2026-04-28 12:32:03 NPdock start
2026-04-28 12:32:03 ver: server
2026-04-28 12:32:03 mode: 11111
2026-04-28 12:32:03 is RNA? 1
2026-04-28 12:32:03 Interface: prot: '' na: ''
2026-04-28 12:32:03 Curr dir:/home/rpdock/web/media/jobs/3d411e53-5cb9-4307-9924-83be5dc86afe/
2026-04-28 12:32:03 GRAMM in progress...
2026-04-28 12:32:03 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 13:47:07 GRAMM done
2026-04-28 13:47:07 DARS scoring in progress...
2026-04-28 13:47:07 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 13:47:08 DARS start [DARS_potential_v3_scoring.py]
2026-04-28 13:47:08 Show log every 100 structures [DARS_potential_v3_scoring.py]
2026-04-28 13:47:10 1/20000 prot-na_1000.pdb	-1417233.81
2026-04-28 13:49:01 100/20000 prot-na_94.pdb	-1355999.24
2026-04-28 13:51:01 200/20000 prot-na_194.pdb	-1552901.98
2026-04-28 13:53:07 300/20000 prot-na_294.pdb	-1629262.77
2026-04-28 13:55:14 400/20000 prot-na_394.pdb	-752707.86
2026-04-28 13:57:22 500/20000 prot-na_494.pdb	-2022332.20
2026-04-28 13:59:30 600/20000 prot-na_594.pdb	-2068636.31
2026-04-28 14:01:39 700/20000 prot-na_694.pdb	-1779683.52
2026-04-28 14:03:50 800/20000 prot-na_794.pdb	-1751311.91
2026-04-28 14:05:59 900/20000 prot-na_894.pdb	-2327852.92
2026-04-28 14:08:07 1000/20000 prot-na_994.pdb	-2157761.37
2026-04-28 14:10:14 1100/20000 prot-na_1100.pdb	-2236587.43
2026-04-28 14:12:20 1200/20000 prot-na_1200.pdb	-2012402.57
2026-04-28 14:14:26 1300/20000 prot-na_1300.pdb	-1408235.12
2026-04-28 14:16:31 1400/20000 prot-na_1400.pdb	-1740280.38
2026-04-28 14:18:38 1500/20000 prot-na_1500.pdb	-2509986.76
2026-04-28 14:20:42 1600/20000 prot-na_1600.pdb	-1309854.15
2026-04-28 14:22:45 1700/20000 prot-na_1700.pdb	-2153257.24
2026-04-28 14:24:48 1800/20000 prot-na_1800.pdb	-825880.65
2026-04-28 14:26:48 1900/20000 prot-na_1900.pdb	-867965.78
2026-04-28 14:28:50 2000/20000 prot-na_2000.pdb	-1524419.83
2026-04-28 14:30:59 2100/20000 prot-na_2100.pdb	-1241460.66
2026-04-28 14:32:59 2200/20000 prot-na_2200.pdb	-516801.72
2026-04-28 14:34:59 2300/20000 prot-na_2300.pdb	-1481986.88
2026-04-28 14:36:59 2400/20000 prot-na_2400.pdb	-1623714.70
2026-04-28 14:39:00 2500/20000 prot-na_2500.pdb	-1533016.63
2026-04-28 14:40:59 2600/20000 prot-na_2600.pdb	-450285.69
2026-04-28 14:43:09 2700/20000 prot-na_2700.pdb	-1343118.76
2026-04-28 14:45:08 2800/20000 prot-na_2800.pdb	-1750216.07
2026-04-28 14:47:07 2900/20000 prot-na_2900.pdb	-927827.01
2026-04-28 14:49:05 3000/20000 prot-na_3000.pdb	-1166999.55
2026-04-28 14:51:04 3100/20000 prot-na_3100.pdb	-1831592.67
2026-04-28 14:53:02 3200/20000 prot-na_3200.pdb	-1597707.46
2026-04-28 14:55:02 3300/20000 prot-na_3300.pdb	-1896694.86
2026-04-28 14:57:03 3400/20000 prot-na_3400.pdb	-2046827.32
2026-04-28 14:59:01 3500/20000 prot-na_3500.pdb	-1555321.59
2026-04-28 15:00:59 3600/20000 prot-na_3600.pdb	-486489.19
2026-04-28 15:02:55 3700/20000 prot-na_3700.pdb	-610897.62
2026-04-28 15:04:52 3800/20000 prot-na_3800.pdb	-803295.15
2026-04-28 15:06:50 3900/20000 prot-na_3900.pdb	-2370318.38
2026-04-28 15:08:48 4000/20000 prot-na_4000.pdb	-1622199.01
2026-04-28 15:10:47 4100/20000 prot-na_4100.pdb	-2348964.12
2026-04-28 15:12:44 4200/20000 prot-na_4200.pdb	-1544102.75
2026-04-28 15:14:41 4300/20000 prot-na_4300.pdb	-1395985.43
2026-04-28 15:16:36 4400/20000 prot-na_4400.pdb	-1255270.61
2026-04-28 15:18:32 4500/20000 prot-na_4500.pdb	-1127682.75
2026-04-28 15:20:29 4600/20000 prot-na_4600.pdb	-907162.32
2026-04-28 15:22:25 4700/20000 prot-na_4700.pdb	-2105607.43
2026-04-28 15:24:22 4800/20000 prot-na_4800.pdb	-1208415.04
2026-04-28 15:26:18 4900/20000 prot-na_4900.pdb	-1871547.17
2026-04-28 15:28:13 5000/20000 prot-na_5000.pdb	-817084.95
2026-04-28 15:30:09 5100/20000 prot-na_5100.pdb	-1171719.00
2026-04-28 15:32:04 5200/20000 prot-na_5200.pdb	-1582871.19
2026-04-28 15:34:13 5300/20000 prot-na_5300.pdb	-688521.18
2026-04-28 15:36:29 5400/20000 prot-na_5400.pdb	-1958723.05
2026-04-28 15:38:46 5500/20000 prot-na_5500.pdb	-1512465.22
2026-04-28 15:41:03 5600/20000 prot-na_5600.pdb	-1587230.90
2026-04-28 15:43:20 5700/20000 prot-na_5700.pdb	-1473523.02
2026-04-28 15:45:37 5800/20000 prot-na_5800.pdb	-841225.97
2026-04-28 15:47:53 5900/20000 prot-na_5900.pdb	-1449975.12
2026-04-28 15:50:12 6000/20000 prot-na_6000.pdb	-787444.53
2026-04-28 15:52:30 6100/20000 prot-na_6100.pdb	-1590945.42
2026-04-28 15:54:47 6200/20000 prot-na_6200.pdb	-1556825.86
2026-04-28 15:57:05 6300/20000 prot-na_6300.pdb	-1785979.95
2026-04-28 15:59:23 6400/20000 prot-na_6400.pdb	-1228252.47
2026-04-28 16:01:41 6500/20000 prot-na_6500.pdb	-1805126.00
2026-04-28 16:04:00 6600/20000 prot-na_6600.pdb	-1479315.92
2026-04-28 16:06:16 6700/20000 prot-na_6700.pdb	-856218.84
2026-04-28 16:08:33 6800/20000 prot-na_6800.pdb	-668814.60
2026-04-28 16:10:50 6900/20000 prot-na_6900.pdb	-1820841.52
2026-04-28 16:13:08 7000/20000 prot-na_7000.pdb	-1699774.08
2026-04-28 16:15:25 7100/20000 prot-na_7100.pdb	-1480519.24
2026-04-28 16:17:42 7200/20000 prot-na_7200.pdb	-2053474.66
2026-04-28 16:20:00 7300/20000 prot-na_7300.pdb	-1372898.66
2026-04-28 16:22:18 7400/20000 prot-na_7400.pdb	-687057.63
2026-04-28 16:24:36 7500/20000 prot-na_7500.pdb	-1056963.02
2026-04-28 16:26:54 7600/20000 prot-na_7600.pdb	-965147.34
2026-04-28 16:29:12 7700/20000 prot-na_7700.pdb	-1610283.32
2026-04-28 16:31:31 7800/20000 prot-na_7800.pdb	-1750184.59
2026-04-28 16:33:52 7900/20000 prot-na_7900.pdb	-729560.90
2026-04-28 16:36:14 8000/20000 prot-na_8000.pdb	-1667430.96
2026-04-28 16:38:34 8100/20000 prot-na_8100.pdb	-806843.64
2026-04-28 16:40:42 8200/20000 prot-na_8200.pdb	-1723025.76
2026-04-28 16:42:50 8300/20000 prot-na_8300.pdb	-970612.19
2026-04-28 16:44:54 8400/20000 prot-na_8400.pdb	-861565.40
2026-04-28 16:46:57 8500/20000 prot-na_8500.pdb	-1660386.39
2026-04-28 16:48:57 8600/20000 prot-na_8600.pdb	-1307314.13
2026-04-28 16:51:00 8700/20000 prot-na_8700.pdb	-1578896.29
2026-04-28 16:53:04 8800/20000 prot-na_8800.pdb	-1175498.97
2026-04-28 16:55:10 8900/20000 prot-na_8900.pdb	-1572957.92
2026-04-28 16:57:12 9000/20000 prot-na_9000.pdb	-1086368.06
2026-04-28 16:59:10 9100/20000 prot-na_9100.pdb	-2498159.96
2026-04-28 17:01:12 9200/20000 prot-na_9200.pdb	-471400.78
2026-04-28 17:03:13 9300/20000 prot-na_9300.pdb	-366545.92
2026-04-28 17:05:15 9400/20000 prot-na_9400.pdb	-1356558.48
2026-04-28 17:07:16 9500/20000 prot-na_9500.pdb	-1146856.76
2026-04-28 17:09:19 9600/20000 prot-na_9600.pdb	-1451610.11
2026-04-28 17:11:21 9700/20000 prot-na_9700.pdb	-2355545.27
2026-04-28 17:13:23 9800/20000 prot-na_9800.pdb	-1423829.82
2026-04-28 17:15:26 9900/20000 prot-na_9900.pdb	-1340772.13
2026-04-28 17:17:28 10000/20000 prot-na_10000.pdb	-1273474.42
2026-04-28 17:19:31 10100/20000 prot-na_10100.pdb	-991993.43
2026-04-28 17:21:35 10200/20000 prot-na_10200.pdb	-1530588.95
2026-04-28 17:23:37 10300/20000 prot-na_10300.pdb	-1010017.38
2026-04-28 17:25:42 10400/20000 prot-na_10400.pdb	-696224.13
2026-04-28 17:27:46 10500/20000 prot-na_10500.pdb	-518563.53
2026-04-28 17:29:50 10600/20000 prot-na_10600.pdb	-924675.20
2026-04-28 17:31:53 10700/20000 prot-na_10700.pdb	-1057951.79
2026-04-28 17:33:57 10800/20000 prot-na_10800.pdb	-1526319.71
2026-04-28 17:36:02 10900/20000 prot-na_10900.pdb	-1845991.74
2026-04-28 17:38:06 11000/20000 prot-na_11000.pdb	-1566005.92
2026-04-28 17:40:12 11100/20000 prot-na_11100.pdb	-780310.93
2026-04-28 17:42:18 11200/20000 prot-na_11200.pdb	-1509260.44
2026-04-28 17:44:26 11300/20000 prot-na_11300.pdb	-2190837.67
2026-04-28 17:46:31 11400/20000 prot-na_11400.pdb	-1514548.45
2026-04-28 17:48:34 11500/20000 prot-na_11500.pdb	-577026.72
2026-04-28 17:50:39 11600/20000 prot-na_11600.pdb	-1044116.74
2026-04-28 17:52:43 11700/20000 prot-na_11700.pdb	-988620.36
2026-04-28 17:54:48 11800/20000 prot-na_11800.pdb	-830873.21
2026-04-28 17:56:52 11900/20000 prot-na_11900.pdb	-1600447.92
2026-04-28 17:58:54 12000/20000 prot-na_12000.pdb	-1424957.65
2026-04-28 18:00:56 12100/20000 prot-na_12100.pdb	-1362094.15
2026-04-28 18:02:57 12200/20000 prot-na_12200.pdb	-1775777.45
2026-04-28 18:04:59 12300/20000 prot-na_12300.pdb	-890877.54
2026-04-28 18:07:01 12400/20000 prot-na_12400.pdb	-1412961.61
2026-04-28 18:09:02 12500/20000 prot-na_12500.pdb	-813182.08
2026-04-28 18:11:03 12600/20000 prot-na_12600.pdb	-1185289.18
2026-04-28 18:13:04 12700/20000 prot-na_12700.pdb	-1500743.36
2026-04-28 18:15:04 12800/20000 prot-na_12800.pdb	-1556680.11
2026-04-28 18:17:04 12900/20000 prot-na_12900.pdb	-1370403.25
2026-04-28 18:19:05 13000/20000 prot-na_13000.pdb	-1368576.35
2026-04-28 18:21:06 13100/20000 prot-na_13100.pdb	-997408.74
2026-04-28 18:23:07 13200/20000 prot-na_13200.pdb	-2125482.73
2026-04-28 18:25:07 13300/20000 prot-na_13300.pdb	-1103010.28
2026-04-28 18:27:14 13400/20000 prot-na_13400.pdb	-1216361.59
2026-04-28 18:29:15 13500/20000 prot-na_13500.pdb	-1286231.51
2026-04-28 18:31:17 13600/20000 prot-na_13600.pdb	-572237.48
2026-04-28 18:33:18 13700/20000 prot-na_13700.pdb	-1325204.24
2026-04-28 18:35:19 13800/20000 prot-na_13800.pdb	-1311926.40
2026-04-28 18:37:31 13900/20000 prot-na_13900.pdb	-1460145.23
2026-04-28 18:39:51 14000/20000 prot-na_14000.pdb	-1127813.85
2026-04-28 18:42:14 14100/20000 prot-na_14100.pdb	-1221019.03
2026-04-28 18:44:36 14200/20000 prot-na_14200.pdb	-678946.93
2026-04-28 18:47:00 14300/20000 prot-na_14300.pdb	-1509612.58
2026-04-28 18:49:24 14400/20000 prot-na_14400.pdb	-1822171.83
2026-04-28 18:51:46 14500/20000 prot-na_14500.pdb	-1221338.63
2026-04-28 18:54:10 14600/20000 prot-na_14600.pdb	-1367770.95
2026-04-28 18:56:34 14700/20000 prot-na_14700.pdb	-1568481.33
2026-04-28 18:58:58 14800/20000 prot-na_14800.pdb	-1185681.41
2026-04-28 19:01:22 14900/20000 prot-na_14900.pdb	-1514877.46
2026-04-28 19:03:41 15000/20000 prot-na_15000.pdb	-1533610.76
2026-04-28 19:06:02 15100/20000 prot-na_15100.pdb	-1305956.40
2026-04-28 19:08:23 15200/20000 prot-na_15200.pdb	-1635120.62
2026-04-28 19:10:36 15300/20000 prot-na_15300.pdb	-1489623.95
2026-04-28 19:12:44 15400/20000 prot-na_15400.pdb	-1361213.80
2026-04-28 19:14:45 15500/20000 prot-na_15500.pdb	-766285.65
2026-04-28 19:16:47 15600/20000 prot-na_15600.pdb	-1166757.20
2026-04-28 19:18:50 15700/20000 prot-na_15700.pdb	-619794.47
2026-04-28 19:20:52 15800/20000 prot-na_15800.pdb	-1084640.56
2026-04-28 19:22:54 15900/20000 prot-na_15900.pdb	-836162.35
2026-04-28 19:24:55 16000/20000 prot-na_16000.pdb	-1539498.22
2026-04-28 19:26:58 16100/20000 prot-na_16100.pdb	-1503225.41
2026-04-28 19:28:58 16200/20000 prot-na_16200.pdb	-945183.94
2026-04-28 19:30:58 16300/20000 prot-na_16300.pdb	-1695843.26
2026-04-28 19:32:59 16400/20000 prot-na_16400.pdb	-1189812.71
2026-04-28 19:35:00 16500/20000 prot-na_16500.pdb	-1263635.26
2026-04-28 19:37:02 16600/20000 prot-na_16600.pdb	-996542.84
2026-04-28 19:39:03 16700/20000 prot-na_16700.pdb	-1106443.71
2026-04-28 19:41:03 16800/20000 prot-na_16800.pdb	-1431447.22
2026-04-28 19:43:04 16900/20000 prot-na_16900.pdb	-730740.58
2026-04-28 19:45:05 17000/20000 prot-na_17000.pdb	-2113668.10
2026-04-28 19:47:05 17100/20000 prot-na_17100.pdb	-640173.73
2026-04-28 19:49:05 17200/20000 prot-na_17200.pdb	-1481318.33
2026-04-28 19:51:05 17300/20000 prot-na_17300.pdb	-1475011.18
2026-04-28 19:53:10 17400/20000 prot-na_17400.pdb	-1481119.22
2026-04-28 19:55:11 17500/20000 prot-na_17500.pdb	-1390088.42
2026-04-28 19:57:12 17600/20000 prot-na_17600.pdb	-1116493.05
2026-04-28 19:59:13 17700/20000 prot-na_17700.pdb	-1389991.28
2026-04-28 20:01:15 17800/20000 prot-na_17800.pdb	-1181137.86
2026-04-28 20:03:23 17900/20000 prot-na_17900.pdb	-1265593.83
2026-04-28 20:05:23 18000/20000 prot-na_18000.pdb	-1597650.44
2026-04-28 20:07:23 18100/20000 prot-na_18100.pdb	-1358583.17
2026-04-28 20:09:21 18200/20000 prot-na_18200.pdb	-1407692.19
2026-04-28 20:11:19 18300/20000 prot-na_18300.pdb	-424629.82
2026-04-28 20:13:19 18400/20000 prot-na_18400.pdb	-1386843.61
2026-04-28 20:15:18 18500/20000 prot-na_18500.pdb	-1587000.82
2026-04-28 20:17:18 18600/20000 prot-na_18600.pdb	-1063911.72
2026-04-28 20:19:18 18700/20000 prot-na_18700.pdb	-835879.57
2026-04-28 20:21:18 18800/20000 prot-na_18800.pdb	-1079281.19
2026-04-28 20:23:19 18900/20000 prot-na_18900.pdb	-1656409.68
2026-04-28 20:25:18 19000/20000 prot-na_19000.pdb	-1470125.90
2026-04-28 20:27:18 19100/20000 prot-na_19100.pdb	-1099305.70
2026-04-28 20:29:18 19200/20000 prot-na_19200.pdb	-1556470.80
2026-04-28 20:31:19 19300/20000 prot-na_19300.pdb	-1419803.36
2026-04-28 20:33:19 19400/20000 prot-na_19400.pdb	-1192432.33
2026-04-28 20:35:17 19500/20000 prot-na_19500.pdb	-789975.72
2026-04-28 20:37:16 19600/20000 prot-na_19600.pdb	-469208.99
2026-04-28 20:39:15 19700/20000 prot-na_19700.pdb	-1252880.26
2026-04-28 20:41:12 19800/20000 prot-na_19800.pdb	-1444256.60
2026-04-28 20:43:09 19900/20000 prot-na_19900.pdb	-1540069.29
2026-04-28 20:45:06 20000/20000 prot-na_20000.pdb	-1532902.23
2026-04-28 20:45:06 DARS scoring end
2026-04-28 20:45:06 Clustering (cuttoff: 5, nr_clust: 100 ) in progress...
2026-04-28 20:45:06 time python /home/rpdock/run_gramm//clustering_v4.py dars_out.txt list.txt 5 100
2026-04-28 20:45:06 100 best scored structures
2026-04-28 20:45:06     1 prot-na_14232.pdb -5059461.1
2026-04-28 20:45:06     2 prot-na_334.pdb -4431372.73
2026-04-28 20:45:06     3 prot-na_18619.pdb -4321237.36
2026-04-28 20:45:06     4 prot-na_7304.pdb -3895315.66
2026-04-28 20:45:06     5 prot-na_8705.pdb -3886009.97
2026-04-28 20:45:06     6 prot-na_15593.pdb -3866495.32
2026-04-28 20:45:06     7 prot-na_19091.pdb -3848431.19
2026-04-28 20:45:06     8 prot-na_11787.pdb -3794684.39
2026-04-28 20:45:06     9 prot-na_2959.pdb -3789315.67
2026-04-28 20:45:06     10 prot-na_15283.pdb -3700804.49
2026-04-28 20:45:06     11 prot-na_4743.pdb -3689932.54
2026-04-28 20:45:06     12 prot-na_1348.pdb -3677286.34
2026-04-28 20:45:06     13 prot-na_622.pdb -3656835.79
2026-04-28 20:45:06     14 prot-na_6345.pdb -3610326.84
2026-04-28 20:45:06     15 prot-na_4.pdb -3602186.73
2026-04-28 20:45:06     16 prot-na_8752.pdb -3599734.8
2026-04-28 20:45:06     17 prot-na_237.pdb -3595741.7
2026-04-28 20:45:06     18 prot-na_4373.pdb -3565095.51
2026-04-28 20:45:06     19 prot-na_350.pdb -3541971.22
2026-04-28 20:45:06     20 prot-na_5581.pdb -3510700.89
2026-04-28 20:45:06     21 prot-na_2210.pdb -3507004.16
2026-04-28 20:45:06     22 prot-na_62.pdb -3506285.85
2026-04-28 20:45:06     23 prot-na_516.pdb -3502915.19
2026-04-28 20:45:06     24 prot-na_3910.pdb -3499401.27
2026-04-28 20:45:06     25 prot-na_6465.pdb -3492275.23
2026-04-28 20:45:06     26 prot-na_15353.pdb -3470790.82
2026-04-28 20:45:06     27 prot-na_12366.pdb -3465930.82
2026-04-28 20:45:06     28 prot-na_6741.pdb -3461255.65
2026-04-28 20:45:06     29 prot-na_9698.pdb -3449875.15
2026-04-28 20:45:06     30 prot-na_2438.pdb -3449355.23
2026-04-28 20:45:06     31 prot-na_3729.pdb -3446229.57
2026-04-28 20:45:06     32 prot-na_13023.pdb -3442384.25
2026-04-28 20:45:06     33 prot-na_364.pdb -3438076.06
2026-04-28 20:45:06     34 prot-na_1690.pdb -3434775.65
2026-04-28 20:45:06     35 prot-na_16872.pdb -3432006.81
2026-04-28 20:45:06     36 prot-na_1302.pdb -3427322.14
2026-04-28 20:45:06     37 prot-na_134.pdb -3424368.42
2026-04-28 20:45:06     38 prot-na_2535.pdb -3420353.17
2026-04-28 20:45:06     39 prot-na_12.pdb -3392305.03
2026-04-28 20:45:06     40 prot-na_630.pdb -3388948.44
2026-04-28 20:45:06     41 prot-na_396.pdb -3383076.3
2026-04-28 20:45:06     42 prot-na_12936.pdb -3373581.63
2026-04-28 20:45:06     43 prot-na_3346.pdb -3364692.43
2026-04-28 20:45:06     44 prot-na_3319.pdb -3358760.14
2026-04-28 20:45:06     45 prot-na_13311.pdb -3354080.63
2026-04-28 20:45:06     46 prot-na_3785.pdb -3350567.78
2026-04-28 20:45:06     47 prot-na_668.pdb -3348435.24
2026-04-28 20:45:06     48 prot-na_373.pdb -3340672.45
2026-04-28 20:45:06     49 prot-na_24.pdb -3329340.91
2026-04-28 20:45:06     50 prot-na_12493.pdb -3295667.53
2026-04-28 20:45:06     51 prot-na_1985.pdb -3292774.25
2026-04-28 20:45:06     52 prot-na_2985.pdb -3286832.8
2026-04-28 20:45:06     53 prot-na_10071.pdb -3272819.12
2026-04-28 20:45:06     54 prot-na_11265.pdb -3269786.03
2026-04-28 20:45:06     55 prot-na_17282.pdb -3258266.4
2026-04-28 20:45:06     56 prot-na_1076.pdb -3254008.09
2026-04-28 20:45:06     57 prot-na_11942.pdb -3247973.07
2026-04-28 20:45:06     58 prot-na_3052.pdb -3245702.15
2026-04-28 20:45:06     59 prot-na_10135.pdb -3239565.22
2026-04-28 20:45:06     60 prot-na_11285.pdb -3234477.37
2026-04-28 20:45:06     61 prot-na_499.pdb -3228676.61
2026-04-28 20:45:06     62 prot-na_13123.pdb -3215618.52
2026-04-28 20:45:06     63 prot-na_11269.pdb -3207533.61
2026-04-28 20:45:06     64 prot-na_9363.pdb -3206023.4
2026-04-28 20:45:06     65 prot-na_2.pdb -3197918.87
2026-04-28 20:45:06     66 prot-na_753.pdb -3193964.66
2026-04-28 20:45:06     67 prot-na_9785.pdb -3176821.28
2026-04-28 20:45:06     68 prot-na_826.pdb -3160843.45
2026-04-28 20:45:06     69 prot-na_2525.pdb -3150118.13
2026-04-28 20:45:06     70 prot-na_15.pdb -3150018.67
2026-04-28 20:45:06     71 prot-na_199.pdb -3147717.65
2026-04-28 20:45:06     72 prot-na_9799.pdb -3141787.31
2026-04-28 20:45:06     73 prot-na_628.pdb -3140360.07
2026-04-28 20:45:06     74 prot-na_436.pdb -3138830.7
2026-04-28 20:45:06     75 prot-na_272.pdb -3134812.27
2026-04-28 20:45:06     76 prot-na_2494.pdb -3133954.42
2026-04-28 20:45:06     77 prot-na_16117.pdb -3122876.07
2026-04-28 20:45:06     78 prot-na_12336.pdb -3120110.7
2026-04-28 20:45:06     79 prot-na_5939.pdb -3119620.32
2026-04-28 20:45:06     80 prot-na_288.pdb -3111762.25
2026-04-28 20:45:06     81 prot-na_2107.pdb -3110397.0
2026-04-28 20:45:06     82 prot-na_7.pdb -3106678.73
2026-04-28 20:45:06     83 prot-na_1945.pdb -3102219.96
2026-04-28 20:45:06     84 prot-na_1162.pdb -3095013.47
2026-04-28 20:45:06     85 prot-na_5372.pdb -3092152.76
2026-04-28 20:45:06     86 prot-na_5819.pdb -3090559.51
2026-04-28 20:45:06     87 prot-na_3435.pdb -3089307.83
2026-04-28 20:45:06     88 prot-na_1018.pdb -3087621.23
2026-04-28 20:45:06     89 prot-na_3204.pdb -3075372.34
2026-04-28 20:45:06     90 prot-na_6387.pdb -3071330.27
2026-04-28 20:45:06     91 prot-na_1548.pdb -3067890.73
2026-04-28 20:45:06     92 prot-na_4964.pdb -3065100.89
2026-04-28 20:45:06     93 prot-na_16580.pdb -3054790.14
2026-04-28 20:45:06     94 prot-na_37.pdb -3049730.76
2026-04-28 20:45:06     95 prot-na_10285.pdb -3046402.68
2026-04-28 20:45:06     96 prot-na_3406.pdb -3045695.95
2026-04-28 20:45:06     97 prot-na_11.pdb -3041264.48
2026-04-28 20:45:06     98 prot-na_5769.pdb -3037007.61
2026-04-28 20:45:06     99 prot-na_1.pdb -3035986.57
2026-04-28 20:45:06     100 prot-na_2049.pdb -3030135.93
2026-04-28 20:45:06 Chains: C
2026-04-28 20:45:41 100 best scored structures
2026-04-28 20:45:41 GRAMM analysis selected for further analysis: prot-na_15
2026-04-28 20:45:41 Cluster #1 with 6 structures
2026-04-28 20:45:41    1 prot-na_3910.pdb  -3499401.27
2026-04-28 20:45:41    2 prot-na_15353.pdb  -3470790.82
2026-04-28 20:45:41    3 prot-na_12.pdb  -3392305.03
2026-04-28 20:45:41    4 prot-na_13311.pdb  -3354080.63
2026-04-28 20:45:41    5 prot-na_15.pdb  -3150018.67
2026-04-28 20:45:41    6 prot-na_1.pdb  -3035986.57
2026-04-28 20:45:41 Cluster #2 with 5 structures
2026-04-28 20:45:41    1 prot-na_4.pdb  -3602186.73
2026-04-28 20:45:41    2 prot-na_2210.pdb  -3507004.16
2026-04-28 20:45:41    3 prot-na_6741.pdb  -3461255.65
2026-04-28 20:45:41    4 prot-na_396.pdb  -3383076.3
2026-04-28 20:45:41    5 prot-na_7.pdb  -3106678.73
2026-04-28 20:45:41 Sent to refinement: clusters_found|prot-na_3910.pdb|prot-na_4.pdb
2026-04-28 20:45:41 Sent to refinement: clusters_found|prot-na_3910.pdb|prot-na_4.pdb
2026-04-28 20:45:41 DARS clustering end
2026-04-28 20:45:41 MC (refinement) init
2026-04-28 20:45:41 python /home/rpdock/run_gramm//run_mc.py -f dars_to_mc.txt -d /home/rpdock/web/media/jobs/3d411e53-5cb9-4307-9924-83be5dc86afe/
2026-04-28 20:45:41 Refinement of #1 /home/rpdock/web/media/jobs/3d411e53-5cb9-4307-9924-83be5dc86afe/prot-na_3910.pdb
2026-04-28 20:45:41 python /home/rpdock/mc/MC.py -s 1000 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/3d411e53-5cb9-4307-9924-83be5dc86afe//ref_struc/prot-na_3910/prot-na_3910.pdb
2026-04-28 20:54:17 run_mc::stderr:/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CA defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 806.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CB defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 810.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CG defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 812.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CD defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 814.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom NE defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 816.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CZ defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 818.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom NH1 defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 820.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom NH2 defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 822.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CA defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 4512.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CB defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 4516.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CG defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 4518.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CD defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 4520.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom NE defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 4522.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CZ defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 4524.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom NH1 defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 4526.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom NH2 defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 4528.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom P defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7863.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C5' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7864.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom O5' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7865.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C4' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7866.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom O4' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7867.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C3' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7868.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom O3' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7869.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C2' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7870.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom O2' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7871.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C1' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7872.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom N1 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7873.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C2 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7874.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom O2 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7875.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom N3 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7876.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C4 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7877.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom O4 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7878.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C5 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7879.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C6 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7880.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom OP1 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7881.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom OP2 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7882.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
Traceback (most recent call last):
  File "/home/rpdock/mc/MC.py", line 709, in <module>
    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
2026-04-28 20:54:17 Refinement of #2 /home/rpdock/web/media/jobs/3d411e53-5cb9-4307-9924-83be5dc86afe/prot-na_4.pdb
2026-04-28 20:54:17 python /home/rpdock/mc/MC.py -s 1000 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/3d411e53-5cb9-4307-9924-83be5dc86afe//ref_struc/prot-na_4/prot-na_4.pdb
2026-04-28 21:14:11 run_mc::stderr:/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CA defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 806.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CB defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 810.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CG defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 812.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CD defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 814.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom NE defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 816.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CZ defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 818.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom NH1 defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 820.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom NH2 defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 822.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CA defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 4512.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CB defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 4516.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CG defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 4518.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CD defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 4520.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom NE defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 4522.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CZ defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 4524.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom NH1 defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 4526.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom NH2 defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 4528.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom P defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7863.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C5' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7864.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom O5' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7865.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C4' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7866.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom O4' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7867.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C3' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7868.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom O3' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7869.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C2' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7870.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom O2' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7871.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C1' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7872.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom N1 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7873.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C2 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7874.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom O2 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7875.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom N3 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7876.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C4 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7877.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom O4 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7878.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C5 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7879.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C6 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7880.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom OP1 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7881.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom OP2 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7882.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
2026-04-28 21:14:11 /usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CA defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 806.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CB defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 810.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CG defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 812.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CD defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 814.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom NE defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 816.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CZ defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 818.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom NH1 defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 820.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom NH2 defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 822.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CA defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 4512.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CB defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 4516.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CG defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 4518.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CD defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 4520.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom NE defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 4522.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CZ defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 4524.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom NH1 defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 4526.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom NH2 defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 4528.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom P defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7863.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C5' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7864.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom O5' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7865.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C4' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7866.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom O4' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7867.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C3' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7868.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom O3' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7869.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C2' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7870.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom O2' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7871.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C1' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7872.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom N1 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7873.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C2 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7874.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom O2 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7875.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom N3 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7876.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C4 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7877.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom O4 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7878.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C5 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7879.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C6 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7880.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom OP1 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7881.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom OP2 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7882.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
start - parameters:
    File name /home/rpdock/web/media/jobs/3d411e53-5cb9-4307-9924-83be5dc86afe//ref_struc/prot-na_3910/prot-na_3910.pdb
    Steps 1000
    Temp. start 15000.0
    Temp. end 295.0
    False
    
msg start - parameters:
    File name /home/rpdock/web/media/jobs/3d411e53-5cb9-4307-9924-83be5dc86afe//ref_struc/prot-na_3910/prot-na_3910.pdb
    Steps 1000
    Temp. start 15000.0
    Temp. end 295.0
    False
    


    Step	E	Edist	Eang	Epen
Missed atom CG in the LEU 1011
Missed atom CD1 in the LEU 1011
Missed atom CD2 in the LEU 1011
Missed atom CG in the HIS 1012
Missed atom ND1 in the HIS 1012
Missed atom CD2 in the HIS 1012
Missed atom CE1 in the HIS 1012
Missed atom NE2 in the HIS 1012
Missed atom CG in the GLU 1013
Missed atom CD in the GLU 1013
Missed atom OE1 in the GLU 1013
Missed atom OE2 in the GLU 1013
Missed atom CG1 in the VAL 1014
Missed atom CG2 in the VAL 1014
Missed atom CG in the LEU 1015
Missed atom CD1 in the LEU 1015
Missed atom CD2 in the LEU 1015
Missed atom CG in the HIS 1016
Missed atom ND1 in the HIS 1016
Missed atom CD2 in the HIS 1016
Missed atom CE1 in the HIS 1016
Missed atom NE2 in the HIS 1016
Missed atom CG in the HIS 1017
Missed atom ND1 in the HIS 1017
Missed atom CD2 in the HIS 1017
Missed atom CE1 in the HIS 1017
Missed atom NE2 in the HIS 1017
Missed atom OG1 in the THR 1018
Missed atom CG2 in the THR 1018
Missed atom OG1 in the THR 1020
Missed atom CG2 in the THR 1020
Missed atom CG in the ASN 1021
Missed atom OD1 in the ASN 1021
Missed atom ND2 in the ASN 1021
Missed atom CG1 in the VAL 1022
Missed atom CG2 in the VAL 1022
Missed atom CG in the ASP 1023
Missed atom OD1 in the ASP 1023
Missed atom OD2 in the ASP 1023
Missed atom CG in the LYS 1025
Missed atom CD in the LYS 1025
Missed atom CE in the LYS 1025
Missed atom NZ in the LYS 1025
Missed atom CG in the ARG 1028
Missed atom CD in the ARG 1028
Missed atom NE in the ARG 1028
Missed atom CZ in the ARG 1028
Missed atom NH1 in the ARG 1028
Missed atom NH2 in the ARG 1028
Missed atom OG1 in the THR 1029
Missed atom CG2 in the THR 1029
Missed atom CG in the MET 1031
Missed atom SD in the MET 1031
Missed atom CE in the MET 1031
Missed atom CG in the GLN 1033
Missed atom CD in the GLN 1033
Missed atom OE1 in the GLN 1033
Missed atom NE2 in the GLN 1033
Missed atom CG in the ARG 1038
Missed atom CD in the ARG 1038
Missed atom NE in the ARG 1038
Missed atom CZ in the ARG 1038
Missed atom NH1 in the ARG 1038
Missed atom NH2 in the ARG 1038
Missed atom CG in the ARG 1093
Missed atom CD in the ARG 1093
Missed atom NE in the ARG 1093
Missed atom CZ in the ARG 1093
Missed atom NH1 in the ARG 1093
Missed atom NH2 in the ARG 1093
Missed atom CG in the GLU 1097
Missed atom CD in the GLU 1097
Missed atom OE1 in the GLU 1097
Missed atom OE2 in the GLU 1097
Missed atom CG in the LEU 1148
Missed atom CD1 in the LEU 1148
Missed atom CD2 in the LEU 1148
Missed atom OG1 in the THR 1168
Missed atom CG2 in the THR 1168
Missed atom CG in the GLU 1217
Missed atom CD in the GLU 1217
Missed atom OE1 in the GLU 1217
Missed atom OE2 in the GLU 1217
Missed atom CG in the ASP 1218
Missed atom OD1 in the ASP 1218
Missed atom OD2 in the ASP 1218
Missed atom CG1 in the VAL 1231
Missed atom CG2 in the VAL 1231
Missed atom CG in the LYS 1234
Missed atom CD in the LYS 1234
Missed atom CE in the LYS 1234
Missed atom NZ in the LYS 1234
Missed atom CG in the GLU 1239
Missed atom CD in the GLU 1239
Missed atom OE1 in the GLU 1239
Missed atom OE2 in the GLU 1239
Missed atom CG in the GLU 1241
Missed atom CD in the GLU 1241
Missed atom OE1 in the GLU 1241
Missed atom OE2 in the GLU 1241
Missed atom CG in the PHE 1244
Missed atom CD1 in the PHE 1244
Missed atom CD2 in the PHE 1244
Missed atom CE1 in the PHE 1244
Missed atom CE2 in the PHE 1244
Missed atom CZ in the PHE 1244
Missed atom CG in the ASN 1246
Missed atom OD1 in the ASN 1246
Missed atom ND2 in the ASN 1246
Missed atom CG in the GLN 1268
Missed atom CD in the GLN 1268
Missed atom OE1 in the GLN 1268
Missed atom NE2 in the GLN 1268
Missed atom CG in the LYS 1279
Missed atom CD in the LYS 1279
Missed atom CE in the LYS 1279
Missed atom NZ in the LYS 1279
Missed atom CG in the GLN 1280
Missed atom CD in the GLN 1280
Missed atom OE1 in the GLN 1280
Missed atom NE2 in the GLN 1280
Missed atom CG in the LYS 1281
Missed atom CD in the LYS 1281
Missed atom CE in the LYS 1281
Missed atom NZ in the LYS 1281
Missed atom OG1 in the THR 1282
Missed atom CG2 in the THR 1282
Missed atom CG in the LYS 1289
Missed atom CD in the LYS 1289
Missed atom CE in the LYS 1289
Missed atom NZ in the LYS 1289
Missed atom CG in the LYS 1336
Missed atom CD in the LYS 1336
Missed atom CE in the LYS 1336
Missed atom NZ in the LYS 1336
Missed atom CG in the ARG 1337
Missed atom CD in the ARG 1337
Missed atom NE in the ARG 1337
Missed atom CZ in the ARG 1337
Missed atom NH1 in the ARG 1337
Missed atom NH2 in the ARG 1337
Missed atom CG in the ARG 1338
Missed atom CD in the ARG 1338
Missed atom NE in the ARG 1338
Missed atom CZ in the ARG 1338
Missed atom NH1 in the ARG 1338
Missed atom NH2 in the ARG 1338
Missed atom CG in the ARG 1340
Missed atom CD in the ARG 1340
Missed atom NE in the ARG 1340
Missed atom CZ in the ARG 1340
Missed atom NH1 in the ARG 1340
Missed atom NH2 in the ARG 1340
Missed atom CG in the GLU 1344
Missed atom CD in the GLU 1344
Missed atom OE1 in the GLU 1344
Missed atom OE2 in the GLU 1344
Missed atom CG in the LEU 1365
Missed atom CD1 in the LEU 1365
Missed atom CD2 in the LEU 1365
Missed atom CG in the LYS 1457
Missed atom CD in the LYS 1457
Missed atom CE in the LYS 1457
Missed atom NZ in the LYS 1457
Missed atom CG in the LYS 1469
Missed atom CD in the LYS 1469
Missed atom CE in the LYS 1469
Missed atom NZ in the LYS 1469
Missed atom CG in the GLU 1470
Missed atom CD in the GLU 1470
Missed atom OE1 in the GLU 1470
Missed atom OE2 in the GLU 1470
Missed atom CG in the ARG 1471
Missed atom CD in the ARG 1471
Missed atom NE in the ARG 1471
Missed atom CZ in the ARG 1471
Missed atom NH1 in the ARG 1471
Missed atom NH2 in the ARG 1471
Missed atom CG in the LYS 1475
Missed atom CD in the LYS 1475
Missed atom CE in the LYS 1475
Missed atom NZ in the LYS 1475
Missed atom CG in the LEU 1478
Missed atom CD1 in the LEU 1478
Missed atom CD2 in the LEU 1478
Missed atom CG in the LYS 1489
Missed atom CD in the LYS 1489
Missed atom CE in the LYS 1489
Missed atom NZ in the LYS 1489
Missed atom CG in the ARG 1491
Missed atom CD in the ARG 1491
Missed atom NE in the ARG 1491
Missed atom CZ in the ARG 1491
Missed atom NH1 in the ARG 1491
Missed atom NH2 in the ARG 1491
Missed atom OG1 in the THR 1492
Missed atom CG2 in the THR 1492
Missed atom CG in the LYS 1493
Missed atom CD in the LYS 1493
Missed atom CE in the LYS 1493
Missed atom NZ in the LYS 1493
Missed atom CG in the LEU 1011
Missed atom CD1 in the LEU 1011
Missed atom CD2 in the LEU 1011
Missed atom CG in the HIS 1012
Missed atom ND1 in the HIS 1012
Missed atom CD2 in the HIS 1012
Missed atom CE1 in the HIS 1012
Missed atom NE2 in the HIS 1012
Missed atom CG in the GLU 1013
Missed atom CD in the GLU 1013
Missed atom OE1 in the GLU 1013
Missed atom OE2 in the GLU 1013
Missed atom CG1 in the VAL 1014
Missed atom CG2 in the VAL 1014
Missed atom CG in the LEU 1015
Missed atom CD1 in the LEU 1015
Missed atom CD2 in the LEU 1015
Missed atom CG in the HIS 1016
Missed atom ND1 in the HIS 1016
Missed atom CD2 in the HIS 1016
Missed atom CE1 in the HIS 1016
Missed atom NE2 in the HIS 1016
Missed atom CG in the HIS 1017
Missed atom ND1 in the HIS 1017
Missed atom CD2 in the HIS 1017
Missed atom CE1 in the HIS 1017
Missed atom NE2 in the HIS 1017
Missed atom OG1 in the THR 1018
Missed atom CG2 in the THR 1018
Missed atom OG1 in the THR 1020
Missed atom CG2 in the THR 1020
Missed atom CG in the ASN 1021
Missed atom OD1 in the ASN 1021
Missed atom ND2 in the ASN 1021
Missed atom CG1 in the VAL 1022
Missed atom CG2 in the VAL 1022
Missed atom CG in the ASP 1023
Missed atom OD1 in the ASP 1023
Missed atom OD2 in the ASP 1023
Missed atom CG in the LYS 1025
Missed atom CD in the LYS 1025
Missed atom CE in the LYS 1025
Missed atom NZ in the LYS 1025
Missed atom CG in the ARG 1028
Missed atom CD in the ARG 1028
Missed atom NE in the ARG 1028
Missed atom CZ in the ARG 1028
Missed atom NH1 in the ARG 1028
Missed atom NH2 in the ARG 1028
Missed atom OG1 in the THR 1029
Missed atom CG2 in the THR 1029
Missed atom CG in the MET 1031
Missed atom SD in the MET 1031
Missed atom CE in the MET 1031
Missed atom CG in the GLN 1033
Missed atom CD in the GLN 1033
Missed atom OE1 in the GLN 1033
Missed atom NE2 in the GLN 1033
Missed atom CG in the ARG 1038
Missed atom CD in the ARG 1038
Missed atom NE in the ARG 1038
Missed atom CZ in the ARG 1038
Missed atom NH1 in the ARG 1038
Missed atom NH2 in the ARG 1038
Missed atom CG in the ARG 1093
Missed atom CD in the ARG 1093
Missed atom NE in the ARG 1093
Missed atom CZ in the ARG 1093
Missed atom NH1 in the ARG 1093
Missed atom NH2 in the ARG 1093
Missed atom CG in the GLU 1097
Missed atom CD in the GLU 1097
Missed atom OE1 in the GLU 1097
Missed atom OE2 in the GLU 1097
Missed atom OG1 in the THR 1168
Missed atom CG2 in the THR 1168
Missed atom CG in the GLU 1217
Missed atom CD in the GLU 1217
Missed atom OE1 in the GLU 1217
Missed atom OE2 in the GLU 1217
Missed atom CG in the ASP 1218
Missed atom OD1 in the ASP 1218
Missed atom OD2 in the ASP 1218
Missed atom CG1 in the VAL 1231
Missed atom CG2 in the VAL 1231
Missed atom CG in the LYS 1234
Missed atom CD in the LYS 1234
Missed atom CE in the LYS 1234
Missed atom NZ in the LYS 1234
Missed atom CG in the LEU 1235
Missed atom CD1 in the LEU 1235
Missed atom CD2 in the LEU 1235
Missed atom CG in the GLU 1241
Missed atom CD in the GLU 1241
Missed atom OE1 in the GLU 1241
Missed atom OE2 in the GLU 1241
Missed atom CG in the PHE 1244
Missed atom CD1 in the PHE 1244
Missed atom CD2 in the PHE 1244
Missed atom CE1 in the PHE 1244
Missed atom CE2 in the PHE 1244
Missed atom CZ in the PHE 1244
Missed atom CG in the GLN 1268
Missed atom CD in the GLN 1268
Missed atom OE1 in the GLN 1268
Missed atom NE2 in the GLN 1268
Missed atom CG in the LYS 1279
Missed atom CD in the LYS 1279
Missed atom CE in the LYS 1279
Missed atom NZ in the LYS 1279
Missed atom CG in the GLN 1280
Missed atom CD in the GLN 1280
Missed atom OE1 in the GLN 1280
Missed atom NE2 in the GLN 1280
Missed atom CG in the LYS 1281
Missed atom CD in the LYS 1281
Missed atom CE in the LYS 1281
Missed atom NZ in the LYS 1281
Missed atom CG in the LYS 1289
Missed atom CD in the LYS 1289
Missed atom CE in the LYS 1289
Missed atom NZ in the LYS 1289
Missed atom CG in the LYS 1336
Missed atom CD in the LYS 1336
Missed atom CE in the LYS 1336
Missed atom NZ in the LYS 1336
Missed atom CG in the ARG 1337
Missed atom CD in the ARG 1337
Missed atom NE in the ARG 1337
Missed atom CZ in the ARG 1337
Missed atom NH1 in the ARG 1337
Missed atom NH2 in the ARG 1337
Missed atom CG in the ARG 1338
Missed atom CD in the ARG 1338
Missed atom NE in the ARG 1338
Missed atom CZ in the ARG 1338
Missed atom NH1 in the ARG 1338
Missed atom NH2 in the ARG 1338
Missed atom CG in the ARG 1340
Missed atom CD in the ARG 1340
Missed atom NE in the ARG 1340
Missed atom CZ in the ARG 1340
Missed atom NH1 in the ARG 1340
Missed atom NH2 in the ARG 1340
Missed atom CG in the GLU 1344
Missed atom CD in the GLU 1344
Missed atom OE1 in the GLU 1344
Missed atom OE2 in the GLU 1344
Missed atom CG in the LEU 1365
Missed atom CD1 in the LEU 1365
Missed atom CD2 in the LEU 1365
Missed atom CG in the LYS 1469
Missed atom CD in the LYS 1469
Missed atom CE in the LYS 1469
Missed atom NZ in the LYS 1469
Missed atom CG in the GLU 1470
Missed atom CD in the GLU 1470
Missed atom OE1 in the GLU 1470
Missed atom OE2 in the GLU 1470
Missed atom CG in the ARG 1471
Missed atom CD in the ARG 1471
Missed atom NE in the ARG 1471
Missed atom CZ in the ARG 1471
Missed atom NH1 in the ARG 1471
Missed atom NH2 in the ARG 1471
Missed atom CG in the LYS 1489
Missed atom CD in the LYS 1489
Missed atom CE in the LYS 1489
Missed atom NZ in the LYS 1489
Missed atom CG in the ARG 1491
Missed atom CD in the ARG 1491
Missed atom NE in the ARG 1491
Missed atom CZ in the ARG 1491
Missed atom NH1 in the ARG 1491
Missed atom NH2 in the ARG 1491
Missed atom OG1 in the THR 1492
Missed atom CG2 in the THR 1492
Missed atom CG in the LYS 1493
Missed atom CD in the LYS 1493
Missed atom CE in the LYS 1493
Missed atom NZ in the LYS 1493
0 - -2800455.89	-1531473.20	-1468982.70	200000.00
1 R -2814922.69	-1541497.76	-1473424.93	200000.00 T= 15000.0 K
progress 0.1
2 R -2608930.94	-1538655.56	-1470275.38	400000.00 T= 14955.885 K
progress 0.2
3 R -2609362.81	-1546666.76	-1462696.05	400000.00 T= 14941.18 K
progress 0.3
4 R -2640565.30	-1557041.53	-1483523.78	400000.00 T= 14882.36 K
progress 0.4
5 R -2818975.37	-1550704.37	-1468271.00	200000.00 T= 14867.655 K
progress 0.5
6 R -3001643.14	-1533608.89	-1468034.25	0.00 T= 14823.54 K
progress 0.6
7 R -2869840.30	-1473835.90	-1396004.39	0.00 T= 14794.13 K
progress 0.7
8 T -2870491.83	-1507130.78	-1463361.05	100000.00 T= 14779.425 K
progress 0.8
9 R -2653463.77	-1512172.13	-1441291.64	300000.00 T= 14705.9 K
progress 0.9
10 R -2761489.83	-1501203.90	-1460285.92	200000.00 T= 14661.785 K
progress 1.0
11 R -2874624.65	-1513854.54	-1460770.11	100000.00 T= 14632.375 K
progress 1.1
12 R -2757240.97	-1514436.97	-1442804.00	200000.00 T= 14602.965 K
progress 1.2
13 T -2682252.07	-1427677.06	-1354575.01	100000.00 T= 14514.735 K
progress 1.3
14 R -2698816.42	-1391273.41	-1307543.01	0.00 T= 14411.8 K
progress 1.4
15 R -2721063.78	-1395609.28	-1325454.50	0.00 T= 14397.095 K
progress 1.5
16 R -2641111.70	-1410709.21	-1330402.50	100000.00 T= 14382.39 K
progress 1.6
17 T -2441061.80	-1321442.40	-1219619.40	100000.00 T= 14352.98 K
progress 1.7
18 R -2603384.22	-1356918.52	-1246465.71	0.00 T= 14338.275 K
progress 1.8
19 R -2496367.29	-1298145.59	-1198221.70	0.00 T= 14308.865 K
progress 1.9
20 R -2444868.51	-1266655.83	-1178212.69	0.00 T= 14294.16 K
progress 2.0
21 T -2373787.03	-1243789.93	-1129997.10	0.00 T= 14279.455 K
progress 2.1
22 R -2398763.32	-1244604.44	-1154158.89	0.00 T= 14264.75 K
progress 2.2
23 R -2420149.40	-1257687.89	-1162461.51	0.00 T= 14250.045 K
progress 2.3
24 R -2445637.68	-1273207.14	-1172430.54	0.00 T= 14235.34 K
progress 2.4
25 T -2599530.48	-1361287.51	-1238242.97	0.00 T= 14220.635 K
progress 2.5
26 R -2589818.30	-1355267.06	-1234551.24	0.00 T= 14191.225 K
progress 2.6
27 T -2497901.71	-1276128.68	-1221773.04	0.00 T= 14176.52 K
progress 2.7
28 R -2587583.08	-1338732.12	-1248850.96	0.00 T= 14161.815 K
progress 2.8
29 R -2584203.14	-1338735.40	-1245467.74	0.00 T= 14147.11 K
progress 2.9
30 T -2589447.26	-1329783.19	-1259664.07	0.00 T= 14058.88 K
progress 3.0
31 R -2588329.36	-1327577.93	-1260751.43	0.00 T= 14029.47 K
progress 3.1
32 R -2599104.49	-1335038.79	-1264065.70	0.00 T= 14000.06 K
progress 3.2
33 T -2778058.91	-1568335.94	-1509722.97	300000.00 T= 13985.355 K
progress 3.3
34 T -2935712.08	-1595533.06	-1540179.02	200000.00 T= 13926.535 K
progress 3.4
35 R -2829752.59	-1555863.38	-1473889.21	200000.00 T= 13853.01 K
progress 3.5
36 T -2897615.63	-1541113.99	-1456501.63	100000.00 T= 13808.895 K
progress 3.6
37 R -2914131.02	-1549003.69	-1465127.33	100000.00 T= 13794.19 K
progress 3.7
38 R -2851490.72	-1509077.34	-1442413.39	100000.00 T= 13750.075 K
progress 3.8
39 T -2694748.50	-1487037.61	-1407710.89	200000.00 T= 13647.14 K
progress 3.9
40 T -2721874.29	-1489254.49	-1432619.80	200000.00 T= 13632.435 K
progress 4.0
41 R -2899150.40	-1532169.85	-1466980.55	100000.00 T= 13603.025 K
progress 4.1
42 R -2679578.16	-1583099.66	-1496478.51	400000.00 T= 13573.615 K
progress 4.2
43 R -2724122.87	-1608038.26	-1516084.60	400000.00 T= 13544.205 K
progress 4.3
44 T -2740684.86	-1562960.63	-1477724.22	300000.00 T= 13514.795 K
progress 4.4
45 R -2651735.67	-1516690.55	-1435045.12	300000.00 T= 13500.09 K
progress 4.5
46 R -2808303.28	-1561615.90	-1446687.37	200000.00 T= 13485.385 K
progress 4.6
47 R -2604686.43	-1537494.24	-1467192.18	400000.00 T= 13426.565 K
progress 4.7
48 T -2824650.53	-1651395.78	-1573254.75	400000.00 T= 13397.155 K
progress 4.8
49 T -2903765.74	-1640302.56	-1563463.18	300000.00 T= 13323.63 K
progress 4.9
50 T -2643064.49	-1757514.94	-1685549.54	800000.00 T= 13014.825 K
progress 5.0
51 R -2316042.33	-1802161.05	-1713881.28	1200000.00 T= 13000.12 K
progress 5.1
52 T -2526890.99	-1707354.18	-1619536.81	800000.00 T= 12985.415 K
progress 5.2
53 T -2537716.05	-1560950.81	-1476765.24	500000.00 T= 12956.005 K
progress 5.3
54 T -2631499.52	-1557231.06	-1474268.47	400000.00 T= 12926.595 K
progress 5.4
55 T -2665251.57	-1542724.41	-1422527.16	300000.00 T= 12867.775 K
progress 5.5
56 T -2606254.94	-1581537.80	-1524717.14	500000.00 T= 12853.07 K
progress 5.6
57 R -2398644.32	-1518560.85	-1480083.47	600000.00 T= 12808.955 K
progress 5.7
58 T -2510312.23	-1391187.09	-1319125.14	200000.00 T= 12779.545 K
progress 5.8
59 T -2432676.44	-1302185.46	-1230490.98	100000.00 T= 12735.43 K
progress 5.9
60 T -2582190.20	-1478379.52	-1403810.68	300000.00 T= 12720.725 K
progress 6.0
61 R -2577612.38	-1478150.86	-1399461.53	300000.00 T= 12691.315 K
progress 6.1
62 R -2663507.60	-1759146.09	-1604361.51	700000.00 T= 12676.61 K
progress 6.2
63 R -2983914.63	-1689402.39	-1594512.24	300000.00 T= 12603.085 K
progress 6.3
64 R -3111146.90	-1773350.79	-1637796.11	300000.00 T= 12573.675 K
progress 6.4
65 T -3072649.80	-1900183.94	-1772465.85	600000.00 T= 12544.265 K
progress 6.5
66 R -3095481.27	-1837805.26	-1757676.02	500000.00 T= 12485.445 K
progress 6.6
67 R -3088861.67	-1841066.53	-1747795.15	500000.00 T= 12411.92 K
progress 6.7
68 R -2974214.91	-1773200.43	-1701014.47	500000.00 T= 12323.69 K
progress 6.8
69 R -3035758.83	-1805317.64	-1730441.19	500000.00 T= 12264.87 K
progress 6.9
70 R -3091886.77	-1843863.07	-1748023.69	500000.00 T= 12250.165 K
progress 7.0
71 T -3042464.78	-1727536.54	-1614928.25	300000.00 T= 12147.23 K
progress 7.1
72 T -2874191.67	-1520006.49	-1454185.18	100000.00 T= 12132.525 K
progress 7.2
73 R -2888992.02	-1517363.63	-1471628.39	100000.00 T= 12103.115 K
progress 7.3
74 T -2844768.12	-1460076.58	-1384691.54	0.00 T= 12073.705 K
progress 7.4
75 T -2773707.46	-1435333.22	-1338374.24	0.00 T= 12029.59 K
progress 7.5
76 T -2846264.06	-1548166.18	-1498097.88	200000.00 T= 11985.475 K
progress 7.6
77 R -2854607.33	-1552089.73	-1502517.60	200000.00 T= 11970.77 K
progress 7.7
78 R -2806546.30	-1636058.59	-1570487.72	400000.00 T= 11941.36 K
progress 7.8
79 R -2984705.98	-1646878.75	-1537827.23	200000.00 T= 11926.655 K
progress 7.9
80 R -3003172.21	-1697323.04	-1605849.17	300000.00 T= 11911.95 K
progress 8.0
81 R -3135598.07	-1619754.70	-1515843.37	0.00 T= 11838.425 K
progress 8.1
Traceback (most recent call last):
  File "/home/rpdock/mc/MC.py", line 671, in <module>
    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())
MemoryError
Tue Apr 28 20:45:41 2026
['prot-na_3910.pdb', 'prot-na_4.pdb']
msg Refinement of #1 /home/rpdock/web/media/jobs/3d411e53-5cb9-4307-9924-83be5dc86afe/prot-na_3910.pdb
dir: /home/rpdock/web/media/jobs/3d411e53-5cb9-4307-9924-83be5dc86afe/
file: prot-na_3910.pdb
find `pwd` -iname prot-na_3910.pdb 
 copy /home/rpdock/web/media/jobs/3d411e53-5cb9-4307-9924-83be5dc86afe/prot-na_15/prot-na_3910.pdb to /home/rpdock/web/media/jobs/3d411e53-5cb9-4307-9924-83be5dc86afe//ref_struc/prot-na_3910/prot-na_3910.pdb
cmd: python /home/rpdock/mc/MC.py -s 1000 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/3d411e53-5cb9-4307-9924-83be5dc86afe//ref_struc/prot-na_3910/prot-na_3910.pdb
msg python /home/rpdock/mc/MC.py -s 1000 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/3d411e53-5cb9-4307-9924-83be5dc86afe//ref_struc/prot-na_3910/prot-na_3910.pdb
msg run_mc::stderr:/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CA defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 806.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CB defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 810.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CG defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 812.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CD defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 814.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom NE defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 816.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CZ defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 818.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom NH1 defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 820.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom NH2 defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 822.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CA defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 4512.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CB defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 4516.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CG defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 4518.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CD defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 4520.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom NE defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 4522.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CZ defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 4524.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom NH1 defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 4526.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom NH2 defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 4528.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom P defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7863.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C5' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7864.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom O5' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7865.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C4' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7866.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom O4' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7867.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C3' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7868.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom O3' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7869.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C2' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7870.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom O2' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7871.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C1' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7872.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom N1 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7873.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C2 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7874.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom O2 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7875.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom N3 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7876.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C4 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7877.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom O4 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7878.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C5 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7879.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C6 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7880.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom OP1 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7881.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom OP2 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7882.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConError in run_mc /usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CA defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 806.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CB defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 810.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CG defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 812.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CD defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 814.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom NE defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 816.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CZ defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 818.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom NH1 defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 820.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom NH2 defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 822.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CA defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 4512.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CB defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 4516.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CG defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 4518.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CD defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 4520.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom NE defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 4522.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CZ defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 4524.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom NH1 defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 4526.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom NH2 defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 4528.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom P defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7863.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C5' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7864.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom O5' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7865.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C4' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7866.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom O4' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7867.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C3' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7868.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom O3' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7869.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C2' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7870.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom O2' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7871.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C1' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7872.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom N1 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7873.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C2 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7874.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom O2 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7875.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom N3 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7876.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C4 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7877.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom O4 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7878.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C5 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7879.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C6 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7880.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom OP1 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7881.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom OP2 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7882.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
Traceback (most recent call last):
  File "/home/rpdock/mc/MC.py", line 709, in <module>
    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
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CA defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 806.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CB defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 810.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CG defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 812.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CD defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 814.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom NE defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 816.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CZ defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 818.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom NH1 defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 820.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom NH2 defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 822.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CA defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 4512.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CB defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 4516.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CG defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 4518.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CD defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 4520.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom NE defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 4522.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CZ defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 4524.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom NH1 defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 4526.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom NH2 defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 4528.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom P defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7863.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C5' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7864.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom O5' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7865.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C4' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7866.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom O4' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7867.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C3' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7868.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom O3' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7869.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C2' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7870.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom O2' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7871.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C1' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7872.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom N1 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7873.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C2 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7874.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom O2 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7875.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom N3 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7876.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C4 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7877.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom O4 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7878.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C5 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7879.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C6 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7880.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom OP1 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7881.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom OP2 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7882.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
start - parameters:
    File name /home/rpdock/web/media/jobs/3d411e53-5cb9-4307-9924-83be5dc86afe//ref_struc/prot-na_4/prot-na_4.pdb
    Steps 1000
    Temp. start 15000.0
    Temp. end 295.0
    False
    
msg start - parameters:
    File name /home/rpdock/web/media/jobs/3d411e53-5cb9-4307-9924-83be5dc86afe//ref_struc/prot-na_4/prot-na_4.pdb
    Steps 1000
    Temp. start 15000.0
    Temp. end 295.0
    False
    


    Step	E	Edist	Eang	Epen
Missed atom CG in the LEU 1011
Missed atom CD1 in the LEU 1011
Missed atom CD2 in the LEU 1011
Missed atom CG in the HIS 1012
Missed atom ND1 in the HIS 1012
Missed atom CD2 in the HIS 1012
Missed atom CE1 in the HIS 1012
Missed atom NE2 in the HIS 1012
Missed atom CG in the GLU 1013
Missed atom CD in the GLU 1013
Missed atom OE1 in the GLU 1013
Missed atom OE2 in the GLU 1013
Missed atom CG1 in the VAL 1014
Missed atom CG2 in the VAL 1014
Missed atom CG in the LEU 1015
Missed atom CD1 in the LEU 1015
Missed atom CD2 in the LEU 1015
Missed atom CG in the HIS 1016
Missed atom ND1 in the HIS 1016
Missed atom CD2 in the HIS 1016
Missed atom CE1 in the HIS 1016
Missed atom NE2 in the HIS 1016
Missed atom CG in the HIS 1017
Missed atom ND1 in the HIS 1017
Missed atom CD2 in the HIS 1017
Missed atom CE1 in the HIS 1017
Missed atom NE2 in the HIS 1017
Missed atom OG1 in the THR 1018
Missed atom CG2 in the THR 1018
Missed atom OG1 in the THR 1020
Missed atom CG2 in the THR 1020
Missed atom CG in the ASN 1021
Missed atom OD1 in the ASN 1021
Missed atom ND2 in the ASN 1021
Missed atom CG1 in the VAL 1022
Missed atom CG2 in the VAL 1022
Missed atom CG in the ASP 1023
Missed atom OD1 in the ASP 1023
Missed atom OD2 in the ASP 1023
Missed atom CG in the LYS 1025
Missed atom CD in the LYS 1025
Missed atom CE in the LYS 1025
Missed atom NZ in the LYS 1025
Missed atom CG in the ARG 1028
Missed atom CD in the ARG 1028
Missed atom NE in the ARG 1028
Missed atom CZ in the ARG 1028
Missed atom NH1 in the ARG 1028
Missed atom NH2 in the ARG 1028
Missed atom OG1 in the THR 1029
Missed atom CG2 in the THR 1029
Missed atom CG in the MET 1031
Missed atom SD in the MET 1031
Missed atom CE in the MET 1031
Missed atom CG in the GLN 1033
Missed atom CD in the GLN 1033
Missed atom OE1 in the GLN 1033
Missed atom NE2 in the GLN 1033
Missed atom CG in the ARG 1038
Missed atom CD in the ARG 1038
Missed atom NE in the ARG 1038
Missed atom CZ in the ARG 1038
Missed atom NH1 in the ARG 1038
Missed atom NH2 in the ARG 1038
Missed atom CG in the ARG 1093
Missed atom CD in the ARG 1093
Missed atom NE in the ARG 1093
Missed atom CZ in the ARG 1093
Missed atom NH1 in the ARG 1093
Missed atom NH2 in the ARG 1093
Missed atom CG in the GLU 1097
Missed atom CD in the GLU 1097
Missed atom OE1 in the GLU 1097
Missed atom OE2 in the GLU 1097
Missed atom CG in the LEU 1148
Missed atom CD1 in the LEU 1148
Missed atom CD2 in the LEU 1148
Missed atom OG1 in the THR 1168
Missed atom CG2 in the THR 1168
Missed atom CG in the GLU 1217
Missed atom CD in the GLU 1217
Missed atom OE1 in the GLU 1217
Missed atom OE2 in the GLU 1217
Missed atom CG in the ASP 1218
Missed atom OD1 in the ASP 1218
Missed atom OD2 in the ASP 1218
Missed atom CG1 in the VAL 1231
Missed atom CG2 in the VAL 1231
Missed atom CG in the LYS 1234
Missed atom CD in the LYS 1234
Missed atom CE in the LYS 1234
Missed atom NZ in the LYS 1234
Missed atom CG in the GLU 1239
Missed atom CD in the GLU 1239
Missed atom OE1 in the GLU 1239
Missed atom OE2 in the GLU 1239
Missed atom CG in the GLU 1241
Missed atom CD in the GLU 1241
Missed atom OE1 in the GLU 1241
Missed atom OE2 in the GLU 1241
Missed atom CG in the PHE 1244
Missed atom CD1 in the PHE 1244
Missed atom CD2 in the PHE 1244
Missed atom CE1 in the PHE 1244
Missed atom CE2 in the PHE 1244
Missed atom CZ in the PHE 1244
Missed atom CG in the ASN 1246
Missed atom OD1 in the ASN 1246
Missed atom ND2 in the ASN 1246
Missed atom CG in the GLN 1268
Missed atom CD in the GLN 1268
Missed atom OE1 in the GLN 1268
Missed atom NE2 in the GLN 1268
Missed atom CG in the LYS 1279
Missed atom CD in the LYS 1279
Missed atom CE in the LYS 1279
Missed atom NZ in the LYS 1279
Missed atom CG in the GLN 1280
Missed atom CD in the GLN 1280
Missed atom OE1 in the GLN 1280
Missed atom NE2 in the GLN 1280
Missed atom CG in the LYS 1281
Missed atom CD in the LYS 1281
Missed atom CE in the LYS 1281
Missed atom NZ in the LYS 1281
Missed atom OG1 in the THR 1282
Missed atom CG2 in the THR 1282
Missed atom CG in the LYS 1289
Missed atom CD in the LYS 1289
Missed atom CE in the LYS 1289
Missed atom NZ in the LYS 1289
Missed atom CG in the LYS 1336
Missed atom CD in the LYS 1336
Missed atom CE in the LYS 1336
Missed atom NZ in the LYS 1336
Missed atom CG in the ARG 1337
Missed atom CD in the ARG 1337
Missed atom NE in the ARG 1337
Missed atom CZ in the ARG 1337
Missed atom NH1 in the ARG 1337
Missed atom NH2 in the ARG 1337
Missed atom CG in the ARG 1338
Missed atom CD in the ARG 1338
Missed atom NE in the ARG 1338
Missed atom CZ in the ARG 1338
Missed atom NH1 in the ARG 1338
Missed atom NH2 in the ARG 1338
Missed atom CG in the ARG 1340
Missed atom CD in the ARG 1340
Missed atom NE in the ARG 1340
Missed atom CZ in the ARG 1340
Missed atom NH1 in the ARG 1340
Missed atom NH2 in the ARG 1340
Missed atom CG in the GLU 1344
Missed atom CD in the GLU 1344
Missed atom OE1 in the GLU 1344
Missed atom OE2 in the GLU 1344
Missed atom CG in the LEU 1365
Missed atom CD1 in the LEU 1365
Missed atom CD2 in the LEU 1365
Missed atom CG in the LYS 1457
Missed atom CD in the LYS 1457
Missed atom CE in the LYS 1457
Missed atom NZ in the LYS 1457
Missed atom CG in the LYS 1469
Missed atom CD in the LYS 1469
Missed atom CE in the LYS 1469
Missed atom NZ in the LYS 1469
Missed atom CG in the GLU 1470
Missed atom CD in the GLU 1470
Missed atom OE1 in the GLU 1470
Missed atom OE2 in the GLU 1470
Missed atom CG in the ARG 1471
Missed atom CD in the ARG 1471
Missed atom NE in the ARG 1471
Missed atom CZ in the ARG 1471
Missed atom NH1 in the ARG 1471
Missed atom NH2 in the ARG 1471
Missed atom CG in the LYS 1475
Missed atom CD in the LYS 1475
Missed atom CE in the LYS 1475
Missed atom NZ in the LYS 1475
Missed atom CG in the LEU 1478
Missed atom CD1 in the LEU 1478
Missed atom CD2 in the LEU 1478
Missed atom CG in the LYS 1489
Missed atom CD in the LYS 1489
Missed atom CE in the LYS 1489
Missed atom NZ in the LYS 1489
Missed atom CG in the ARG 1491
Missed atom CD in the ARG 1491
Missed atom NE in the ARG 1491
Missed atom CZ in the ARG 1491
Missed atom NH1 in the ARG 1491
Missed atom NH2 in the ARG 1491
Missed atom OG1 in the THR 1492
Missed atom CG2 in the THR 1492
Missed atom CG in the LYS 1493
Missed atom CD in the LYS 1493
Missed atom CE in the LYS 1493
Missed atom NZ in the LYS 1493
Missed atom CG in the LEU 1011
Missed atom CD1 in the LEU 1011
Missed atom CD2 in the LEU 1011
Missed atom CG in the HIS 1012
Missed atom ND1 in the HIS 1012
Missed atom CD2 in the HIS 1012
Missed atom CE1 in the HIS 1012
Missed atom NE2 in the HIS 1012
Missed atom CG in the GLU 1013
Missed atom CD in the GLU 1013
Missed atom OE1 in the GLU 1013
Missed atom OE2 in the GLU 1013
Missed atom CG1 in the VAL 1014
Missed atom CG2 in the VAL 1014
Missed atom CG in the LEU 1015
Missed atom CD1 in the LEU 1015
Missed atom CD2 in the LEU 1015
Missed atom CG in the HIS 1016
Missed atom ND1 in the HIS 1016
Missed atom CD2 in the HIS 1016
Missed atom CE1 in the HIS 1016
Missed atom NE2 in the HIS 1016
Missed atom CG in the HIS 1017
Missed atom ND1 in the HIS 1017
Missed atom CD2 in the HIS 1017
Missed atom CE1 in the HIS 1017
Missed atom NE2 in the HIS 1017
Missed atom OG1 in the THR 1018
Missed atom CG2 in the THR 1018
Missed atom OG1 in the THR 1020
Missed atom CG2 in the THR 1020
Missed atom CG in the ASN 1021
Missed atom OD1 in the ASN 1021
Missed atom ND2 in the ASN 1021
Missed atom CG1 in the VAL 1022
Missed atom CG2 in the VAL 1022
Missed atom CG in the ASP 1023
Missed atom OD1 in the ASP 1023
Missed atom OD2 in the ASP 1023
Missed atom CG in the LYS 1025
Missed atom CD in the LYS 1025
Missed atom CE in the LYS 1025
Missed atom NZ in the LYS 1025
Missed atom CG in the ARG 1028
Missed atom CD in the ARG 1028
Missed atom NE in the ARG 1028
Missed atom CZ in the ARG 1028
Missed atom NH1 in the ARG 1028
Missed atom NH2 in the ARG 1028
Missed atom OG1 in the THR 1029
Missed atom CG2 in the THR 1029
Missed atom CG in the MET 1031
Missed atom SD in the MET 1031
Missed atom CE in the MET 1031
Missed atom CG in the GLN 1033
Missed atom CD in the GLN 1033
Missed atom OE1 in the GLN 1033
Missed atom NE2 in the GLN 1033
Missed atom CG in the ARG 1038
Missed atom CD in the ARG 1038
Missed atom NE in the ARG 1038
Missed atom CZ in the ARG 1038
Missed atom NH1 in the ARG 1038
Missed atom NH2 in the ARG 1038
Missed atom CG in the ARG 1093
Missed atom CD in the ARG 1093
Missed atom NE in the ARG 1093
Missed atom CZ in the ARG 1093
Missed atom NH1 in the ARG 1093
Missed atom NH2 in the ARG 1093
Missed atom CG in the GLU 1097
Missed atom CD in the GLU 1097
Missed atom OE1 in the GLU 1097
Missed atom OE2 in the GLU 1097
Missed atom OG1 in the THR 1168
Missed atom CG2 in the THR 1168
Missed atom CG in the GLU 1217
Missed atom CD in the GLU 1217
Missed atom OE1 in the GLU 1217
Missed atom OE2 in the GLU 1217
Missed atom CG in the ASP 1218
Missed atom OD1 in the ASP 1218
Missed atom OD2 in the ASP 1218
Missed atom CG1 in the VAL 1231
Missed atom CG2 in the VAL 1231
Missed atom CG in the LYS 1234
Missed atom CD in the LYS 1234
Missed atom CE in the LYS 1234
Missed atom NZ in the LYS 1234
Missed atom CG in the LEU 1235
Missed atom CD1 in the LEU 1235
Missed atom CD2 in the LEU 1235
Missed atom CG in the GLU 1241
Missed atom CD in the GLU 1241
Missed atom OE1 in the GLU 1241
Missed atom OE2 in the GLU 1241
Missed atom CG in the PHE 1244
Missed atom CD1 in the PHE 1244
Missed atom CD2 in the PHE 1244
Missed atom CE1 in the PHE 1244
Missed atom CE2 in the PHE 1244
Missed atom CZ in the PHE 1244
Missed atom CG in the GLN 1268
Missed atom CD in the GLN 1268
Missed atom OE1 in the GLN 1268
Missed atom NE2 in the GLN 1268
Missed atom CG in the LYS 1279
Missed atom CD in the LYS 1279
Missed atom CE in the LYS 1279
Missed atom NZ in the LYS 1279
Missed atom CG in the GLN 1280
Missed atom CD in the GLN 1280
Missed atom OE1 in the GLN 1280
Missed atom NE2 in the GLN 1280
Missed atom CG in the LYS 1281
Missed atom CD in the LYS 1281
Missed atom CE in the LYS 1281
Missed atom NZ in the LYS 1281
Missed atom CG in the LYS 1289
Missed atom CD in the LYS 1289
Missed atom CE in the LYS 1289
Missed atom NZ in the LYS 1289
Missed atom CG in the LYS 1336
Missed atom CD in the LYS 1336
Missed atom CE in the LYS 1336
Missed atom NZ in the LYS 1336
Missed atom CG in the ARG 1337
Missed atom CD in the ARG 1337
Missed atom NE in the ARG 1337
Missed atom CZ in the ARG 1337
Missed atom NH1 in the ARG 1337
Missed atom NH2 in the ARG 1337
Missed atom CG in the ARG 1338
Missed atom CD in the ARG 1338
Missed atom NE in the ARG 1338
Missed atom CZ in the ARG 1338
Missed atom NH1 in the ARG 1338
Missed atom NH2 in the ARG 1338
Missed atom CG in the ARG 1340
Missed atom CD in the ARG 1340
Missed atom NE in the ARG 1340
Missed atom CZ in the ARG 1340
Missed atom NH1 in the ARG 1340
Missed atom NH2 in the ARG 1340
Missed atom CG in the GLU 1344
Missed atom CD in the GLU 1344
Missed atom OE1 in the GLU 1344
Missed atom OE2 in the GLU 1344
Missed atom CG in the LEU 1365
Missed atom CD1 in the LEU 1365
Missed atom CD2 in the LEU 1365
Missed atom CG in the LYS 1469
Missed atom CD in the LYS 1469
Missed atom CE in the LYS 1469
Missed atom NZ in the LYS 1469
Missed atom CG in the GLU 1470
Missed atom CD in the GLU 1470
Missed atom OE1 in the GLU 1470
Missed atom OE2 in the GLU 1470
Missed atom CG in the ARG 1471
Missed atom CD in the ARG 1471
Missed atom NE in the ARG 1471
Missed atom CZ in the ARG 1471
Missed atom NH1 in the ARG 1471
Missed atom NH2 in the ARG 1471
Missed atom CG in the LYS 1489
Missed atom CD in the LYS 1489
Missed atom CE in the LYS 1489
Missed atom NZ in the LYS 1489
Missed atom CG in the ARG 1491
Missed atom CD in the ARG 1491
Missed atom NE in the ARG 1491
Missed atom CZ in the ARG 1491
Missed atom NH1 in the ARG 1491
Missed atom NH2 in the ARG 1491
Missed atom OG1 in the THR 1492
Missed atom CG2 in the THR 1492
Missed atom CG in the LYS 1493
Missed atom CD in the LYS 1493
Missed atom CE in the LYS 1493
Missed atom NZ in the LYS 1493
0 - -2363787.39	-1618722.16	-1545065.23	800000.00
1 T -2815328.41	-1706195.96	-1609132.45	500000.00 T= 14985.295 K
progress 0.1
2 T -2829365.19	-1923818.87	-1805546.32	900000.00 T= 14926.475 K
progress 0.2
3 T -3039269.16	-1829036.92	-1710232.24	500000.00 T= 14823.54 K
progress 0.3
4 T -2874470.16	-2007776.68	-1866693.48	1000000.00 T= 14794.13 K
progress 0.4
5 R -2841226.14	-2042657.92	-1898568.22	1100000.00 T= 14750.015 K
progress 0.5
6 T -3171469.84	-2336735.81	-2134734.03	1300000.00 T= 14735.31 K
progress 0.6
7 R -3178645.53	-2284553.68	-2094091.85	1200000.00 T= 14676.49 K
progress 0.7
8 T -2973688.48	-2482073.27	-2291615.22	1800000.00 T= 14632.375 K
progress 0.8
9 T -2746600.06	-2120881.08	-1925718.98	1300000.00 T= 14529.44 K
progress 0.9
10 T -2688805.80	-1954615.25	-1834190.54	1100000.00 T= 14514.735 K
progress 1.0
11 T -3100687.41	-2019169.53	-1881517.88	800000.00 T= 14500.03 K
progress 1.1
12 R -3232352.59	-2084188.33	-1948164.26	800000.00 T= 14470.62 K
progress 1.2
13 R -3238989.05	-2088982.76	-1950006.30	800000.00 T= 14279.455 K
progress 1.3
14 T -3446801.31	-2031506.02	-1915295.29	500000.00 T= 14191.225 K
progress 1.4
15 R -3444311.71	-2032531.21	-1911780.50	500000.00 T= 13926.535 K
progress 1.5
16 T -3462013.05	-1982355.47	-1879657.58	400000.00 T= 13544.205 K
progress 1.6
17 R -3504174.05	-2062548.59	-1941625.46	500000.00 T= 13529.5 K
progress 1.7
18 R -3481080.98	-2060337.35	-1920743.64	500000.00 T= 13382.45 K
progress 1.8
19 T -3180913.67	-2122613.27	-1958300.39	900000.00 T= 13235.4 K
progress 1.9
20 T -3211226.16	-1969947.02	-1841279.14	600000.00 T= 13205.99 K
progress 2.0
21 T -3240347.55	-1846919.51	-1793428.03	400000.00 T= 13117.76 K
progress 2.1
22 R -2948925.76	-1844641.45	-1804284.31	700000.00 T= 13073.645 K
progress 2.2
23 T -3176445.84	-1922611.42	-1853834.42	600000.00 T= 13044.235 K
progress 2.3
24 T -2984621.17	-1714014.13	-1670607.03	400000.00 T= 12985.415 K
progress 2.4
25 T -3169835.60	-1864489.16	-1805346.44	500000.00 T= 12956.005 K
progress 2.5
26 T -2935072.64	-2082650.01	-1952422.63	1100000.00 T= 12750.135 K
progress 2.6
27 R -3439564.16	-2018792.88	-1920771.28	500000.00 T= 12676.61 K
progress 2.7
28 R -3433871.94	-2015739.01	-1918132.93	500000.00 T= 12573.675 K
progress 2.8
29 R -3442774.11	-2011722.05	-1931052.06	500000.00 T= 12544.265 K
progress 2.9
30 R -3387448.37	-1989856.08	-1897592.30	500000.00 T= 12441.33 K
progress 3.0
31 R -3220030.13	-2016389.42	-1903640.71	700000.00 T= 12353.1 K
progress 3.1
32 R -3232948.01	-2073099.04	-1959848.98	800000.00 T= 12294.28 K
progress 3.2
33 R -3180575.71	-2026888.93	-1953686.77	800000.00 T= 12220.755 K
progress 3.3
34 R -3103560.60	-2000380.14	-1903180.46	800000.00 T= 12176.64 K
progress 3.4
35 T -3132020.06	-1796203.25	-1735816.81	400000.00 T= 12161.935 K
progress 3.5
36 T -3068565.98	-1670008.96	-1598557.03	200000.00 T= 12147.23 K
progress 3.6
37 T -2868012.72	-1608448.53	-1559564.19	300000.00 T= 12088.41 K
progress 3.7
38 T -2604645.30	-1567084.35	-1437560.96	400000.00 T= 12059.0 K
progress 3.8
39 R -2607030.94	-1494971.15	-1412059.79	300000.00 T= 12044.295 K
progress 3.9
40 T -2781755.10	-1657138.03	-1524617.07	400000.00 T= 12014.885 K
progress 4.0
41 R -2785238.80	-1660347.55	-1524891.25	400000.00 T= 11956.065 K
progress 4.1
42 T -2673315.19	-1440937.98	-1332377.22	100000.00 T= 11926.655 K
progress 4.2
43 T -2615144.94	-1419992.10	-1295152.84	100000.00 T= 11897.245 K
progress 4.3
44 R -2724794.30	-1462199.00	-1362595.30	100000.00 T= 11882.54 K
progress 4.4
45 T -2787100.21	-1440919.65	-1346180.56	0.00 T= 11809.015 K
progress 4.5
46 T -2899513.56	-1564994.11	-1434519.45	100000.00 T= 11750.195 K
progress 4.6
47 R -2994584.36	-1603097.03	-1491487.33	100000.00 T= 11706.08 K
progress 4.7
48 R -2838019.36	-1576755.82	-1461263.54	200000.00 T= 11661.965 K
progress 4.8
49 T -3077636.30	-1906613.17	-1771023.13	600000.00 T= 11647.26 K
progress 4.9
50 T -3117488.68	-1715835.82	-1601652.87	200000.00 T= 11529.62 K
progress 5.0
51 R -3055161.10	-1678982.76	-1576178.34	200000.00 T= 11485.505 K
progress 5.1
52 T -3208666.07	-1749897.13	-1658768.94	200000.00 T= 11456.095 K
progress 5.2
53 R -3246352.59	-1772696.85	-1673655.74	200000.00 T= 11441.39 K
progress 5.3
54 T -3197361.43	-1862072.67	-1735288.76	400000.00 T= 11279.635 K
progress 5.4
55 R -3162344.58	-1953841.89	-1808502.68	600000.00 T= 11250.225 K
progress 5.5
56 T -3013216.73	-1865785.58	-1747431.15	600000.00 T= 11220.815 K
progress 5.6
57 R -2991359.48	-1851813.41	-1739546.07	600000.00 T= 11176.7 K
progress 5.7
58 R -2867362.44	-1763790.41	-1703572.03	600000.00 T= 11147.29 K
progress 5.8
59 R -2968931.23	-1833675.81	-1735255.42	600000.00 T= 11059.06 K
progress 5.9
60 R -2994957.80	-1902236.46	-1792721.34	700000.00 T= 11029.65 K
progress 6.0
61 T -3170934.65	-2018318.37	-1852616.28	700000.00 T= 10985.535 K
progress 6.1
62 R -3339063.37	-2005522.82	-1833540.56	500000.00 T= 10956.125 K
progress 6.2
63 T -3134260.19	-1876392.93	-1757867.26	500000.00 T= 10794.37 K
progress 6.3
64 R -3151571.76	-1947451.96	-1804119.80	600000.00 T= 10735.55 K
progress 6.4
65 R -3129545.49	-1925364.01	-1804181.48	600000.00 T= 10720.845 K
progress 6.5
66 R -3276518.98	-1849634.44	-1726884.54	300000.00 T= 10706.14 K
progress 6.6
67 R -2901144.06	-1642877.22	-1558266.83	300000.00 T= 10514.975 K
progress 6.7
68 R -2912854.68	-1645253.81	-1567600.87	300000.00 T= 10485.565 K
progress 6.8
69 R -3030225.50	-1846489.26	-1783736.24	600000.00 T= 10456.155 K
progress 6.9
70 R -3237108.27	-1852730.01	-1784378.26	400000.00 T= 10441.45 K
progress 7.0
71 T -3339091.45	-1848549.97	-1790541.48	300000.00 T= 10088.53 K
progress 7.1
72 T -3263977.79	-1872309.06	-1791668.73	400000.00 T= 10073.825 K
progress 7.2
73 T -3335413.48	-1904130.09	-1831283.38	400000.00 T= 10015.005 K
progress 7.3
74 T -3261364.71	-1870764.87	-1790599.83	400000.00 T= 10000.3 K
progress 7.4
75 R -3254080.56	-1867699.96	-1786380.60	400000.00 T= 9897.365 K
progress 7.5
76 R -3209511.15	-1729633.07	-1679878.08	200000.00 T= 9838.545 K
progress 7.6
77 T -3217162.09	-1806612.80	-1710549.30	300000.00 T= 9765.02 K
progress 7.7
78 R -3229019.03	-1816250.22	-1712768.81	300000.00 T= 9706.2 K
progress 7.8
79 R -3061640.04	-1852309.08	-1709330.96	500000.00 T= 9632.675 K
progress 7.9
80 T -3150752.53	-1646746.98	-1604005.55	100000.00 T= 9588.56 K
progress 8.0
Traceback (most recent call last):
  File "/home/rpdock/mc/MC.py", line 589, in <module>
    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 328, in all_atom
    at.set_coord(list(coo))
MemoryError
structionWarning)
Traceback (most recent call last):
  File "/home/rpdock/mc/MC.py", line 709, in <module>
    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/3d411e53-5cb9-4307-9924-83be5dc86afe/prot-na_4.pdb
dir: /home/rpdock/web/media/jobs/3d411e53-5cb9-4307-9924-83be5dc86afe/
file: prot-na_4.pdb
find `pwd` -iname prot-na_4.pdb 
 copy /home/rpdock/web/media/jobs/3d411e53-5cb9-4307-9924-83be5dc86afe/prot-na_15/prot-na_4.pdb to /home/rpdock/web/media/jobs/3d411e53-5cb9-4307-9924-83be5dc86afe//ref_struc/prot-na_4/prot-na_4.pdb
cmd: python /home/rpdock/mc/MC.py -s 1000 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/3d411e53-5cb9-4307-9924-83be5dc86afe//ref_struc/prot-na_4/prot-na_4.pdb
msg python /home/rpdock/mc/MC.py -s 1000 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/3d411e53-5cb9-4307-9924-83be5dc86afe//ref_struc/prot-na_4/prot-na_4.pdb
msg run_mc::stderr:/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CA defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 806.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CB defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 810.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CG defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 812.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CD defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 814.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom NE defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 816.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CZ defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 818.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom NH1 defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 820.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom NH2 defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 822.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CA defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 4512.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CB defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 4516.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CG defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 4518.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CD defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 4520.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom NE defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 4522.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CZ defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 4524.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom NH1 defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 4526.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom NH2 defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 4528.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom P defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7863.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C5' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7864.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom O5' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7865.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C4' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7866.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom O4' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7867.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C3' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7868.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom O3' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7869.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C2' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7870.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom O2' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7871.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C1' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7872.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom N1 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7873.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C2 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7874.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom O2 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7875.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom N3 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7876.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C4 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7877.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom O4 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7878.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionExError in run_mc /usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CA defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 806.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CB defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 810.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CG defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 812.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CD defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 814.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom NE defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 816.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CZ defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 818.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom NH1 defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 820.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom NH2 defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 822.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CA defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 4512.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CB defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 4516.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CG defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 4518.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CD defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 4520.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom NE defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 4522.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CZ defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 4524.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom NH1 defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 4526.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom NH2 defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 4528.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom P defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7863.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C5' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7864.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom O5' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7865.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C4' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7866.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom O4' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7867.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C3' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7868.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom O3' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7869.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C2' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7870.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom O2' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7871.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C1' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7872.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom N1 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7873.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C2 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7874.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom O2 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7875.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom N3 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7876.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C4 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7877.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom O4 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7878.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C5 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7879.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C6 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7880.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom OP1 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7881.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom OP2 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7882.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
ception: Atom C5 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7879.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C6 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7880.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom OP1 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7881.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom OP2 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7882.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
2026-04-28 21:14:11 npdock::MC (refinement) end
2026-04-28 21:14:11 npdock::OK
2026-04-28 21:14:11 Set finished status of 3d411e53-5cb9-4307-9924-83be5dc86afe