2026-07-24 19:37:02 NPdock start 2026-07-24 19:37:02 ver: server 2026-07-24 19:37:02 mode: 11111 2026-07-24 19:37:02 is RNA? 1 2026-07-24 19:37:02 Interface: prot: '' na: '' 2026-07-24 19:37:02 Curr dir:/home/rpdock/web/media/jobs/7b0a82ff-9a6b-468f-ac08-72c9319fcf62/ 2026-07-24 19:37:02 GRAMM in progress... 2026-07-24 19:37:02 python /home/rpdock/run_gramm//run_gramm1.py -d 20000 -p prot.pdb -r na.pdb -pi '' -ri '' -n 1 -pf '*' -rf '*' 2026-07-24 20:49:50 GRAMM done 2026-07-24 20:49:50 DARS scoring in progress... 2026-07-24 20:49:50 time python /home/rpdock/run_gramm//DARS-RNP_v3//DARS_potential_v3_scoring.py -m 100 -f list.txt -o dars_out.txt 2026-07-24 20:49:51 DARS start [DARS_potential_v3_scoring.py] 2026-07-24 20:49:51 Show log every 100 structures [DARS_potential_v3_scoring.py] 2026-07-24 20:49:51 1/20000 prot-na_1000.pdb 91963.86 2026-07-24 20:50:32 100/20000 prot-na_94.pdb 370000.00 2026-07-24 20:51:14 200/20000 prot-na_194.pdb 311261.48 2026-07-24 20:51:56 300/20000 prot-na_294.pdb 163094.97 2026-07-24 20:52:41 400/20000 prot-na_394.pdb 211756.54 2026-07-24 20:53:25 500/20000 prot-na_494.pdb 205152.02 2026-07-24 20:54:08 600/20000 prot-na_594.pdb 220000.00 2026-07-24 20:54:51 700/20000 prot-na_694.pdb 72303.36 2026-07-24 20:55:34 800/20000 prot-na_794.pdb 241424.12 2026-07-24 20:56:16 900/20000 prot-na_894.pdb 131352.80 2026-07-24 20:56:57 1000/20000 prot-na_994.pdb 30000.00 2026-07-24 20:57:38 1100/20000 prot-na_1100.pdb 306029.44 2026-07-24 20:58:20 1200/20000 prot-na_1200.pdb 123543.26 2026-07-24 20:59:01 1300/20000 prot-na_1300.pdb 26380.02 2026-07-24 20:59:42 1400/20000 prot-na_1400.pdb 142564.07 2026-07-24 21:00:24 1500/20000 prot-na_1500.pdb 212577.44 2026-07-24 21:01:05 1600/20000 prot-na_1600.pdb 56380.02 2026-07-24 21:01:48 1700/20000 prot-na_1700.pdb 191163.18 2026-07-24 21:02:30 1800/20000 prot-na_1800.pdb 581104.83 2026-07-24 21:03:12 1900/20000 prot-na_1900.pdb 77297.46 2026-07-24 21:03:54 2000/20000 prot-na_2000.pdb 70000.00 2026-07-24 21:04:37 2100/20000 prot-na_2100.pdb 250224.50 2026-07-24 21:05:19 2200/20000 prot-na_2200.pdb 107151.34 2026-07-24 21:06:02 2300/20000 prot-na_2300.pdb 106615.79 2026-07-24 21:06:45 2400/20000 prot-na_2400.pdb 529734.34 2026-07-24 21:07:28 2500/20000 prot-na_2500.pdb 271999.32 2026-07-24 21:08:10 2600/20000 prot-na_2600.pdb 267918.21 2026-07-24 21:08:53 2700/20000 prot-na_2700.pdb 60000.00 2026-07-24 21:09:36 2800/20000 prot-na_2800.pdb 221900.42 2026-07-24 21:10:18 2900/20000 prot-na_2900.pdb 306692.48 2026-07-24 21:11:01 3000/20000 prot-na_3000.pdb 370755.81 2026-07-24 21:11:45 3100/20000 prot-na_3100.pdb 286380.02 2026-07-24 21:12:28 3200/20000 prot-na_3200.pdb 130000.00 2026-07-24 21:13:11 3300/20000 prot-na_3300.pdb 270000.00 2026-07-24 21:13:54 3400/20000 prot-na_3400.pdb 217641.49 2026-07-24 21:14:36 3500/20000 prot-na_3500.pdb 112921.05 2026-07-24 21:15:18 3600/20000 prot-na_3600.pdb 103722.56 2026-07-24 21:16:00 3700/20000 prot-na_3700.pdb 266604.52 2026-07-24 21:16:43 3800/20000 prot-na_3800.pdb 46811.59 2026-07-24 21:17:26 3900/20000 prot-na_3900.pdb -11925.50 2026-07-24 21:18:08 4000/20000 prot-na_4000.pdb 172717.82 2026-07-24 21:18:50 4100/20000 prot-na_4100.pdb 64438.71 2026-07-24 21:19:32 4200/20000 prot-na_4200.pdb 185619.30 2026-07-24 21:20:13 4300/20000 prot-na_4300.pdb 89877.88 2026-07-24 21:20:55 4400/20000 prot-na_4400.pdb 138108.77 2026-07-24 21:21:37 4500/20000 prot-na_4500.pdb 60000.00 2026-07-24 21:22:19 4600/20000 prot-na_4600.pdb 113587.31 2026-07-24 21:23:00 4700/20000 prot-na_4700.pdb 110189.97 2026-07-24 21:23:42 4800/20000 prot-na_4800.pdb 116884.86 2026-07-24 21:24:22 4900/20000 prot-na_4900.pdb 94725.86 2026-07-24 21:25:04 5000/20000 prot-na_5000.pdb 202779.04 2026-07-24 21:25:45 5100/20000 prot-na_5100.pdb 355152.02 2026-07-24 21:26:26 5200/20000 prot-na_5200.pdb 160000.00 2026-07-24 21:27:07 5300/20000 prot-na_5300.pdb 125152.02 2026-07-24 21:27:48 5400/20000 prot-na_5400.pdb 279710.84 2026-07-24 21:28:30 5500/20000 prot-na_5500.pdb 30000.00 2026-07-24 21:29:11 5600/20000 prot-na_5600.pdb 446109.45 2026-07-24 21:29:53 5700/20000 prot-na_5700.pdb 160000.00 2026-07-24 21:30:39 5800/20000 prot-na_5800.pdb 211820.08 2026-07-24 21:31:21 5900/20000 prot-na_5900.pdb 111532.04 2026-07-24 21:32:02 6000/20000 prot-na_6000.pdb 146811.59 2026-07-24 21:32:43 6100/20000 prot-na_6100.pdb 329141.21 2026-07-24 21:33:24 6200/20000 prot-na_6200.pdb 82760.03 2026-07-24 21:34:06 6300/20000 prot-na_6300.pdb 115226.81 2026-07-24 21:34:47 6400/20000 prot-na_6400.pdb 1192.85 2026-07-24 21:35:28 6500/20000 prot-na_6500.pdb 160000.00 2026-07-24 21:36:09 6600/20000 prot-na_6600.pdb 120000.00 2026-07-24 21:36:50 6700/20000 prot-na_6700.pdb 73631.45 2026-07-24 21:37:31 6800/20000 prot-na_6800.pdb 144725.86 2026-07-24 21:38:12 6900/20000 prot-na_6900.pdb 0.00 2026-07-24 21:38:53 7000/20000 prot-na_7000.pdb 120000.00 2026-07-24 21:39:34 7100/20000 prot-na_7100.pdb 100000.00 2026-07-24 21:40:16 7200/20000 prot-na_7200.pdb 240507.42 2026-07-24 21:40:57 7300/20000 prot-na_7300.pdb 32057.49 2026-07-24 21:41:39 7400/20000 prot-na_7400.pdb 60000.00 2026-07-24 21:42:20 7500/20000 prot-na_7500.pdb 96160.88 2026-07-24 21:43:01 7600/20000 prot-na_7600.pdb 39099.68 2026-07-24 21:43:42 7700/20000 prot-na_7700.pdb 200000.00 2026-07-24 21:44:24 7800/20000 prot-na_7800.pdb 56380.02 2026-07-24 21:45:06 7900/20000 prot-na_7900.pdb 127152.64 2026-07-24 21:45:48 8000/20000 prot-na_8000.pdb 180849.05 2026-07-24 21:46:29 8100/20000 prot-na_8100.pdb 143227.50 2026-07-24 21:47:10 8200/20000 prot-na_8200.pdb 280282.47 2026-07-24 21:47:51 8300/20000 prot-na_8300.pdb 290000.00 2026-07-24 21:48:32 8400/20000 prot-na_8400.pdb 160000.00 2026-07-24 21:49:14 8500/20000 prot-na_8500.pdb 121490.88 2026-07-24 21:49:55 8600/20000 prot-na_8600.pdb 195163.28 2026-07-24 21:50:42 8700/20000 prot-na_8700.pdb 188354.87 2026-07-24 21:51:25 8800/20000 prot-na_8800.pdb 190000.00 2026-07-24 21:52:07 8900/20000 prot-na_8900.pdb 236574.52 2026-07-24 21:52:49 9000/20000 prot-na_9000.pdb 102580.80 2026-07-24 21:53:30 9100/20000 prot-na_9100.pdb 123105.38 2026-07-24 21:54:12 9200/20000 prot-na_9200.pdb 210000.00 2026-07-24 21:54:53 9300/20000 prot-na_9300.pdb 41336.27 2026-07-24 21:55:35 9400/20000 prot-na_9400.pdb 149106.35 2026-07-24 21:56:16 9500/20000 prot-na_9500.pdb 77033.44 2026-07-24 21:56:58 9600/20000 prot-na_9600.pdb 214655.54 2026-07-24 21:57:39 9700/20000 prot-na_9700.pdb -22228.11 2026-07-24 21:58:21 9800/20000 prot-na_9800.pdb 291261.48 2026-07-24 21:59:03 9900/20000 prot-na_9900.pdb 231608.64 2026-07-24 21:59:44 10000/20000 prot-na_10000.pdb 383099.23 2026-07-24 22:00:26 10100/20000 prot-na_10100.pdb 293838.91 2026-07-24 22:01:07 10200/20000 prot-na_10200.pdb 178196.73 2026-07-24 22:01:49 10300/20000 prot-na_10300.pdb 232501.83 2026-07-24 22:02:30 10400/20000 prot-na_10400.pdb 93042.50 2026-07-24 22:03:15 10500/20000 prot-na_10500.pdb 242218.91 2026-07-24 22:03:57 10600/20000 prot-na_10600.pdb -49401.69 2026-07-24 22:04:39 10700/20000 prot-na_10700.pdb 539507.87 2026-07-24 22:05:21 10800/20000 prot-na_10800.pdb 12921.05 2026-07-24 22:06:02 10900/20000 prot-na_10900.pdb 79734.34 2026-07-24 22:06:44 11000/20000 prot-na_11000.pdb 48598.92 2026-07-24 22:07:25 11100/20000 prot-na_11100.pdb 56380.02 2026-07-24 22:08:06 11200/20000 prot-na_11200.pdb 78846.80 2026-07-24 22:08:48 11300/20000 prot-na_11300.pdb 30000.00 2026-07-24 22:09:29 11400/20000 prot-na_11400.pdb 109267.07 2026-07-24 22:10:11 11500/20000 prot-na_11500.pdb 150000.00 2026-07-24 22:10:53 11600/20000 prot-na_11600.pdb 145521.23 2026-07-24 22:11:34 11700/20000 prot-na_11700.pdb 128058.70 2026-07-24 22:12:16 11800/20000 prot-na_11800.pdb 141100.56 2026-07-24 22:12:58 11900/20000 prot-na_11900.pdb 228391.69 2026-07-24 22:13:40 12000/20000 prot-na_12000.pdb 203692.37 2026-07-24 22:14:21 12100/20000 prot-na_12100.pdb 144886.37 2026-07-24 22:15:03 12200/20000 prot-na_12200.pdb 126144.40 2026-07-24 22:15:44 12300/20000 prot-na_12300.pdb 41226.94 2026-07-24 22:16:26 12400/20000 prot-na_12400.pdb 154293.23 2026-07-24 22:17:08 12500/20000 prot-na_12500.pdb 90000.00 2026-07-24 22:17:50 12600/20000 prot-na_12600.pdb 314115.05 2026-07-24 22:18:31 12700/20000 prot-na_12700.pdb 46528.25 2026-07-24 22:19:13 12800/20000 prot-na_12800.pdb 173077.55 2026-07-24 22:19:54 12900/20000 prot-na_12900.pdb 160000.00 2026-07-24 22:20:36 13000/20000 prot-na_13000.pdb 181261.48 2026-07-24 22:21:18 13100/20000 prot-na_13100.pdb 160000.00 2026-07-24 22:22:00 13200/20000 prot-na_13200.pdb 163260.79 2026-07-24 22:22:42 13300/20000 prot-na_13300.pdb 152830.09 2026-07-24 22:23:24 13400/20000 prot-na_13400.pdb 256557.15 2026-07-24 22:24:05 13500/20000 prot-na_13500.pdb 144725.86 2026-07-24 22:24:46 13600/20000 prot-na_13600.pdb 260000.00 2026-07-24 22:25:28 13700/20000 prot-na_13700.pdb 134269.63 2026-07-24 22:26:10 13800/20000 prot-na_13800.pdb 111105.88 2026-07-24 22:26:51 13900/20000 prot-na_13900.pdb 60000.00 2026-07-24 22:27:33 14000/20000 prot-na_14000.pdb 51261.48 2026-07-24 22:28:15 14100/20000 prot-na_14100.pdb 60000.00 2026-07-24 22:28:57 14200/20000 prot-na_14200.pdb 318098.66 2026-07-24 22:29:38 14300/20000 prot-na_14300.pdb 226109.45 2026-07-24 22:30:20 14400/20000 prot-na_14400.pdb 69965.14 2026-07-24 22:31:01 14500/20000 prot-na_14500.pdb 47348.05 2026-07-24 22:31:43 14600/20000 prot-na_14600.pdb 175481.26 2026-07-24 22:32:25 14700/20000 prot-na_14700.pdb 164348.03 2026-07-24 22:33:07 14800/20000 prot-na_14800.pdb 298600.05 2026-07-24 22:33:49 14900/20000 prot-na_14900.pdb 56380.02 2026-07-24 22:34:30 15000/20000 prot-na_15000.pdb 250000.00 2026-07-24 22:35:12 15100/20000 prot-na_15100.pdb 160000.00 2026-07-24 22:35:54 15200/20000 prot-na_15200.pdb 71203.73 2026-07-24 22:36:35 15300/20000 prot-na_15300.pdb 48869.49 2026-07-24 22:37:17 15400/20000 prot-na_15400.pdb 71264.77 2026-07-24 22:37:59 15500/20000 prot-na_15500.pdb 9727.23 2026-07-24 22:38:41 15600/20000 prot-na_15600.pdb 145521.23 2026-07-24 22:39:23 15700/20000 prot-na_15700.pdb 276380.02 2026-07-24 22:40:04 15800/20000 prot-na_15800.pdb 432798.86 2026-07-24 22:40:46 15900/20000 prot-na_15900.pdb 23745.75 2026-07-24 22:41:28 16000/20000 prot-na_16000.pdb 84115.05 2026-07-24 22:42:10 16100/20000 prot-na_16100.pdb 133923.01 2026-07-24 22:42:51 16200/20000 prot-na_16200.pdb 190000.00 2026-07-24 22:43:33 16300/20000 prot-na_16300.pdb 65776.24 2026-07-24 22:44:14 16400/20000 prot-na_16400.pdb 146604.52 2026-07-24 22:44:56 16500/20000 prot-na_16500.pdb 250000.00 2026-07-24 22:45:37 16600/20000 prot-na_16600.pdb 212066.70 2026-07-24 22:46:18 16700/20000 prot-na_16700.pdb 190286.54 2026-07-24 22:47:00 16800/20000 prot-na_16800.pdb 79607.52 2026-07-24 22:47:41 16900/20000 prot-na_16900.pdb 126380.02 2026-07-24 22:48:22 17000/20000 prot-na_17000.pdb 184115.05 2026-07-24 22:49:04 17100/20000 prot-na_17100.pdb 60000.00 2026-07-24 22:49:45 17200/20000 prot-na_17200.pdb 25619.30 2026-07-24 22:50:25 17300/20000 prot-na_17300.pdb 210129.16 2026-07-24 22:51:06 17400/20000 prot-na_17400.pdb -20990.22 2026-07-24 22:51:48 17500/20000 prot-na_17500.pdb 245554.71 2026-07-24 22:52:29 17600/20000 prot-na_17600.pdb 319596.31 2026-07-24 22:53:11 17700/20000 prot-na_17700.pdb 60000.00 2026-07-24 22:53:52 17800/20000 prot-na_17800.pdb 85152.02 2026-07-24 22:54:33 17900/20000 prot-na_17900.pdb 202755.62 2026-07-24 22:55:15 18000/20000 prot-na_18000.pdb 120000.00 2026-07-24 22:55:56 18100/20000 prot-na_18100.pdb 146380.02 2026-07-24 22:56:38 18200/20000 prot-na_18200.pdb 346380.02 2026-07-24 22:57:19 18300/20000 prot-na_18300.pdb 145945.15 2026-07-24 22:58:00 18400/20000 prot-na_18400.pdb 202367.36 2026-07-24 22:58:42 18500/20000 prot-na_18500.pdb 86380.02 2026-07-24 22:59:23 18600/20000 prot-na_18600.pdb 109319.39 2026-07-24 23:00:09 18700/20000 prot-na_18700.pdb 115619.30 2026-07-24 23:00:51 18800/20000 prot-na_18800.pdb 56380.02 2026-07-24 23:01:33 18900/20000 prot-na_18900.pdb 395026.16 2026-07-24 23:02:15 19000/20000 prot-na_19000.pdb 70000.00 2026-07-24 23:02:56 19100/20000 prot-na_19100.pdb 90000.00 2026-07-24 23:03:37 19200/20000 prot-na_19200.pdb 161532.04 2026-07-24 23:04:19 19300/20000 prot-na_19300.pdb 180000.00 2026-07-24 23:05:00 19400/20000 prot-na_19400.pdb 109766.67 2026-07-24 23:05:41 19500/20000 prot-na_19500.pdb 68391.69 2026-07-24 23:06:22 19600/20000 prot-na_19600.pdb 171238.60 2026-07-24 23:07:03 19700/20000 prot-na_19700.pdb 120000.00 2026-07-24 23:07:44 19800/20000 prot-na_19800.pdb 52316.38 2026-07-24 23:08:26 19900/20000 prot-na_19900.pdb 12359.31 2026-07-24 23:09:07 20000/20000 prot-na_20000.pdb 145619.30 2026-07-24 23:09:07 DARS scoring end 2026-07-24 23:09:07 Clustering (cuttoff: 5, nr_clust: 100 ) in progress... 2026-07-24 23:09:07 time python /home/rpdock/run_gramm//clustering_v4.py dars_out.txt list.txt 5 100 2026-07-24 23:09:07 100 best scored structures 2026-07-24 23:09:07 1 prot-na_7208.pdb -117317.97 2026-07-24 23:09:07 2 prot-na_8425.pdb -89222.49 2026-07-24 23:09:07 3 prot-na_16969.pdb -71223.21 2026-07-24 23:09:07 4 prot-na_15699.pdb -68065.84 2026-07-24 23:09:07 5 prot-na_18521.pdb -66210.25 2026-07-24 23:09:07 6 prot-na_7921.pdb -65927.26 2026-07-24 23:09:07 7 prot-na_10438.pdb -63293.51 2026-07-24 23:09:07 8 prot-na_7576.pdb -62050.24 2026-07-24 23:09:07 9 prot-na_10223.pdb -60085.32 2026-07-24 23:09:07 10 prot-na_17523.pdb -57269.82 2026-07-24 23:09:07 11 prot-na_10187.pdb -54279.5 2026-07-24 23:09:07 12 prot-na_15269.pdb -51688.42 2026-07-24 23:09:07 13 prot-na_6275.pdb -51677.78 2026-07-24 23:09:07 14 prot-na_4461.pdb -51505.87 2026-07-24 23:09:07 15 prot-na_8920.pdb -51279.31 2026-07-24 23:09:07 16 prot-na_4811.pdb -51193.46 2026-07-24 23:09:07 17 prot-na_16959.pdb -51167.54 2026-07-24 23:09:07 18 prot-na_18492.pdb -51166.31 2026-07-24 23:09:07 19 prot-na_13252.pdb -50945.81 2026-07-24 23:09:07 20 prot-na_651.pdb -50918.73 2026-07-24 23:09:07 21 prot-na_5576.pdb -50571.93 2026-07-24 23:09:07 22 prot-na_10600.pdb -49401.69 2026-07-24 23:09:07 23 prot-na_13112.pdb -48843.56 2026-07-24 23:09:07 24 prot-na_8946.pdb -48190.65 2026-07-24 23:09:07 25 prot-na_4787.pdb -47142.22 2026-07-24 23:09:07 26 prot-na_8933.pdb -46671.36 2026-07-24 23:09:07 27 prot-na_4459.pdb -45517.09 2026-07-24 23:09:07 28 prot-na_17995.pdb -45506.94 2026-07-24 23:09:07 29 prot-na_6677.pdb -44947.38 2026-07-24 23:09:07 30 prot-na_13495.pdb -44664.48 2026-07-24 23:09:07 31 prot-na_7893.pdb -44638.47 2026-07-24 23:09:07 32 prot-na_19758.pdb -44199.05 2026-07-24 23:09:07 33 prot-na_7346.pdb -43575.38 2026-07-24 23:09:07 34 prot-na_13862.pdb -43269.8 2026-07-24 23:09:07 35 prot-na_4440.pdb -42185.57 2026-07-24 23:09:07 36 prot-na_16909.pdb -42048.35 2026-07-24 23:09:07 37 prot-na_11067.pdb -42012.97 2026-07-24 23:09:07 38 prot-na_18254.pdb -41101.86 2026-07-24 23:09:07 39 prot-na_4780.pdb -40727.61 2026-07-24 23:09:07 40 prot-na_13618.pdb -40204.39 2026-07-24 23:09:07 41 prot-na_3017.pdb -39084.25 2026-07-24 23:09:07 42 prot-na_13284.pdb -38915.49 2026-07-24 23:09:07 43 prot-na_5389.pdb -38510.15 2026-07-24 23:09:07 44 prot-na_3657.pdb -38259.55 2026-07-24 23:09:07 45 prot-na_4463.pdb -37908.49 2026-07-24 23:09:07 46 prot-na_16621.pdb -37690.43 2026-07-24 23:09:07 47 prot-na_19926.pdb -36917.89 2026-07-24 23:09:07 48 prot-na_19572.pdb -36699.06 2026-07-24 23:09:07 49 prot-na_12830.pdb -36532.63 2026-07-24 23:09:07 50 prot-na_14667.pdb -35926.63 2026-07-24 23:09:07 51 prot-na_19023.pdb -35352.16 2026-07-24 23:09:07 52 prot-na_15381.pdb -35234.45 2026-07-24 23:09:07 53 prot-na_4260.pdb -34869.28 2026-07-24 23:09:07 54 prot-na_2087.pdb -34277.71 2026-07-24 23:09:07 55 prot-na_14346.pdb -34265.76 2026-07-24 23:09:07 56 prot-na_4176.pdb -33247.3 2026-07-24 23:09:07 57 prot-na_11948.pdb -33229.56 2026-07-24 23:09:07 58 prot-na_3397.pdb -32880.21 2026-07-24 23:09:07 59 prot-na_8504.pdb -32632.56 2026-07-24 23:09:07 60 prot-na_10214.pdb -32521.95 2026-07-24 23:09:07 61 prot-na_18852.pdb -32463.09 2026-07-24 23:09:07 62 prot-na_8995.pdb -32253.85 2026-07-24 23:09:07 63 prot-na_1302.pdb -32124.56 2026-07-24 23:09:07 64 prot-na_10943.pdb -31637.26 2026-07-24 23:09:07 65 prot-na_16821.pdb -30451.57 2026-07-24 23:09:07 66 prot-na_1535.pdb -30351.37 2026-07-24 23:09:07 67 prot-na_18079.pdb -30300.52 2026-07-24 23:09:07 68 prot-na_7452.pdb -30100.66 2026-07-24 23:09:07 69 prot-na_15586.pdb -29993.77 2026-07-24 23:09:07 70 prot-na_12073.pdb -29922.02 2026-07-24 23:09:07 71 prot-na_5106.pdb -29861.18 2026-07-24 23:09:07 72 prot-na_17411.pdb -29616.45 2026-07-24 23:09:07 73 prot-na_18093.pdb -29593.37 2026-07-24 23:09:07 74 prot-na_12564.pdb -29421.1 2026-07-24 23:09:07 75 prot-na_5202.pdb -29207.27 2026-07-24 23:09:07 76 prot-na_13362.pdb -29136.25 2026-07-24 23:09:07 77 prot-na_16296.pdb -28989.49 2026-07-24 23:09:07 78 prot-na_6487.pdb -28468.58 2026-07-24 23:09:07 79 prot-na_5814.pdb -28185.49 2026-07-24 23:09:07 80 prot-na_16116.pdb -27969.97 2026-07-24 23:09:07 81 prot-na_18318.pdb -27892.86 2026-07-24 23:09:07 82 prot-na_18407.pdb -27886.54 2026-07-24 23:09:07 83 prot-na_17545.pdb -27810.14 2026-07-24 23:09:07 84 prot-na_18497.pdb -27703.94 2026-07-24 23:09:07 85 prot-na_13570.pdb -27626.5 2026-07-24 23:09:07 86 prot-na_8852.pdb -27430.64 2026-07-24 23:09:07 87 prot-na_13037.pdb -27402.7 2026-07-24 23:09:07 88 prot-na_14626.pdb -27293.41 2026-07-24 23:09:07 89 prot-na_7162.pdb -27107.84 2026-07-24 23:09:07 90 prot-na_16308.pdb -27106.72 2026-07-24 23:09:07 91 prot-na_6490.pdb -27044.57 2026-07-24 23:09:07 92 prot-na_16488.pdb -26984.6 2026-07-24 23:09:07 93 prot-na_1092.pdb -26369.87 2026-07-24 23:09:07 94 prot-na_10770.pdb -25902.59 2026-07-24 23:09:07 95 prot-na_11548.pdb -25741.61 2026-07-24 23:09:07 96 prot-na_6158.pdb -25419.7 2026-07-24 23:09:07 97 prot-na_4538.pdb -25311.96 2026-07-24 23:09:07 98 prot-na_16361.pdb -25286.64 2026-07-24 23:09:07 99 prot-na_9533.pdb -25285.03 2026-07-24 23:09:07 100 prot-na_19931.pdb -25228.29 2026-07-24 23:09:07 Chains: I 2026-07-24 23:09:25 100 best scored structures 2026-07-24 23:09:25 GRAMM analysis selected for further analysis: prot-na_10 2026-07-24 23:09:25 Cluster #1 with 6 structures 2026-07-24 23:09:25 1 prot-na_8425.pdb -89222.49 2026-07-24 23:09:25 2 prot-na_16969.pdb -71223.21 2026-07-24 23:09:25 3 prot-na_18521.pdb -66210.25 2026-07-24 23:09:25 4 prot-na_10438.pdb -63293.51 2026-07-24 23:09:25 5 prot-na_14667.pdb -35926.63 2026-07-24 23:09:25 6 prot-na_13362.pdb -29136.25 2026-07-24 23:09:25 Cluster #2 with 5 structures 2026-07-24 23:09:25 1 prot-na_7576.pdb -62050.24 2026-07-24 23:09:25 2 prot-na_8920.pdb -51279.31 2026-07-24 23:09:25 3 prot-na_4440.pdb -42185.57 2026-07-24 23:09:25 4 prot-na_8504.pdb -32632.56 2026-07-24 23:09:25 5 prot-na_16308.pdb -27106.72 2026-07-24 23:09:25 Sent to refinement: clusters_found|prot-na_8425.pdb|prot-na_7576.pdb 2026-07-24 23:09:25 Sent to refinement: clusters_found|prot-na_8425.pdb|prot-na_7576.pdb 2026-07-24 23:09:25 DARS clustering end 2026-07-24 23:09:25 MC (refinement) init 2026-07-24 23:09:25 python /home/rpdock/run_gramm//run_mc.py -f dars_to_mc.txt -d /home/rpdock/web/media/jobs/7b0a82ff-9a6b-468f-ac08-72c9319fcf62/ 2026-07-24 23:09:25 Refinement of #1 /home/rpdock/web/media/jobs/7b0a82ff-9a6b-468f-ac08-72c9319fcf62/prot-na_8425.pdb 2026-07-24 23:09:25 python /home/rpdock/mc/MC.py -s 1000 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/7b0a82ff-9a6b-468f-ac08-72c9319fcf62//ref_struc/prot-na_8425/prot-na_8425.pdb 2026-07-24 23:11:07 run_mc::stderr:Traceback (most recent call last): File "/home/rpdock/mc/MC.py", line 709, in s, datas = write_all_atoms (datas, step_real, cal.split()[0], plik, pars, historyT, historyR, rna) File "/home/rpdock/mc/MC.py", line 360, in write_all_atoms all_at_ch_rna, all_at_ch_prot = all_atom (plik, pars, transl, rotation, rna) File "/home/rpdock/mc/MC.py", line 297, in all_atom pro_ch, rna_ch = check_chains(plik, pars) File "/home/rpdock/mc/MC.py", line 106, in check_chains struc = pars.get_structure('native', plik) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py", line 83, in get_structure self._parse(handle.readlines()) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py", line 109, in _parse self.trailer = self._parse_coordinates(coords_trailer) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py", line 225, in _parse_coordinates fullname, serial_number, element) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/StructureBuilder.py", line 197, in init_atom fullname, serial_number, element) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/Atom.py", line 58, in __init__ self.bfactor=bfactor MemoryError 2026-07-24 23:11:07 Refinement of #2 /home/rpdock/web/media/jobs/7b0a82ff-9a6b-468f-ac08-72c9319fcf62/prot-na_7576.pdb 2026-07-24 23:11:07 python /home/rpdock/mc/MC.py -s 1000 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/7b0a82ff-9a6b-468f-ac08-72c9319fcf62//ref_struc/prot-na_7576/prot-na_7576.pdb 2026-07-24 23:12:52 run_mc::stderr:Traceback (most recent call last): File "/home/rpdock/mc/MC.py", line 628, in s, datas = write_all_atoms (datas, step_real, cal.split()[0], plik, pars, historyT, historyR,rna) File "/home/rpdock/mc/MC.py", line 360, in write_all_atoms all_at_ch_rna, all_at_ch_prot = all_atom (plik, pars, transl, rotation, rna) File "/home/rpdock/mc/MC.py", line 297, in all_atom pro_ch, rna_ch = check_chains(plik, pars) File "/home/rpdock/mc/MC.py", line 106, in check_chains struc = pars.get_structure('native', plik) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py", line 83, in get_structure self._parse(handle.readlines()) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py", line 109, in _parse self.trailer = self._parse_coordinates(coords_trailer) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py", line 225, in _parse_coordinates fullname, serial_number, element) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/StructureBuilder.py", line 197, in init_atom fullname, serial_number, element) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/Atom.py", line 51, in __init__ self.level="A" MemoryError 2026-07-24 23:12:52 start - parameters: File name /home/rpdock/web/media/jobs/7b0a82ff-9a6b-468f-ac08-72c9319fcf62//ref_struc/prot-na_8425/prot-na_8425.pdb Steps 1000 Temp. start 15000.0 Temp. end 295.0 False msg start - parameters: File name /home/rpdock/web/media/jobs/7b0a82ff-9a6b-468f-ac08-72c9319fcf62//ref_struc/prot-na_8425/prot-na_8425.pdb Steps 1000 Temp. start 15000.0 Temp. end 295.0 False Step E Edist Eang Epen Missed atom CG in the GLU 13 Missed atom CD in the GLU 13 Missed atom OE1 in the GLU 13 Missed atom OE2 in the GLU 13 Missed atom CG in the LYS 108 Missed atom CD in the LYS 108 Missed atom CE in the LYS 108 Missed atom NZ in the LYS 108 Missed atom CG in the ASP 109 Missed atom OD1 in the ASP 109 Missed atom OD2 in the ASP 109 Missed atom CG in the GLU 13 Missed atom CD in the GLU 13 Missed atom OE1 in the GLU 13 Missed atom OE2 in the GLU 13 Missed atom CG in the GLU 13 Missed atom CD in the GLU 13 Missed atom OE1 in the GLU 13 Missed atom OE2 in the GLU 13 Missed atom CG in the GLU 13 Missed atom CD in the GLU 13 Missed atom OE1 in the GLU 13 Missed atom OE2 in the GLU 13 Missed atom CG in the GLU 13 Missed atom CD in the GLU 13 Missed atom OE1 in the GLU 13 Missed atom OE2 in the GLU 13 Missed atom CG in the LYS 108 Missed atom CD in the LYS 108 Missed atom CE in the LYS 108 Missed atom NZ in the LYS 108 Missed atom CG in the GLU 13 Missed atom CD in the GLU 13 Missed atom OE1 in the GLU 13 Missed atom OE2 in the GLU 13 0 - -89222.49 -56786.01 -32436.48 0.00 1 R -81538.87 -56786.01 -24752.86 0.00 T= 15000.0 K progress 0.1 2 R -85775.78 -53339.30 -32436.48 0.00 T= 14970.59 K progress 0.2 3 T -86873.57 -46861.21 -40012.36 0.00 T= 14955.885 K progress 0.3 4 R 19478.88 -54964.88 -25556.24 100000.00 T= 14941.18 K progress 0.4 5 T 131928.52 -59437.70 -8633.79 200000.00 T= 14911.77 K progress 0.5 6 R 18017.29 -57229.85 -24752.86 100000.00 T= 14897.065 K progress 0.6 7 R -79632.41 -47195.93 -32436.48 0.00 T= 14867.655 K progress 0.7 8 R 10926.80 -56636.71 -32436.48 100000.00 T= 14852.95 K progress 0.8 9 T -92352.93 -59916.45 -32436.48 0.00 T= 14838.245 K progress 0.9 10 T 140283.11 -41736.52 -17980.36 200000.00 T= 14794.13 K progress 1.0 11 T 135309.28 -46710.36 -17980.36 200000.00 T= 14779.425 K progress 1.1 12 T 176736.39 -23263.61 0.00 200000.00 T= 14750.015 K progress 1.2 13 T 45794.45 -39749.43 -14456.12 100000.00 T= 14735.31 K progress 1.3 14 R -59479.68 -45023.57 -14456.12 0.00 T= 14720.605 K progress 1.4 15 T -50394.55 -35938.43 -14456.12 0.00 T= 14691.195 K progress 1.5 16 R -43265.06 -27667.18 -15597.89 0.00 T= 14676.49 K progress 1.6 17 R -43518.46 -27920.57 -15597.89 0.00 T= 14661.785 K progress 1.7 18 R -38670.48 -23072.59 -15597.89 0.00 T= 14647.08 K progress 1.8 19 R -38670.48 -23072.59 -15597.89 0.00 T= 14632.375 K progress 1.9 20 T -47916.33 -32318.45 -15597.89 0.00 T= 14617.67 K progress 2.0 21 R 79912.53 -20087.47 0.00 100000.00 T= 14602.965 K progress 2.1 22 R 84167.37 -15832.63 0.00 100000.00 T= 14573.555 K progress 2.2 23 R 84167.37 -15832.63 0.00 100000.00 T= 14514.735 K progress 2.3 24 R 84167.37 -15832.63 0.00 100000.00 T= 14500.03 K progress 2.4 25 R 74050.04 -18266.34 -7683.62 100000.00 T= 14485.325 K progress 2.5 26 R -54775.25 -40319.13 -14456.12 0.00 T= 14455.915 K progress 2.6 27 R -49501.11 -35044.99 -14456.12 0.00 T= 14441.21 K progress 2.7 28 T -64881.94 -41079.24 -23802.70 0.00 T= 14426.505 K progress 2.8 29 T -78894.60 -55091.90 -23802.70 0.00 T= 14279.455 K progress 2.9 30 T -56108.03 -40510.15 -15597.89 0.00 T= 14264.75 K progress 3.0 31 T 17319.59 -50243.92 -32436.48 100000.00 T= 14220.635 K progress 3.1 32 T 108828.75 -58734.77 -32436.48 200000.00 T= 14191.225 K progress 3.2 33 T 15203.86 -52359.66 -32436.48 100000.00 T= 14176.52 K progress 3.3 34 R 35747.20 -31816.32 -32436.48 100000.00 T= 14147.11 K progress 3.4 35 R 40713.08 -36197.02 -23089.90 100000.00 T= 14117.7 K progress 3.5 36 R 52147.74 -32445.98 -15406.29 100000.00 T= 14102.995 K progress 3.6 37 R 51276.53 -32175.41 -16548.05 100000.00 T= 14088.29 K progress 3.7 38 R 52211.08 -31240.86 -16548.05 100000.00 T= 14073.585 K progress 3.8 39 R 39893.88 -35874.45 -24231.67 100000.00 T= 14044.175 K progress 3.9 40 R -48256.19 -31708.14 -16548.05 0.00 T= 14029.47 K progress 4.0 41 R -55811.83 -40405.55 -15406.29 0.00 T= 14014.765 K progress 4.1 42 T -46156.99 -30750.71 -15406.29 0.00 T= 14000.06 K progress 4.2 43 R 47363.11 -36088.84 -16548.05 100000.00 T= 13985.355 K progress 4.3 44 T -43409.97 -35495.71 -7914.27 0.00 T= 13970.65 K progress 4.4 45 R -36186.18 -20849.35 -15336.83 0.00 T= 13955.945 K progress 4.5 46 R -36186.18 -20849.35 -15336.83 0.00 T= 13941.24 K progress 4.6 47 R -43409.97 -35495.71 -7914.27 0.00 T= 13926.535 K progress 4.7 48 R -28763.62 -20849.35 -7914.27 0.00 T= 13911.83 K progress 4.8 49 R -41612.28 -33698.01 -7914.27 0.00 T= 13897.125 K progress 4.9 50 R -28763.62 -20849.35 -7914.27 0.00 T= 13882.42 K progress 5.0 51 T -38583.67 -22035.62 -16548.05 0.00 T= 13823.6 K progress 5.1 52 R -44168.93 -27620.88 -16548.05 0.00 T= 13808.895 K progress 5.2 53 T -35535.15 -27620.88 -7914.27 0.00 T= 13779.485 K progress 5.3 54 T -39178.56 -31264.30 -7914.27 0.00 T= 13764.78 K progress 5.4 55 T -38585.43 -30671.16 -7914.27 0.00 T= 13750.075 K progress 5.5 56 T -31621.72 -23707.45 -7914.27 0.00 T= 13705.96 K progress 5.6 57 T -26007.33 -18093.06 -7914.27 0.00 T= 13691.255 K progress 5.7 58 T -42879.72 -34965.45 -7914.27 0.00 T= 13676.55 K progress 5.8 59 T -43640.43 -35726.17 -7914.27 0.00 T= 13661.845 K progress 5.9 60 R -37271.02 -29356.75 -7914.27 0.00 T= 13647.14 K progress 6.0 61 T -25736.77 -25736.77 0.00 0.00 T= 13632.435 K progress 6.1 62 R 174597.28 -25402.72 0.00 200000.00 T= 13603.025 K progress 6.2 63 R 180482.23 -19517.77 0.00 200000.00 T= 13588.32 K progress 6.3 64 T 185330.21 -14669.79 0.00 200000.00 T= 13573.615 K progress 6.4 65 T 79009.78 -13567.66 -7422.56 100000.00 T= 13558.91 K progress 6.5 66 T -34196.31 -26773.74 -7422.56 0.00 T= 13529.5 K progress 6.6 67 R -34196.31 -26773.74 -7422.56 0.00 T= 13514.795 K progress 6.7 68 T 70460.65 -22116.78 -7422.56 100000.00 T= 13485.385 K progress 6.8 69 T 62506.28 -30071.16 -7422.56 100000.00 T= 13455.975 K progress 6.9 70 T 79602.91 -12974.52 -7422.56 100000.00 T= 13441.27 K progress 7.0 71 T 179602.91 -12974.52 -7422.56 200000.00 T= 13397.155 K progress 7.1 72 T 68512.56 -24064.88 -7422.56 100000.00 T= 13382.45 K progress 7.2 73 T 183816.03 -8761.40 -7422.56 200000.00 T= 13367.745 K progress 7.3 74 R 70016.81 -22560.63 -7422.56 100000.00 T= 13353.04 K progress 7.4 75 R 70016.81 -22560.63 -7422.56 100000.00 T= 13338.335 K progress 7.5 76 T 172044.58 -27955.42 0.00 200000.00 T= 13308.925 K progress 7.6 77 T 189734.34 -10265.66 0.00 200000.00 T= 13294.22 K progress 7.7 78 T 291238.60 -8761.40 0.00 300000.00 T= 13279.515 K progress 7.8 79 R 285353.64 -14646.36 0.00 300000.00 T= 13264.81 K progress 7.9 80 R 191238.60 -8761.40 0.00 200000.00 T= 13250.105 K progress 8.0 81 R 285353.64 -14646.36 0.00 300000.00 T= 13235.4 K progress 8.1 82 R 191238.60 -8761.40 0.00 200000.00 T= 13220.695 K progress 8.2 83 R 179704.34 -12381.39 -7914.27 200000.00 T= 13191.285 K progress 8.3 84 T 79111.21 -12974.52 -7914.27 100000.00 T= 13176.58 K progress 8.4 85 R 79111.21 -12974.52 -7914.27 100000.00 T= 13147.17 K progress 8.5 86 R 75491.23 -16594.50 -7914.27 100000.00 T= 13132.465 K progress 8.6 87 R 79111.21 -12974.52 -7914.27 100000.00 T= 13117.76 K progress 8.7 88 T 62014.58 -30071.16 -7914.27 100000.00 T= 13103.055 K progress 8.8 89 T 59893.15 -32192.59 -7914.27 100000.00 T= 13088.35 K progress 8.9 90 R 59893.15 -32192.59 -7914.27 100000.00 T= 13073.645 K progress 9.0 91 T 452470.58 -32192.59 -15336.83 500000.00 T= 13058.94 K progress 9.1 92 R 453698.58 -30964.59 -15336.83 500000.00 T= 13044.235 K progress 9.2 93 T 269438.69 -22647.04 -7914.27 300000.00 T= 13029.53 K progress 9.3 94 R 266396.83 -18266.34 -15336.83 300000.00 T= 13014.825 K progress 9.4 95 T 173819.39 -18266.34 -7914.27 200000.00 T= 13000.12 K progress 9.5 96 R 173819.39 -18266.34 -7914.27 200000.00 T= 12985.415 K progress 9.6 97 T 73226.26 -18859.48 -7914.27 100000.00 T= 12970.71 K progress 9.7 98 R 84760.51 -15239.49 0.00 100000.00 T= 12956.005 K progress 9.8 99 R 79704.34 -12381.39 -7914.27 100000.00 T= 12941.3 K progress 9.9 100 T 79704.34 -12381.39 -7914.27 100000.00 T= 12911.89 K progress 10.0 101 T 73819.39 -18266.34 -7914.27 100000.00 T= 12882.48 K progress 10.1 102 R -43594.12 -35679.85 -7914.27 0.00 T= 12867.775 K progress 10.2 Traceback (most recent call last): File "/home/rpdock/mc/MC.py", line 671, in s, datas = write_all_atoms (datas, step_real, cal.split()[0], plik, pars, historyT, historyR, rna) File "/home/rpdock/mc/MC.py", line 360, in write_all_atoms all_at_ch_rna, all_at_ch_prot = all_atom (plik, pars, transl, rotation, rna) File "/home/rpdock/mc/MC.py", line 297, in all_atom pro_ch, rna_ch = check_chains(plik, pars) File "/home/rpdock/mc/MC.py", line 106, in check_chains struc = pars.get_structure('native', plik) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py", line 83, in get_structure self._parse(handle.readlines()) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py", line 109, in _parse self.trailer = self._parse_coordinates(coords_trailer) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py", line 219, in _parse_coordinates structure_builder.init_residue(resname, hetero_flag, resseq, icode) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/StructureBuilder.py", line 156, in init_residue residue=Residue(res_id, resname, self.segid) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/Residue.py", line 30, in __init__ Entity.__init__(self, id) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/Entity.py", line 23, in __init__ self.full_id=None MemoryError Error in run_mc Traceback (most recent call last): File "/home/rpdock/mc/MC.py", line 709, in s, datas = write_all_atoms (datas, step_real, cal.split()[0], plik, pars, historyT, historyR, rna) File "/home/rpdock/mc/MC.py", line 360, in write_all_atoms all_at_ch_rna, all_at_ch_prot = all_atom (plik, pars, transl, rotation, rna) File "/home/rpdock/mc/MC.py", line 297, in all_atom pro_ch, rna_ch = check_chains(plik, pars) File "/home/rpdock/mc/MC.py", line 106, in check_chains struc = pars.get_structure('native', plik) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py", line 83, in get_structure self._parse(handle.readlines()) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py", line 109, in _parse self.trailer = self._parse_coordinates(coords_trailer) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py", line 225, in _parse_coordinates fullname, serial_number, element) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/StructureBuilder.py", line 197, in init_atom fullname, serial_number, element) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/Atom.py", line 58, in __init__ self.bfactor=bfactor MemoryError start - parameters: File name /home/rpdock/web/media/jobs/7b0a82ff-9a6b-468f-ac08-72c9319fcf62//ref_struc/prot-na_7576/prot-na_7576.pdb Steps 1000 Temp. start 15000.0 Temp. end 295.0 False msg start - parameters: File name /home/rpdock/web/media/jobs/7b0a82ff-9a6b-468f-ac08-72c9319fcf62//ref_struc/prot-na_7576/prot-na_7576.pdb Steps 1000 Temp. start 15000.0 Temp. end 295.0 False Step E Edist Eang Epen Missed atom CG in the GLU 13 Missed atom CD in the GLU 13 Missed atom OE1 in the GLU 13 Missed atom OE2 in the GLU 13 Missed atom CG in the LYS 108 Missed atom CD in the LYS 108 Missed atom CE in the LYS 108 Missed atom NZ in the LYS 108 Missed atom CG in the ASP 109 Missed atom OD1 in the ASP 109 Missed atom OD2 in the ASP 109 Missed atom CG in the GLU 13 Missed atom CD in the GLU 13 Missed atom OE1 in the GLU 13 Missed atom OE2 in the GLU 13 Missed atom CG in the GLU 13 Missed atom CD in the GLU 13 Missed atom OE1 in the GLU 13 Missed atom OE2 in the GLU 13 Missed atom CG in the GLU 13 Missed atom CD in the GLU 13 Missed atom OE1 in the GLU 13 Missed atom OE2 in the GLU 13 Missed atom CG in the GLU 13 Missed atom CD in the GLU 13 Missed atom OE1 in the GLU 13 Missed atom OE2 in the GLU 13 Missed atom CG in the LYS 108 Missed atom CD in the LYS 108 Missed atom CE in the LYS 108 Missed atom NZ in the LYS 108 Missed atom CG in the GLU 13 Missed atom CD in the GLU 13 Missed atom OE1 in the GLU 13 Missed atom OE2 in the GLU 13 0 - -62050.24 -25823.18 -36227.05 0.00 1 T 27683.22 -34717.30 -37599.47 100000.00 T= 15000.0 K progress 0.1 2 T -57837.12 -21610.07 -36227.05 0.00 T= 14985.295 K progress 0.2 3 T -59416.42 -30504.19 -28912.23 0.00 T= 14970.59 K progress 0.3 4 T -76235.99 -32325.32 -43910.67 0.00 T= 14926.475 K progress 0.4 5 R -76235.99 -32325.32 -43910.67 0.00 T= 14911.77 K progress 0.5 6 R -53743.77 -23689.77 -30054.00 0.00 T= 14897.065 K progress 0.6 7 R -63204.73 -26716.62 -36488.11 0.00 T= 14882.36 K progress 0.7 8 R -50440.86 -28070.47 -22370.39 0.00 T= 14867.655 K progress 0.8 9 R -35344.91 -12974.52 -22370.39 0.00 T= 14852.95 K progress 0.9 10 R -36572.90 -14202.52 -22370.39 0.00 T= 14838.245 K progress 1.0 11 R -41546.74 -19176.35 -22370.39 0.00 T= 14808.835 K progress 1.1 12 T -53636.03 -23689.77 -29946.26 0.00 T= 14794.13 K progress 1.2 13 R -69059.28 -31690.46 -37368.82 0.00 T= 14779.425 K progress 1.3 14 T -60129.55 -30336.60 -29792.95 0.00 T= 14764.72 K progress 1.4 15 R 43404.20 -27944.61 -28651.18 100000.00 T= 14750.015 K progress 1.5 16 R 47871.13 -22335.92 -29792.95 100000.00 T= 14735.31 K progress 1.6 17 R 47871.13 -22335.92 -29792.95 100000.00 T= 14720.605 K progress 1.7 18 T 43598.68 -31564.60 -24836.72 100000.00 T= 14705.9 K progress 1.8 19 T 44227.00 -32428.30 -23344.70 100000.00 T= 14691.195 K progress 1.9 20 R 40775.53 -36683.14 -22541.33 100000.00 T= 14676.49 K progress 2.0 21 R 31260.44 -36048.28 -32691.28 100000.00 T= 14647.08 K progress 2.1 22 R 40775.53 -36683.14 -22541.33 100000.00 T= 14632.375 K progress 2.2 23 R 37155.55 -40303.12 -22541.33 100000.00 T= 14617.67 K progress 2.3 24 T 41368.67 -36090.00 -22541.33 100000.00 T= 14602.965 K progress 2.4 25 R 31768.19 -39409.69 -28822.13 100000.00 T= 14588.26 K progress 2.5 26 R 36394.83 -41063.84 -22541.33 100000.00 T= 14573.555 K progress 2.6 27 R 61750.55 -22480.62 -15768.83 100000.00 T= 14558.85 K progress 2.7 28 R 52403.46 -17632.64 -29963.89 100000.00 T= 14544.145 K progress 2.8 29 T -62696.37 -40325.99 -22370.39 0.00 T= 14529.44 K progress 2.9 30 R 42847.42 -35120.58 -22031.99 100000.00 T= 14514.735 K progress 3.0 31 R 57454.76 -21316.62 -21228.62 100000.00 T= 14500.03 K progress 3.1 32 R -48739.81 -20088.63 -28651.18 0.00 T= 14485.325 K progress 3.2 33 R 43980.59 -26226.46 -29792.95 100000.00 T= 14455.915 K progress 3.3 34 R 43980.59 -26226.46 -29792.95 100000.00 T= 14441.21 K progress 3.4 35 T 64901.84 -27183.89 -7914.27 100000.00 T= 14426.505 K progress 3.5 36 R 57325.96 -27183.89 -15490.14 100000.00 T= 14411.8 K progress 3.6 37 R 57325.96 -27183.89 -15490.14 100000.00 T= 14397.095 K progress 3.7 38 R 64545.24 -21909.76 -13545.00 100000.00 T= 14382.39 K progress 3.8 39 R 53662.41 -32792.59 -13545.00 100000.00 T= 14367.685 K progress 3.9 40 T 51087.82 -27944.61 -20967.56 100000.00 T= 14352.98 K progress 4.0 41 T -46380.25 -32031.87 -14348.37 0.00 T= 14338.275 K progress 4.1 42 R -60107.53 -36412.57 -23694.95 0.00 T= 14323.57 K progress 4.2 43 R -60107.53 -36412.57 -23694.95 0.00 T= 14308.865 K progress 4.3 44 T -38160.62 -22670.48 -15490.14 0.00 T= 14294.16 K progress 4.4 45 R -33186.78 -17696.64 -15490.14 0.00 T= 14264.75 K progress 4.5 46 R -31052.02 -23137.75 -7914.27 0.00 T= 14250.045 K progress 4.6 47 R -42674.04 -27183.89 -15490.14 0.00 T= 14235.34 K progress 4.7 48 T -46294.02 -30803.88 -15490.14 0.00 T= 14205.93 K progress 4.8 49 R -44683.44 -31138.44 -13545.00 0.00 T= 14191.225 K progress 4.9 50 R -46294.02 -30803.88 -15490.14 0.00 T= 14161.815 K progress 5.0 51 T -57629.31 -32792.59 -24836.72 0.00 T= 14147.11 K progress 5.1 52 R -56994.45 -32157.73 -24836.72 0.00 T= 14132.405 K progress 5.2 53 R -56994.45 -32157.73 -24836.72 0.00 T= 14117.7 K progress 5.3 54 R -43426.80 -18590.07 -24836.72 0.00 T= 14102.995 K progress 5.4 55 R -67144.27 -40596.55 -26547.72 0.00 T= 14088.29 K progress 5.5 56 T -29907.35 -14138.52 -15768.83 0.00 T= 14044.175 K progress 5.6 57 T -20669.20 -12754.93 -7914.27 0.00 T= 14029.47 K progress 5.7 58 T -44705.07 -21252.63 -23452.45 0.00 T= 14014.765 K progress 5.8 59 T -53656.32 -30203.87 -23452.45 0.00 T= 14000.06 K progress 5.9 60 T 47122.58 -37339.24 -15538.18 100000.00 T= 13941.24 K progress 6.0 61 T -51661.91 -28209.47 -23452.45 0.00 T= 13926.535 K progress 6.1 62 T -68705.96 -45253.51 -23452.45 0.00 T= 13911.83 K progress 6.2 63 R 141799.09 -25569.34 -32631.57 200000.00 T= 13853.01 K progress 6.3 64 T 118823.28 -30843.47 -50333.25 200000.00 T= 13838.305 K progress 6.4 65 R 118823.28 -30843.47 -50333.25 200000.00 T= 13808.895 K progress 6.5 66 R 151145.67 -25569.34 -23285.00 200000.00 T= 13794.19 K progress 6.6 67 R 132731.20 -25569.34 -41699.47 200000.00 T= 13779.485 K progress 6.7 68 R 118823.28 -30843.47 -50333.25 200000.00 T= 13764.78 K progress 6.8 69 R -45463.36 -30203.87 -15259.49 0.00 T= 13735.37 K progress 6.9 70 R -59262.58 -36088.83 -23173.76 0.00 T= 13705.96 K progress 7.0 71 R -68609.16 -36088.83 -32520.34 0.00 T= 13691.255 K progress 7.1 72 R -45463.36 -30203.87 -15259.49 0.00 T= 13676.55 K progress 7.2 73 R 68105.21 -24318.92 -7575.87 100000.00 T= 13661.845 K progress 7.3 74 T -33304.68 -16382.23 -16922.45 0.00 T= 13647.14 K progress 7.4 75 T 70653.70 -4847.98 -24498.33 100000.00 T= 13603.025 K progress 7.5 76 T 81691.20 -10732.93 -7575.87 100000.00 T= 13588.32 K progress 7.6 77 T 56417.43 -20237.87 -23344.70 100000.00 T= 13573.615 K progress 7.7 78 R 64904.42 -19326.75 -15768.83 100000.00 T= 13544.205 K progress 7.8 79 R 78071.21 -14352.91 -7575.87 100000.00 T= 13514.795 K progress 7.9 80 T 88804.14 -3619.98 -7575.87 100000.00 T= 13500.09 K progress 8.0 81 R 75004.92 -9504.94 -15490.14 100000.00 T= 13485.385 K progress 8.1 82 R 82919.19 -9504.94 -7575.87 100000.00 T= 13470.68 K progress 8.2 83 R 63530.38 -13124.92 -23344.70 100000.00 T= 13455.975 K progress 8.3 84 R 63530.38 -13124.92 -23344.70 100000.00 T= 13426.565 K progress 8.4 85 R 63530.38 -13124.92 -23344.70 100000.00 T= 13411.86 K progress 8.5 86 R 63530.38 -13124.92 -23344.70 100000.00 T= 13382.45 K progress 8.6 87 T 64904.42 -19326.75 -15768.83 100000.00 T= 13353.04 K progress 8.7 88 R 70154.51 -14076.66 -15768.83 100000.00 T= 13338.335 K progress 8.8 89 T 75002.49 -9228.68 -15768.83 100000.00 T= 13323.63 K progress 8.9 90 T 76144.26 -9228.68 -14627.06 100000.00 T= 13308.925 K progress 9.0 91 T 69752.40 -14478.77 -15768.83 100000.00 T= 13294.22 K progress 9.1 92 R 74726.23 -9504.94 -15768.83 100000.00 T= 13279.515 K progress 9.2 93 T -54332.48 -23304.16 -31028.32 0.00 T= 13264.81 K progress 9.3 94 T -66206.03 -35177.71 -31028.32 0.00 T= 13250.105 K progress 9.4 95 T -65064.26 -35177.71 -29886.55 0.00 T= 13220.695 K progress 9.5 96 R -60090.42 -30203.87 -29886.55 0.00 T= 13205.99 K progress 9.6 97 R -68684.24 -38797.69 -29886.55 0.00 T= 13117.76 K progress 9.7 98 T -65334.83 -35448.27 -29886.55 0.00 T= 13103.055 K progress 9.8 99 T 49393.44 -28295.88 -22310.68 100000.00 T= 13044.235 K progress 9.9 100 T 127154.64 -42958.80 -29886.55 200000.00 T= 13029.53 K progress 10.0 101 T 53013.42 -24675.90 -22310.68 100000.00 T= 13014.825 K progress 10.1 102 T 65330.81 -12358.51 -22310.68 100000.00 T= 13000.12 K progress 10.2 Traceback (most recent call last): File "/home/rpdock/mc/MC.py", line 628, in s, datas = write_all_atoms (datas, step_real, cal.split()[0], plik, pars, historyT, historyR,rna) File "/home/rpdock/mc/MC.py", line 360, in write_all_atoms all_at_ch_rna, all_at_ch_prot = all_atom (plik, pars, transl, rotation, rna) File "/home/rpdock/mc/MC.py", line 297, in all_atom pro_ch, rna_ch = check_chains(plik, pars) File "/home/rpdock/mc/MC.py", line 106, in check_chains struc = pars.get_structure('native', plik) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py", line 83, in get_structure self._parse(handle.readlines()) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py", line 109, in _parse self.trailer = self._parse_coordinates(coords_trailer) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py", line 225, in _parse_coordinates fullname, serial_number, element) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/StructureBuilder.py", line 197, in init_atom fullname, serial_number, element) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/Atom.py", line 58, in __init__ self.bfactor=bfactor MemoryError Error in run_mc Traceback (most recent call last): File "/home/rpdock/mc/MC.py", line 628, in s, datas = write_all_atoms (datas, step_real, cal.split()[0], plik, pars, historyT, historyR,rna) File "/home/rpdock/mc/MC.py", line 360, in write_all_atoms all_at_ch_rna, all_at_ch_prot = all_atom (plik, pars, transl, rotation, rna) File "/home/rpdock/mc/MC.py", line 297, in all_atom pro_ch, rna_ch = check_chains(plik, pars) File "/home/rpdock/mc/MC.py", line 106, in check_chains struc = pars.get_structure('native', plik) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py", line 83, in get_structure self._parse(handle.readlines()) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py", line 109, in _parse self.trailer = self._parse_coordinates(coords_trailer) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py", line 225, in _parse_coordinates fullname, serial_number, element) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/StructureBuilder.py", line 197, in init_atom fullname, serial_number, element) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/Atom.py", line 51, in __init__ self.level="A" MemoryError Fri Jul 24 23:09:25 2026 ['prot-na_8425.pdb', 'prot-na_7576.pdb'] msg Refinement of #1 /home/rpdock/web/media/jobs/7b0a82ff-9a6b-468f-ac08-72c9319fcf62/prot-na_8425.pdb dir: /home/rpdock/web/media/jobs/7b0a82ff-9a6b-468f-ac08-72c9319fcf62/ file: prot-na_8425.pdb find `pwd` -iname prot-na_8425.pdb copy /home/rpdock/web/media/jobs/7b0a82ff-9a6b-468f-ac08-72c9319fcf62/prot-na_10/prot-na_8425.pdb to /home/rpdock/web/media/jobs/7b0a82ff-9a6b-468f-ac08-72c9319fcf62//ref_struc/prot-na_8425/prot-na_8425.pdb cmd: python /home/rpdock/mc/MC.py -s 1000 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/7b0a82ff-9a6b-468f-ac08-72c9319fcf62//ref_struc/prot-na_8425/prot-na_8425.pdb msg python /home/rpdock/mc/MC.py -s 1000 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/7b0a82ff-9a6b-468f-ac08-72c9319fcf62//ref_struc/prot-na_8425/prot-na_8425.pdb msg run_mc::stderr:Traceback (most recent call last): File "/home/rpdock/mc/MC.py", line 709, in s, datas = write_all_atoms (datas, step_real, cal.split()[0], plik, pars, historyT, historyR, rna) File "/home/rpdock/mc/MC.py", line 360, in write_all_atoms all_at_ch_rna, all_at_ch_prot = all_atom (plik, pars, transl, rotation, rna) File "/home/rpdock/mc/MC.py", line 297, in all_atom pro_ch, rna_ch = check_chains(plik, pars) File "/home/rpdock/mc/MC.py", line 106, in check_chains struc = pars.get_structure('native', plik) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py", line 83, in get_structure self._parse(handle.readlines()) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py", line 109, in _parse self.trailer = self._parse_coordinates(coords_trailer) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py", line 225, in _parse_coordinates fullname, serial_number, element) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/StructureBuilder.py", line 197, in init_atom fullname, serial_number, element) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/Atom.py", line 58, in __init__ self.bfactor=bfactor MemoryError msg Refinement of #2 /home/rpdock/web/media/jobs/7b0a82ff-9a6b-468f-ac08-72c9319fcf62/prot-na_7576.pdb dir: /home/rpdock/web/media/jobs/7b0a82ff-9a6b-468f-ac08-72c9319fcf62/ file: prot-na_7576.pdb find `pwd` -iname prot-na_7576.pdb copy /home/rpdock/web/media/jobs/7b0a82ff-9a6b-468f-ac08-72c9319fcf62/prot-na_10/prot-na_7576.pdb to /home/rpdock/web/media/jobs/7b0a82ff-9a6b-468f-ac08-72c9319fcf62//ref_struc/prot-na_7576/prot-na_7576.pdb cmd: python /home/rpdock/mc/MC.py -s 1000 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/7b0a82ff-9a6b-468f-ac08-72c9319fcf62//ref_struc/prot-na_7576/prot-na_7576.pdb msg python /home/rpdock/mc/MC.py -s 1000 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/7b0a82ff-9a6b-468f-ac08-72c9319fcf62//ref_struc/prot-na_7576/prot-na_7576.pdb msg run_mc::stderr:Traceback (most recent call last): File "/home/rpdock/mc/MC.py", line 628, in s, datas = write_all_atoms (datas, step_real, cal.split()[0], plik, pars, historyT, historyR,rna) File "/home/rpdock/mc/MC.py", line 360, in write_all_atoms all_at_ch_rna, all_at_ch_prot = all_atom (plik, pars, transl, rotation, rna) File "/home/rpdock/mc/MC.py", line 297, in all_atom pro_ch, rna_ch = check_chains(plik, pars) File "/home/rpdock/mc/MC.py", line 106, in check_chains struc = pars.get_structure('native', plik) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py", line 83, in get_structure self._parse(handle.readlines()) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py", line 109, in _parse self.trailer = self._parse_coordinates(coords_trailer) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py", line 225, in _parse_coordinates fullname, serial_number, element) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/StructureBuilder.py", line 197, in init_atom fullname, serial_number, element) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/Atom.py", line 51, in __init__ self.level="A" MemoryError 2026-07-24 23:12:52 npdock::MC (refinement) end 2026-07-24 23:12:52 npdock::OK 2026-07-24 23:12:52 Set finished status of 7b0a82ff-9a6b-468f-ac08-72c9319fcf62