2026-10-24 17:07:02 NPdock start 2026-10-24 17:07:02 ver: v1.2-23-gfce5bd3-dirty 2026-10-24 17:07:02 mode: None 2026-10-24 17:07:02 is RNA? True 2026-10-24 17:07:02 Interface: prot: '' na: '' 2026-10-24 17:07:02 Curr dir:/home/rpdock/web/media/jobs/e220063b-f4fb-4a69-84d7-314924df7088/ 2026-10-24 17:07:02 GRAMM in progress... 2026-10-24 17:07:02 timeout 72h python /home/rpdock/run_gramm//run_gramm1.py -d 20000 -p prot.pdb -r na.pdb -pi '' -ri '' -n '1' -pf 'A' -rf 'B' 2026-10-24 18:19:40 GRAMM done 2026-10-24 18:19:40 DARS scoring in progress... 2026-10-24 18:19:40 timeout 72h /home/rpdock/run_gramm//DARS-RNP_v3//DARS_potential_v3_scoring.py -m 100 -f list.txt -o dars_out.txt 2026-10-24 18:19:40 DARS start [DARS_potential_v3_scoring.py] 2026-10-24 18:19:40 Show log every 100 structures [DARS_potential_v3_scoring.py] 2026-10-24 18:19:41 1/20000 prot-na_1000.pdb -1474888.54 2026-10-24 18:20:09 100/20000 prot-na_94.pdb -1252800.53 2026-10-24 18:20:38 200/20000 prot-na_194.pdb -1544110.68 2026-10-24 18:21:06 300/20000 prot-na_294.pdb -1298678.93 2026-10-24 18:21:35 400/20000 prot-na_394.pdb -1007616.60 2026-10-24 18:22:04 500/20000 prot-na_494.pdb -1917366.57 2026-10-24 18:22:33 600/20000 prot-na_594.pdb -1640290.49 2026-10-24 18:23:02 700/20000 prot-na_694.pdb -1506098.26 2026-10-24 18:23:31 800/20000 prot-na_794.pdb -1276592.00 2026-10-24 18:23:59 900/20000 prot-na_894.pdb -1602258.01 2026-10-24 18:24:28 1000/20000 prot-na_994.pdb -1616890.29 2026-10-24 18:24:56 1100/20000 prot-na_1100.pdb -1878998.59 2026-10-24 18:25:25 1200/20000 prot-na_1200.pdb -1329768.95 2026-10-24 18:25:53 1300/20000 prot-na_1300.pdb -1377021.09 2026-10-24 18:26:22 1400/20000 prot-na_1400.pdb -1162130.08 2026-10-24 18:26:50 1500/20000 prot-na_1500.pdb -1939336.17 2026-10-24 18:27:19 1600/20000 prot-na_1600.pdb -1327168.61 2026-10-24 18:27:47 1700/20000 prot-na_1700.pdb -1705531.45 2026-10-24 18:28:16 1800/20000 prot-na_1800.pdb -1851892.00 2026-10-24 18:28:44 1900/20000 prot-na_1900.pdb -964095.24 2026-10-24 18:29:12 2000/20000 prot-na_2000.pdb -1545070.42 2026-10-24 18:29:41 2100/20000 prot-na_2100.pdb -1947509.51 2026-10-24 18:30:09 2200/20000 prot-na_2200.pdb -1825012.89 2026-10-24 18:30:37 2300/20000 prot-na_2300.pdb -1034981.25 2026-10-24 18:31:05 2400/20000 prot-na_2400.pdb -1070353.07 2026-10-24 18:31:33 2500/20000 prot-na_2500.pdb -1659084.64 2026-10-24 18:32:01 2600/20000 prot-na_2600.pdb -1126173.67 2026-10-24 18:32:29 2700/20000 prot-na_2700.pdb -1395549.85 2026-10-24 18:32:57 2800/20000 prot-na_2800.pdb -1735611.77 2026-10-24 18:33:25 2900/20000 prot-na_2900.pdb -1652957.06 2026-10-24 18:33:53 3000/20000 prot-na_3000.pdb -930190.35 2026-10-24 18:34:22 3100/20000 prot-na_3100.pdb -1742326.43 2026-10-24 18:34:50 3200/20000 prot-na_3200.pdb -1085601.58 2026-10-24 18:35:18 3300/20000 prot-na_3300.pdb -1219310.23 2026-10-24 18:35:46 3400/20000 prot-na_3400.pdb -1342743.43 2026-10-24 18:36:15 3500/20000 prot-na_3500.pdb -1396033.88 2026-10-24 18:36:43 3600/20000 prot-na_3600.pdb -2073982.19 2026-10-24 18:37:11 3700/20000 prot-na_3700.pdb -1553163.07 2026-10-24 18:37:40 3800/20000 prot-na_3800.pdb -1496377.40 2026-10-24 18:38:08 3900/20000 prot-na_3900.pdb -1234605.52 2026-10-24 18:38:37 4000/20000 prot-na_4000.pdb -1131617.42 2026-10-24 18:39:06 4100/20000 prot-na_4100.pdb -1215499.85 2026-10-24 18:39:34 4200/20000 prot-na_4200.pdb -813024.59 2026-10-24 18:40:03 4300/20000 prot-na_4300.pdb -1701612.52 2026-10-24 18:40:32 4400/20000 prot-na_4400.pdb -1061370.52 2026-10-24 18:41:00 4500/20000 prot-na_4500.pdb -1183286.30 2026-10-24 18:41:29 4600/20000 prot-na_4600.pdb -1160717.09 2026-10-24 18:41:57 4700/20000 prot-na_4700.pdb -1374729.15 2026-10-24 18:42:26 4800/20000 prot-na_4800.pdb -1515746.58 2026-10-24 18:42:54 4900/20000 prot-na_4900.pdb -1070356.44 2026-10-24 18:43:23 5000/20000 prot-na_5000.pdb -753483.16 2026-10-24 18:43:51 5100/20000 prot-na_5100.pdb -1748773.82 2026-10-24 18:44:20 5200/20000 prot-na_5200.pdb -1035035.13 2026-10-24 18:44:48 5300/20000 prot-na_5300.pdb -710591.90 2026-10-24 18:45:17 5400/20000 prot-na_5400.pdb -915319.74 2026-10-24 18:45:45 5500/20000 prot-na_5500.pdb -1078113.21 2026-10-24 18:46:14 5600/20000 prot-na_5600.pdb -991609.14 2026-10-24 18:46:42 5700/20000 prot-na_5700.pdb -1026245.60 2026-10-24 18:47:11 5800/20000 prot-na_5800.pdb -921122.61 2026-10-24 18:47:39 5900/20000 prot-na_5900.pdb -1043522.94 2026-10-24 18:48:09 6000/20000 prot-na_6000.pdb -1069960.74 2026-10-24 18:48:38 6100/20000 prot-na_6100.pdb -1497241.62 2026-10-24 18:49:06 6200/20000 prot-na_6200.pdb -1280667.19 2026-10-24 18:49:35 6300/20000 prot-na_6300.pdb -1031966.73 2026-10-24 18:50:04 6400/20000 prot-na_6400.pdb -1138619.46 2026-10-24 18:50:33 6500/20000 prot-na_6500.pdb -2112436.87 2026-10-24 18:51:01 6600/20000 prot-na_6600.pdb -906500.92 2026-10-24 18:51:30 6700/20000 prot-na_6700.pdb -2370507.20 2026-10-24 18:51:59 6800/20000 prot-na_6800.pdb -910444.26 2026-10-24 18:52:27 6900/20000 prot-na_6900.pdb -1496796.95 2026-10-24 18:52:56 7000/20000 prot-na_7000.pdb -1508047.62 2026-10-24 18:53:25 7100/20000 prot-na_7100.pdb -1554608.27 2026-10-24 18:53:53 7200/20000 prot-na_7200.pdb -1381814.81 2026-10-24 18:54:22 7300/20000 prot-na_7300.pdb -898635.70 2026-10-24 18:54:51 7400/20000 prot-na_7400.pdb -1641166.73 2026-10-24 18:55:20 7500/20000 prot-na_7500.pdb -1147314.65 2026-10-24 18:55:49 7600/20000 prot-na_7600.pdb -1402869.07 2026-10-24 18:56:17 7700/20000 prot-na_7700.pdb -865808.05 2026-10-24 18:56:46 7800/20000 prot-na_7800.pdb -1207981.18 2026-10-24 18:57:15 7900/20000 prot-na_7900.pdb -814957.79 2026-10-24 18:57:44 8000/20000 prot-na_8000.pdb -1482787.87 2026-10-24 18:58:13 8100/20000 prot-na_8100.pdb -1312951.44 2026-10-24 18:58:43 8200/20000 prot-na_8200.pdb -783262.92 2026-10-24 18:59:12 8300/20000 prot-na_8300.pdb -1341539.24 2026-10-24 18:59:41 8400/20000 prot-na_8400.pdb -1187668.14 2026-10-24 19:00:10 8500/20000 prot-na_8500.pdb -1065378.25 2026-10-24 19:00:38 8600/20000 prot-na_8600.pdb -1183288.94 2026-10-24 19:01:07 8700/20000 prot-na_8700.pdb -884469.39 2026-10-24 19:01:36 8800/20000 prot-na_8800.pdb -1725165.54 2026-10-24 19:02:05 8900/20000 prot-na_8900.pdb -944307.88 2026-10-24 19:02:34 9000/20000 prot-na_9000.pdb -852464.50 2026-10-24 19:03:02 9100/20000 prot-na_9100.pdb -1088906.50 2026-10-24 19:03:31 9200/20000 prot-na_9200.pdb -1067568.19 2026-10-24 19:04:00 9300/20000 prot-na_9300.pdb -1466891.46 2026-10-24 19:04:29 9400/20000 prot-na_9400.pdb -1391288.26 2026-10-24 19:04:58 9500/20000 prot-na_9500.pdb -1738817.08 2026-10-24 19:05:26 9600/20000 prot-na_9600.pdb -947870.88 2026-10-24 19:05:55 9700/20000 prot-na_9700.pdb -891740.77 2026-10-24 19:06:24 9800/20000 prot-na_9800.pdb -1016372.36 2026-10-24 19:06:52 9900/20000 prot-na_9900.pdb -1286329.90 2026-10-24 19:07:21 10000/20000 prot-na_10000.pdb -1151000.58 2026-10-24 19:07:50 10100/20000 prot-na_10100.pdb -1333504.09 2026-10-24 19:08:18 10200/20000 prot-na_10200.pdb -1097565.17 2026-10-24 19:08:47 10300/20000 prot-na_10300.pdb -755280.92 2026-10-24 19:09:16 10400/20000 prot-na_10400.pdb -1136310.35 2026-10-24 19:09:46 10500/20000 prot-na_10500.pdb -1073304.40 2026-10-24 19:10:15 10600/20000 prot-na_10600.pdb -838320.08 2026-10-24 19:10:43 10700/20000 prot-na_10700.pdb -1134272.15 2026-10-24 19:11:12 10800/20000 prot-na_10800.pdb -1698370.01 2026-10-24 19:11:41 10900/20000 prot-na_10900.pdb -1219474.13 2026-10-24 19:12:09 11000/20000 prot-na_11000.pdb -1412928.38 2026-10-24 19:12:38 11100/20000 prot-na_11100.pdb -1331110.83 2026-10-24 19:13:07 11200/20000 prot-na_11200.pdb -1172001.71 2026-10-24 19:13:36 11300/20000 prot-na_11300.pdb -877347.79 2026-10-24 19:14:05 11400/20000 prot-na_11400.pdb -758613.89 2026-10-24 19:14:33 11500/20000 prot-na_11500.pdb -1097415.34 2026-10-24 19:15:03 11600/20000 prot-na_11600.pdb -1393544.53 2026-10-24 19:15:32 11700/20000 prot-na_11700.pdb -922150.07 2026-10-24 19:16:01 11800/20000 prot-na_11800.pdb -904778.14 2026-10-24 19:16:30 11900/20000 prot-na_11900.pdb -868056.65 2026-10-24 19:16:58 12000/20000 prot-na_12000.pdb -740627.76 2026-10-24 19:17:27 12100/20000 prot-na_12100.pdb -1356272.43 2026-10-24 19:17:56 12200/20000 prot-na_12200.pdb -1008168.87 2026-10-24 19:18:25 12300/20000 prot-na_12300.pdb -735329.65 2026-10-24 19:18:54 12400/20000 prot-na_12400.pdb -1360830.81 2026-10-24 19:19:23 12500/20000 prot-na_12500.pdb -1578127.79 2026-10-24 19:19:52 12600/20000 prot-na_12600.pdb -794246.56 2026-10-24 19:20:21 12700/20000 prot-na_12700.pdb -845255.27 2026-10-24 19:20:50 12800/20000 prot-na_12800.pdb -1337570.33 2026-10-24 19:21:19 12900/20000 prot-na_12900.pdb -1900095.86 2026-10-24 19:21:47 13000/20000 prot-na_13000.pdb -712901.43 2026-10-24 19:22:17 13100/20000 prot-na_13100.pdb -954581.20 2026-10-24 19:22:45 13200/20000 prot-na_13200.pdb -1385911.28 2026-10-24 19:23:14 13300/20000 prot-na_13300.pdb -732526.68 2026-10-24 19:23:43 13400/20000 prot-na_13400.pdb -1288598.55 2026-10-24 19:24:12 13500/20000 prot-na_13500.pdb -1677251.92 2026-10-24 19:24:41 13600/20000 prot-na_13600.pdb -1056071.57 2026-10-24 19:25:10 13700/20000 prot-na_13700.pdb -918064.15 2026-10-24 19:25:39 13800/20000 prot-na_13800.pdb -1291748.59 2026-10-24 19:26:08 13900/20000 prot-na_13900.pdb -843004.81 2026-10-24 19:26:37 14000/20000 prot-na_14000.pdb -759817.97 2026-10-24 19:27:06 14100/20000 prot-na_14100.pdb -1373149.12 2026-10-24 19:27:35 14200/20000 prot-na_14200.pdb -1011145.55 2026-10-24 19:28:04 14300/20000 prot-na_14300.pdb -847454.22 2026-10-24 19:28:33 14400/20000 prot-na_14400.pdb -1119716.09 2026-10-24 19:29:02 14500/20000 prot-na_14500.pdb -890426.72 2026-10-24 19:29:31 14600/20000 prot-na_14600.pdb -1063224.06 2026-10-24 19:30:00 14700/20000 prot-na_14700.pdb -1259912.30 2026-10-24 19:30:29 14800/20000 prot-na_14800.pdb -1130645.63 2026-10-24 19:30:58 14900/20000 prot-na_14900.pdb -1580921.85 2026-10-24 19:31:27 15000/20000 prot-na_15000.pdb -1341295.67 2026-10-24 19:31:56 15100/20000 prot-na_15100.pdb -1062000.45 2026-10-24 19:32:25 15200/20000 prot-na_15200.pdb -1599146.55 2026-10-24 19:32:53 15300/20000 prot-na_15300.pdb -1169677.35 2026-10-24 19:33:22 15400/20000 prot-na_15400.pdb -1201722.29 2026-10-24 19:33:51 15500/20000 prot-na_15500.pdb -1707136.25 2026-10-24 19:34:20 15600/20000 prot-na_15600.pdb -1614402.04 2026-10-24 19:34:49 15700/20000 prot-na_15700.pdb -958430.65 2026-10-24 19:35:18 15800/20000 prot-na_15800.pdb -982719.01 2026-10-24 19:35:47 15900/20000 prot-na_15900.pdb -1568453.28 2026-10-24 19:36:16 16000/20000 prot-na_16000.pdb -1102583.72 2026-10-24 19:36:45 16100/20000 prot-na_16100.pdb -956344.81 2026-10-24 19:37:14 16200/20000 prot-na_16200.pdb -1021328.29 2026-10-24 19:37:42 16300/20000 prot-na_16300.pdb -1172810.56 2026-10-24 19:38:11 16400/20000 prot-na_16400.pdb -1051273.44 2026-10-24 19:38:41 16500/20000 prot-na_16500.pdb -1080744.45 2026-10-24 19:39:10 16600/20000 prot-na_16600.pdb -906238.91 2026-10-24 19:39:39 16700/20000 prot-na_16700.pdb -1238361.77 2026-10-24 19:40:08 16800/20000 prot-na_16800.pdb -998570.53 2026-10-24 19:40:37 16900/20000 prot-na_16900.pdb -1333038.57 2026-10-24 19:41:07 17000/20000 prot-na_17000.pdb -737966.09 2026-10-24 19:41:36 17100/20000 prot-na_17100.pdb -1035201.10 2026-10-24 19:42:05 17200/20000 prot-na_17200.pdb -1023130.89 2026-10-24 19:42:33 17300/20000 prot-na_17300.pdb -923142.16 2026-10-24 19:43:02 17400/20000 prot-na_17400.pdb -1294392.42 2026-10-24 19:43:31 17500/20000 prot-na_17500.pdb -850590.99 2026-10-24 19:44:00 17600/20000 prot-na_17600.pdb -822425.92 2026-10-24 19:44:29 17700/20000 prot-na_17700.pdb -929328.67 2026-10-24 19:44:58 17800/20000 prot-na_17800.pdb -919223.85 2026-10-24 19:45:27 17900/20000 prot-na_17900.pdb -1241191.73 2026-10-24 19:45:55 18000/20000 prot-na_18000.pdb -1443388.81 2026-10-24 19:46:24 18100/20000 prot-na_18100.pdb -1317236.26 2026-10-24 19:46:53 18200/20000 prot-na_18200.pdb -1445648.80 2026-10-24 19:47:22 18300/20000 prot-na_18300.pdb -908167.76 2026-10-24 19:47:51 18400/20000 prot-na_18400.pdb -847261.93 2026-10-24 19:48:20 18500/20000 prot-na_18500.pdb -1376848.72 2026-10-24 19:48:50 18600/20000 prot-na_18600.pdb -1233607.77 2026-10-24 19:49:19 18700/20000 prot-na_18700.pdb -1096431.14 2026-10-24 19:49:48 18800/20000 prot-na_18800.pdb -883909.67 2026-10-24 19:50:18 18900/20000 prot-na_18900.pdb -794346.93 2026-10-24 19:50:47 19000/20000 prot-na_19000.pdb -1164868.87 2026-10-24 19:51:16 19100/20000 prot-na_19100.pdb -1991696.75 2026-10-24 19:51:45 19200/20000 prot-na_19200.pdb -1023684.69 2026-10-24 19:52:15 19300/20000 prot-na_19300.pdb -1123763.55 2026-10-24 19:52:44 19400/20000 prot-na_19400.pdb -676787.58 2026-10-24 19:53:14 19500/20000 prot-na_19500.pdb -1079403.22 2026-10-24 19:53:43 19600/20000 prot-na_19600.pdb -1262309.75 2026-10-24 19:54:13 19700/20000 prot-na_19700.pdb -1264932.58 2026-10-24 19:54:42 19800/20000 prot-na_19800.pdb -1111580.87 2026-10-24 19:55:11 19900/20000 prot-na_19900.pdb -813590.48 2026-10-24 19:55:40 20000/20000 prot-na_20000.pdb -1881062.53 2026-10-24 19:55:40 DARS scoring end 2026-10-24 19:55:40 Clustering (cuttoff: 5, nr_clust: 100 ) in progress... 2026-10-24 19:55:40 timeout 72h python /home/rpdock/run_gramm//clustering_v4.py dars_out.txt list.txt 5 100 2026-10-24 19:55:40 100 best scored structures 2026-10-24 19:55:40 1 prot-na_10438.pdb -2533232.32 2026-10-24 19:55:40 2 prot-na_1287.pdb -2523323.16 2026-10-24 19:55:40 3 prot-na_8516.pdb -2518751.26 2026-10-24 19:55:40 4 prot-na_5892.pdb -2486146.23 2026-10-24 19:55:40 5 prot-na_14620.pdb -2483048.41 2026-10-24 19:55:40 6 prot-na_18954.pdb -2480245.69 2026-10-24 19:55:40 7 prot-na_761.pdb -2459361.56 2026-10-24 19:55:40 8 prot-na_14053.pdb -2455608.85 2026-10-24 19:55:40 9 prot-na_2050.pdb -2446959.7 2026-10-24 19:55:40 10 prot-na_9983.pdb -2446409.56 2026-10-24 19:55:40 11 prot-na_19816.pdb -2443801.53 2026-10-24 19:55:40 12 prot-na_963.pdb -2427953.17 2026-10-24 19:55:40 13 prot-na_18308.pdb -2424020.48 2026-10-24 19:55:40 14 prot-na_13508.pdb -2423708.18 2026-10-24 19:55:40 15 prot-na_6084.pdb -2412953.34 2026-10-24 19:55:40 16 prot-na_222.pdb -2405139.23 2026-10-24 19:55:40 17 prot-na_9686.pdb -2402527.1 2026-10-24 19:55:40 18 prot-na_4076.pdb -2397079.14 2026-10-24 19:55:40 19 prot-na_18223.pdb -2383217.04 2026-10-24 19:55:40 20 prot-na_6700.pdb -2370507.2 2026-10-24 19:55:40 21 prot-na_2973.pdb -2369312.16 2026-10-24 19:55:40 22 prot-na_8011.pdb -2366659.41 2026-10-24 19:55:40 23 prot-na_2558.pdb -2360615.61 2026-10-24 19:55:40 24 prot-na_18079.pdb -2358124.47 2026-10-24 19:55:40 25 prot-na_18984.pdb -2357254.25 2026-10-24 19:55:40 26 prot-na_17279.pdb -2344270.53 2026-10-24 19:55:40 27 prot-na_50.pdb -2342114.21 2026-10-24 19:55:40 28 prot-na_5243.pdb -2337945.46 2026-10-24 19:55:40 29 prot-na_38.pdb -2326201.62 2026-10-24 19:55:40 30 prot-na_5475.pdb -2325339.23 2026-10-24 19:55:40 31 prot-na_2690.pdb -2323860.46 2026-10-24 19:55:40 32 prot-na_12702.pdb -2323654.99 2026-10-24 19:55:40 33 prot-na_4004.pdb -2323127.39 2026-10-24 19:55:40 34 prot-na_6966.pdb -2320649.46 2026-10-24 19:55:40 35 prot-na_755.pdb -2320313.65 2026-10-24 19:55:40 36 prot-na_129.pdb -2319325.81 2026-10-24 19:55:40 37 prot-na_501.pdb -2318687.31 2026-10-24 19:55:40 38 prot-na_1450.pdb -2318562.37 2026-10-24 19:55:40 39 prot-na_4560.pdb -2317953.33 2026-10-24 19:55:40 40 prot-na_450.pdb -2314630.55 2026-10-24 19:55:40 41 prot-na_7447.pdb -2314519.39 2026-10-24 19:55:40 42 prot-na_13413.pdb -2313394.17 2026-10-24 19:55:40 43 prot-na_18603.pdb -2311244.61 2026-10-24 19:55:40 44 prot-na_6374.pdb -2310284.31 2026-10-24 19:55:40 45 prot-na_15446.pdb -2302666.87 2026-10-24 19:55:40 46 prot-na_8722.pdb -2297980.73 2026-10-24 19:55:40 47 prot-na_11164.pdb -2293412.45 2026-10-24 19:55:40 48 prot-na_3959.pdb -2284684.27 2026-10-24 19:55:40 49 prot-na_17750.pdb -2280647.13 2026-10-24 19:55:40 50 prot-na_12919.pdb -2277323.49 2026-10-24 19:55:40 51 prot-na_12863.pdb -2273588.1 2026-10-24 19:55:40 52 prot-na_1613.pdb -2272675.84 2026-10-24 19:55:40 53 prot-na_4030.pdb -2272111.11 2026-10-24 19:55:40 54 prot-na_11842.pdb -2267724.64 2026-10-24 19:55:40 55 prot-na_2531.pdb -2267123.05 2026-10-24 19:55:40 56 prot-na_18535.pdb -2266662.16 2026-10-24 19:55:40 57 prot-na_19905.pdb -2266309.87 2026-10-24 19:55:40 58 prot-na_3640.pdb -2266283.1 2026-10-24 19:55:40 59 prot-na_417.pdb -2260270.85 2026-10-24 19:55:40 60 prot-na_6802.pdb -2256535.07 2026-10-24 19:55:40 61 prot-na_12592.pdb -2255014.74 2026-10-24 19:55:40 62 prot-na_87.pdb -2253307.33 2026-10-24 19:55:40 63 prot-na_4253.pdb -2251328.44 2026-10-24 19:55:40 64 prot-na_5601.pdb -2244815.42 2026-10-24 19:55:40 65 prot-na_15232.pdb -2243570.0 2026-10-24 19:55:40 66 prot-na_5383.pdb -2243319.17 2026-10-24 19:55:40 67 prot-na_19659.pdb -2237989.73 2026-10-24 19:55:40 68 prot-na_3554.pdb -2235093.92 2026-10-24 19:55:40 69 prot-na_11854.pdb -2235041.88 2026-10-24 19:55:40 70 prot-na_1120.pdb -2234840.59 2026-10-24 19:55:40 71 prot-na_1246.pdb -2233121.21 2026-10-24 19:55:40 72 prot-na_2464.pdb -2231070.52 2026-10-24 19:55:40 73 prot-na_1651.pdb -2229873.66 2026-10-24 19:55:40 74 prot-na_17082.pdb -2228076.24 2026-10-24 19:55:40 75 prot-na_1025.pdb -2224059.77 2026-10-24 19:55:40 76 prot-na_17999.pdb -2222264.29 2026-10-24 19:55:40 77 prot-na_152.pdb -2220431.97 2026-10-24 19:55:40 78 prot-na_528.pdb -2215379.11 2026-10-24 19:55:40 79 prot-na_17163.pdb -2212033.07 2026-10-24 19:55:40 80 prot-na_9425.pdb -2209573.27 2026-10-24 19:55:40 81 prot-na_11578.pdb -2208071.73 2026-10-24 19:55:40 82 prot-na_7752.pdb -2206477.62 2026-10-24 19:55:40 83 prot-na_213.pdb -2204532.77 2026-10-24 19:55:40 84 prot-na_3709.pdb -2204527.33 2026-10-24 19:55:40 85 prot-na_9988.pdb -2202982.92 2026-10-24 19:55:40 86 prot-na_97.pdb -2202642.12 2026-10-24 19:55:40 87 prot-na_6610.pdb -2201979.08 2026-10-24 19:55:40 88 prot-na_4181.pdb -2201791.32 2026-10-24 19:55:40 89 prot-na_66.pdb -2199510.43 2026-10-24 19:55:40 90 prot-na_6671.pdb -2199117.59 2026-10-24 19:55:40 91 prot-na_10615.pdb -2197984.31 2026-10-24 19:55:40 92 prot-na_19504.pdb -2197500.58 2026-10-24 19:55:40 93 prot-na_8273.pdb -2197215.05 2026-10-24 19:55:40 94 prot-na_18856.pdb -2196432.32 2026-10-24 19:55:40 95 prot-na_16670.pdb -2195317.76 2026-10-24 19:55:40 96 prot-na_11946.pdb -2195281.06 2026-10-24 19:55:40 97 prot-na_4324.pdb -2193498.23 2026-10-24 19:55:40 98 prot-na_6218.pdb -2192673.58 2026-10-24 19:55:40 99 prot-na_1430.pdb -2188970.0 2026-10-24 19:55:40 100 prot-na_1887.pdb -2186987.16 2026-10-24 19:55:40 Chains: B 2026-10-24 19:55:55 100 best scored structures 2026-10-24 19:55:55 GRAMM analysis selected for further analysis: prot-na_10 2026-10-24 19:55:55 Cluster #1 with 19 structures 2026-10-24 19:55:55 1 prot-na_1287.pdb -2523323.16 2026-10-24 19:55:55 2 prot-na_8516.pdb -2518751.26 2026-10-24 19:55:55 3 prot-na_761.pdb -2459361.56 2026-10-24 19:55:55 4 prot-na_222.pdb -2405139.23 2026-10-24 19:55:55 5 prot-na_4076.pdb -2397079.14 2026-10-24 19:55:55 6 prot-na_18984.pdb -2357254.25 2026-10-24 19:55:55 7 prot-na_50.pdb -2342114.21 2026-10-24 19:55:55 8 prot-na_129.pdb -2319325.81 2026-10-24 19:55:55 9 prot-na_450.pdb -2314630.55 2026-10-24 19:55:55 10 prot-na_6374.pdb -2310284.31 2026-10-24 19:55:55 11 prot-na_11164.pdb -2293412.45 2026-10-24 19:55:55 12 prot-na_12919.pdb -2277323.49 2026-10-24 19:55:55 13 prot-na_4253.pdb -2251328.44 2026-10-24 19:55:55 14 prot-na_213.pdb -2204532.77 2026-10-24 19:55:55 15 prot-na_3709.pdb -2204527.33 2026-10-24 19:55:55 16 prot-na_97.pdb -2202642.12 2026-10-24 19:55:55 17 prot-na_66.pdb -2199510.43 2026-10-24 19:55:55 18 prot-na_8273.pdb -2197215.05 2026-10-24 19:55:55 19 prot-na_11946.pdb -2195281.06 2026-10-24 19:55:55 Cluster #2 with 16 structures 2026-10-24 19:55:55 1 prot-na_14620.pdb -2483048.41 2026-10-24 19:55:55 2 prot-na_17279.pdb -2344270.53 2026-10-24 19:55:55 3 prot-na_4560.pdb -2317953.33 2026-10-24 19:55:55 4 prot-na_18603.pdb -2311244.61 2026-10-24 19:55:55 5 prot-na_15446.pdb -2302666.87 2026-10-24 19:55:55 6 prot-na_3959.pdb -2284684.27 2026-10-24 19:55:55 7 prot-na_18535.pdb -2266662.16 2026-10-24 19:55:55 8 prot-na_3640.pdb -2266283.1 2026-10-24 19:55:55 9 prot-na_12592.pdb -2255014.74 2026-10-24 19:55:55 10 prot-na_1246.pdb -2233121.21 2026-10-24 19:55:55 11 prot-na_1651.pdb -2229873.66 2026-10-24 19:55:55 12 prot-na_1025.pdb -2224059.77 2026-10-24 19:55:55 13 prot-na_11578.pdb -2208071.73 2026-10-24 19:55:55 14 prot-na_4181.pdb -2201791.32 2026-10-24 19:55:55 15 prot-na_18856.pdb -2196432.32 2026-10-24 19:55:55 16 prot-na_1887.pdb -2186987.16 2026-10-24 19:55:55 Cluster #3 with 14 structures 2026-10-24 19:55:55 1 prot-na_2050.pdb -2446959.7 2026-10-24 19:55:55 2 prot-na_18308.pdb -2424020.48 2026-10-24 19:55:55 3 prot-na_6084.pdb -2412953.34 2026-10-24 19:55:55 4 prot-na_38.pdb -2326201.62 2026-10-24 19:55:55 5 prot-na_5475.pdb -2325339.23 2026-10-24 19:55:55 6 prot-na_6966.pdb -2320649.46 2026-10-24 19:55:55 7 prot-na_501.pdb -2318687.31 2026-10-24 19:55:55 8 prot-na_13413.pdb -2313394.17 2026-10-24 19:55:55 9 prot-na_417.pdb -2260270.85 2026-10-24 19:55:55 10 prot-na_6802.pdb -2256535.07 2026-10-24 19:55:55 11 prot-na_87.pdb -2253307.33 2026-10-24 19:55:55 12 prot-na_3554.pdb -2235093.92 2026-10-24 19:55:55 13 prot-na_17163.pdb -2212033.07 2026-10-24 19:55:55 14 prot-na_6218.pdb -2192673.58 2026-10-24 19:55:55 Cluster #4 with 12 structures 2026-10-24 19:55:55 1 prot-na_5892.pdb -2486146.23 2026-10-24 19:55:55 2 prot-na_19816.pdb -2443801.53 2026-10-24 19:55:55 3 prot-na_963.pdb -2427953.17 2026-10-24 19:55:55 4 prot-na_18223.pdb -2383217.04 2026-10-24 19:55:55 5 prot-na_6700.pdb -2370507.2 2026-10-24 19:55:55 6 prot-na_2973.pdb -2369312.16 2026-10-24 19:55:55 7 prot-na_755.pdb -2320313.65 2026-10-24 19:55:55 8 prot-na_12863.pdb -2273588.1 2026-10-24 19:55:55 9 prot-na_19905.pdb -2266309.87 2026-10-24 19:55:55 10 prot-na_5601.pdb -2244815.42 2026-10-24 19:55:55 11 prot-na_17999.pdb -2222264.29 2026-10-24 19:55:55 12 prot-na_16670.pdb -2195317.76 2026-10-24 19:55:55 Cluster #5 with 10 structures 2026-10-24 19:55:55 1 prot-na_10438.pdb -2533232.32 2026-10-24 19:55:55 2 prot-na_14053.pdb -2455608.85 2026-10-24 19:55:55 3 prot-na_9686.pdb -2402527.1 2026-10-24 19:55:55 4 prot-na_8011.pdb -2366659.41 2026-10-24 19:55:55 5 prot-na_4004.pdb -2323127.39 2026-10-24 19:55:55 6 prot-na_1450.pdb -2318562.37 2026-10-24 19:55:55 7 prot-na_11842.pdb -2267724.64 2026-10-24 19:55:55 8 prot-na_1120.pdb -2234840.59 2026-10-24 19:55:55 9 prot-na_152.pdb -2220431.97 2026-10-24 19:55:55 10 prot-na_6610.pdb -2201979.08 2026-10-24 19:55:55 Cluster #6 with 5 structures 2026-10-24 19:55:55 1 prot-na_2690.pdb -2323860.46 2026-10-24 19:55:55 2 prot-na_7447.pdb -2314519.39 2026-10-24 19:55:55 3 prot-na_1613.pdb -2272675.84 2026-10-24 19:55:55 4 prot-na_4030.pdb -2272111.11 2026-10-24 19:55:55 5 prot-na_528.pdb -2215379.11 2026-10-24 19:55:55 Sent to refinement: clusters_found|prot-na_1287.pdb|prot-na_14620.pdb|prot-na_2050.pdb 2026-10-24 19:55:55 Sent to refinement: clusters_found|prot-na_1287.pdb|prot-na_14620.pdb|prot-na_2050.pdb 2026-10-24 19:55:55 DARS clustering end 2026-10-24 19:55:55 MC (refinement) init 2026-10-24 19:55:55 timeout 72h python /home/rpdock/run_gramm//run_mc.py -f dars_to_mc.txt -d /home/rpdock/web/media/jobs/e220063b-f4fb-4a69-84d7-314924df7088/ 2026-10-24 19:55:55 Refinement of #1 /home/rpdock/web/media/jobs/e220063b-f4fb-4a69-84d7-314924df7088/prot-na_1287.pdb 2026-10-24 19:55:55 python /home/rpdock/mc/MC.py -s 1000 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/e220063b-f4fb-4a69-84d7-314924df7088//ref_struc/prot-na_1287/prot-na_1287.pdb 2026-10-24 19:57:38 run_mc::stderr:Traceback (most recent call last): File "/home/rpdock/mc/MC.py", line 671, in s, datas = write_all_atoms (datas, step_real, cal.split()[0], plik, pars, historyT, historyR, rna) File "/home/rpdock/mc/MC.py", line 360, in write_all_atoms all_at_ch_rna, all_at_ch_prot = all_atom (plik, pars, transl, rotation, rna) File "/home/rpdock/mc/MC.py", line 297, in all_atom pro_ch, rna_ch = check_chains(plik, pars) File "/home/rpdock/mc/MC.py", line 106, in check_chains struc = pars.get_structure('native', plik) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py", line 83, in get_structure self._parse(handle.readlines()) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py", line 109, in _parse self.trailer = self._parse_coordinates(coords_trailer) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py", line 225, in _parse_coordinates fullname, serial_number, element) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/StructureBuilder.py", line 197, in init_atom fullname, serial_number, element) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/Atom.py", line 58, in __init__ self.bfactor=bfactor MemoryError 2026-10-24 19:57:38 Refinement of #2 /home/rpdock/web/media/jobs/e220063b-f4fb-4a69-84d7-314924df7088/prot-na_14620.pdb 2026-10-24 19:57:38 python /home/rpdock/mc/MC.py -s 1000 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/e220063b-f4fb-4a69-84d7-314924df7088//ref_struc/prot-na_14620/prot-na_14620.pdb 2026-10-24 19:59:16 run_mc::stderr:Traceback (most recent call last): File "/home/rpdock/mc/MC.py", line 709, in s, datas = write_all_atoms (datas, step_real, cal.split()[0], plik, pars, historyT, historyR, rna) File "/home/rpdock/mc/MC.py", line 360, in write_all_atoms all_at_ch_rna, all_at_ch_prot = all_atom (plik, pars, transl, rotation, rna) File "/home/rpdock/mc/MC.py", line 297, in all_atom pro_ch, rna_ch = check_chains(plik, pars) File "/home/rpdock/mc/MC.py", line 106, in check_chains struc = pars.get_structure('native', plik) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py", line 83, in get_structure self._parse(handle.readlines()) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py", line 109, in _parse self.trailer = self._parse_coordinates(coords_trailer) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py", line 225, in _parse_coordinates fullname, serial_number, element) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/StructureBuilder.py", line 197, in init_atom fullname, serial_number, element) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/Atom.py", line 58, in __init__ self.bfactor=bfactor MemoryError 2026-10-24 19:59:16 Refinement of #3 /home/rpdock/web/media/jobs/e220063b-f4fb-4a69-84d7-314924df7088/prot-na_2050.pdb 2026-10-24 19:59:16 python /home/rpdock/mc/MC.py -s 1000 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/e220063b-f4fb-4a69-84d7-314924df7088//ref_struc/prot-na_2050/prot-na_2050.pdb 2026-10-24 20:00:51 run_mc::stderr:Traceback (most recent call last): File "/home/rpdock/mc/MC.py", line 709, in s, datas = write_all_atoms (datas, step_real, cal.split()[0], plik, pars, historyT, historyR, rna) File "/home/rpdock/mc/MC.py", line 360, in write_all_atoms all_at_ch_rna, all_at_ch_prot = all_atom (plik, pars, transl, rotation, rna) File "/home/rpdock/mc/MC.py", line 297, in all_atom pro_ch, rna_ch = check_chains(plik, pars) File "/home/rpdock/mc/MC.py", line 106, in check_chains struc = pars.get_structure('native', plik) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py", line 83, in get_structure self._parse(handle.readlines()) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py", line 109, in _parse self.trailer = self._parse_coordinates(coords_trailer) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py", line 225, in _parse_coordinates fullname, serial_number, element) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/StructureBuilder.py", line 197, in init_atom fullname, serial_number, element) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/Atom.py", line 58, in __init__ self.bfactor=bfactor MemoryError 2026-10-24 20:00:51 start - parameters: File name /home/rpdock/web/media/jobs/e220063b-f4fb-4a69-84d7-314924df7088//ref_struc/prot-na_1287/prot-na_1287.pdb Steps 1000 Temp. start 15000.0 Temp. end 295.0 False msg start - parameters: File name /home/rpdock/web/media/jobs/e220063b-f4fb-4a69-84d7-314924df7088//ref_struc/prot-na_1287/prot-na_1287.pdb Steps 1000 Temp. start 15000.0 Temp. end 295.0 False Step E Edist Eang Epen Warning, residue G1 in the chain B has not P atom 0 - -1547082.35 -1119548.53 -927533.82 500000.00 1 R -1496271.07 -1084522.94 -911748.13 500000.00 T= 14970.59 K progress 0.1 2 T -1831337.39 -1063907.01 -867430.38 100000.00 T= 14955.885 K progress 0.2 3 T -1819902.76 -1068004.59 -851898.18 100000.00 T= 14911.77 K progress 0.3 4 R -1809406.14 -1064132.99 -845273.14 100000.00 T= 14867.655 K progress 0.4 5 R -1810904.21 -1065807.05 -845097.16 100000.00 T= 14838.245 K progress 0.5 6 R -1814378.39 -1065927.19 -848451.20 100000.00 T= 14823.54 K progress 0.6 7 R -1804428.88 -1060699.94 -843728.93 100000.00 T= 14794.13 K progress 0.7 8 R -1683482.60 -1029817.64 -853664.96 200000.00 T= 14764.72 K progress 0.8 9 T -1893598.40 -1133656.26 -959942.14 200000.00 T= 14750.015 K progress 0.9 10 R -1886142.28 -1103236.94 -982905.34 200000.00 T= 14720.605 K progress 1.0 11 R -1886158.97 -1103253.62 -982905.34 200000.00 T= 14661.785 K progress 1.1 12 R -1900948.42 -1109869.99 -991078.43 200000.00 T= 14647.08 K progress 1.2 13 T -1544239.13 -1040565.46 -903673.67 400000.00 T= 14617.67 K progress 1.3 14 R -1403543.12 -1023464.47 -880078.65 500000.00 T= 14573.555 K progress 1.4 15 T -1561519.48 -1018350.13 -843169.35 300000.00 T= 14558.85 K progress 1.5 16 R -1556587.54 -1015130.66 -841456.88 300000.00 T= 14500.03 K progress 1.6 17 T -1476486.72 -964904.21 -811582.51 300000.00 T= 14485.325 K progress 1.7 18 R -1482650.37 -966864.66 -815785.71 300000.00 T= 14470.62 K progress 1.8 19 T -1638737.63 -1032806.41 -905931.21 300000.00 T= 14441.21 K progress 1.9 20 R -1630494.42 -1030271.74 -900222.68 300000.00 T= 14426.505 K progress 2.0 21 T -1692138.82 -1065282.97 -926855.85 300000.00 T= 14382.39 K progress 2.1 22 T -1834922.84 -1069630.54 -965292.31 200000.00 T= 14264.75 K progress 2.2 23 R -1770098.59 -1050972.46 -919126.13 200000.00 T= 14250.045 K progress 2.3 24 R -1804187.06 -1058365.93 -945821.14 200000.00 T= 14205.93 K progress 2.4 25 R -1941301.20 -1087675.14 -953626.06 100000.00 T= 14191.225 K progress 2.5 26 R -1845207.36 -1070830.21 -974377.14 200000.00 T= 14161.815 K progress 2.6 27 T -1956199.96 -1086321.34 -969878.62 100000.00 T= 14147.11 K progress 2.7 28 R -2106931.70 -1113523.67 -993408.03 0.00 T= 14132.405 K progress 2.8 29 T -2060147.72 -1105801.93 -954345.79 0.00 T= 14058.88 K progress 2.9 30 R -1699900.45 -1022618.04 -877282.40 200000.00 T= 14014.765 K progress 3.0 31 T -1887762.83 -1097631.16 -990131.68 200000.00 T= 13911.83 K progress 3.1 32 T -1948404.44 -1084137.58 -964266.86 100000.00 T= 13882.42 K progress 3.2 33 R -1931740.62 -1068373.13 -963367.50 100000.00 T= 13867.715 K progress 3.3 34 R -1929289.39 -1051961.74 -977327.65 100000.00 T= 13853.01 K progress 3.4 35 R -2017382.37 -1067463.65 -949918.72 0.00 T= 13808.895 K progress 3.5 36 T -2133422.85 -1121747.83 -1011675.03 0.00 T= 13764.78 K progress 3.6 37 R -2114560.31 -1112511.91 -1002048.41 0.00 T= 13676.55 K progress 3.7 38 R -1946345.52 -1066190.22 -980155.30 100000.00 T= 13647.14 K progress 3.8 39 R -1984655.55 -1090932.19 -993723.35 100000.00 T= 13632.435 K progress 3.9 40 R -2098076.72 -1109944.52 -988132.20 0.00 T= 13617.73 K progress 4.0 41 R -2106377.48 -1113525.92 -992851.56 0.00 T= 13573.615 K progress 4.1 42 R -2106637.10 -1113785.54 -992851.56 0.00 T= 13500.09 K progress 4.2 43 R -2119897.11 -1117169.55 -1002727.56 0.00 T= 13470.68 K progress 4.3 44 R -1959575.66 -1068877.32 -990698.34 100000.00 T= 13367.745 K progress 4.4 45 R -1996174.57 -1104725.12 -991449.45 100000.00 T= 13353.04 K progress 4.5 46 R -1873802.67 -1111953.23 -961849.45 200000.00 T= 13264.81 K progress 4.6 47 R -2001276.45 -1106466.26 -994810.20 100000.00 T= 13235.4 K progress 4.7 48 T -2012858.17 -1117669.56 -995188.61 100000.00 T= 13205.99 K progress 4.8 49 R -2020681.82 -1123251.80 -997430.02 100000.00 T= 13176.58 K progress 4.9 50 R -2007325.02 -1117275.55 -990049.47 100000.00 T= 13103.055 K progress 5.0 51 R -2030945.69 -1124783.48 -1006162.21 100000.00 T= 13029.53 K progress 5.1 52 R -2029608.88 -1121208.98 -1008399.90 100000.00 T= 13014.825 K progress 5.2 53 R -2036609.22 -1127333.18 -1009276.04 100000.00 T= 12970.71 K progress 5.3 54 R -1854691.15 -1085176.47 -969514.68 200000.00 T= 12956.005 K progress 5.4 55 R -2056135.64 -1146061.38 -1010074.26 100000.00 T= 12941.3 K progress 5.5 56 R -2060162.39 -1147407.04 -1012755.35 100000.00 T= 12926.595 K progress 5.6 57 R -2057639.83 -1146256.24 -1011383.59 100000.00 T= 12911.89 K progress 5.7 58 R -2035907.67 -1128462.47 -1007445.20 100000.00 T= 12867.775 K progress 5.8 59 R -2039428.22 -1128962.46 -1010465.76 100000.00 T= 12853.07 K progress 5.9 60 R -2038944.34 -1132217.42 -1006726.92 100000.00 T= 12735.43 K progress 6.0 61 R -2037896.77 -1129067.15 -1008829.62 100000.00 T= 12720.725 K progress 6.1 62 T -2070474.55 -1138851.63 -1031622.92 100000.00 T= 12691.315 K progress 6.2 63 T -1936303.27 -1145561.16 -990742.11 200000.00 T= 12676.61 K progress 6.3 64 T -1910235.60 -1184219.99 -1026015.61 300000.00 T= 12661.905 K progress 6.4 65 T -1856212.89 -1212671.29 -1043541.60 400000.00 T= 12647.2 K progress 6.5 66 R -2014786.53 -1229834.79 -1084951.73 300000.00 T= 12632.495 K progress 6.6 67 R -2002397.89 -1223621.18 -1078776.71 300000.00 T= 12558.97 K progress 6.7 68 R -1998602.58 -1219090.15 -1079512.42 300000.00 T= 12544.265 K progress 6.8 69 R -2008515.52 -1224615.99 -1083899.53 300000.00 T= 12529.56 K progress 6.9 70 T -1823608.93 -1129986.95 -993621.98 300000.00 T= 12485.445 K progress 7.0 71 T -2143993.33 -1173240.63 -1070752.70 100000.00 T= 12470.74 K progress 7.1 72 T -2222801.38 -1225152.07 -1097649.32 100000.00 T= 12411.92 K progress 7.2 73 R -2259047.41 -1262904.55 -1096142.86 100000.00 T= 12367.805 K progress 7.3 74 R -2232740.74 -1244883.78 -1087856.96 100000.00 T= 12353.1 K progress 7.4 75 T -2184169.77 -1213233.89 -1070935.88 100000.00 T= 12338.395 K progress 7.5 76 R -2204914.51 -1221450.41 -1083464.10 100000.00 T= 12308.985 K progress 7.6 77 R -2149795.95 -1193459.79 -1056336.17 100000.00 T= 12294.28 K progress 7.7 78 R -2173518.81 -1172213.99 -1101304.81 100000.00 T= 12264.87 K progress 7.8 79 R -2185313.76 -1211742.31 -1073571.45 100000.00 T= 12235.46 K progress 7.9 80 R -2209037.20 -1223676.63 -1085360.57 100000.00 T= 12191.345 K progress 8.0 81 R -2215080.75 -1228205.53 -1086875.22 100000.00 T= 12117.82 K progress 8.1 82 R -2190047.43 -1197767.27 -1092280.16 100000.00 T= 12088.41 K progress 8.2 83 T -2289187.50 -1273554.03 -1115633.47 100000.00 T= 12029.59 K progress 8.3 84 R -2296638.80 -1280083.14 -1116555.66 100000.00 T= 12014.885 K progress 8.4 85 R -2299964.32 -1279957.85 -1120006.47 100000.00 T= 12000.18 K progress 8.5 86 R -2302163.67 -1284221.72 -1117941.95 100000.00 T= 11985.475 K progress 8.6 87 R -2294670.87 -1278239.33 -1116431.54 100000.00 T= 11897.245 K progress 8.7 88 T -2301462.85 -1272113.30 -1129349.55 100000.00 T= 11867.835 K progress 8.8 89 T -2331395.57 -1296061.77 -1135333.80 100000.00 T= 11838.425 K progress 8.9 90 R -2285016.71 -1265112.35 -1119904.36 100000.00 T= 11809.015 K progress 9.0 91 R -2258124.72 -1260516.76 -1097607.96 100000.00 T= 11735.49 K progress 9.1 92 R -2263047.74 -1262939.90 -1100107.84 100000.00 T= 11720.785 K progress 9.2 93 R -2248266.89 -1247085.02 -1101181.87 100000.00 T= 11691.375 K progress 9.3 94 R -2279451.93 -1257308.69 -1122143.24 100000.00 T= 11676.67 K progress 9.4 95 R -2123292.22 -1235718.76 -1087573.46 200000.00 T= 11661.965 K progress 9.5 96 T -2262237.29 -1306230.34 -1156006.95 200000.00 T= 11647.26 K progress 9.6 97 T -2274920.26 -1327093.48 -1147826.79 200000.00 T= 11588.44 K progress 9.7 98 R -2212179.38 -1217209.16 -1094970.22 100000.00 T= 11573.735 K progress 9.8 99 R -2257976.54 -1254593.22 -1103383.32 100000.00 T= 11559.03 K progress 9.9 100 T -2172268.78 -1254434.87 -1117833.91 200000.00 T= 11500.21 K progress 10.0 101 T -2208392.64 -1271324.90 -1137067.74 200000.00 T= 11485.505 K progress 10.1 102 R -2212442.67 -1275374.94 -1137067.74 200000.00 T= 11441.39 K progress 10.2 103 T -1990711.02 -1211878.67 -1078832.35 300000.00 T= 11382.57 K progress 10.3 104 R -1992131.18 -1209442.07 -1082689.11 300000.00 T= 11353.16 K progress 10.4 105 T -2198542.73 -1273153.88 -1125388.85 200000.00 T= 11323.75 K progress 10.5 106 R -2268757.22 -1248470.70 -1120286.52 100000.00 T= 11309.045 K progress 10.6 107 R -2262421.17 -1243314.71 -1119106.46 100000.00 T= 11264.93 K progress 10.7 108 T -2226343.66 -1239887.58 -1086456.08 100000.00 T= 11235.52 K progress 10.8 109 R -2229388.58 -1242067.62 -1087320.95 100000.00 T= 11220.815 K progress 10.9 110 R -2204607.51 -1231789.53 -1072817.98 100000.00 T= 11206.11 K progress 11.0 111 T -2272924.58 -1268258.47 -1104666.11 100000.00 T= 11191.405 K progress 11.1 112 R -2295756.52 -1286589.77 -1109166.76 100000.00 T= 11161.995 K progress 11.2 113 T -2168818.44 -1269581.83 -1099236.61 200000.00 T= 11147.29 K progress 11.3 114 T -2196057.03 -1254273.07 -1141783.96 200000.00 T= 11117.88 K progress 11.4 115 T -2230481.28 -1240237.51 -1090243.78 100000.00 T= 11088.47 K progress 11.5 116 R -2241112.94 -1237636.47 -1103476.47 100000.00 T= 11073.765 K progress 11.6 117 R -2224978.21 -1237901.03 -1087077.18 100000.00 T= 11059.06 K progress 11.7 118 T -2154813.49 -1198069.78 -1056743.70 100000.00 T= 11014.945 K progress 11.8 119 R -2266974.27 -1260862.00 -1106112.27 100000.00 T= 10956.125 K progress 11.9 120 T -2299271.29 -1275448.30 -1123822.99 100000.00 T= 10926.715 K progress 12.0 Traceback (most recent call last): File "/home/rpdock/mc/MC.py", line 589, in s, datas = write_all_atoms (datas, step_real, cal.split()[0], plik, pars, historyT, historyR, rna) File "/home/rpdock/mc/MC.py", line 360, in write_all_atoms all_at_ch_rna, all_at_ch_prot = all_atom (plik, pars, transl, rotation, rna) File "/home/rpdock/mc/MC.py", line 297, in all_atom pro_ch, rna_ch = check_chains(plik, pars) File "/home/rpdock/mc/MC.py", line 106, in check_chains struc = pars.get_structure('native', plik) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py", line 83, in get_structure self._parse(handle.readlines()) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py", line 109, in _parse self.trailer = self._parse_coordinates(coords_trailer) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py", line 225, in _parse_coordinates fullname, serial_number, element) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/StructureBuilder.py", line 197, in init_atom fullname, serial_number, element) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/Atom.py", line 58, in __init__ self.bfactor=bfactor MemoryError Error in run_mc Traceback (most recent call last): File "/home/rpdock/mc/MC.py", line 671, in s, datas = write_all_atoms (datas, step_real, cal.split()[0], plik, pars, historyT, historyR, rna) File "/home/rpdock/mc/MC.py", line 360, in write_all_atoms all_at_ch_rna, all_at_ch_prot = all_atom (plik, pars, transl, rotation, rna) File "/home/rpdock/mc/MC.py", line 297, in all_atom pro_ch, rna_ch = check_chains(plik, pars) File "/home/rpdock/mc/MC.py", line 106, in check_chains struc = pars.get_structure('native', plik) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py", line 83, in get_structure self._parse(handle.readlines()) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py", line 109, in _parse self.trailer = self._parse_coordinates(coords_trailer) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py", line 225, in _parse_coordinates fullname, serial_number, element) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/StructureBuilder.py", line 197, in init_atom fullname, serial_number, element) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/Atom.py", line 58, in __init__ self.bfactor=bfactor MemoryError start - parameters: File name /home/rpdock/web/media/jobs/e220063b-f4fb-4a69-84d7-314924df7088//ref_struc/prot-na_14620/prot-na_14620.pdb Steps 1000 Temp. start 15000.0 Temp. end 295.0 False msg start - parameters: File name /home/rpdock/web/media/jobs/e220063b-f4fb-4a69-84d7-314924df7088//ref_struc/prot-na_14620/prot-na_14620.pdb Steps 1000 Temp. start 15000.0 Temp. end 295.0 False Step E Edist Eang Epen Warning, residue G1 in the chain B has not P atom 0 - -1833852.96 -1032283.79 -901569.17 100000.00 1 T -1673837.10 -1000172.99 -873664.11 200000.00 T= 14985.295 K progress 0.1 2 R -1671025.47 -1010062.62 -860962.85 200000.00 T= 14970.59 K progress 0.2 3 T -1668816.45 -958477.14 -810339.31 100000.00 T= 14955.885 K progress 0.3 4 R -1704741.32 -971241.40 -833499.91 100000.00 T= 14926.475 K progress 0.4 5 R -1744024.76 -989826.41 -854198.34 100000.00 T= 14794.13 K progress 0.5 6 R -1703297.69 -970444.69 -832853.01 100000.00 T= 14764.72 K progress 0.6 7 R -1677334.74 -958320.17 -819014.57 100000.00 T= 14720.605 K progress 0.7 8 R -1632610.87 -939471.16 -793139.71 100000.00 T= 14705.9 K progress 0.8 9 T -1661405.21 -1003145.71 -858259.50 200000.00 T= 14691.195 K progress 0.9 10 T -1544699.63 -942934.97 -801764.66 200000.00 T= 14661.785 K progress 1.0 11 T -1474435.69 -901184.19 -773251.50 200000.00 T= 14632.375 K progress 1.1 12 T -1570730.76 -894322.91 -776407.86 100000.00 T= 14602.965 K progress 1.2 13 R -1521072.02 -856737.75 -764334.27 100000.00 T= 14588.26 K progress 1.3 14 T -1568299.96 -847034.78 -721265.19 0.00 T= 14573.555 K progress 1.4 15 R -1573703.48 -845354.09 -728349.39 0.00 T= 14558.85 K progress 1.5 16 T -1595170.07 -863805.43 -731364.64 0.00 T= 14544.145 K progress 1.6 17 R -1584520.93 -854558.14 -729962.79 0.00 T= 14529.44 K progress 1.7 18 R -1561439.70 -845250.83 -716188.87 0.00 T= 14514.735 K progress 1.8 19 R -1586000.99 -860096.63 -725904.35 0.00 T= 14500.03 K progress 1.9 20 R -1437991.79 -833832.35 -704159.44 100000.00 T= 14485.325 K progress 2.0 21 R -1450973.84 -849372.91 -701600.92 100000.00 T= 14470.62 K progress 2.1 22 T -1467815.56 -836394.06 -731421.49 100000.00 T= 14455.915 K progress 2.2 23 R -1491146.49 -859261.97 -731884.51 100000.00 T= 14441.21 K progress 2.3 24 R -1509195.26 -868728.11 -740467.15 100000.00 T= 14397.095 K progress 2.4 25 R -1446559.15 -851843.73 -694715.42 100000.00 T= 14382.39 K progress 2.5 26 R -1513117.74 -861211.26 -751906.48 100000.00 T= 14308.865 K progress 2.6 27 R -1509474.30 -854598.04 -754876.27 100000.00 T= 14294.16 K progress 2.7 28 T -1484043.71 -851318.97 -732724.73 100000.00 T= 14264.75 K progress 2.8 29 T -1422658.28 -808961.21 -713697.06 100000.00 T= 14250.045 K progress 2.9 30 T -1411363.62 -812031.23 -699332.39 100000.00 T= 14235.34 K progress 3.0 31 T -1530432.81 -866695.08 -763737.73 100000.00 T= 14205.93 K progress 3.1 32 T -1717766.13 -925059.24 -792706.88 0.00 T= 14176.52 K progress 3.2 33 T -1544129.27 -889788.97 -754340.30 100000.00 T= 14147.11 K progress 3.3 34 R -1585285.13 -914020.53 -771264.60 100000.00 T= 14132.405 K progress 3.4 35 R -1580493.58 -911441.72 -769051.87 100000.00 T= 14117.7 K progress 3.5 36 R -1567121.16 -891998.59 -775122.57 100000.00 T= 14073.585 K progress 3.6 37 T -1690608.83 -960975.75 -829633.08 100000.00 T= 14058.88 K progress 3.7 38 T -1689838.60 -968826.90 -821011.70 100000.00 T= 14044.175 K progress 3.8 39 T -1620236.36 -937907.97 -782328.40 100000.00 T= 14014.765 K progress 3.9 40 R -1622886.00 -933682.92 -789203.08 100000.00 T= 14000.06 K progress 4.0 41 T -1324816.50 -869681.56 -755134.94 300000.00 T= 13970.65 K progress 4.1 42 T -1356999.49 -880715.47 -776284.02 300000.00 T= 13955.945 K progress 4.2 43 R -1376223.57 -897724.52 -778499.05 300000.00 T= 13926.535 K progress 4.3 44 T -1183151.17 -781486.04 -701665.12 300000.00 T= 13911.83 K progress 4.4 45 R -1185486.99 -783368.24 -702118.75 300000.00 T= 13838.305 K progress 4.5 46 R -1185684.01 -782635.30 -703048.71 300000.00 T= 13823.6 K progress 4.6 47 T -1254362.03 -832623.84 -721738.19 300000.00 T= 13808.895 K progress 4.7 48 R -1320447.33 -862162.15 -758285.17 300000.00 T= 13794.19 K progress 4.8 49 R -1337828.54 -875631.99 -762196.55 300000.00 T= 13779.485 K progress 4.9 50 R -923071.44 -865743.23 -757328.21 700000.00 T= 13764.78 K progress 5.0 51 T -1439068.59 -921303.88 -817764.71 300000.00 T= 13735.37 K progress 5.1 52 T -1485659.47 -945506.36 -840153.12 300000.00 T= 13720.665 K progress 5.2 53 R -1403797.27 -898158.25 -805639.02 300000.00 T= 13632.435 K progress 5.3 54 R -1204270.72 -852662.96 -751607.76 400000.00 T= 13617.73 K progress 5.4 55 R -1388039.38 -887828.58 -800210.81 300000.00 T= 13603.025 K progress 5.5 56 T -1440306.68 -926674.43 -813632.26 300000.00 T= 13558.91 K progress 5.6 57 T -1372562.98 -886761.06 -785801.92 300000.00 T= 13544.205 K progress 5.7 58 R -1178692.10 -825868.90 -752823.21 400000.00 T= 13470.68 K progress 5.8 59 T -1263816.73 -828192.74 -735623.99 300000.00 T= 13455.975 K progress 5.9 60 R -1187069.86 -842625.06 -744444.80 400000.00 T= 13367.745 K progress 6.0 61 T -1481554.13 -956573.94 -824980.19 300000.00 T= 13338.335 K progress 6.1 62 R -1417702.61 -909336.06 -808366.55 300000.00 T= 13308.925 K progress 6.2 63 T -1687195.28 -968586.68 -818608.60 100000.00 T= 13294.22 K progress 6.3 64 R -1630541.97 -937624.05 -792917.92 100000.00 T= 13279.515 K progress 6.4 65 T -1625358.33 -932026.32 -793332.01 100000.00 T= 13264.81 K progress 6.5 66 T -1626859.49 -948400.89 -778458.60 100000.00 T= 13250.105 K progress 6.6 67 R -1618389.38 -936789.87 -781599.51 100000.00 T= 13235.4 K progress 6.7 68 R -1591858.35 -925828.92 -766029.43 100000.00 T= 13191.285 K progress 6.8 69 R -1698413.43 -977061.70 -821351.74 100000.00 T= 13176.58 K progress 6.9 70 T -1605766.41 -914640.08 -791126.32 100000.00 T= 13132.465 K progress 7.0 71 R -1637169.79 -935066.48 -802103.31 100000.00 T= 13103.055 K progress 7.1 72 R -1567353.76 -890641.53 -776712.23 100000.00 T= 13088.35 K progress 7.2 73 T -1626020.20 -987677.63 -838342.57 200000.00 T= 13073.645 K progress 7.3 74 R -1620921.02 -972578.77 -848342.26 200000.00 T= 13029.53 K progress 7.4 75 R -1623791.45 -968991.99 -854799.45 200000.00 T= 13014.825 K progress 7.5 76 T -1573305.36 -935266.59 -838038.76 200000.00 T= 12985.415 K progress 7.6 77 R -1579315.18 -948407.52 -830907.66 200000.00 T= 12956.005 K progress 7.7 78 R -1543958.29 -945417.63 -798540.66 200000.00 T= 12926.595 K progress 7.8 79 T -1615583.89 -974497.05 -841086.84 200000.00 T= 12911.89 K progress 7.9 80 T -1652927.27 -1048789.68 -904137.59 300000.00 T= 12897.185 K progress 8.0 81 R -1622548.00 -1024371.71 -898176.29 300000.00 T= 12882.48 K progress 8.1 82 R -1682390.04 -1059573.53 -922816.51 300000.00 T= 12867.775 K progress 8.2 83 R -1651338.04 -1047200.44 -904137.59 300000.00 T= 12853.07 K progress 8.3 84 T -1675731.89 -1051096.88 -924635.01 300000.00 T= 12823.66 K progress 8.4 85 R -1707292.32 -1066648.95 -940643.37 300000.00 T= 12764.84 K progress 8.5 86 R -1742691.46 -1085532.59 -957158.87 300000.00 T= 12735.43 K progress 8.6 87 R -1692169.29 -1056869.10 -935300.20 300000.00 T= 12720.725 K progress 8.7 88 R -1892082.85 -1090482.44 -1001600.41 200000.00 T= 12706.02 K progress 8.8 89 R -1737198.48 -1071129.50 -966068.98 300000.00 T= 12588.38 K progress 8.9 90 R -1896147.66 -1096286.72 -999860.94 200000.00 T= 12573.675 K progress 9.0 91 R -1891830.33 -1091863.57 -999966.76 200000.00 T= 12485.445 K progress 9.1 92 R -1882529.14 -1081553.36 -1000975.78 200000.00 T= 12456.035 K progress 9.2 93 R -1870549.26 -1079116.01 -991433.26 200000.00 T= 12426.625 K progress 9.3 94 R -1877339.38 -1093491.17 -983848.22 200000.00 T= 12382.51 K progress 9.4 95 R -1873989.55 -1084678.46 -989311.09 200000.00 T= 12323.69 K progress 9.5 96 T -1861357.50 -1079597.99 -981759.51 200000.00 T= 12308.985 K progress 9.6 97 R -1863019.58 -1080901.08 -982118.51 200000.00 T= 12294.28 K progress 9.7 98 T -1802438.33 -1063213.41 -939224.92 200000.00 T= 12279.575 K progress 9.8 99 T -1683948.14 -1123417.29 -960530.85 400000.00 T= 12250.165 K progress 9.9 100 R -1696023.62 -1127940.08 -968083.55 400000.00 T= 12220.755 K progress 10.0 101 T -1814491.11 -1069620.60 -944870.51 200000.00 T= 12176.64 K progress 10.1 102 R -1616661.53 -1004838.44 -911823.09 300000.00 T= 12161.935 K progress 10.2 103 T -1647533.87 -1010195.63 -937338.24 300000.00 T= 12103.115 K progress 10.3 104 T -1675415.93 -996562.81 -878853.12 200000.00 T= 12073.705 K progress 10.4 105 T -1741174.93 -1029102.98 -912071.95 200000.00 T= 12044.295 K progress 10.5 106 T -1911823.69 -1103829.78 -1007993.91 200000.00 T= 12000.18 K progress 10.6 107 R -1921982.22 -1110883.50 -1011098.71 200000.00 T= 11985.475 K progress 10.7 108 R -1929179.63 -1114546.58 -1014633.05 200000.00 T= 11911.95 K progress 10.8 109 R -1895223.87 -1096873.37 -998350.50 200000.00 T= 11882.54 K progress 10.9 110 R -1921982.22 -1110883.50 -1011098.71 200000.00 T= 11779.605 K progress 11.0 111 R -1896703.80 -1095789.82 -1000913.98 200000.00 T= 11573.735 K progress 11.1 112 T -1802447.49 -1053010.34 -949437.15 200000.00 T= 11470.8 K progress 11.2 113 R -1811368.91 -1064804.82 -946564.09 200000.00 T= 11426.685 K progress 11.3 114 R -1816274.15 -1062572.11 -953702.04 200000.00 T= 11411.98 K progress 11.4 115 R -1801764.31 -1054224.24 -947540.07 200000.00 T= 11323.75 K progress 11.5 116 R -1762020.27 -1029605.13 -932415.14 200000.00 T= 11309.045 K progress 11.6 117 R -1826046.88 -1066311.95 -959734.93 200000.00 T= 11279.635 K progress 11.7 118 R -1823569.98 -1066311.95 -957258.03 200000.00 T= 11264.93 K progress 11.8 119 R -1820292.44 -1065939.79 -954352.64 200000.00 T= 11161.995 K progress 11.9 120 R -1703824.05 -1076220.00 -927604.05 300000.00 T= 11147.29 K progress 12.0 Traceback (most recent call last): File "/home/rpdock/mc/MC.py", line 709, in s, datas = write_all_atoms (datas, step_real, cal.split()[0], plik, pars, historyT, historyR, rna) File "/home/rpdock/mc/MC.py", line 360, in write_all_atoms all_at_ch_rna, all_at_ch_prot = all_atom (plik, pars, transl, rotation, rna) File "/home/rpdock/mc/MC.py", line 297, in all_atom pro_ch, rna_ch = check_chains(plik, pars) File "/home/rpdock/mc/MC.py", line 106, in check_chains struc = pars.get_structure('native', plik) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py", line 83, in get_structure self._parse(handle.readlines()) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py", line 109, in _parse self.trailer = self._parse_coordinates(coords_trailer) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py", line 225, in _parse_coordinates fullname, serial_number, element) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/StructureBuilder.py", line 197, in init_atom fullname, serial_number, element) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/Atom.py", line 58, in __init__ self.bfactor=bfactor MemoryError Sat Oct 24 19:55:55 2026 ['prot-na_1287.pdb', 'prot-na_14620.pdb', 'prot-na_2050.pdb'] msg Refinement of #1 /home/rpdock/web/media/jobs/e220063b-f4fb-4a69-84d7-314924df7088/prot-na_1287.pdb dir: /home/rpdock/web/media/jobs/e220063b-f4fb-4a69-84d7-314924df7088/ file: prot-na_1287.pdb find `pwd` -iname prot-na_1287.pdb copy /home/rpdock/web/media/jobs/e220063b-f4fb-4a69-84d7-314924df7088/prot-na_10/prot-na_1287.pdb to /home/rpdock/web/media/jobs/e220063b-f4fb-4a69-84d7-314924df7088//ref_struc/prot-na_1287/prot-na_1287.pdb cmd: python /home/rpdock/mc/MC.py -s 1000 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/e220063b-f4fb-4a69-84d7-314924df7088//ref_struc/prot-na_1287/prot-na_1287.pdb msg python /home/rpdock/mc/MC.py -s 1000 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/e220063b-f4fb-4a69-84d7-314924df7088//ref_struc/prot-na_1287/prot-na_1287.pdb msg run_mc::stderr:Traceback (most recent call last): File "/home/rpdock/mc/MC.py", line 671, in s, datas = write_all_atoms (datas, step_real, cal.split()[0], plik, pars, historyT, historyR, rna) File "/home/rpdock/mc/MC.py", line 360, in write_all_atoms all_at_ch_rna, all_at_ch_prot = all_atom (plik, pars, transl, rotation, rna) File "/home/rpdock/mc/MC.py", line 297, in all_atom pro_ch, rna_ch = check_chains(plik, pars) File "/home/rpdock/mc/MC.py", line 106, in check_chains struc = pars.get_structure('native', plik) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py", line 83, in get_structure self._parse(handle.readlines()) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py", line 109, in _parse self.trailer = self._parse_coordinates(coords_trailer) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py", line 225, in _parse_coordinates fullname, serial_number, element) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/StructureBuilder.py", line 197, in init_atom fullname, serial_number, element) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/Atom.py", line 58, in __init__ self.bfactor=bfactor MemoryError msg Refinement of #2 /home/rpdock/web/media/jobs/e220063b-f4fb-4a69-84d7-314924df7088/prot-na_14620.pdb dir: /home/rpdock/web/media/jobs/e220063b-f4fb-4a69-84d7-314924df7088/ file: prot-na_14620.pdb find `pwd` -iname prot-na_14620.pdb copy /home/rpdock/web/media/jobs/e220063b-f4fb-4a69-84d7-314924df7088/prot-na_10/prot-na_14620.pdb to /home/rpdock/web/media/jobs/e220063b-f4fb-4a69-84d7-314924df7088//ref_struc/prot-na_14620/prot-na_14620.pdb cmd: python /home/rpdock/mc/MC.py -s 1000 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/e220063b-f4fb-4a69-84d7-314924df7088//ref_struc/prot-na_14620/prot-na_14620.pdb msg python /home/rpdock/mc/MC.py -s 1000 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/e220063b-f4fb-4a69-84d7-314924df7088//ref_struc/prot-na_14620/prot-na_14620.pdb msg run_mc::stderr:Traceback (most recent call last): File "/home/rpdock/mc/MC.py", line 709, in s, datas = write_all_atoms (datas, step_real, cal.split()[0], plik, pars, historyT, historyR, rna) File "/home/rpdock/mc/MC.py", line 360, in write_all_atoms all_at_ch_rna, all_at_ch_prot = all_atom (plik, pars, transl, rotation, rna) File "/home/rpdock/mc/MC.py", line 297, in all_atom pro_ch, rna_ch = check_chains(plik, pars) File "/home/rpdock/mc/MC.py", line 106, in check_chains struc = pars.get_structure('native', plik) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py", line 83, in get_structure self._parse(handle.readlines()) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py", line 109, in _parse self.trailer = self._parse_coordinates(coords_trailer) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py", line 225, in _parse_coordinates fullname, serial_number, element) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/StructureBuilder.py", line 197, in init_atom fullname, serial_number, element) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/Atom.py", line 58, in __init__ selfError in run_mc Traceback (most recent call last): File "/home/rpdock/mc/MC.py", line 709, in s, datas = write_all_atoms (datas, step_real, cal.split()[0], plik, pars, historyT, historyR, rna) File "/home/rpdock/mc/MC.py", line 360, in write_all_atoms all_at_ch_rna, all_at_ch_prot = all_atom (plik, pars, transl, rotation, rna) File "/home/rpdock/mc/MC.py", line 297, in all_atom pro_ch, rna_ch = check_chains(plik, pars) File "/home/rpdock/mc/MC.py", line 106, in check_chains struc = pars.get_structure('native', plik) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py", line 83, in get_structure self._parse(handle.readlines()) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py", line 109, in _parse self.trailer = self._parse_coordinates(coords_trailer) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py", line 225, in _parse_coordinates fullname, serial_number, element) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/StructureBuilder.py", line 197, in init_atom fullname, serial_number, element) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/Atom.py", line 58, in __init__ self.bfactor=bfactor MemoryError start - parameters: File name /home/rpdock/web/media/jobs/e220063b-f4fb-4a69-84d7-314924df7088//ref_struc/prot-na_2050/prot-na_2050.pdb Steps 1000 Temp. start 15000.0 Temp. end 295.0 False msg start - parameters: File name /home/rpdock/web/media/jobs/e220063b-f4fb-4a69-84d7-314924df7088//ref_struc/prot-na_2050/prot-na_2050.pdb Steps 1000 Temp. start 15000.0 Temp. end 295.0 False Step E Edist Eang Epen Warning, residue G1 in the chain B has not P atom 0 - -1886755.25 -1043272.36 -943482.88 100000.00 1 R -1996178.77 -1079125.07 -917053.70 0.00 T= 14970.59 K progress 0.1 2 T -1841626.94 -1051823.31 -889803.63 100000.00 T= 14955.885 K progress 0.2 3 R -1888798.09 -1055716.81 -933081.28 100000.00 T= 14941.18 K progress 0.3 4 R -1836467.36 -1032791.46 -903675.90 100000.00 T= 14926.475 K progress 0.4 5 T -1892616.85 -1111222.12 -981394.73 200000.00 T= 14911.77 K progress 0.5 6 R -1885389.00 -1111171.62 -974217.38 200000.00 T= 14897.065 K progress 0.6 7 R -1852042.53 -1094756.84 -957285.68 200000.00 T= 14882.36 K progress 0.7 8 R -1843541.73 -1094296.71 -949245.01 200000.00 T= 14867.655 K progress 0.8 9 T -1829345.77 -1150038.23 -979307.54 300000.00 T= 14852.95 K progress 0.9 10 R -1617502.66 -1075033.68 -942468.97 400000.00 T= 14823.54 K progress 1.0 11 T -1784546.82 -1057421.23 -927125.59 200000.00 T= 14779.425 K progress 1.1 12 R -1789902.34 -1052268.45 -937633.89 200000.00 T= 14750.015 K progress 1.2 13 T -1879133.00 -1055583.19 -923549.81 100000.00 T= 14735.31 K progress 1.3 14 T -1849063.53 -1104093.82 -944969.71 200000.00 T= 14705.9 K progress 1.4 15 R -1793097.32 -1081518.73 -911578.59 200000.00 T= 14676.49 K progress 1.5 16 T -1779211.50 -1090390.65 -888820.85 200000.00 T= 14661.785 K progress 1.6 17 R -1746519.19 -1066595.33 -879923.85 200000.00 T= 14647.08 K progress 1.7 18 R -1729248.55 -1053276.22 -875972.33 200000.00 T= 14632.375 K progress 1.8 19 R -1753631.23 -1054349.42 -899281.80 200000.00 T= 14602.965 K progress 1.9 20 R -1770931.34 -1072656.30 -898275.04 200000.00 T= 14588.26 K progress 2.0 21 T -2029218.80 -1171932.61 -957286.19 100000.00 T= 14544.145 K progress 2.1 22 T -1959578.09 -1067398.78 -892179.31 0.00 T= 14514.735 K progress 2.2 23 R -1997149.17 -1083705.51 -913443.66 0.00 T= 14426.505 K progress 2.3 24 T -1890890.38 -1083804.60 -907085.78 100000.00 T= 14411.8 K progress 2.4 25 T -1894927.39 -1126307.59 -968619.80 200000.00 T= 14294.16 K progress 2.5 26 R -1898893.77 -1129297.79 -969595.98 200000.00 T= 14279.455 K progress 2.6 27 R -1906743.04 -1131445.50 -975297.54 200000.00 T= 14220.635 K progress 2.7 28 R -1928776.48 -1143090.48 -985686.00 200000.00 T= 14191.225 K progress 2.8 29 R -2024480.63 -1147210.98 -977269.65 100000.00 T= 14161.815 K progress 2.9 30 T -1828935.54 -1103480.64 -925454.90 200000.00 T= 14088.29 K progress 3.0 31 T -1586982.93 -1073661.34 -913321.60 400000.00 T= 14073.585 K progress 3.1 32 R -1607535.67 -1105158.36 -902377.31 400000.00 T= 14058.88 K progress 3.2 33 T -1608261.83 -1080886.87 -927374.96 400000.00 T= 14044.175 K progress 3.3 34 R -1341458.77 -987996.62 -853462.15 500000.00 T= 14000.06 K progress 3.4 35 T -1292569.98 -1048961.48 -943608.50 700000.00 T= 13985.355 K progress 3.5 36 T -1259501.22 -1025674.17 -933827.05 700000.00 T= 13970.65 K progress 3.6 37 R -1141718.24 -1014129.29 -927588.96 800000.00 T= 13941.24 K progress 3.7 38 T -908977.47 -1022476.32 -886501.15 1000000.00 T= 13926.535 K progress 3.8 39 R -855505.84 -999352.60 -856153.24 1000000.00 T= 13838.305 K progress 3.9 40 R -1018542.97 -1025341.05 -893201.92 900000.00 T= 13823.6 K progress 4.0 41 R -1054524.49 -1037324.06 -917200.43 900000.00 T= 13764.78 K progress 4.1 42 R -1064057.65 -1026052.75 -938004.91 900000.00 T= 13750.075 K progress 4.2 43 T -1461029.46 -984612.89 -876416.56 400000.00 T= 13735.37 K progress 4.3 44 R -1467457.17 -987111.72 -880345.45 400000.00 T= 13720.665 K progress 4.4 45 R -1590705.01 -1003428.40 -887276.62 300000.00 T= 13705.96 K progress 4.5 46 R -1460541.39 -985832.64 -874708.75 400000.00 T= 13676.55 K progress 4.6 47 R -1609887.56 -1008374.50 -901513.06 300000.00 T= 13661.845 K progress 4.7 48 T -1659680.02 -977059.89 -882620.13 200000.00 T= 13647.14 K progress 4.8 49 R -1494643.93 -947246.60 -847397.33 300000.00 T= 13632.435 K progress 4.9 50 T -1686795.69 -1000496.87 -886298.83 200000.00 T= 13617.73 K progress 5.0 51 T -1728419.36 -1017967.33 -910452.03 200000.00 T= 13588.32 K progress 5.1 52 T -1619289.62 -1015814.70 -903474.92 300000.00 T= 13544.205 K progress 5.2 53 T -1835359.29 -1151537.14 -983822.15 300000.00 T= 13529.5 K progress 5.3 54 R -1817368.73 -1142098.50 -975270.23 300000.00 T= 13470.68 K progress 5.4 55 R -1804402.30 -1140253.40 -964148.90 300000.00 T= 13426.565 K progress 5.5 56 R -1793831.26 -1139443.04 -954388.22 300000.00 T= 13382.45 K progress 5.6 57 R -1785309.10 -1126945.70 -958363.40 300000.00 T= 13353.04 K progress 5.7 58 R -1794669.98 -1133938.30 -960731.68 300000.00 T= 13235.4 K progress 5.8 59 T -1609447.66 -1026940.47 -882507.19 300000.00 T= 13191.285 K progress 5.9 60 R -1654536.91 -1050884.16 -903652.75 300000.00 T= 13176.58 K progress 6.0 61 T -1794552.74 -1125805.31 -968747.43 300000.00 T= 13147.17 K progress 6.1 62 R -1791452.46 -1124647.40 -966805.06 300000.00 T= 13103.055 K progress 6.2 63 R -1529130.82 -1040186.11 -888944.71 400000.00 T= 13073.645 K progress 6.3 64 T -1551623.30 -1030188.63 -921434.67 400000.00 T= 13058.94 K progress 6.4 65 T -1772848.23 -1110787.88 -962060.35 300000.00 T= 13029.53 K progress 6.5 66 R -1758282.47 -1104785.02 -953497.45 300000.00 T= 12970.71 K progress 6.6 67 R -1754121.38 -1100268.47 -953852.91 300000.00 T= 12897.185 K progress 6.7 68 R -1748274.38 -1098044.44 -950229.94 300000.00 T= 12867.775 K progress 6.8 69 R -1753590.55 -1100907.53 -952683.02 300000.00 T= 12823.66 K progress 6.9 70 R -1741006.05 -1088672.58 -952333.47 300000.00 T= 12808.955 K progress 7.0 71 R -1724998.61 -1081429.85 -943568.76 300000.00 T= 12794.25 K progress 7.1 72 R -1739301.45 -1089208.42 -950093.04 300000.00 T= 12764.84 K progress 7.2 73 R -1752520.20 -1095253.10 -957267.10 300000.00 T= 12720.725 K progress 7.3 74 T -1729589.64 -1065136.02 -964453.63 300000.00 T= 12706.02 K progress 7.4 75 R -1729589.64 -1065136.02 -964453.63 300000.00 T= 12676.61 K progress 7.5 76 R -1731674.42 -1067220.79 -964453.63 300000.00 T= 12632.495 K progress 7.6 77 R -1427748.37 -1131024.81 -996723.56 700000.00 T= 12603.085 K progress 7.7 78 R -1418975.74 -1128099.89 -990875.86 700000.00 T= 12588.38 K progress 7.8 79 R -1766108.93 -1096545.62 -969563.32 300000.00 T= 12573.675 K progress 7.9 80 R -1768621.01 -1084403.67 -984217.34 300000.00 T= 12544.265 K progress 8.0 81 R -1761837.25 -1080096.08 -981741.17 300000.00 T= 12500.15 K progress 8.1 82 R -1756797.27 -1077474.14 -979323.14 300000.00 T= 12338.395 K progress 8.2 83 R -1880352.46 -1101961.22 -978391.24 200000.00 T= 12323.69 K progress 8.3 84 T -1805869.79 -1064622.51 -941247.29 200000.00 T= 12294.28 K progress 8.4 85 R -1789977.38 -1053937.90 -936039.48 200000.00 T= 12264.87 K progress 8.5 86 R -1815598.19 -1088163.91 -927434.28 200000.00 T= 12235.46 K progress 8.6 87 R -1800498.47 -1062146.99 -938351.48 200000.00 T= 12206.05 K progress 8.7 88 R -1736155.41 -1032584.10 -903571.31 200000.00 T= 12147.23 K progress 8.8 89 R -1805869.79 -1064622.51 -941247.29 200000.00 T= 12103.115 K progress 8.9 90 R -1739046.92 -1034825.88 -904221.04 200000.00 T= 12088.41 K progress 9.0 91 T -1800399.44 -1078463.79 -921935.64 200000.00 T= 12059.0 K progress 9.1 92 T -1757276.97 -1085288.60 -971988.38 300000.00 T= 11926.655 K progress 9.2 93 R -1760136.72 -1080480.46 -979656.25 300000.00 T= 11911.95 K progress 9.3 94 R -1783328.03 -1102413.42 -980914.61 300000.00 T= 11897.245 K progress 9.4 95 R -1933276.44 -1127660.76 -1005615.67 200000.00 T= 11882.54 K progress 9.5 96 R -1776773.49 -1104590.42 -972183.07 300000.00 T= 11794.31 K progress 9.6 97 R -1766876.20 -1090926.50 -975949.70 300000.00 T= 11750.195 K progress 9.7 98 T -1453047.33 -1028629.09 -924418.23 500000.00 T= 11735.49 K progress 9.8 99 T -1577206.09 -1034043.22 -943162.87 400000.00 T= 11676.67 K progress 9.9 100 R -1374877.83 -985378.47 -889499.36 500000.00 T= 11588.44 K progress 10.0 101 T -1431752.91 -1040887.58 -890865.32 500000.00 T= 11573.735 K progress 10.1 102 R -1427453.79 -1037953.14 -889500.65 500000.00 T= 11559.03 K progress 10.2 103 T -1507920.26 -1039304.55 -868615.71 400000.00 T= 11485.505 K progress 10.3 104 R -1514092.03 -1042653.13 -871438.90 400000.00 T= 11441.39 K progress 10.4 105 T -1503035.44 -1022895.84 -880139.60 400000.00 T= 11397.275 K progress 10.5 106 T -1635162.56 -1046053.22 -889109.34 300000.00 T= 11382.57 K progress 10.6 107 R -1645606.02 -1042724.19 -902881.83 300000.00 T= 11353.16 K progress 10.7 108 R -1638769.10 -1043678.82 -895090.28 300000.00 T= 11250.225 K progress 10.8 109 T -1696781.43 -1039447.53 -857333.90 200000.00 T= 11147.29 K progress 10.9 110 T -1716634.83 -1069616.68 -847018.15 200000.00 T= 11117.88 K progress 11.0 111 R -1714183.49 -1049736.46 -864447.02 200000.00 T= 11000.24 K progress 11.1 112 R -1704749.12 -1066145.59 -838603.53 200000.00 T= 10970.83 K progress 11.2 113 R -1681258.28 -1050870.57 -830387.71 200000.00 T= 10956.125 K progress 11.3 114 R -1678480.83 -1052130.97 -826349.87 200000.00 T= 10912.01 K progress 11.4 Traceback (most recent call last): File "/home/rpdock/mc/MC.py", line 709, in s, datas = write_all_atoms (datas, step_real, cal.split()[0], plik, pars, historyT, historyR, rna) File "/home/rpdock/mc/MC.py", line 360, in write_all_atoms all_at_ch_rna, all_at_ch_prot = all_atom (plik, pars, transl, rotation, rna) File "/home/rpdock/mc/MC.py", line 297, in all_atom pro_ch, rna_ch = check_chains(plik, pars) File "/home/rpdock/mc/MC.py", line 106, in check_chains struc = pars.get_structure('native', plik) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py", line 83, in get_structure self._parse(handle.readlines()) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py", line 109, in _parse self.trailer = self._parse_coordinates(coords_trailer) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py", line 199, in _parse_coordinates global_line_counter) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py", line 284, in _handle_PDB_exception % message, PDBConstructionWarning) MemoryError Error in run_mc Traceback (most recent call last): File "/home/rpdock/mc/MC.py", line 709, in s, datas = write_all_atoms (datas, step_real, cal.split()[0], plik, pars, historyT, historyR, rna) File "/home/rpdock/mc/MC.py", line 360, in write_all_atoms all_at_ch_rna, all_at_ch_prot = all_atom (plik, pars, transl, rotation, rna) File "/home/rpdock/mc/MC.py", line 297, in all_atom pro_ch, rna_ch = check_chains(plik, pars) File "/home/rpdock/mc/MC.py", line 106, in check_chains struc = pars.get_structure('native', plik) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py", line 83, in get_structure self._parse(handle.readlines()) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py", line 109, in _parse self.trailer = self._parse_coordinates(coords_trailer) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py", line 225, in _parse_coordinates fullname, serial_number, element) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/StructureBuilder.py", line 197, in init_atom fullname, serial_number, element) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/Atom.py", line 58, in __init__ self.bfactor=bfactor MemoryError .bfactor=bfactor MemoryError msg Refinement of #3 /home/rpdock/web/media/jobs/e220063b-f4fb-4a69-84d7-314924df7088/prot-na_2050.pdb dir: /home/rpdock/web/media/jobs/e220063b-f4fb-4a69-84d7-314924df7088/ file: prot-na_2050.pdb find `pwd` -iname prot-na_2050.pdb copy /home/rpdock/web/media/jobs/e220063b-f4fb-4a69-84d7-314924df7088/prot-na_10/prot-na_2050.pdb to /home/rpdock/web/media/jobs/e220063b-f4fb-4a69-84d7-314924df7088//ref_struc/prot-na_2050/prot-na_2050.pdb cmd: python /home/rpdock/mc/MC.py -s 1000 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/e220063b-f4fb-4a69-84d7-314924df7088//ref_struc/prot-na_2050/prot-na_2050.pdb msg python /home/rpdock/mc/MC.py -s 1000 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/e220063b-f4fb-4a69-84d7-314924df7088//ref_struc/prot-na_2050/prot-na_2050.pdb msg run_mc::stderr:Traceback (most recent call last): File "/home/rpdock/mc/MC.py", line 709, in s, datas = write_all_atoms (datas, step_real, cal.split()[0], plik, pars, historyT, historyR, rna) File "/home/rpdock/mc/MC.py", line 360, in write_all_atoms all_at_ch_rna, all_at_ch_prot = all_atom (plik, pars, transl, rotation, rna) File "/home/rpdock/mc/MC.py", line 297, in all_atom pro_ch, rna_ch = check_chains(plik, pars) File "/home/rpdock/mc/MC.py", line 106, in check_chains struc = pars.get_structure('native', plik) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py", line 83, in get_structure self._parse(handle.readlines()) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py", line 109, in _parse self.trailer = self._parse_coordinates(coords_trailer) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py", line 225, in _parse_coordinates fullname, serial_number, element) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/StructureBuilder.py", line 197, in init_atom fullname, serial_number, element) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/Atom.py", line 58, in __init__ self.bfactor=bfactor MemoryError 2026-10-24 20:00:51 MC (refinement) end 2026-10-24 20:00:51 OK 2026-10-24 20:00:51 Set finished status of e220063b-f4fb-4a69-84d7-314924df7088