288136 K progress 7.79661016949 24 R -1840346.05 -1267071.81 -1073274.24 500000.00 T= 10414.0338983 K progress 8.13559322034 25 R -1843968.78 -1269992.85 -1073975.92 500000.00 T= 10214.6440678 K progress 8.47457627119 26 R -1808379.07 -1244309.73 -1064069.34 500000.00 T= 9915.55932203 K progress 8.81355932203 27 T -1905318.63 -1245818.08 -1059500.54 400000.00 T= 9766.01694915 K progress 9.15254237288 28 R -1869597.58 -1227558.75 -1042038.83 400000.00 T= 9566.62711864 K progress 9.49152542373 29 R -1874847.39 -1232208.04 -1042639.35 400000.00 T= 9417.08474576 K progress 9.83050847458 30 R -1757789.08 -1226471.43 -1031317.65 500000.00 T= 9267.54237288 K progress 10.1694915254 31 T -1844099.52 -1271850.56 -1072248.95 500000.00 T= 8968.45762712 K progress 10.5084745763 32 R -1833842.15 -1261669.09 -1072173.05 500000.00 T= 8868.76271186 K progress 10.8474576271 33 R -1833842.15 -1261669.09 -1072173.05 500000.00 T= 8818.91525424 K progress 11.186440678 34 R -1963947.84 -1267776.27 -1096171.57 400000.00 T= 8619.52542373 K progress 11.5254237288 35 R -1962666.64 -1266495.07 -1096171.57 400000.00 T= 7772.11864407 K progress 11.8644067797 36 R -1828162.17 -1259935.82 -1068226.35 500000.00 T= 7722.27118644 K progress 12.2033898305 37 R -1833901.34 -1257880.66 -1076020.68 500000.00 T= 7672.42372881 K progress 12.5423728814 38 R -1845990.98 -1273857.78 -1072133.20 500000.00 T= 7473.03389831 K progress 12.8813559322 39 R -1837151.39 -1264759.84 -1072391.55 500000.00 T= 7423.18644068 K progress 13.2203389831 40 R -1906568.82 -1254127.99 -1052440.83 400000.00 T= 7373.33898305 K progress 13.5593220339 41 T -1957378.72 -1282637.37 -1074741.34 400000.00 T= 7323.49152542 K progress 13.8983050847 42 R -1965366.49 -1282896.94 -1082469.55 400000.00 T= 7024.40677966 K progress 14.2372881356 43 T -1978826.37 -1286701.99 -1092124.38 400000.00 T= 6825.01694915 K progress 14.5762711864 44 R -1972367.84 -1281504.86 -1090862.99 400000.00 T= 6775.16949153 K progress 14.9152542373 45 R -2001668.29 -1302819.70 -1098848.59 400000.00 T= 6675.47457627 K progress 15.2542372881 46 R -2004776.74 -1296336.44 -1108440.30 400000.00 T= 5229.89830508 K progress 15.593220339 47 R -1987671.41 -1278759.85 -1108911.55 400000.00 T= 5130.20338983 K progress 15.9322033898 48 R -1986265.88 -1272831.90 -1113433.98 400000.00 T= 5030.50847458 K progress 16.2711864407 49 R -2028948.82 -1295202.40 -1133746.41 400000.00 T= 4731.42372881 K progress 16.6101694915 50 R -1977282.36 -1271817.59 -1105464.77 400000.00 T= 4382.49152542 K progress 16.9491525424 51 R -2041229.75 -1303254.19 -1137975.56 400000.00 T= 4183.10169492 K progress 17.2881355932 52 R -2042942.27 -1303409.01 -1139533.27 400000.00 T= 4033.55932203 K progress 17.6271186441 53 R -1851377.63 -1261882.95 -1089494.68 500000.00 T= 3584.93220339 K progress 17.9661016949 54 R -1868945.64 -1265760.08 -1103185.56 500000.00 T= 3385.54237288 K progress 18.3050847458 55 R -1832696.00 -1250130.99 -1082565.01 500000.00 T= 3236.0 K progress 18.6440677966 56 R -1850367.63 -1257419.13 -1092948.50 500000.00 T= 3186.15254237 K progress 18.9830508475 57 R -1828043.27 -1243326.58 -1084716.69 500000.00 T= 3136.30508475 K progress 19.3220338983 58 R -1876202.29 -1279760.82 -1096441.47 500000.00 T= 3036.61016949 K progress 19.6610169492 59 R -1879171.74 -1276127.66 -1103044.08 500000.00 T= 2587.98305085 K progress 20.0 60 R -1875108.55 -1282544.61 -1092563.94 500000.00 T= 2538.13559322 K progress 20.3389830508 61 R -1886375.41 -1286864.73 -1099510.68 500000.00 T= 2488.28813559 K progress 20.6779661017 62 T -1901812.54 -1294450.11 -1107362.43 500000.00 T= 2438.44067797 K progress 21.0169491525 63 T -2040525.74 -1351867.40 -1188658.34 500000.00 T= 2139.3559322 K progress 21.3559322034 64 T -2247188.84 -1416269.74 -1230919.10 400000.00 T= 1890.11864407 K progress 21.6949152542 65 R -2247919.74 -1423789.88 -1224129.86 400000.00 T= 1790.42372881 K progress 22.0338983051 66 R -2266493.99 -1417097.13 -1249396.86 400000.00 T= 1591.03389831 K progress 22.3728813559 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/629e21dd-2962-42b3-94ab-0391bc554550//ref_struc/prot-na_11802/prot-na_11802.pdb Steps 295 Temp. start 15000.0 Temp. end 295.0 False msg start - parameters: File name /home/rpdock/web/media/jobs/629e21dd-2962-42b3-94ab-0391bc554550//ref_struc/prot-na_11802/prot-na_11802.pdb Steps 295 Temp. start 15000.0 Temp. end 295.0 False Step E Edist Eang Epen Warning, residue A400 in the chain B is not compleet Warning, residue A400 in the chain B has not P atom Missed atom C4' in the A 400 Missed atom C3' in the A 400 Missed atom C1' in the A 400 Missed atom C2' in the A 400 Missed atom O4' in the A 400 Missed atom N9 in the A 400 Missed atom C8 in the A 400 Missed atom N7 in the A 400 Missed atom C5 in the A 400 Missed atom C4 in the A 400 Missed atom N1 in the A 400 Missed atom C2 in the A 400 Missed atom N3 in the A 400 Missed atom C4 in the A 400 Missed atom C6 in the A 400 Missed atom C5 in the A 400 Missed atom CA in the ILE 275 Missed atom CB in the ILE 275 Missed atom CG1 in the ILE 275 Missed atom CG2 in the ILE 275 Missed atom CD1 in the ILE 275 0 - -2006769.72 -1320853.39 -1185916.33 500000.00 1 T -2166349.15 -1323306.24 -1143042.91 300000.00 T= 15000.0 K progress 0.338983050847 2 R -2164136.79 -1314415.01 -1149721.78 300000.00 T= 14950.1525424 K progress 0.677966101695 3 R -2147959.49 -1306962.85 -1140996.63 300000.00 T= 14900.3050847 K progress 1.01694915254 4 R -2137959.18 -1312644.47 -1125314.71 300000.00 T= 14850.4576271 K progress 1.35593220339 5 R -2167591.74 -1319261.44 -1148330.29 300000.00 T= 14750.7627119 K progress 1.69491525424 6 R -2140563.55 -1313702.26 -1126861.29 300000.00 T= 14700.9152542 K progress 2.03389830508 7 R -2141196.83 -1314335.54 -1126861.29 300000.00 T= 14651.0677966 K progress 2.37288135593 8 R -2134809.67 -1307948.38 -1126861.29 300000.00 T= 14401.8305085 K progress 2.71186440678 9 T -2233385.92 -1299782.75 -1133603.17 200000.00 T= 14351.9830508 K progress 3.05084745763 10 T -2335631.83 -1336883.59 -1198748.25 200000.00 T= 14302.1355932 K progress 3.38983050847 11 R -2413982.02 -1376849.32 -1237132.70 200000.00 T= 14252.2881356 K progress 3.72881355932 12 R -2412257.03 -1372880.70 -1239376.32 200000.00 T= 14003.0508475 K progress 4.06779661017 13 R -2400627.65 -1362830.59 -1237797.06 200000.00 T= 13903.3559322 K progress 4.40677966102 14 T -2250607.87 -1309529.77 -1141078.10 200000.00 T= 13803.6610169 K progress 4.74576271186 15 R -2266620.65 -1314260.69 -1152359.96 200000.00 T= 13703.9661017 K progress 5.08474576271 16 R -2274217.61 -1318055.29 -1156162.32 200000.00 T= 13604.2711864 K progress 5.42372881356 17 T -2120218.14 -1301045.50 -1119172.64 300000.00 T= 13504.5762712 K progress 5.76271186441 18 R -2151250.80 -1304120.93 -1147129.86 300000.00 T= 13454.7288136 K progress 6.10169491525 19 R -2157881.04 -1314556.16 -1143324.88 300000.00 T= 13404.8813559 K progress 6.4406779661 20 R -2157881.04 -1314556.16 -1143324.88 300000.00 T= 13255.3389831 K progress 6.77966101695 21 R -2157425.52 -1313054.79 -1144370.73 300000.00 T= 13205.4915254 K progress 7.1186440678 22 R -2144258.06 -1296668.72 -1147589.34 300000.00 T= 13155.6440678 K progress 7.45762711864 23 R -2155187.90 -1313054.79 -1142133.11 300000.00 T= 13105.7966102 K progress 7.79661016949 24 R -2207882.87 -1317849.12 -1190033.75 300000.00 T= 13055.9491525 K progress 8.13559322034 25 R -2205828.43 -1318671.57 -1187156.85 300000.00 T= 12956.2542373 K progress 8.47457627119 26 R -2220382.35 -1332614.74 -1187767.60 300000.00 T= 12856.559322 K progress 8.81355932203 27 R -2109474.81 -1265610.31 -1143864.50 300000.00 T= 12756.8644068 K progress 9.15254237288 28 R -2095685.58 -1252497.98 -1143187.60 300000.00 T= 12657.1694915 K progress 9.49152542373 29 R -1937473.26 -1232732.86 -1104740.40 400000.00 T= 12407.9322034 K progress 9.83050847458 30 R -2223862.93 -1337065.17 -1186797.76 300000.00 T= 12358.0847458 K progress 10.1694915254 31 T -2282150.91 -1307558.86 -1174592.05 200000.00 T= 12059.0 K progress 10.5084745763 32 R -2291270.29 -1307738.90 -1183531.39 200000.00 T= 11859.6101695 K progress 10.8474576271 33 R -2305900.59 -1316239.43 -1189661.16 200000.00 T= 11759.9152542 K progress 11.186440678 34 R -2442686.58 -1331905.49 -1210781.09 100000.00 T= 11660.220339 K progress 11.5254237288 35 R -2443540.64 -1334744.21 -1208796.43 100000.00 T= 11560.5254237 K progress 11.8644067797 36 R -2445449.94 -1316896.31 -1228553.63 100000.00 T= 11211.5932203 K progress 12.2033898305 37 R -2303595.02 -1314360.38 -1189234.63 200000.00 T= 11161.7457627 K progress 12.5423728814 38 R -2304157.70 -1313949.94 -1190207.76 200000.00 T= 10912.5084746 K progress 12.8813559322 39 R -2308727.45 -1315226.48 -1193500.97 200000.00 T= 10812.8135593 K progress 13.2203389831 40 R -2287688.32 -1293374.76 -1194313.57 200000.00 T= 10563.5762712 K progress 13.5593220339 41 R -2296093.44 -1312040.30 -1184053.14 200000.00 T= 10513.7288136 K progress 13.8983050847 42 T -2318042.11 -1326437.82 -1191604.29 200000.00 T= 10463.8813559 K progress 14.2372881356 43 R -2305003.84 -1325450.27 -1179553.57 200000.00 T= 10414.0338983 K progress 14.5762711864 44 R -2349961.24 -1362001.16 -1187960.09 200000.00 T= 10264.4915254 K progress 14.9152542373 45 T -2465904.46 -1357820.37 -1208084.09 100000.00 T= 10214.6440678 K progress 15.2542372881 46 R -2500016.81 -1378087.27 -1221929.54 100000.00 T= 10164.7966102 K progress 15.593220339 47 R -2510367.14 -1376335.66 -1234031.48 100000.00 T= 10114.9491525 K progress 15.9322033898 48 R -2446354.21 -1353389.00 -1192965.21 100000.00 T= 9965.40677966 K progress 16.2711864407 49 R -2431178.54 -1345467.70 -1185710.84 100000.00 T= 9865.71186441 K progress 16.6101694915 50 T -2243265.07 -1223126.17 -1120138.90 100000.00 T= 9815.86440678 K progress 16.9491525424 51 R -2239361.02 -1211762.12 -1127598.90 100000.00 T= 9616.47457627 K progress 17.2881355932 52 T -2166955.29 -1232655.22 -1134300.07 200000.00 T= 9566.62711864 K progress 17.6271186441 53 R -2162298.80 -1227850.67 -1134448.13 200000.00 T= 9516.77966102 K progress 17.9661016949 54 R -2200757.18 -1261626.36 -1139130.81 200000.00 T= 9466.93220339 K progress 18.3050847458 55 T -2406937.74 -1346961.06 -1159976.68 100000.00 T= 9417.08474576 K progress 18.6440677966 56 R -2402147.14 -1339545.58 -1162601.56 100000.00 T= 9367.23728814 K progress 18.9830508475 57 R -2328324.33 -1329334.77 -1198989.56 200000.00 T= 9217.69491525 K progress 19.3220338983 58 R -2330458.63 -1321226.89 -1209231.74 200000.00 T= 9167.84745763 K progress 19.6610169492 59 R -2324485.06 -1317246.19 -1207238.87 200000.00 T= 9068.15254237 K progress 20.0 60 R -2334688.51 -1318109.77 -1216578.74 200000.00 T= 8968.45762712 K progress 20.3389830508 61 R -2341581.48 -1319797.43 -1221784.05 200000.00 T= 8868.76271186 K progress 20.6779661017 62 R -2341677.31 -1318775.48 -1222901.83 200000.00 T= 8719.22033898 K progress 21.0169491525 63 T -2141178.63 -1223104.15 -1118074.49 200000.00 T= 8569.6779661 K progress 21.3559322034 64 R -2388815.98 -1297534.14 -1191281.84 100000.00 T= 8519.83050847 K progress 21.6949152542 65 R -2320435.39 -1272013.90 -1148421.50 100000.00 T= 8469.98305085 K progress 22.0338983051 66 R -2309781.64 -1264368.98 -1145412.65 100000.00 T= 8370.28813559 K progress 22.3728813559 67 T -2160934.52 -1198950.57 -1061983.94 100000.00 T= 8320.44067797 K progress 22.7118644068 68 T -2226831.78 -1259157.25 -1167674.53 200000.00 T= 8220.74576271 K progress 23.0508474576 69 R -2255796.55 -1280170.73 -1175625.82 200000.00 T= 8170.89830508 K progress 23.3898305085 70 R -2296330.85 -1242518.23 -1153812.62 100000.00 T= 8121.05084746 K progress 23.7288135593 71 R -2296132.69 -1242283.99 -1153848.69 100000.00 T= 8021.3559322 K progress 24.0677966102 72 R -2315961.74 -1244748.09 -1171213.65 100000.00 T= 7622.57627119 K progress 24.406779661 73 R -2315605.37 -1249990.36 -1165615.01 100000.00 T= 7572.72881356 K progress 24.7457627119 74 T -2488881.64 -1353560.68 -1235320.96 100000.00 T= 7473.03389831 K progress 25.0847457627 75 R -2500065.89 -1351758.15 -1248307.74 100000.00 T= 7323.49152542 K progress 25.4237288136 76 R -2495460.33 -1347152.59 -1248307.74 100000.00 T= 7223.79661017 K progress 25.7627118644 77 R -2536336.28 -1375513.46 -1260822.82 100000.00 T= 7124.10169492 K progress 26.1016949153 78 R -2536281.57 -1373962.18 -1262319.39 100000.00 T= 7074.25423729 K progress 26.4406779661 79 R -2533764.39 -1368475.85 -1265288.54 100000.00 T= 6974.55932203 K progress 26.7796610169 80 R -2536055.99 -1376121.51 -1259934.48 100000.00 T= 6825.01694915 K progress 27.1186440678 81 R -2524428.08 -1377867.52 -1246560.57 100000.00 T= 6725.3220339 K progress 27.4576271186 82 R -2527240.49 -1370635.71 -1256604.78 100000.00 T= 6625.62711864 K progress 27.7966101695 83 R -2535957.03 -1378665.88 -1257291.14 100000.00 T= 6575.77966102 K progress 28.1355932203 84 R -2488235.49 -1347219.06 -1241016.43 100000.00 T= 6525.93220339 K progress 28.4745762712 85 R -2517595.65 -1371185.62 -1246410.03 100000.00 T= 6376.38983051 K progress 28.813559322 86 R -2534487.93 -1376998.46 -1257489.47 100000.00 T= 6226.84745763 K progress 29.1525423729 87 R -2515399.20 -1362933.59 -1252465.61 100000.00 T= 5877.91525424 K progress 29.4915254237 88 R -2517825.73 -1364816.21 -1253009.52 100000.00 T= 5828.06779661 K progress 29.8305084746 89 R -2518352.85 -1360022.20 -1258330.65 100000.00 T= 5628.6779661 K progress 30.1694915254 90 R -2494112.61 -1343335.30 -1250777.31 100000.00 T= 5578.83050847 K progress 30.5084745763 91 R -2513869.44 -1358983.84 -1254885.61 100000.00 T= 5429.28813559 K progress 30.8474576271 92 R -2535597.37 -1373155.29 -1262442.07 100000.00 T= 5329.59322034 K progress 31.186440678 93 R -2540584.95 -1377031.47 -1263553.48 100000.00 T= 5030.50847458 K progress 31.5254237288 94 R -2517366.22 -1369044.38 -1248321.83 100000.00 T= 4681.57627119 K progress 31.8644067797 95 R -2503563.77 -1353890.60 -1249673.17 100000.00 T= 4581.88135593 K progress 32.2033898305 96 R -2561141.50 -1389064.28 -1272077.21 100000.00 T= 4432.33898305 K progress 32.5423728814 97 R -2534470.11 -1374624.48 -1259845.63 100000.00 T= 3834.16949153 K progress 32.8813559322 98 R -2563087.05 -1389064.28 -1274022.77 100000.00 T= 3236.0 K progress 33.2203389831 99 R -2543058.71 -1377031.47 -1266027.24 100000.00 T= 1441.49152542 K progress 33.5593220339 100 R -2539603.26 -1376031.38 -1263571.88 100000.00 T= 893.169491525 K progress 33.8983050847 101 R -2545751.80 -1379147.59 -1266604.22 100000.00 T= 793.474576271 K progress 34.2372881356 Save no big msg save short traj msg save best.pdb msg save plot e_step.png Tue Apr 28 20:02:47 2026 ['prot-na_10707.pdb', 'prot-na_5450.pdb', 'prot-na_11802.pdb'] msg Refinement of #1 /home/rpdock/web/media/jobs/629e21dd-2962-42b3-94ab-0391bc554550/prot-na_10707.pdb dir: /home/rpdock/web/media/jobs/629e21dd-2962-42b3-94ab-0391bc554550/ file: prot-na_10707.pdb find `pwd` -iname prot-na_10707.pdb copy /home/rpdock/web/media/jobs/629e21dd-2962-42b3-94ab-0391bc554550/prot-na_15/prot-na_10707.pdb to /home/rpdock/web/media/jobs/629e21dd-2962-42b3-94ab-0391bc554550//ref_struc/prot-na_10707/prot-na_10707.pdb cmd: python /home/rpdock/mc/MC.py -s 295 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/629e21dd-2962-42b3-94ab-0391bc554550//ref_struc/prot-na_10707/prot-na_10707.pdb msg python /home/rpdock/mc/MC.py -s 295 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/629e21dd-2962-42b3-94ab-0391bc554550//ref_struc/prot-na_10707/prot-na_10707.pdb run_mc::OK! = stderr empty msg Refinement of #2 /home/rpdock/web/media/jobs/629e21dd-2962-42b3-94ab-0391bc554550/prot-na_5450.pdb dir: /home/rpdock/web/media/jobs/629e21dd-2962-42b3-94ab-0391bc554550/ file: prot-na_5450.pdb find `pwd` -iname prot-na_5450.pdb copy /home/rpdock/web/media/jobs/629e21dd-2962-42b3-94ab-0391bc554550/prot-na_15/prot-na_5450.pdb to /home/rpdock/web/media/jobs/629e21dd-2962-42b3-94ab-0391bc554550//ref_struc/prot-na_5450/prot-na_5450.pdb cmd: python /home/rpdock/mc/MC.py -s 295 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/629e21dd-2962-42b3-94ab-0391bc554550//ref_struc/prot-na_5450/prot-na_5450.pdb msg python /home/rpdock/mc/MC.py -s 295 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/629e21dd-2962-42b3-94ab-0391bc554550//ref_struc/prot-na_5450/prot-na_5450.pdb run_mc::OK! = stderr empty msg Refinement of #3 /home/rpdock/web/media/jobs/629e21dd-2962-42b3-94ab-0391bc554550/prot-na_11802.pdb dir: /home/rpdock/web/media/jobs/629e21dd-2962-42b3-94ab-0391bc554550/ file: prot-na_11802.pdb find `pwd` -iname prot-na_11802.pdb copy /home/rpdock/web/media/jobs/629e21dd-2962-42b3-94ab-0391bc554550/prot-na_15/prot-na_11802.pdb to /home/rpdock/web/media/jobs/629e21dd-2962-42b3-94ab-0391bc554550//ref_struc/prot-na_11802/prot-na_11802.pdb cmd: python /home/rpdock/mc/MC.py -s 295 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/629e21dd-2962-42b3-94ab-0391bc554550//ref_struc/prot-na_11802/prot-na_11802.pdb msg python /home/rpdock/mc/MC.py -s 295 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/629e21dd-2962-42b3-94ab-0391bc554550//ref_struc/prot-na_11802/prot-na_11802.pdb run_mc::OK! = stderr empty 2026-04-28 20:05:19 npdock::MC (refinement) end 2026-04-28 20:05:19 npdock::OK 2026-04-28 20:05:19 Set finished status of 629e21dd-2962-42b3-94ab-0391bc554550