2026-04-27 16:26:04 NPdock start 2026-04-27 16:26:04 ver: server 2026-04-27 16:26:04 mode: 11111 2026-04-27 16:26:04 is RNA? 0 2026-04-27 16:26:04 Interface: prot: '' na: '' 2026-04-27 16:26:04 Curr dir:/home/rpdock/web/media/jobs/deb82bf2-cc38-4464-8ae9-3ce758cd0b27/ 2026-04-27 16:26:04 GRAMM in progress... 2026-04-27 16:26:04 python /home/rpdock/run_gramm//run_gramm1.py -d 20000 -p prot.pdb -r na.pdb -pi '' -ri '' -n 1 -pf '*' -rf '*' 2026-04-27 17:01:47 GRAMM done 2026-04-27 17:01:47 DNP scoring in progress... 2026-04-27 17:01:48 time python /home/rpdock/run_gramm//DNP/laczony/QUASI-DNP-QDV_potential_1.0.py -m 100 -f list.txt -o dnp_out.txt 2026-04-27 17:01:48 QDV-DNP starts 2026-04-27 17:01:48 Show log every 100 structures 2026-04-27 17:01:48 QUASI-DNP starts 2026-04-27 17:01:48 na-prot_1000.pdb -177250.71397 2026-04-27 17:02:08 na-prot_94.pdb -890520.614962 2026-04-27 17:02:27 na-prot_194.pdb -640442.275451 2026-04-27 17:02:45 na-prot_294.pdb -581190.885545 2026-04-27 17:03:03 na-prot_394.pdb -291147.15054 2026-04-27 17:03:22 na-prot_494.pdb -449866.735882 2026-04-27 17:03:40 na-prot_594.pdb -339906.304382 2026-04-27 17:03:58 na-prot_694.pdb -302098.509256 2026-04-27 17:04:17 na-prot_794.pdb -266288.386964 2026-04-27 17:04:35 na-prot_894.pdb -492121.82194 2026-04-27 17:04:53 na-prot_994.pdb -279001.402942 2026-04-27 17:05:12 na-prot_1100.pdb -198954.180617 2026-04-27 17:05:31 na-prot_1200.pdb -191124.212526 2026-04-27 17:05:49 na-prot_1300.pdb -666916.776029 2026-04-27 17:06:08 na-prot_1400.pdb -301985.225353 2026-04-27 17:06:27 na-prot_1500.pdb -168813.826859 2026-04-27 17:06:46 na-prot_1600.pdb -663016.285203 2026-04-27 17:07:05 na-prot_1700.pdb -515194.023316 2026-04-27 17:07:24 na-prot_1800.pdb -331561.02474 2026-04-27 17:07:43 na-prot_1900.pdb -270828.862418 2026-04-27 17:08:02 na-prot_2000.pdb -222827.753504 2026-04-27 17:08:20 na-prot_2100.pdb -278819.553979 2026-04-27 17:08:39 na-prot_2200.pdb -191143.972283 2026-04-27 17:08:58 na-prot_2300.pdb -767518.285972 2026-04-27 17:09:17 na-prot_2400.pdb -371399.90402 2026-04-27 17:09:36 na-prot_2500.pdb -588782.029407 2026-04-27 17:09:55 na-prot_2600.pdb -190800.624057 2026-04-27 17:10:14 na-prot_2700.pdb -204197.57746 2026-04-27 17:10:33 na-prot_2800.pdb -154077.851466 2026-04-27 17:10:51 na-prot_2900.pdb -433726.931049 2026-04-27 17:11:10 na-prot_3000.pdb -400214.341113 2026-04-27 17:11:29 na-prot_3100.pdb -444163.872495 2026-04-27 17:11:48 na-prot_3200.pdb -448504.261918 2026-04-27 17:12:07 na-prot_3300.pdb -286778.819598 2026-04-27 17:12:26 na-prot_3400.pdb -246228.336023 2026-04-27 17:12:45 na-prot_3500.pdb -142784.088186 2026-04-27 17:13:04 na-prot_3600.pdb -142724.580696 2026-04-27 17:13:23 na-prot_3700.pdb -284929.485371 2026-04-27 17:13:42 na-prot_3800.pdb -290435.398349 2026-04-27 17:14:01 na-prot_3900.pdb -187606.506885 2026-04-27 17:14:20 na-prot_4000.pdb -142893.475998 2026-04-27 17:14:39 na-prot_4100.pdb -343520.188156 2026-04-27 17:14:58 na-prot_4200.pdb -257212.400433 2026-04-27 17:15:17 na-prot_4300.pdb -173269.759552 2026-04-27 17:15:36 na-prot_4400.pdb -670058.388224 2026-04-27 17:15:55 na-prot_4500.pdb -651002.152701 2026-04-27 17:16:14 na-prot_4600.pdb -516644.090108 2026-04-27 17:16:33 na-prot_4700.pdb -137339.112284 2026-04-27 17:16:51 na-prot_4800.pdb -190221.51647 2026-04-27 17:17:11 na-prot_4900.pdb -212093.692346 2026-04-27 17:17:30 na-prot_5000.pdb -563948.137568 2026-04-27 17:17:49 na-prot_5100.pdb -275910.118668 2026-04-27 17:18:08 na-prot_5200.pdb -550770.81186 2026-04-27 17:18:27 na-prot_5300.pdb -73238.2958769 2026-04-27 17:18:46 na-prot_5400.pdb -523680.325841 2026-04-27 17:19:05 na-prot_5500.pdb -102460.333891 2026-04-27 17:19:24 na-prot_5600.pdb -179200.166011 2026-04-27 17:19:43 na-prot_5700.pdb -435582.396841 2026-04-27 17:20:02 na-prot_5800.pdb -449404.97313 2026-04-27 17:20:21 na-prot_5900.pdb -73258.4217915 2026-04-27 17:20:40 na-prot_6000.pdb -600202.347097 2026-04-27 17:20:59 na-prot_6100.pdb -659627.392824 2026-04-27 17:21:18 na-prot_6200.pdb -326606.463392 2026-04-27 17:21:37 na-prot_6300.pdb -651615.919025 2026-04-27 17:21:56 na-prot_6400.pdb -675072.178597 2026-04-27 17:22:15 na-prot_6500.pdb -259082.129972 2026-04-27 17:22:34 na-prot_6600.pdb -373909.888174 2026-04-27 17:22:53 na-prot_6700.pdb -310688.817578 2026-04-27 17:23:12 na-prot_6800.pdb -279510.734693 2026-04-27 17:23:31 na-prot_6900.pdb -538994.267627 2026-04-27 17:23:50 na-prot_7000.pdb -224117.66126 2026-04-27 17:24:10 na-prot_7100.pdb -475590.023774 2026-04-27 17:24:29 na-prot_7200.pdb -459761.578101 2026-04-27 17:24:48 na-prot_7300.pdb -337095.526165 2026-04-27 17:25:07 na-prot_7400.pdb -320882.92778 2026-04-27 17:25:26 na-prot_7500.pdb -339469.504504 2026-04-27 17:25:45 na-prot_7600.pdb -239851.942187 2026-04-27 17:26:04 na-prot_7700.pdb -786013.459487 2026-04-27 17:26:24 na-prot_7800.pdb -461188.552521 2026-04-27 17:26:43 na-prot_7900.pdb -539459.820267 2026-04-27 17:27:02 na-prot_8000.pdb -170750.665405 2026-04-27 17:27:21 na-prot_8100.pdb -297709.546105 2026-04-27 17:27:40 na-prot_8200.pdb -549048.077539 2026-04-27 17:27:59 na-prot_8300.pdb -30754.0175287 2026-04-27 17:28:19 na-prot_8400.pdb -169281.632107 2026-04-27 17:28:38 na-prot_8500.pdb -404359.724824 2026-04-27 17:28:57 na-prot_8600.pdb -169276.575418 2026-04-27 17:29:17 na-prot_8700.pdb -475715.304757 2026-04-27 17:29:36 na-prot_8800.pdb -285180.682521 2026-04-27 17:29:55 na-prot_8900.pdb -282073.995079 2026-04-27 17:30:14 na-prot_9000.pdb -348739.197265 2026-04-27 17:30:33 na-prot_9100.pdb -160062.046544 2026-04-27 17:30:52 na-prot_9200.pdb -496251.52026 2026-04-27 17:31:12 na-prot_9300.pdb -3708.57096713 2026-04-27 17:31:31 na-prot_9400.pdb -287200.792281 2026-04-27 17:31:50 na-prot_9500.pdb -410023.162238 2026-04-27 17:32:09 na-prot_9600.pdb -203313.753486 2026-04-27 17:32:28 na-prot_9700.pdb -300061.763759 2026-04-27 17:32:47 na-prot_9800.pdb -306711.83462 2026-04-27 17:33:06 na-prot_9900.pdb -368615.536292 2026-04-27 17:33:25 na-prot_10000.pdb -281254.468969 2026-04-27 17:33:44 na-prot_10100.pdb -230609.032414 2026-04-27 17:34:04 na-prot_10200.pdb -256636.528904 2026-04-27 17:34:23 na-prot_10300.pdb -654698.892777 2026-04-27 17:34:42 na-prot_10400.pdb -571211.764366 2026-04-27 17:35:01 na-prot_10500.pdb -217800.464438 2026-04-27 17:35:20 na-prot_10600.pdb -561206.320837 2026-04-27 17:35:39 na-prot_10700.pdb -390440.162011 2026-04-27 17:35:58 na-prot_10800.pdb -350237.999668 2026-04-27 17:36:18 na-prot_10900.pdb -320481.507528 2026-04-27 17:36:36 na-prot_11000.pdb -201913.137563 2026-04-27 17:36:56 na-prot_11100.pdb -188377.133384 2026-04-27 17:37:15 na-prot_11200.pdb -377658.403794 2026-04-27 17:37:34 na-prot_11300.pdb -204814.931409 2026-04-27 17:37:53 na-prot_11400.pdb -371949.139678 2026-04-27 17:38:13 na-prot_11500.pdb -347971.74669 2026-04-27 17:38:32 na-prot_11600.pdb -297255.3061 2026-04-27 17:38:51 na-prot_11700.pdb -218157.3838 2026-04-27 17:39:11 na-prot_11800.pdb -224860.061706 2026-04-27 17:39:30 na-prot_11900.pdb -355633.117874 2026-04-27 17:39:49 na-prot_12000.pdb -336141.566715 2026-04-27 17:40:08 na-prot_12100.pdb -527878.764873 2026-04-27 17:40:27 na-prot_12200.pdb -587275.444404 2026-04-27 17:40:46 na-prot_12300.pdb -420255.689502 2026-04-27 17:41:05 na-prot_12400.pdb -612480.344314 2026-04-27 17:41:24 na-prot_12500.pdb -287887.002927 2026-04-27 17:41:43 na-prot_12600.pdb -231146.77906 2026-04-27 17:42:02 na-prot_12700.pdb -210574.85618 2026-04-27 17:42:21 na-prot_12800.pdb -670775.695061 2026-04-27 17:42:40 na-prot_12900.pdb -226580.373696 2026-04-27 17:42:59 na-prot_13000.pdb -553732.829727 2026-04-27 17:43:18 na-prot_13100.pdb -592981.849986 2026-04-27 17:43:37 na-prot_13200.pdb -811922.274786 2026-04-27 17:43:56 na-prot_13300.pdb -367258.467573 2026-04-27 17:44:16 na-prot_13400.pdb -264103.87329 2026-04-27 17:44:35 na-prot_13500.pdb -330616.439986 2026-04-27 17:44:54 na-prot_13600.pdb -299276.151746 2026-04-27 17:45:14 na-prot_13700.pdb -340114.833985 2026-04-27 17:45:33 na-prot_13800.pdb -437908.235479 2026-04-27 17:45:52 na-prot_13900.pdb -285549.388502 2026-04-27 17:46:11 na-prot_14000.pdb -233836.925385 2026-04-27 17:46:30 na-prot_14100.pdb -151645.095185 2026-04-27 17:46:49 na-prot_14200.pdb -475830.224323 2026-04-27 17:47:08 na-prot_14300.pdb -327072.420841 2026-04-27 17:47:27 na-prot_14400.pdb -318085.048112 2026-04-27 17:47:46 na-prot_14500.pdb -149478.789962 2026-04-27 17:48:05 na-prot_14600.pdb -234467.699231 2026-04-27 17:48:24 na-prot_14700.pdb -557893.181302 2026-04-27 17:48:43 na-prot_14800.pdb -213818.643417 2026-04-27 17:49:02 na-prot_14900.pdb -309629.980336 2026-04-27 17:49:22 na-prot_15000.pdb -106908.017822 2026-04-27 17:49:41 na-prot_15100.pdb -275304.855887 2026-04-27 17:50:00 na-prot_15200.pdb -368426.702762 2026-04-27 17:50:19 na-prot_15300.pdb -565151.792022 2026-04-27 17:50:39 na-prot_15400.pdb -859876.456966 2026-04-27 17:50:58 na-prot_15500.pdb -322367.763972 2026-04-27 17:51:17 na-prot_15600.pdb -291529.310339 2026-04-27 17:51:36 na-prot_15700.pdb -419996.10926 2026-04-27 17:51:55 na-prot_15800.pdb -330852.130784 2026-04-27 17:52:14 na-prot_15900.pdb -661223.67685 2026-04-27 17:52:33 na-prot_16000.pdb -411703.451286 2026-04-27 17:52:52 na-prot_16100.pdb -384627.743896 2026-04-27 17:53:11 na-prot_16200.pdb -365721.647352 2026-04-27 17:53:30 na-prot_16300.pdb -573192.279923 2026-04-27 17:53:49 na-prot_16400.pdb -213620.064061 2026-04-27 17:54:09 na-prot_16500.pdb -199408.062397 2026-04-27 17:54:28 na-prot_16600.pdb -777375.556503 2026-04-27 17:54:47 na-prot_16700.pdb -349702.776994 2026-04-27 17:55:06 na-prot_16800.pdb -832818.356247 2026-04-27 17:55:25 na-prot_16900.pdb -376448.015988 2026-04-27 17:55:44 na-prot_17000.pdb -389095.109377 2026-04-27 17:56:03 na-prot_17100.pdb -267679.998214 2026-04-27 17:56:22 na-prot_17200.pdb -446109.305277 2026-04-27 17:56:41 na-prot_17300.pdb -272512.313874 2026-04-27 17:57:00 na-prot_17400.pdb -67685.8259402 2026-04-27 17:57:19 na-prot_17500.pdb -300142.242099 2026-04-27 17:57:38 na-prot_17600.pdb -502442.945602 2026-04-27 17:57:57 na-prot_17700.pdb -561027.526921 2026-04-27 17:58:16 na-prot_17800.pdb -109600.820967 2026-04-27 17:58:35 na-prot_17900.pdb -327889.547672 2026-04-27 17:58:54 na-prot_18000.pdb -414545.838553 2026-04-27 17:59:13 na-prot_18100.pdb -321194.646713 2026-04-27 17:59:32 na-prot_18200.pdb -215622.799027 2026-04-27 17:59:51 na-prot_18300.pdb -174077.500212 2026-04-27 18:00:11 na-prot_18400.pdb -437025.245008 2026-04-27 18:00:30 na-prot_18500.pdb -273082.987813 2026-04-27 18:00:48 na-prot_18600.pdb -289574.967802 2026-04-27 18:01:08 na-prot_18700.pdb -463886.650745 2026-04-27 18:01:27 na-prot_18800.pdb -246954.098797 2026-04-27 18:01:46 na-prot_18900.pdb -345102.280053 2026-04-27 18:02:05 na-prot_19000.pdb -431924.057836 2026-04-27 18:02:24 na-prot_19100.pdb -314828.847807 2026-04-27 18:02:43 na-prot_19200.pdb -213245.054322 2026-04-27 18:03:02 na-prot_19300.pdb -434006.084997 2026-04-27 18:03:21 na-prot_19400.pdb -265870.521832 2026-04-27 18:03:40 na-prot_19500.pdb -549855.720846 2026-04-27 18:03:59 na-prot_19600.pdb -398291.587147 2026-04-27 18:04:18 na-prot_19700.pdb -177428.626309 2026-04-27 18:04:37 na-prot_19800.pdb -397905.523907 2026-04-27 18:04:56 na-prot_19900.pdb -457339.013086 2026-04-27 18:05:15 na-prot_20000.pdb -212935.562388 2026-04-27 18:05:15 Varani starts 2026-04-27 18:05:16 na-prot_1000.pdb 378.84 2026-04-27 18:05:47 na-prot_94.pdb 303.873 2026-04-27 18:06:19 na-prot_194.pdb 150.318 2026-04-27 18:06:51 na-prot_294.pdb 180.327 2026-04-27 18:07:23 na-prot_394.pdb 251.128 2026-04-27 18:07:54 na-prot_494.pdb 153.856 2026-04-27 18:08:26 na-prot_594.pdb 369.628 2026-04-27 18:08:57 na-prot_694.pdb 503.164 2026-04-27 18:09:28 na-prot_794.pdb 216.117 2026-04-27 18:10:00 na-prot_894.pdb 260.428 2026-04-27 18:10:32 na-prot_994.pdb 289.768 2026-04-27 18:11:04 na-prot_1100.pdb 274.856 2026-04-27 18:11:35 na-prot_1200.pdb 227.095 2026-04-27 18:12:07 na-prot_1300.pdb 370.393 2026-04-27 18:12:38 na-prot_1400.pdb 287.25 2026-04-27 18:13:10 na-prot_1500.pdb 248.743 2026-04-27 18:13:41 na-prot_1600.pdb 309.014 2026-04-27 18:14:13 na-prot_1700.pdb 209.078 2026-04-27 18:14:45 na-prot_1800.pdb 304.209 2026-04-27 18:15:16 na-prot_1900.pdb 146.227 2026-04-27 18:15:48 na-prot_2000.pdb 331.764 2026-04-27 18:16:19 na-prot_2100.pdb 182.386 2026-04-27 18:16:51 na-prot_2200.pdb 361.081 2026-04-27 18:17:23 na-prot_2300.pdb 172.413 2026-04-27 18:17:54 na-prot_2400.pdb 222.962 2026-04-27 18:18:26 na-prot_2500.pdb 308.531 2026-04-27 18:18:57 na-prot_2600.pdb 179.677 2026-04-27 18:19:29 na-prot_2700.pdb 246.24 2026-04-27 18:20:02 na-prot_2800.pdb 229.122 2026-04-27 18:20:34 na-prot_2900.pdb 62.85 2026-04-27 18:21:05 na-prot_3000.pdb 250.323 2026-04-27 18:21:37 na-prot_3100.pdb 245.435 2026-04-27 18:22:08 na-prot_3200.pdb 276.209 2026-04-27 18:22:39 na-prot_3300.pdb 412.506 2026-04-27 18:23:11 na-prot_3400.pdb 508.302 2026-04-27 18:23:42 na-prot_3500.pdb 278.825 2026-04-27 18:24:14 na-prot_3600.pdb 228.422 2026-04-27 18:24:46 na-prot_3700.pdb 432.081 2026-04-27 18:25:17 na-prot_3800.pdb 220.609 2026-04-27 18:25:49 na-prot_3900.pdb 408.225 2026-04-27 18:26:21 na-prot_4000.pdb 145.818 2026-04-27 18:26:53 na-prot_4100.pdb 214.926 2026-04-27 18:27:25 na-prot_4200.pdb 177.116 2026-04-27 18:27:57 na-prot_4300.pdb 184.816 2026-04-27 18:28:28 na-prot_4400.pdb 444.186 2026-04-27 18:29:00 na-prot_4500.pdb 178.43 2026-04-27 18:29:32 na-prot_4600.pdb 132.036 2026-04-27 18:30:03 na-prot_4700.pdb 284.593 2026-04-27 18:30:34 na-prot_4800.pdb 551.763 2026-04-27 18:31:06 na-prot_4900.pdb 316 2026-04-27 18:31:37 na-prot_5000.pdb 271.824 2026-04-27 18:32:08 na-prot_5100.pdb 365.411 2026-04-27 18:32:39 na-prot_5200.pdb 123.085 2026-04-27 18:33:11 na-prot_5300.pdb 146.243 2026-04-27 18:33:42 na-prot_5400.pdb 170.642 2026-04-27 18:34:14 na-prot_5500.pdb 289.76 2026-04-27 18:34:45 na-prot_5600.pdb 171.169 2026-04-27 18:35:17 na-prot_5700.pdb 328.842 2026-04-27 18:35:48 na-prot_5800.pdb 165.508 2026-04-27 18:36:19 na-prot_5900.pdb 279.414 2026-04-27 18:36:51 na-prot_6000.pdb 290.029 2026-04-27 18:37:22 na-prot_6100.pdb 313.732 2026-04-27 18:37:53 na-prot_6200.pdb 171.82 2026-04-27 18:38:25 na-prot_6300.pdb 163.967 2026-04-27 18:38:56 na-prot_6400.pdb 288.375 2026-04-27 18:39:28 na-prot_6500.pdb 407.505 2026-04-27 18:39:59 na-prot_6600.pdb 182.874 2026-04-27 18:40:30 na-prot_6700.pdb 456.73 2026-04-27 18:41:02 na-prot_6800.pdb 154.703 2026-04-27 18:41:34 na-prot_6900.pdb 286.951 2026-04-27 18:42:05 na-prot_7000.pdb 180.851 2026-04-27 18:42:37 na-prot_7100.pdb 217.112 2026-04-27 18:43:09 na-prot_7200.pdb 162.886 2026-04-27 18:43:41 na-prot_7300.pdb 246.575 2026-04-27 18:44:12 na-prot_7400.pdb 169.545 2026-04-27 18:44:44 na-prot_7500.pdb 98.239 2026-04-27 18:45:15 na-prot_7600.pdb 150.653 2026-04-27 18:45:46 na-prot_7700.pdb 378.917 2026-04-27 18:46:18 na-prot_7800.pdb 177.553 2026-04-27 18:46:49 na-prot_7900.pdb 248.669 2026-04-27 18:47:22 na-prot_8000.pdb 341.435 2026-04-27 18:47:55 na-prot_8100.pdb 150.035 2026-04-27 18:48:27 na-prot_8200.pdb 187.95 2026-04-27 18:48:58 na-prot_8300.pdb 156.501 2026-04-27 18:49:30 na-prot_8400.pdb 148.613 2026-04-27 18:50:01 na-prot_8500.pdb 435.542 2026-04-27 18:50:33 na-prot_8600.pdb 200.217 2026-04-27 18:51:04 na-prot_8700.pdb 137.372 2026-04-27 18:51:36 na-prot_8800.pdb 188.029 2026-04-27 18:52:07 na-prot_8900.pdb 121.639 2026-04-27 18:52:38 na-prot_9000.pdb 235.067 2026-04-27 18:53:10 na-prot_9100.pdb 331.559 2026-04-27 18:53:41 na-prot_9200.pdb 193.815 2026-04-27 18:54:12 na-prot_9300.pdb 216.222 2026-04-27 18:54:44 na-prot_9400.pdb 252.393 2026-04-27 18:55:16 na-prot_9500.pdb 199.973 2026-04-27 18:55:47 na-prot_9600.pdb 245.691 2026-04-27 18:56:19 na-prot_9700.pdb 197.648 2026-04-27 18:56:50 na-prot_9800.pdb 257.537 2026-04-27 18:57:22 na-prot_9900.pdb 95.293 2026-04-27 18:57:53 na-prot_10000.pdb 257.285 2026-04-27 18:58:24 na-prot_10100.pdb 512.248 2026-04-27 18:58:55 na-prot_10200.pdb 260.837 2026-04-27 18:59:27 na-prot_10300.pdb 142.094 2026-04-27 18:59:58 na-prot_10400.pdb 220.189 2026-04-27 19:00:29 na-prot_10500.pdb 196.814 2026-04-27 19:01:01 na-prot_10600.pdb 137.617 2026-04-27 19:01:32 na-prot_10700.pdb 190.723 2026-04-27 19:02:03 na-prot_10800.pdb 181.316 2026-04-27 19:02:35 na-prot_10900.pdb 467.886 2026-04-27 19:03:06 na-prot_11000.pdb 166.148 2026-04-27 19:03:37 na-prot_11100.pdb 193.578 2026-04-27 19:04:09 na-prot_11200.pdb 164.135 2026-04-27 19:04:40 na-prot_11300.pdb 235.81 2026-04-27 19:05:12 na-prot_11400.pdb 319.883 2026-04-27 19:05:43 na-prot_11500.pdb 193.56 2026-04-27 19:06:15 na-prot_11600.pdb 196.23 2026-04-27 19:06:46 na-prot_11700.pdb 330.9 2026-04-27 19:07:18 na-prot_11800.pdb 190.775 2026-04-27 19:07:49 na-prot_11900.pdb 672.902 2026-04-27 19:08:21 na-prot_12000.pdb 267.62 2026-04-27 19:08:52 na-prot_12100.pdb 299.741 2026-04-27 19:09:24 na-prot_12200.pdb 154.871 2026-04-27 19:09:55 na-prot_12300.pdb 229.538 2026-04-27 19:10:27 na-prot_12400.pdb 170.536 2026-04-27 19:10:58 na-prot_12500.pdb 157.185 2026-04-27 19:11:30 na-prot_12600.pdb 113.895 2026-04-27 19:12:01 na-prot_12700.pdb 207.46 2026-04-27 19:12:33 na-prot_12800.pdb 314.768 2026-04-27 19:13:04 na-prot_12900.pdb 261.035 2026-04-27 19:13:36 na-prot_13000.pdb 400.973 2026-04-27 19:14:07 na-prot_13100.pdb 155.848 2026-04-27 19:14:38 na-prot_13200.pdb 579.518 2026-04-27 19:15:10 na-prot_13300.pdb 209.825 2026-04-27 19:15:41 na-prot_13400.pdb 267.709 2026-04-27 19:16:13 na-prot_13500.pdb 173.871 2026-04-27 19:16:44 na-prot_13600.pdb 24.715 2026-04-27 19:17:17 na-prot_13700.pdb 203.154 2026-04-27 19:17:50 na-prot_13800.pdb 276.447 2026-04-27 19:18:22 na-prot_13900.pdb 251.543 2026-04-27 19:18:54 na-prot_14000.pdb 181.753 2026-04-27 19:19:25 na-prot_14100.pdb 208.056 2026-04-27 19:19:57 na-prot_14200.pdb 86.317 2026-04-27 19:20:28 na-prot_14300.pdb 182.584 2026-04-27 19:20:59 na-prot_14400.pdb 95.475 2026-04-27 19:21:31 na-prot_14500.pdb 260.727 2026-04-27 19:22:02 na-prot_14600.pdb 461.931 2026-04-27 19:22:34 na-prot_14700.pdb 203.548 2026-04-27 19:23:05 na-prot_14800.pdb 132.034 2026-04-27 19:23:37 na-prot_14900.pdb 294.292 2026-04-27 19:24:08 na-prot_15000.pdb 217.775 2026-04-27 19:24:40 na-prot_15100.pdb 248.522 2026-04-27 19:25:12 na-prot_15200.pdb 299.758 2026-04-27 19:25:43 na-prot_15300.pdb 184.743 2026-04-27 19:26:15 na-prot_15400.pdb 286.781 2026-04-27 19:26:47 na-prot_15500.pdb 194.674 2026-04-27 19:27:19 na-prot_15600.pdb 113.185 2026-04-27 19:27:50 na-prot_15700.pdb 359.653 2026-04-27 19:28:22 na-prot_15800.pdb 278.317 2026-04-27 19:28:55 na-prot_15900.pdb 265.234 2026-04-27 19:29:27 na-prot_16000.pdb 98.154 2026-04-27 19:29:58 na-prot_16100.pdb 288.56 2026-04-27 19:30:30 na-prot_16200.pdb 183.004 2026-04-27 19:31:02 na-prot_16300.pdb 253.128 2026-04-27 19:31:33 na-prot_16400.pdb 336.986 2026-04-27 19:32:05 na-prot_16500.pdb 239.527 2026-04-27 19:32:36 na-prot_16600.pdb 384.488 2026-04-27 19:33:08 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19:44:42 na-prot_18900.pdb 133.366 2026-04-27 19:45:14 na-prot_19000.pdb 198.244 2026-04-27 19:45:45 na-prot_19100.pdb 267.213 2026-04-27 19:46:17 na-prot_19200.pdb 228.297 2026-04-27 19:46:49 na-prot_19300.pdb 385.973 2026-04-27 19:47:20 na-prot_19400.pdb 322.964 2026-04-27 19:47:51 na-prot_19500.pdb 138.118 2026-04-27 19:48:23 na-prot_19600.pdb 564.472 2026-04-27 19:48:54 na-prot_19700.pdb 181.372 2026-04-27 19:49:26 na-prot_19800.pdb 409.042 2026-04-27 19:49:57 na-prot_19900.pdb 292.974 2026-04-27 19:50:29 na-prot_20000.pdb 324.196 2026-04-27 19:50:29 DFIRE starts 2026-04-27 19:50:29 na-prot_1000.pdb -31.340075 2026-04-27 19:51:08 na-prot_94.pdb -75.697194 2026-04-27 19:51:47 na-prot_194.pdb -62.917730 2026-04-27 19:52:26 na-prot_294.pdb -54.446322 2026-04-27 19:53:05 na-prot_394.pdb -37.993468 2026-04-27 19:53:45 na-prot_494.pdb -44.146009 2026-04-27 19:54:25 na-prot_594.pdb -33.303216 2026-04-27 19:55:04 na-prot_694.pdb -39.565363 2026-04-27 19:55:44 na-prot_794.pdb -31.532704 2026-04-27 19:56:23 na-prot_894.pdb -44.107789 2026-04-27 19:57:02 na-prot_994.pdb -27.655086 2026-04-27 19:57:42 na-prot_1100.pdb -36.671089 2026-04-27 19:58:21 na-prot_1200.pdb -31.994679 2026-04-27 19:59:01 na-prot_1300.pdb -57.614696 2026-04-27 19:59:40 na-prot_1400.pdb -26.880251 2026-04-27 20:00:19 na-prot_1500.pdb -19.956084 2026-04-27 20:00:59 na-prot_1600.pdb -62.342712 2026-04-27 20:01:38 na-prot_1700.pdb -51.124773 2026-04-27 20:02:17 na-prot_1800.pdb -37.548898 2026-04-27 20:02:56 na-prot_1900.pdb -31.792014 2026-04-27 20:03:35 na-prot_2000.pdb -25.839422 2026-04-27 20:04:14 na-prot_2100.pdb -25.655005 2026-04-27 20:04:53 na-prot_2200.pdb -34.386192 2026-04-27 20:05:33 na-prot_2300.pdb -75.569345 2026-04-27 20:06:13 na-prot_2400.pdb -30.269929 2026-04-27 20:06:52 na-prot_2500.pdb -48.737782 2026-04-27 20:07:32 na-prot_2600.pdb -15.835693 2026-04-27 20:08:11 na-prot_2700.pdb -32.435295 2026-04-27 20:08:51 na-prot_2800.pdb -22.146386 2026-04-27 20:09:30 na-prot_2900.pdb 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na-prot_5000.pdb -44.799806 2026-04-27 20:24:01 na-prot_5100.pdb -36.384848 2026-04-27 20:24:41 na-prot_5200.pdb -50.908751 2026-04-27 20:25:21 na-prot_5300.pdb -19.069587 2026-04-27 20:26:01 na-prot_5400.pdb -47.898666 2026-04-27 20:26:40 na-prot_5500.pdb -24.948957 2026-04-27 20:27:20 na-prot_5600.pdb -37.053456 2026-04-27 20:28:00 na-prot_5700.pdb -44.283376 2026-04-27 20:28:40 na-prot_5800.pdb -36.684070 2026-04-27 20:29:20 na-prot_5900.pdb -21.503717 2026-04-27 20:29:59 na-prot_6000.pdb -45.908349 2026-04-27 20:30:39 na-prot_6100.pdb -76.070434 2026-04-27 20:31:18 na-prot_6200.pdb -31.962518 2026-04-27 20:31:58 na-prot_6300.pdb -59.093295 2026-04-27 20:32:37 na-prot_6400.pdb -69.081927 2026-04-27 20:33:16 na-prot_6500.pdb -29.916298 2026-04-27 20:33:55 na-prot_6600.pdb -41.685058 2026-04-27 20:34:35 na-prot_6700.pdb -42.719803 2026-04-27 20:35:14 na-prot_6800.pdb -32.196561 2026-04-27 20:35:54 na-prot_6900.pdb -47.736385 2026-04-27 20:36:34 na-prot_7000.pdb -28.705931 2026-04-27 20:37:13 na-prot_7100.pdb -31.157111 2026-04-27 20:37:52 na-prot_7200.pdb -47.218050 2026-04-27 20:38:32 na-prot_7300.pdb -54.354621 2026-04-27 20:39:11 na-prot_7400.pdb -26.516357 2026-04-27 20:39:50 na-prot_7500.pdb -24.000082 2026-04-27 20:40:29 na-prot_7600.pdb -27.581389 2026-04-27 20:41:09 na-prot_7700.pdb -69.302053 2026-04-27 20:41:49 na-prot_7800.pdb -37.737381 2026-04-27 20:42:28 na-prot_7900.pdb -64.661823 2026-04-27 20:43:08 na-prot_8000.pdb -23.796931 2026-04-27 20:43:47 na-prot_8100.pdb -30.441621 2026-04-27 20:44:27 na-prot_8200.pdb -58.317916 2026-04-27 20:45:06 na-prot_8300.pdb -15.356013 2026-04-27 20:45:45 na-prot_8400.pdb -24.267876 2026-04-27 20:46:25 na-prot_8500.pdb -65.571146 2026-04-27 20:47:04 na-prot_8600.pdb -22.581066 2026-04-27 20:47:43 na-prot_8700.pdb -56.019429 2026-04-27 20:48:23 na-prot_8800.pdb -45.391190 2026-04-27 20:49:02 na-prot_8900.pdb -31.054999 2026-04-27 20:49:42 na-prot_9000.pdb -22.470999 2026-04-27 20:50:21 na-prot_9100.pdb -25.027352 2026-04-27 20:51:01 na-prot_9200.pdb -40.900331 2026-04-27 20:51:40 na-prot_9300.pdb -14.383799 2026-04-27 20:52:20 na-prot_9400.pdb -37.045010 2026-04-27 20:53:00 na-prot_9500.pdb -34.711202 2026-04-27 20:53:39 na-prot_9600.pdb -30.564129 2026-04-27 20:54:19 na-prot_9700.pdb -31.303771 2026-04-27 20:54:59 na-prot_9800.pdb -20.357997 2026-04-27 20:55:38 na-prot_9900.pdb -27.589812 2026-04-27 20:56:18 na-prot_10000.pdb -32.049363 2026-04-27 20:56:58 na-prot_10100.pdb -29.052051 2026-04-27 20:57:37 na-prot_10200.pdb -39.429931 2026-04-27 20:58:17 na-prot_10300.pdb -56.050817 2026-04-27 20:58:57 na-prot_10400.pdb -46.016180 2026-04-27 20:59:36 na-prot_10500.pdb -28.270759 2026-04-27 21:00:16 na-prot_10600.pdb -54.316442 2026-04-27 21:00:56 na-prot_10700.pdb -29.113981 2026-04-27 21:01:35 na-prot_10800.pdb -26.938920 2026-04-27 21:02:15 na-prot_10900.pdb -32.432306 2026-04-27 21:02:55 na-prot_11000.pdb -22.944728 2026-04-27 21:03:34 na-prot_11100.pdb -24.070738 2026-04-27 21:04:14 na-prot_11200.pdb -36.534920 2026-04-27 21:04:53 na-prot_11300.pdb -22.592811 2026-04-27 21:05:32 na-prot_11400.pdb -41.378967 2026-04-27 21:06:11 na-prot_11500.pdb -37.929888 2026-04-27 21:06:51 na-prot_11600.pdb -22.101849 2026-04-27 21:07:31 na-prot_11700.pdb -34.449850 2026-04-27 21:08:10 na-prot_11800.pdb -27.174812 2026-04-27 21:08:50 na-prot_11900.pdb -44.874128 2026-04-27 21:09:30 na-prot_12000.pdb -37.862684 2026-04-27 21:10:09 na-prot_12100.pdb -54.063867 2026-04-27 21:10:48 na-prot_12200.pdb -38.038019 2026-04-27 21:11:28 na-prot_12300.pdb -37.984614 2026-04-27 21:12:07 na-prot_12400.pdb -47.657703 2026-04-27 21:12:47 na-prot_12500.pdb -19.716352 2026-04-27 21:13:26 na-prot_12600.pdb -27.651952 2026-04-27 21:14:05 na-prot_12700.pdb -21.868188 2026-04-27 21:14:44 na-prot_12800.pdb -52.964401 2026-04-27 21:15:27 na-prot_12900.pdb -23.446717 2026-04-27 21:16:08 na-prot_13000.pdb -51.360541 2026-04-27 21:16:48 na-prot_13100.pdb -47.453188 2026-04-27 21:17:27 na-prot_13200.pdb 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/home/rpdock/web/media/jobs/deb82bf2-cc38-4464-8ae9-3ce758cd0b27/prot-na_30/na-prot_18500.pdb 1.14368493504 2026-04-27 22:02:10 /home/rpdock/web/media/jobs/deb82bf2-cc38-4464-8ae9-3ce758cd0b27/prot-na_30/na-prot_18600.pdb 0.800123022526 2026-04-27 22:02:10 /home/rpdock/web/media/jobs/deb82bf2-cc38-4464-8ae9-3ce758cd0b27/prot-na_30/na-prot_18700.pdb -0.63006900272 2026-04-27 22:02:10 /home/rpdock/web/media/jobs/deb82bf2-cc38-4464-8ae9-3ce758cd0b27/prot-na_30/na-prot_18800.pdb 1.17802283565 2026-04-27 22:02:10 /home/rpdock/web/media/jobs/deb82bf2-cc38-4464-8ae9-3ce758cd0b27/prot-na_30/na-prot_18900.pdb -0.266106098111 2026-04-27 22:02:10 /home/rpdock/web/media/jobs/deb82bf2-cc38-4464-8ae9-3ce758cd0b27/prot-na_30/na-prot_19000.pdb -0.560743607575 2026-04-27 22:02:10 /home/rpdock/web/media/jobs/deb82bf2-cc38-4464-8ae9-3ce758cd0b27/prot-na_30/na-prot_19100.pdb 0.373559602052 2026-04-27 22:02:10 /home/rpdock/web/media/jobs/deb82bf2-cc38-4464-8ae9-3ce758cd0b27/prot-na_30/na-prot_19200.pdb 1.6113131577 2026-04-27 22:02:10 /home/rpdock/web/media/jobs/deb82bf2-cc38-4464-8ae9-3ce758cd0b27/prot-na_30/na-prot_19300.pdb 0.199563537278 2026-04-27 22:02:10 /home/rpdock/web/media/jobs/deb82bf2-cc38-4464-8ae9-3ce758cd0b27/prot-na_30/na-prot_19400.pdb 1.82871367247 2026-04-27 22:02:10 /home/rpdock/web/media/jobs/deb82bf2-cc38-4464-8ae9-3ce758cd0b27/prot-na_30/na-prot_19500.pdb -0.897946423353 2026-04-27 22:02:10 /home/rpdock/web/media/jobs/deb82bf2-cc38-4464-8ae9-3ce758cd0b27/prot-na_30/na-prot_19600.pdb 0.167550639861 2026-04-27 22:02:10 /home/rpdock/web/media/jobs/deb82bf2-cc38-4464-8ae9-3ce758cd0b27/prot-na_30/na-prot_19700.pdb 1.48421088782 2026-04-27 22:02:10 /home/rpdock/web/media/jobs/deb82bf2-cc38-4464-8ae9-3ce758cd0b27/prot-na_30/na-prot_19800.pdb 0.705769244553 2026-04-27 22:02:10 /home/rpdock/web/media/jobs/deb82bf2-cc38-4464-8ae9-3ce758cd0b27/prot-na_30/na-prot_19900.pdb 0.705804357792 2026-04-27 22:02:10 /home/rpdock/web/media/jobs/deb82bf2-cc38-4464-8ae9-3ce758cd0b27/prot-na_30/na-prot_20000.pdb 1.46274541201 2026-04-27 22:02:10 [..]75532917) ('/home/rpdock/web/media/jobs/deb82bf2-cc38-4464-8ae9-3ce758cd0b27/prot-na_30/na-prot_19994.pdb', -0.20431245284216581) ('/home/rpdock/web/media/jobs/deb82bf2-cc38-4464-8ae9-3ce758cd0b27/prot-na_30/na-prot_19995.pdb', 0.4904495316271472) ('/home/rpdock/web/media/jobs/deb82bf2-cc38-4464-8ae9-3ce758cd0b27/prot-na_30/na-prot_19996.pdb', 1.7593934845579675) ('/home/rpdock/web/media/jobs/deb82bf2-cc38-4464-8ae9-3ce758cd0b27/prot-na_30/na-prot_19997.pdb', 0.012060950496161904) ('/home/rpdock/web/media/jobs/deb82bf2-cc38-4464-8ae9-3ce758cd0b27/prot-na_30/na-prot_19998.pdb', 0.4223279522733565) ('/home/rpdock/web/media/jobs/deb82bf2-cc38-4464-8ae9-3ce758cd0b27/prot-na_30/na-prot_19999.pdb', -0.15666467831944364) ('/home/rpdock/web/media/jobs/deb82bf2-cc38-4464-8ae9-3ce758cd0b27/prot-na_30/na-prot_20000.pdb', 1.4627454120060182) 16920.16user 973.40system 5:00:22elapsed 99%CPU (0avgtext+0avgdata 198936maxresident)k 5176480inputs+11524736outputs (31major+194897346minor)pagefaults 0swaps 2026-04-27 22:02:10 Clustering (cuttoff: 5, nr_clust: 100 ) in progress... 2026-04-27 22:02:10 time python /home/rpdock/run_gramm//clustering_v4.py dars_out.txt list.txt 5 100 2026-04-27 22:02:10 100 best scored structures 2026-04-27 22:02:10 1 na-prot_9760.pdb -4.94253042799 2026-04-27 22:02:10 2 na-prot_1963.pdb -4.94236008523 2026-04-27 22:02:10 3 na-prot_10269.pdb -4.92633888775 2026-04-27 22:02:10 4 na-prot_16952.pdb -4.84746389137 2026-04-27 22:02:10 5 na-prot_522.pdb -4.82033841197 2026-04-27 22:02:10 6 na-prot_16029.pdb -4.65793353499 2026-04-27 22:02:10 7 na-prot_14534.pdb -4.42168233534 2026-04-27 22:02:10 8 na-prot_834.pdb -4.40967352521 2026-04-27 22:02:10 9 na-prot_4459.pdb -4.26186708404 2026-04-27 22:02:10 10 na-prot_3807.pdb -4.23678492947 2026-04-27 22:02:10 11 na-prot_7970.pdb -4.20191158887 2026-04-27 22:02:10 12 na-prot_712.pdb -4.17353503186 2026-04-27 22:02:10 13 na-prot_2422.pdb -4.04939489083 2026-04-27 22:02:10 14 na-prot_8434.pdb -4.02456859238 2026-04-27 22:02:10 15 na-prot_5748.pdb -4.01980978525 2026-04-27 22:02:10 16 na-prot_19842.pdb -4.00250459984 2026-04-27 22:02:10 17 na-prot_14124.pdb -4.00242396604 2026-04-27 22:02:10 18 na-prot_6909.pdb -3.99337040144 2026-04-27 22:02:10 19 na-prot_41.pdb -3.99076600286 2026-04-27 22:02:10 20 na-prot_8556.pdb -3.9764371268 2026-04-27 22:02:10 21 na-prot_457.pdb -3.93394424493 2026-04-27 22:02:10 22 na-prot_2418.pdb -3.87275272241 2026-04-27 22:02:10 23 na-prot_7975.pdb -3.86664468625 2026-04-27 22:02:10 24 na-prot_2546.pdb -3.85077491429 2026-04-27 22:02:10 25 na-prot_3644.pdb -3.8445545741 2026-04-27 22:02:10 26 na-prot_6605.pdb -3.84443114988 2026-04-27 22:02:10 27 na-prot_7566.pdb -3.80996621302 2026-04-27 22:02:10 28 na-prot_7177.pdb -3.75796022277 2026-04-27 22:02:10 29 na-prot_16820.pdb -3.74890097522 2026-04-27 22:02:10 30 na-prot_1145.pdb -3.74552324616 2026-04-27 22:02:10 31 na-prot_5245.pdb -3.74309670069 2026-04-27 22:02:10 32 na-prot_11001.pdb -3.73260127704 2026-04-27 22:02:10 33 na-prot_16497.pdb -3.73039001875 2026-04-27 22:02:10 34 na-prot_11190.pdb -3.72851106851 2026-04-27 22:02:10 35 na-prot_1839.pdb -3.72578107619 2026-04-27 22:02:10 36 na-prot_4732.pdb -3.71702669697 2026-04-27 22:02:10 37 na-prot_1502.pdb -3.71030282948 2026-04-27 22:02:10 38 na-prot_7759.pdb -3.68257655728 2026-04-27 22:02:10 39 na-prot_135.pdb -3.67841030786 2026-04-27 22:02:10 40 na-prot_1677.pdb -3.67353241687 2026-04-27 22:02:10 41 na-prot_11415.pdb -3.61306651619 2026-04-27 22:02:10 42 na-prot_3045.pdb -3.61205592932 2026-04-27 22:02:10 43 na-prot_14369.pdb -3.58441301655 2026-04-27 22:02:10 44 na-prot_18807.pdb -3.57886475297 2026-04-27 22:02:10 45 na-prot_5368.pdb -3.57538961095 2026-04-27 22:02:10 46 na-prot_13458.pdb -3.56290668144 2026-04-27 22:02:10 47 na-prot_339.pdb -3.56128289842 2026-04-27 22:02:10 48 na-prot_3256.pdb -3.55605571809 2026-04-27 22:02:10 49 na-prot_15355.pdb -3.55443124794 2026-04-27 22:02:10 50 na-prot_8519.pdb -3.54239270163 2026-04-27 22:02:10 51 na-prot_7043.pdb -3.54035023029 2026-04-27 22:02:10 52 na-prot_8167.pdb -3.53623963694 2026-04-27 22:02:10 53 na-prot_5168.pdb -3.53597098927 2026-04-27 22:02:10 54 na-prot_15021.pdb -3.53593108641 2026-04-27 22:02:10 55 na-prot_17109.pdb -3.52764106147 2026-04-27 22:02:10 56 na-prot_12552.pdb -3.52553392753 2026-04-27 22:02:10 57 na-prot_31.pdb -3.51105627067 2026-04-27 22:02:10 58 na-prot_1232.pdb -3.49181229168 2026-04-27 22:02:10 59 na-prot_16083.pdb -3.48605554441 2026-04-27 22:02:10 60 na-prot_10622.pdb -3.48449515689 2026-04-27 22:02:10 61 na-prot_9297.pdb -3.48237172823 2026-04-27 22:02:10 62 na-prot_2931.pdb -3.47952576192 2026-04-27 22:02:10 63 na-prot_3421.pdb -3.47808382876 2026-04-27 22:02:10 64 na-prot_1293.pdb -3.47415319839 2026-04-27 22:02:10 65 na-prot_6041.pdb -3.45206379822 2026-04-27 22:02:10 66 na-prot_8214.pdb -3.43762671986 2026-04-27 22:02:10 67 na-prot_16015.pdb -3.43712227169 2026-04-27 22:02:10 68 na-prot_3818.pdb -3.43702699265 2026-04-27 22:02:10 69 na-prot_415.pdb -3.43629961661 2026-04-27 22:02:10 70 na-prot_6775.pdb -3.43533633831 2026-04-27 22:02:10 71 na-prot_110.pdb -3.43250665094 2026-04-27 22:02:10 72 na-prot_882.pdb -3.42842567463 2026-04-27 22:02:10 73 na-prot_4036.pdb -3.42611943558 2026-04-27 22:02:10 74 na-prot_2078.pdb -3.40677719385 2026-04-27 22:02:10 75 na-prot_17568.pdb -3.40134668053 2026-04-27 22:02:10 76 na-prot_15703.pdb -3.40013095059 2026-04-27 22:02:10 77 na-prot_19803.pdb -3.39771591918 2026-04-27 22:02:10 78 na-prot_10967.pdb -3.39752095146 2026-04-27 22:02:10 79 na-prot_16351.pdb -3.39161070774 2026-04-27 22:02:10 80 na-prot_1433.pdb -3.38669422151 2026-04-27 22:02:10 81 na-prot_12531.pdb -3.38083591841 2026-04-27 22:02:10 82 na-prot_18307.pdb -3.36846104862 2026-04-27 22:02:10 83 na-prot_723.pdb -3.36228609713 2026-04-27 22:02:10 84 na-prot_2010.pdb -3.34953491824 2026-04-27 22:02:10 85 na-prot_6204.pdb -3.34036323391 2026-04-27 22:02:10 86 na-prot_8543.pdb -3.33968159768 2026-04-27 22:02:10 87 na-prot_15400.pdb -3.33545885169 2026-04-27 22:02:10 88 na-prot_2671.pdb -3.33197319676 2026-04-27 22:02:10 89 na-prot_6245.pdb -3.31354295844 2026-04-27 22:02:10 90 na-prot_10019.pdb -3.31226008026 2026-04-27 22:02:10 91 na-prot_139.pdb -3.30730125761 2026-04-27 22:02:10 92 na-prot_15323.pdb -3.29977589565 2026-04-27 22:02:10 93 na-prot_1064.pdb -3.27979213003 2026-04-27 22:02:10 94 na-prot_10684.pdb -3.27767349719 2026-04-27 22:02:10 95 na-prot_13291.pdb -3.27669751623 2026-04-27 22:02:10 96 na-prot_8067.pdb -3.27043922558 2026-04-27 22:02:10 97 na-prot_6997.pdb -3.26607310573 2026-04-27 22:02:10 98 na-prot_2593.pdb -3.26583781087 2026-04-27 22:02:10 99 na-prot_10437.pdb -3.26244828346 2026-04-27 22:02:10 100 na-prot_5178.pdb -3.25938311464 2026-04-27 22:02:10 Chains: A 2026-04-27 22:02:35 100 best scored structures 2026-04-27 22:02:35 GRAMM analysis selected for further analysis: prot-na_30 2026-04-27 22:02:35 Cluster #1 with 100 structures 2026-04-27 22:02:35 1 na-prot_9760.pdb -4.94253042799 2026-04-27 22:02:35 2 na-prot_1963.pdb -4.94236008523 2026-04-27 22:02:35 3 na-prot_10269.pdb -4.92633888775 2026-04-27 22:02:35 4 na-prot_16952.pdb -4.84746389137 2026-04-27 22:02:35 5 na-prot_522.pdb -4.82033841197 2026-04-27 22:02:35 6 na-prot_16029.pdb -4.65793353499 2026-04-27 22:02:35 7 na-prot_14534.pdb -4.42168233534 2026-04-27 22:02:35 8 na-prot_834.pdb -4.40967352521 2026-04-27 22:02:35 9 na-prot_4459.pdb -4.26186708404 2026-04-27 22:02:35 10 na-prot_3807.pdb -4.23678492947 2026-04-27 22:02:35 11 na-prot_7970.pdb -4.20191158887 2026-04-27 22:02:35 12 na-prot_712.pdb -4.17353503186 2026-04-27 22:02:35 13 na-prot_2422.pdb -4.04939489083 2026-04-27 22:02:35 14 na-prot_8434.pdb -4.02456859238 2026-04-27 22:02:35 15 na-prot_5748.pdb -4.01980978525 2026-04-27 22:02:35 16 na-prot_19842.pdb -4.00250459984 2026-04-27 22:02:35 17 na-prot_14124.pdb -4.00242396604 2026-04-27 22:02:35 18 na-prot_6909.pdb -3.99337040144 2026-04-27 22:02:35 19 na-prot_41.pdb -3.99076600286 2026-04-27 22:02:35 20 na-prot_8556.pdb -3.9764371268 2026-04-27 22:02:35 21 na-prot_457.pdb -3.93394424493 2026-04-27 22:02:35 22 na-prot_2418.pdb -3.87275272241 2026-04-27 22:02:35 23 na-prot_7975.pdb -3.86664468625 2026-04-27 22:02:35 24 na-prot_2546.pdb -3.85077491429 2026-04-27 22:02:35 25 na-prot_3644.pdb -3.8445545741 2026-04-27 22:02:35 26 na-prot_6605.pdb -3.84443114988 2026-04-27 22:02:35 27 na-prot_7566.pdb -3.80996621302 2026-04-27 22:02:35 28 na-prot_7177.pdb -3.75796022277 2026-04-27 22:02:35 29 na-prot_16820.pdb -3.74890097522 2026-04-27 22:02:35 30 na-prot_1145.pdb -3.74552324616 2026-04-27 22:02:35 31 na-prot_5245.pdb -3.74309670069 2026-04-27 22:02:35 32 na-prot_11001.pdb -3.73260127704 2026-04-27 22:02:35 33 na-prot_16497.pdb -3.73039001875 2026-04-27 22:02:35 34 na-prot_11190.pdb -3.72851106851 2026-04-27 22:02:35 35 na-prot_1839.pdb -3.72578107619 2026-04-27 22:02:35 36 na-prot_4732.pdb -3.71702669697 2026-04-27 22:02:35 37 na-prot_1502.pdb -3.71030282948 2026-04-27 22:02:35 38 na-prot_7759.pdb -3.68257655728 2026-04-27 22:02:35 39 na-prot_135.pdb -3.67841030786 2026-04-27 22:02:35 40 na-prot_1677.pdb -3.67353241687 2026-04-27 22:02:35 41 na-prot_11415.pdb -3.61306651619 2026-04-27 22:02:35 42 na-prot_3045.pdb -3.61205592932 2026-04-27 22:02:35 43 na-prot_14369.pdb -3.58441301655 2026-04-27 22:02:35 44 na-prot_18807.pdb -3.57886475297 2026-04-27 22:02:35 45 na-prot_5368.pdb -3.57538961095 2026-04-27 22:02:35 46 na-prot_13458.pdb -3.56290668144 2026-04-27 22:02:35 47 na-prot_339.pdb -3.56128289842 2026-04-27 22:02:35 48 na-prot_3256.pdb -3.55605571809 2026-04-27 22:02:35 49 na-prot_15355.pdb -3.55443124794 2026-04-27 22:02:35 50 na-prot_8519.pdb -3.54239270163 2026-04-27 22:02:35 51 na-prot_7043.pdb -3.54035023029 2026-04-27 22:02:35 52 na-prot_8167.pdb -3.53623963694 2026-04-27 22:02:35 53 na-prot_5168.pdb -3.53597098927 2026-04-27 22:02:35 54 na-prot_15021.pdb -3.53593108641 2026-04-27 22:02:35 55 na-prot_17109.pdb -3.52764106147 2026-04-27 22:02:35 56 na-prot_12552.pdb -3.52553392753 2026-04-27 22:02:35 57 na-prot_31.pdb -3.51105627067 2026-04-27 22:02:35 58 na-prot_1232.pdb -3.49181229168 2026-04-27 22:02:35 59 na-prot_16083.pdb -3.48605554441 2026-04-27 22:02:35 60 na-prot_10622.pdb -3.48449515689 2026-04-27 22:02:35 61 na-prot_9297.pdb -3.48237172823 2026-04-27 22:02:35 62 na-prot_2931.pdb -3.47952576192 2026-04-27 22:02:35 63 na-prot_3421.pdb -3.47808382876 2026-04-27 22:02:35 64 na-prot_1293.pdb -3.47415319839 2026-04-27 22:02:35 65 na-prot_6041.pdb -3.45206379822 2026-04-27 22:02:35 66 na-prot_8214.pdb -3.43762671986 2026-04-27 22:02:35 67 na-prot_16015.pdb -3.43712227169 2026-04-27 22:02:35 68 na-prot_3818.pdb -3.43702699265 2026-04-27 22:02:35 69 na-prot_415.pdb -3.43629961661 2026-04-27 22:02:35 70 na-prot_6775.pdb -3.43533633831 2026-04-27 22:02:35 71 na-prot_110.pdb -3.43250665094 2026-04-27 22:02:35 72 na-prot_882.pdb -3.42842567463 2026-04-27 22:02:35 73 na-prot_4036.pdb -3.42611943558 2026-04-27 22:02:35 74 na-prot_2078.pdb -3.40677719385 2026-04-27 22:02:35 75 na-prot_17568.pdb -3.40134668053 2026-04-27 22:02:35 76 na-prot_15703.pdb -3.40013095059 2026-04-27 22:02:35 77 na-prot_19803.pdb -3.39771591918 2026-04-27 22:02:35 78 na-prot_10967.pdb -3.39752095146 2026-04-27 22:02:35 79 na-prot_16351.pdb -3.39161070774 2026-04-27 22:02:35 80 na-prot_1433.pdb -3.38669422151 2026-04-27 22:02:35 81 na-prot_12531.pdb -3.38083591841 2026-04-27 22:02:35 82 na-prot_18307.pdb -3.36846104862 2026-04-27 22:02:35 83 na-prot_723.pdb -3.36228609713 2026-04-27 22:02:35 84 na-prot_2010.pdb -3.34953491824 2026-04-27 22:02:35 85 na-prot_6204.pdb -3.34036323391 2026-04-27 22:02:35 86 na-prot_8543.pdb -3.33968159768 2026-04-27 22:02:35 87 na-prot_15400.pdb -3.33545885169 2026-04-27 22:02:35 88 na-prot_2671.pdb -3.33197319676 2026-04-27 22:02:35 89 na-prot_6245.pdb -3.31354295844 2026-04-27 22:02:35 90 na-prot_10019.pdb -3.31226008026 2026-04-27 22:02:35 91 na-prot_139.pdb -3.30730125761 2026-04-27 22:02:35 92 na-prot_15323.pdb -3.29977589565 2026-04-27 22:02:35 93 na-prot_1064.pdb -3.27979213003 2026-04-27 22:02:35 94 na-prot_10684.pdb -3.27767349719 2026-04-27 22:02:35 95 na-prot_13291.pdb -3.27669751623 2026-04-27 22:02:35 96 na-prot_8067.pdb -3.27043922558 2026-04-27 22:02:35 97 na-prot_6997.pdb -3.26607310573 2026-04-27 22:02:35 98 na-prot_2593.pdb -3.26583781087 2026-04-27 22:02:35 99 na-prot_10437.pdb -3.26244828346 2026-04-27 22:02:35 100 na-prot_5178.pdb -3.25938311464 2026-04-27 22:02:35 Sent to refinement: clusters_found|na-prot_9760.pdb 2026-04-27 22:02:35 Sent to refinement: clusters_found|na-prot_9760.pdb 2026-04-27 22:02:35 DARS clustering end 2026-04-27 22:02:35 MC (refinement) init 2026-04-27 22:02:35 python /home/rpdock/run_gramm//run_mc.py -f dars_to_mc.txt -d /home/rpdock/web/media/jobs/deb82bf2-cc38-4464-8ae9-3ce758cd0b27/ 2026-04-27 22:02:35 Refinement of #1 /home/rpdock/web/media/jobs/deb82bf2-cc38-4464-8ae9-3ce758cd0b27/na-prot_9760.pdb 2026-04-27 22:02:35 python /home/rpdock/mc/MC_DNA.py -s 1000 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/deb82bf2-cc38-4464-8ae9-3ce758cd0b27//ref_struc/na-prot_9760/na-prot_9760.pdb 2026-04-27 22:06:16 run_mc::stderr:Traceback (most recent call last): File "/home/rpdock/mc/MC_DNA.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_DNA.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_DNA.py", line 297, in all_atom pro_ch, rna_ch = check_chains(plik, pars) File "/home/rpdock/mc/MC_DNA.py", line 103, 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 2026-04-27 22:06:16 start - parameters: File name /home/rpdock/web/media/jobs/deb82bf2-cc38-4464-8ae9-3ce758cd0b27//ref_struc/na-prot_9760/na-prot_9760.pdb Steps 1000 Temp. start 15000.0 Temp. end 295.0 False msg start - parameters: File name /home/rpdock/web/media/jobs/deb82bf2-cc38-4464-8ae9-3ce758cd0b27//ref_struc/na-prot_9760/na-prot_9760.pdb Steps 1000 Temp. start 15000.0 Temp. end 295.0 False Step E Edist Eang Epen Warning, residue DC1 in the chain A has not P atom Missed atom CG in the LYS 94 Missed atom CD in the LYS 94 Missed atom CE in the LYS 94 Missed atom NZ in the LYS 94 Missed atom CG in the LYS 97 Missed atom CD in the LYS 97 Missed atom CE in the LYS 97 Missed atom NZ in the LYS 97 Missed atom OG in the SER 99 Missed atom CG in the LYS 103 Missed atom CD in the LYS 103 Missed atom CE in the LYS 103 Missed atom NZ in the LYS 103 Missed atom CG in the LYS 136 Missed atom CD in the LYS 136 Missed atom CE in the LYS 136 Missed atom NZ in the LYS 136 Missed atom CG in the LYS 137 Missed atom CD in the LYS 137 Missed atom CE in the LYS 137 Missed atom NZ in the LYS 137 Missed atom CG in the GLU 145 Missed atom CD in the GLU 145 Missed atom OE1 in the GLU 145 Missed atom OE2 in the GLU 145 Missed atom CG in the ARG 174 Missed atom CD in the ARG 174 Missed atom NE in the ARG 174 Missed atom CZ in the ARG 174 Missed atom NH1 in the ARG 174 Missed atom NH2 in the ARG 174 Missed atom CG in the ARG 188 Missed atom CD in the ARG 188 Missed atom NE in the ARG 188 Missed atom CZ in the ARG 188 Missed atom NH1 in the ARG 188 Missed atom NH2 in the ARG 188 Missed atom CG in the GLN 190 Missed atom CD in the GLN 190 Missed atom OE1 in the GLN 190 Missed atom NE2 in the GLN 190 Missed atom CG in the LYS 191 Missed atom CD in the LYS 191 Missed atom CE in the LYS 191 Missed atom NZ in the LYS 191 0 - -437304.21 -725202.24 -192101.97 480000.00 1 R -492262.07 -737385.56 -194876.51 440000.00 T= 15000.0 K progress 0.1 2 T -517446.89 -692998.57 -184448.32 360000.00 T= 14985.295 K progress 0.2 3 T -488275.88 -699505.32 -188770.56 400000.00 T= 14955.885 K progress 0.3 4 R -560993.75 -660401.36 -180592.39 280000.00 T= 14941.18 K progress 0.4 5 T -587253.23 -651808.52 -175444.71 240000.00 T= 14926.475 K progress 0.5 6 R -534945.49 -641938.41 -173007.08 280000.00 T= 14897.065 K progress 0.6 7 T -529137.43 -620339.73 -148797.70 240000.00 T= 14882.36 K progress 0.7 8 R -528402.52 -616472.51 -151930.02 240000.00 T= 14867.655 K progress 0.8 9 R -561168.18 -604332.39 -156835.79 200000.00 T= 14852.95 K progress 0.9 10 R -605670.22 -674329.15 -171341.06 240000.00 T= 14838.245 K progress 1.0 11 R -584902.80 -665950.72 -158952.08 240000.00 T= 14823.54 K progress 1.1 12 R -583757.74 -624790.06 -158967.68 200000.00 T= 14808.835 K progress 1.2 13 T -630188.16 -623931.57 -166256.60 160000.00 T= 14794.13 K progress 1.3 14 T -731650.72 -641151.35 -170499.37 80000.00 T= 14779.425 K progress 1.4 15 R -673713.43 -635573.26 -158140.16 120000.00 T= 14705.9 K progress 1.5 16 T -527936.75 -589125.87 -138810.88 200000.00 T= 14676.49 K progress 1.6 17 R -574415.19 -626938.80 -147476.38 200000.00 T= 14661.785 K progress 1.7 18 T -482201.99 -719134.67 -163067.32 400000.00 T= 14647.08 K progress 1.8 19 T -496984.78 -649247.05 -167737.74 320000.00 T= 14602.965 K progress 1.9 20 R -500931.87 -654573.13 -166358.74 320000.00 T= 14588.26 K progress 2.0 21 T -558222.81 -658011.65 -180211.17 280000.00 T= 14573.555 K progress 2.1 22 T -565232.94 -725456.54 -159776.40 320000.00 T= 14529.44 K progress 2.2 23 T -573384.94 -740110.21 -153274.72 320000.00 T= 14500.03 K progress 2.3 24 R -504796.28 -693314.32 -171481.96 360000.00 T= 14485.325 K progress 2.4 25 R -524014.42 -733114.01 -150900.41 360000.00 T= 14455.915 K progress 2.5 26 T -274086.53 -741421.50 -172665.03 640000.00 T= 14426.505 K progress 2.6 27 R -280116.18 -747582.85 -172533.33 640000.00 T= 14411.8 K progress 2.7 28 R -102494.55 -770508.35 -171986.21 840000.00 T= 14397.095 K progress 2.8 29 T -183768.22 -675773.12 -147995.10 640000.00 T= 14382.39 K progress 2.9 30 T -186169.84 -595863.24 -150306.60 560000.00 T= 14367.685 K progress 3.0 31 T -340856.50 -606268.05 -134588.44 400000.00 T= 14352.98 K progress 3.1 32 R -465792.92 -630841.66 -154951.26 320000.00 T= 14338.275 K progress 3.2 33 R -216642.19 -613286.32 -163355.87 560000.00 T= 14323.57 K progress 3.3 34 R 15358.57 -618129.72 -166511.71 800000.00 T= 14279.455 K progress 3.4 35 T -308455.67 -560506.51 -147949.16 400000.00 T= 14264.75 K progress 3.5 36 T -319936.59 -529362.34 -150574.25 360000.00 T= 14250.045 K progress 3.6 37 T -170363.03 -577371.43 -152991.60 560000.00 T= 14205.93 K progress 3.7 38 T -465704.32 -519198.72 -146505.60 200000.00 T= 14191.225 K progress 3.8 39 R -319839.83 -520520.57 -159319.26 360000.00 T= 14176.52 K progress 3.9 40 R -350628.59 -522538.75 -148089.83 320000.00 T= 14161.815 K progress 4.0 41 T -500664.13 -487069.47 -133594.67 120000.00 T= 14147.11 K progress 4.1 42 T -552685.63 -485939.36 -146746.27 80000.00 T= 14102.995 K progress 4.2 43 R -487214.19 -491571.02 -155643.17 160000.00 T= 14088.29 K progress 4.3 44 T -458743.77 -513535.25 -145208.52 200000.00 T= 14073.585 K progress 4.4 45 T -705841.88 -633976.90 -191864.98 120000.00 T= 14058.88 K progress 4.5 46 R -682305.39 -678117.71 -204187.67 200000.00 T= 14044.175 K progress 4.6 47 T -519349.42 -660870.93 -178478.49 320000.00 T= 13985.355 K progress 4.7 48 T -508553.00 -651237.51 -177315.49 320000.00 T= 13970.65 K progress 4.8 49 R -524516.01 -662863.02 -181652.98 320000.00 T= 13941.24 K progress 4.9 50 R -512694.57 -679953.25 -192741.32 360000.00 T= 13926.535 K progress 5.0 51 R -545976.58 -620466.85 -165509.73 240000.00 T= 13911.83 K progress 5.1 52 R -542655.21 -594558.09 -188097.12 240000.00 T= 13838.305 K progress 5.2 53 R -555210.36 -626112.94 -169097.42 240000.00 T= 13808.895 K progress 5.3 54 R -687097.39 -694475.76 -192621.63 200000.00 T= 13794.19 K progress 5.4 55 T -514457.08 -727770.41 -186686.68 400000.00 T= 13779.485 K progress 5.5 56 R -426786.74 -713866.77 -192919.97 480000.00 T= 13764.78 K progress 5.6 57 T -512055.55 -718381.22 -193674.33 400000.00 T= 13750.075 K progress 5.7 58 T -335946.10 -720125.44 -175820.66 560000.00 T= 13676.55 K progress 5.8 59 T -630366.65 -752457.52 -197909.13 320000.00 T= 13647.14 K progress 5.9 60 T -516647.00 -760356.51 -196290.49 440000.00 T= 13632.435 K progress 6.0 61 T -432426.03 -715360.54 -197065.49 480000.00 T= 13617.73 K progress 6.1 62 T -218347.42 -613119.22 -165228.20 560000.00 T= 13573.615 K progress 6.2 63 R 145822.47 -633903.14 -140274.39 920000.00 T= 13558.91 K progress 6.3 64 R 360427.74 -600035.53 -159536.74 1120000.00 T= 13544.205 K progress 6.4 65 T 349887.49 -634420.86 -175691.65 1160000.00 T= 13514.795 K progress 6.5 66 R 4741.34 -627192.72 -168065.94 800000.00 T= 13500.09 K progress 6.6 67 T -157055.80 -617050.41 -180005.39 640000.00 T= 13485.385 K progress 6.7 68 T -385262.94 -541161.70 -164101.24 320000.00 T= 13441.27 K progress 6.8 69 R -377902.86 -509773.17 -148129.69 280000.00 T= 13397.155 K progress 6.9 70 R -454583.90 -464578.28 -150005.63 160000.00 T= 13382.45 K progress 7.0 71 R -365943.07 -497507.71 -148435.36 280000.00 T= 13367.745 K progress 7.1 72 R -347313.75 -484241.11 -143072.64 280000.00 T= 13353.04 K progress 7.2 73 R -344493.05 -481420.41 -143072.64 280000.00 T= 13338.335 K progress 7.3 74 R -352500.23 -517618.53 -154881.70 320000.00 T= 13308.925 K progress 7.4 75 T -363031.78 -481234.11 -161797.67 280000.00 T= 13294.22 K progress 7.5 76 R -403647.32 -508700.65 -174946.66 280000.00 T= 13279.515 K progress 7.6 77 T -609230.36 -627828.19 -181402.18 200000.00 T= 13264.81 K progress 7.7 78 R -520600.28 -587834.68 -172765.61 240000.00 T= 13250.105 K progress 7.8 79 R -511005.12 -577605.82 -173399.30 240000.00 T= 13220.695 K progress 7.9 80 R -482686.85 -562644.26 -160042.58 240000.00 T= 13191.285 K progress 8.0 81 T -506564.90 -583866.77 -162698.13 240000.00 T= 13176.58 K progress 8.1 82 T -350169.85 -550516.37 -159653.48 360000.00 T= 13147.17 K progress 8.2 83 R -371194.31 -564394.94 -166799.37 360000.00 T= 13103.055 K progress 8.3 84 R -358357.44 -554376.18 -163981.26 360000.00 T= 13058.94 K progress 8.4 85 R -509470.63 -549631.90 -159838.73 200000.00 T= 13044.235 K progress 8.5 86 R -165173.99 -567168.91 -158005.08 560000.00 T= 13014.825 K progress 8.6 87 R -155367.34 -557626.69 -157740.65 560000.00 T= 13000.12 K progress 8.7 88 T -524569.87 -571004.99 -153564.88 200000.00 T= 12985.415 K progress 8.8 89 R -598709.10 -556712.23 -161996.87 120000.00 T= 12970.71 K progress 8.9 90 R -579241.20 -542726.70 -156514.50 120000.00 T= 12956.005 K progress 9.0 91 R -614496.71 -565303.34 -169193.37 120000.00 T= 12926.595 K progress 9.1 92 R -686572.19 -620309.25 -186262.95 120000.00 T= 12911.89 K progress 9.2 93 R -634667.08 -585792.79 -168874.29 120000.00 T= 12897.185 K progress 9.3 94 R -569083.68 -615846.93 -193236.75 240000.00 T= 12882.48 K progress 9.4 95 T -567902.81 -628287.68 -179615.14 240000.00 T= 12838.365 K progress 9.5 96 R -539667.29 -614316.02 -165351.28 240000.00 T= 12823.66 K progress 9.6 97 T -479242.40 -682540.06 -196702.34 400000.00 T= 12794.25 K progress 9.7 98 R -397545.63 -617858.07 -179687.55 400000.00 T= 12764.84 K progress 9.8 99 R -438160.53 -649294.65 -188865.88 400000.00 T= 12750.135 K progress 9.9 100 T -654251.43 -604505.24 -169746.19 120000.00 T= 12735.43 K progress 10.0 101 T -683966.24 -585815.99 -178150.25 80000.00 T= 12676.61 K progress 10.1 102 R -621966.41 -529592.76 -172373.65 80000.00 T= 12647.2 K progress 10.2 103 T -500379.61 -445246.84 -135132.77 80000.00 T= 12632.495 K progress 10.3 104 R -485452.52 -461753.72 -143698.80 120000.00 T= 12603.085 K progress 10.4 105 T -345391.36 -548978.33 -156413.04 360000.00 T= 12573.675 K progress 10.5 106 R -446835.92 -584964.21 -181871.71 320000.00 T= 12558.97 K progress 10.6 107 R -455951.90 -536500.71 -159451.19 240000.00 T= 12544.265 K progress 10.7 108 T -410878.06 -614169.79 -156708.27 360000.00 T= 12500.15 K progress 10.8 109 T -329969.60 -656430.20 -153539.40 480000.00 T= 12470.74 K progress 10.9 110 R -160664.48 -680066.17 -160598.31 680000.00 T= 12441.33 K progress 11.0 111 T -248403.82 -747187.12 -181216.70 680000.00 T= 12411.92 K progress 11.1 112 R -429578.09 -705452.08 -164126.01 440000.00 T= 12382.51 K progress 11.2 113 T -481060.88 -668366.67 -172694.20 360000.00 T= 12367.805 K progress 11.3 114 T -588859.18 -630754.40 -198104.78 240000.00 T= 12353.1 K progress 11.4 115 T -439241.03 -522127.51 -157113.52 240000.00 T= 12250.165 K progress 11.5 116 T -389610.18 -575521.69 -174088.49 360000.00 T= 12235.46 K progress 11.6 117 R -197139.18 -547182.04 -169957.15 520000.00 T= 12220.755 K progress 11.7 118 T -373312.61 -552264.12 -181048.48 360000.00 T= 12191.345 K progress 11.8 119 T -522598.26 -654065.10 -188533.16 320000.00 T= 12147.23 K progress 11.9 120 R -491962.69 -564990.96 -166971.73 240000.00 T= 12103.115 K progress 12.0 121 T -456184.18 -653411.00 -162773.18 360000.00 T= 12073.705 K progress 12.1 122 T -385328.87 -616018.26 -169310.60 400000.00 T= 12029.59 K progress 12.2 123 T -376185.10 -636889.88 -179295.22 440000.00 T= 12014.885 K progress 12.3 124 T -447616.45 -590011.12 -177605.32 320000.00 T= 11956.065 K progress 12.4 125 T -561861.85 -590771.64 -171090.21 200000.00 T= 11941.36 K progress 12.5 126 R -397043.28 -622286.28 -174757.00 400000.00 T= 11897.245 K progress 12.6 127 T -234654.08 -655753.30 -178900.78 600000.00 T= 11853.13 K progress 12.7 128 R -400753.13 -639042.55 -161710.58 400000.00 T= 11838.425 K progress 12.8 129 R -584023.58 -616718.77 -167304.81 200000.00 T= 11823.72 K progress 12.9 130 T -536460.40 -557991.34 -138469.06 160000.00 T= 11809.015 K progress 13.0 131 R -380890.21 -555549.88 -145340.33 320000.00 T= 11794.31 K progress 13.1 132 R -530793.64 -550195.18 -140598.46 160000.00 T= 11764.9 K progress 13.2 133 R -523931.51 -545317.32 -138614.19 160000.00 T= 11750.195 K progress 13.3 134 R -562462.82 -578991.50 -143471.32 160000.00 T= 11735.49 K progress 13.4 135 R -552764.99 -569781.60 -142983.39 160000.00 T= 11720.785 K progress 13.5 136 T -550099.79 -592911.97 -157187.82 200000.00 T= 11691.375 K progress 13.6 137 R -591720.32 -617529.02 -174191.29 200000.00 T= 11676.67 K progress 13.7 138 T -605259.93 -607019.46 -158240.47 160000.00 T= 11647.26 K progress 13.8 139 R -521232.51 -550958.47 -130274.04 160000.00 T= 11632.555 K progress 13.9 140 T -491655.38 -518261.31 -133394.06 160000.00 T= 11603.145 K progress 14.0 141 R -565638.52 -535273.50 -150365.02 120000.00 T= 11544.325 K progress 14.1 142 R -486670.83 -471603.76 -135067.07 120000.00 T= 11529.62 K progress 14.2 143 R -546364.19 -522550.65 -143813.54 120000.00 T= 11514.915 K progress 14.3 144 R -508066.83 -489338.60 -138728.23 120000.00 T= 11470.8 K progress 14.4 145 R -462115.26 -453219.25 -128896.01 120000.00 T= 11456.095 K progress 14.5 146 T -248489.84 -468558.53 -139931.31 360000.00 T= 11397.275 K progress 14.6 147 T -351824.76 -421620.09 -130204.68 200000.00 T= 11382.57 K progress 14.7 148 R -401344.26 -426189.60 -135154.65 160000.00 T= 11367.865 K progress 14.8 149 R -369728.14 -415271.50 -114456.64 160000.00 T= 11353.16 K progress 14.9 150 R -376245.61 -418059.79 -118185.82 160000.00 T= 11338.455 K progress 15.0 151 T -215699.38 -416102.26 -119597.12 320000.00 T= 11309.045 K progress 15.1 152 T -386948.72 -422003.77 -124944.95 160000.00 T= 11294.34 K progress 15.2 153 R -393877.83 -425389.25 -128488.58 160000.00 T= 11235.52 K progress 15.3 154 R -328975.24 -407473.02 -121502.22 200000.00 T= 11103.175 K progress 15.4 155 R -399351.74 -435060.12 -124291.62 160000.00 T= 11088.47 K progress 15.5 156 R -389798.38 -428767.70 -121030.68 160000.00 T= 11073.765 K progress 15.6 157 R -397411.79 -433191.59 -124220.20 160000.00 T= 11044.355 K progress 15.7 158 T -355817.43 -404550.71 -111266.73 160000.00 T= 11000.24 K progress 15.8 159 R -341907.11 -413166.15 -128740.97 200000.00 T= 10985.535 K progress 15.9 160 R -334897.10 -407929.54 -126967.57 200000.00 T= 10970.83 K progress 16.0 161 R -332128.55 -406638.30 -125490.25 200000.00 T= 10956.125 K progress 16.1 162 R -338082.81 -410202.31 -127880.50 200000.00 T= 10941.42 K progress 16.2 163 R -341388.92 -414812.66 -126576.26 200000.00 T= 10926.715 K progress 16.3 164 R -341555.50 -412392.98 -129162.53 200000.00 T= 10912.01 K progress 16.4 165 R -346986.95 -415988.45 -130998.50 200000.00 T= 10897.305 K progress 16.5 166 R -347278.32 -417677.76 -129600.56 200000.00 T= 10882.6 K progress 16.6 167 R -359886.43 -427774.06 -132112.38 200000.00 T= 10867.895 K progress 16.7 168 R -350279.15 -418024.82 -132254.32 200000.00 T= 10853.19 K progress 16.8 169 R -376003.03 -469826.49 -146176.54 240000.00 T= 10823.78 K progress 16.9 170 R -364136.96 -429093.85 -135043.11 200000.00 T= 10809.075 K progress 17.0 171 R -348484.63 -418180.31 -130304.32 200000.00 T= 10779.665 K progress 17.1 172 T -395895.09 -460099.01 -135796.08 200000.00 T= 10750.255 K progress 17.2 173 R -401170.76 -461939.98 -139230.79 200000.00 T= 10735.55 K progress 17.3 174 T -386315.07 -451555.24 -134759.83 200000.00 T= 10720.845 K progress 17.4 175 R -404419.47 -455507.72 -148911.75 200000.00 T= 10706.14 K progress 17.5 176 R -438595.01 -483984.18 -154610.83 200000.00 T= 10632.615 K progress 17.6 177 R -423582.36 -469311.36 -154271.00 200000.00 T= 10603.205 K progress 17.7 178 R -388039.27 -451818.21 -136221.06 200000.00 T= 10588.5 K progress 17.8 179 T -371407.76 -439921.51 -131486.25 200000.00 T= 10514.975 K progress 17.9 180 R -369552.70 -441527.65 -128025.05 200000.00 T= 10500.27 K progress 18.0 181 T -314962.64 -499186.38 -135776.26 320000.00 T= 10470.86 K progress 18.1 182 R -421619.34 -518696.08 -142923.26 240000.00 T= 10456.155 K progress 18.2 183 R -477617.97 -527289.56 -150328.41 200000.00 T= 10412.04 K progress 18.3 184 T -452163.45 -507422.13 -144741.33 200000.00 T= 10397.335 K progress 18.4 185 R -496691.38 -523716.13 -132975.25 160000.00 T= 10382.63 K progress 18.5 186 T -352916.85 -493690.46 -139226.38 280000.00 T= 10323.81 K progress 18.6 187 R -351385.08 -493637.08 -137748.00 280000.00 T= 10309.105 K progress 18.7 188 R -376442.82 -518301.96 -138140.85 280000.00 T= 10279.695 K progress 18.8 189 R -305223.25 -455091.82 -130131.43 280000.00 T= 10264.99 K progress 18.9 190 R -496720.53 -488548.74 -128171.80 120000.00 T= 10235.58 K progress 19.0 191 R -471673.97 -469686.58 -121987.39 120000.00 T= 10206.17 K progress 19.1 192 R -467301.23 -461126.71 -126174.52 120000.00 T= 10191.465 K progress 19.2 193 R -301763.18 -457558.31 -124204.87 280000.00 T= 10176.76 K progress 19.3 194 T -278394.90 -433222.22 -125172.68 280000.00 T= 10147.35 K progress 19.4 195 T -410846.49 -408154.59 -122691.90 120000.00 T= 10117.94 K progress 19.5 196 R -395858.30 -400342.16 -115516.14 120000.00 T= 10103.235 K progress 19.6 197 T -341460.37 -381625.63 -119834.74 160000.00 T= 10088.53 K progress 19.7 198 T -369007.39 -444878.13 -124129.27 200000.00 T= 10073.825 K progress 19.8 199 R -444134.72 -474085.85 -130048.87 160000.00 T= 10059.12 K progress 19.9 200 R -445633.04 -471977.54 -133655.50 160000.00 T= 10044.415 K progress 20.0 Long traj 201 R -442517.28 -475311.55 -127205.74 160000.00 T= 10029.71 K progress 20.1 202 R -404604.07 -468568.60 -136035.47 200000.00 T= 10015.005 K progress 20.2 203 T -329042.89 -409853.53 -119189.36 200000.00 T= 9985.595 K progress 20.3 204 R -432998.59 -455627.96 -137370.64 160000.00 T= 9970.89 K progress 20.4 205 T -280661.32 -460399.94 -140261.38 320000.00 T= 9956.185 K progress 20.5 206 R -448499.92 -458450.89 -150049.04 160000.00 T= 9941.48 K progress 20.6 207 T -440418.41 -525476.36 -154942.05 240000.00 T= 9926.775 K progress 20.7 208 R -393517.57 -527285.88 -146231.69 280000.00 T= 9897.365 K progress 20.8 209 R -460110.95 -539943.34 -160167.61 240000.00 T= 9867.955 K progress 20.9 210 T -421182.13 -510876.94 -150305.19 240000.00 T= 9838.545 K progress 21.0 211 R -418800.96 -512700.68 -146100.29 240000.00 T= 9823.84 K progress 21.1 212 R -400999.29 -501302.51 -139696.78 240000.00 T= 9794.43 K progress 21.2 213 R -498296.24 -546729.06 -151567.18 200000.00 T= 9779.725 K progress 21.3 214 R -469971.78 -527942.50 -142029.28 200000.00 T= 9735.61 K progress 21.4 215 T -424317.33 -453243.70 -131073.63 160000.00 T= 9647.38 K progress 21.5 216 R -270671.38 -457608.11 -133063.27 320000.00 T= 9632.675 K progress 21.6 217 R -268357.56 -455993.32 -132364.25 320000.00 T= 9603.265 K progress 21.7 218 R -265920.46 -451177.24 -134743.22 320000.00 T= 9588.56 K progress 21.8 219 R -413341.89 -442301.79 -131040.10 160000.00 T= 9573.855 K progress 21.9 220 R -465502.23 -487717.88 -137784.34 160000.00 T= 9515.035 K progress 22.0 221 R -475453.06 -499033.27 -136419.79 160000.00 T= 9500.33 K progress 22.1 222 R -458627.79 -476041.30 -142586.49 160000.00 T= 9485.625 K progress 22.2 223 R -289530.85 -473323.27 -136207.58 320000.00 T= 9397.395 K progress 22.3 224 R -488809.70 -503145.01 -145664.70 160000.00 T= 9353.28 K progress 22.4 225 T -502295.56 -513226.45 -149069.11 160000.00 T= 9309.165 K progress 22.5 226 R -523640.67 -531730.45 -151910.21 160000.00 T= 9294.46 K progress 22.6 227 T -483348.25 -565980.17 -157368.08 240000.00 T= 9279.755 K progress 22.7 228 T -426126.60 -522492.06 -143634.54 240000.00 T= 9191.525 K progress 22.8 229 R -456160.65 -535242.30 -160918.34 240000.00 T= 9147.41 K progress 22.9 230 T -525169.94 -529631.47 -155538.47 160000.00 T= 9118.0 K progress 23.0 231 T -487870.59 -538054.56 -149816.03 200000.00 T= 9073.885 K progress 23.1 232 R -508568.63 -552902.36 -155666.27 200000.00 T= 9059.18 K progress 23.2 233 R -457126.95 -543147.88 -153979.07 240000.00 T= 9044.475 K progress 23.3 234 T -517149.61 -525816.05 -151333.56 160000.00 T= 9029.77 K progress 23.4 235 T -435379.19 -533066.76 -142312.43 240000.00 T= 8956.245 K progress 23.5 236 T -436269.66 -535991.77 -140277.89 240000.00 T= 8941.54 K progress 23.6 237 R -489224.89 -532338.46 -156886.43 200000.00 T= 8926.835 K progress 23.7 238 R -508630.25 -551705.87 -156924.38 200000.00 T= 8912.13 K progress 23.8 239 R -482772.91 -528842.89 -153930.02 200000.00 T= 8882.72 K progress 23.9 240 R -472215.35 -560670.10 -151545.26 240000.00 T= 8868.015 K progress 24.0 241 R -476261.43 -564716.18 -151545.26 240000.00 T= 8853.31 K progress 24.1 242 R -468460.36 -523250.45 -145209.92 200000.00 T= 8823.9 K progress 24.2 243 R -477301.00 -564314.18 -152986.82 240000.00 T= 8765.08 K progress 24.3 244 R -534186.46 -567708.29 -166478.17 200000.00 T= 8750.375 K progress 24.4 245 R -516274.82 -554403.79 -161871.04 200000.00 T= 8735.67 K progress 24.5 246 T -515489.58 -525429.62 -150059.96 160000.00 T= 8676.85 K progress 24.6 247 R -515489.58 -525429.62 -150059.96 160000.00 T= 8662.145 K progress 24.7 248 R -515240.81 -525431.51 -149809.30 160000.00 T= 8647.44 K progress 24.8 249 R -349713.38 -548590.62 -161122.77 360000.00 T= 8618.03 K progress 24.9 250 R -560279.94 -560873.41 -159406.53 160000.00 T= 8603.325 K progress 25.0 251 R -491904.91 -509993.63 -141911.28 160000.00 T= 8573.915 K progress 25.1 252 R -442307.77 -471909.25 -130398.52 160000.00 T= 8529.8 K progress 25.2 253 T -439385.85 -466190.94 -133194.90 160000.00 T= 8515.095 K progress 25.3 254 R -442145.34 -458051.09 -144094.25 160000.00 T= 8500.39 K progress 25.4 255 R -474009.62 -490649.21 -143360.40 160000.00 T= 8485.685 K progress 25.5 256 R -451015.75 -466789.57 -144226.19 160000.00 T= 8470.98 K progress 25.6 257 R -441358.20 -461015.79 -140342.42 160000.00 T= 8456.275 K progress 25.7 258 R -446372.71 -464501.81 -141870.90 160000.00 T= 8441.57 K progress 25.8 259 R -448890.01 -464576.08 -144313.92 160000.00 T= 8426.865 K progress 25.9 260 R -444391.48 -468120.69 -136270.79 160000.00 T= 8412.16 K progress 26.0 261 R -475747.73 -485589.23 -150158.49 160000.00 T= 8353.34 K progress 26.1 262 R -447703.02 -460327.05 -147375.97 160000.00 T= 8279.815 K progress 26.2 263 R -516974.73 -523262.07 -153712.66 160000.00 T= 8265.11 K progress 26.3 264 R -610794.36 -595242.73 -175551.63 160000.00 T= 8250.405 K progress 26.4 265 T -611612.76 -596298.54 -175314.22 160000.00 T= 8235.7 K progress 26.5 266 T -612057.95 -595824.14 -176233.81 160000.00 T= 8206.29 K progress 26.6 267 R -522282.13 -523993.42 -158288.71 160000.00 T= 8162.175 K progress 26.7 268 T -514584.21 -506784.64 -167799.57 160000.00 T= 8132.765 K progress 26.8 269 R -589482.81 -531305.31 -178177.50 120000.00 T= 8118.06 K progress 26.9 270 R -598749.47 -540468.34 -178281.13 120000.00 T= 8103.355 K progress 27.0 271 T -542109.82 -568233.08 -173876.74 200000.00 T= 8088.65 K progress 27.1 272 T -648810.35 -595908.45 -172901.90 120000.00 T= 8073.945 K progress 27.2 273 T -658284.63 -620643.29 -157641.34 120000.00 T= 8029.83 K progress 27.3 274 T -667607.35 -650471.18 -177136.17 160000.00 T= 8000.42 K progress 27.4 275 T -586451.63 -591751.93 -154699.71 160000.00 T= 7971.01 K progress 27.5 276 T -373594.93 -502271.04 -151323.89 280000.00 T= 7912.19 K progress 27.6 277 T -637752.65 -629930.65 -167822.00 160000.00 T= 7882.78 K progress 27.7 278 R -613259.07 -616535.28 -156723.80 160000.00 T= 7868.075 K progress 27.8 279 R -543596.08 -670559.94 -193036.15 320000.00 T= 7823.96 K progress 27.9 280 R -528058.48 -659085.76 -188972.72 320000.00 T= 7794.55 K progress 28.0 281 R -509462.06 -649711.99 -179750.07 320000.00 T= 7779.845 K progress 28.1 282 R -435450.12 -615954.61 -179495.51 360000.00 T= 7765.14 K progress 28.2 283 T -450308.90 -631276.91 -179031.98 360000.00 T= 7750.435 K progress 28.3 284 T -528643.25 -564740.58 -163902.68 200000.00 T= 7735.73 K progress 28.4 285 T -629928.85 -629507.51 -200421.34 200000.00 T= 7706.32 K progress 28.5 286 T -556424.67 -582320.61 -174104.06 200000.00 T= 7691.615 K progress 28.6 287 T -513658.72 -688521.35 -185137.37 360000.00 T= 7647.5 K progress 28.7 288 R -566041.63 -589007.39 -177034.25 200000.00 T= 7603.385 K progress 28.8 289 R -680157.43 -650749.47 -189407.97 160000.00 T= 7544.565 K progress 28.9 290 R -572544.58 -631810.31 -180734.27 240000.00 T= 7515.155 K progress 29.0 291 T -629085.70 -623477.00 -165608.70 160000.00 T= 7500.45 K progress 29.1 292 R -637805.07 -626764.80 -171040.27 160000.00 T= 7456.335 K progress 29.2 293 R -640033.89 -631887.79 -168146.11 160000.00 T= 7441.63 K progress 29.3 294 R -667313.17 -649277.82 -178035.36 160000.00 T= 7426.925 K progress 29.4 295 R -651938.76 -633425.89 -178512.87 160000.00 T= 7382.81 K progress 29.5 296 R -650407.67 -636714.28 -173693.39 160000.00 T= 7353.4 K progress 29.6 297 R -661324.79 -610502.00 -170822.79 120000.00 T= 7309.285 K progress 29.7 298 R -654542.78 -640849.39 -173693.39 160000.00 T= 7206.35 K progress 29.8 299 R -654798.05 -636285.18 -178512.87 160000.00 T= 7103.415 K progress 29.9 300 T -646736.41 -593055.07 -173681.34 120000.00 T= 7074.005 K progress 30.0 301 T -589021.17 -510055.28 -158965.88 80000.00 T= 7059.3 K progress 30.1 302 T -581299.98 -503239.26 -158060.72 80000.00 T= 7015.185 K progress 30.2 303 R -687209.39 -560190.45 -167018.93 40000.00 T= 7000.48 K progress 30.3 304 R -692208.19 -565297.94 -166910.25 40000.00 T= 6985.775 K progress 30.4 305 R -696676.96 -567157.98 -169518.97 40000.00 T= 6853.43 K progress 30.5 306 R -683937.35 -577689.92 -186247.42 80000.00 T= 6706.38 K progress 30.6 307 R -697451.62 -567965.12 -169486.50 40000.00 T= 6647.56 K progress 30.7 308 T -530483.21 -583273.30 -187209.92 240000.00 T= 6618.15 K progress 30.8 309 T -586908.75 -678016.06 -188892.69 280000.00 T= 6588.74 K progress 30.9 310 R -600238.05 -689713.76 -190524.29 280000.00 T= 6559.33 K progress 31.0 311 R -565149.55 -660542.80 -184606.75 280000.00 T= 6500.51 K progress 31.1 312 T -340988.73 -631629.92 -189358.80 480000.00 T= 6485.805 K progress 31.2 313 T -367285.55 -692925.50 -194360.04 520000.00 T= 6471.1 K progress 31.3 314 T -613179.57 -652477.77 -200701.80 240000.00 T= 6456.395 K progress 31.4 315 T -563534.90 -733746.75 -189788.15 360000.00 T= 6382.87 K progress 31.5 316 R -752621.01 -748095.65 -204525.36 200000.00 T= 6324.05 K progress 31.6 317 T -766584.27 -761845.12 -204739.15 200000.00 T= 6294.64 K progress 31.7 318 T -633891.44 -707327.66 -206563.78 280000.00 T= 6265.23 K progress 31.8 319 T -756638.31 -763138.19 -193500.12 200000.00 T= 6250.525 K progress 31.9 320 T -746077.97 -777351.64 -208726.33 240000.00 T= 6235.82 K progress 32.0 Traceback (most recent call last): File "/home/rpdock/mc/MC_DNA.py", line 551, in change_atom_list, change_chains, change_chains1, trans_vec = translation(change_chains) File "/home/rpdock/mc/MC_DNA.py", line 262, in translation rna_chains1 = deepcopy(rna_chains) File "/usr/lib/python2.7/copy.py", line 163, in deepcopy y = copier(x, memo) File "/usr/lib/python2.7/copy.py", line 230, in _deepcopy_list y.append(deepcopy(a, memo)) File "/usr/lib/python2.7/copy.py", line 190, in deepcopy y = _reconstruct(x, rv, 1, memo) File "/usr/lib/python2.7/copy.py", line 334, in _reconstruct state = deepcopy(state, memo) File "/usr/lib/python2.7/copy.py", line 163, in deepcopy y = copier(x, memo) File "/usr/lib/python2.7/copy.py", line 257, in _deepcopy_dict y[deepcopy(key, memo)] = deepcopy(value, memo) File "/usr/lib/python2.7/copy.py", line 163, in deepcopy y = copier(x, memo) File "/usr/lib/python2.7/copy.py", line 257, in _deepcopy_dict y[deepcopy(key, memo)] = deepcopy(value, memo) File "/usr/lib/python2.7/copy.py", line 190, in deepcopy y = _reconstruct(x, rv, 1, memo) File "/usr/lib/python2.7/copy.py", line 334, in _reconstruct state = deepcopy(state, memo) File "/usr/lib/python2.7/copy.py", line 163, in deepcopy y = copier(x, memo) File "/usr/lib/python2.7/copy.py", line 257, in _deepcopy_dict y[deepcopy(key, memo)] = deepcopy(value, memo) File "/usr/lib/python2.7/copy.py", line 163, in deepcopy y = copier(x, memo) File "/usr/lib/python2.7/copy.py", line 257, in _deepcopy_dict y[deepcopy(key, memo)] = deepcopy(value, memo) File "/usr/lib/python2.7/copy.py", line 190, in deepcopy y = _reconstruct(x, rv, 1, memo) File "/usr/lib/python2.7/copy.py", line 328, in _reconstruct args = deepcopy(args, memo) File "/usr/lib/python2.7/copy.py", line 163, in deepcopy y = copier(x, memo) File "/usr/lib/python2.7/copy.py", line 249, in _deepcopy_tuple memo[d] = y MemoryError Error in run_mc Traceback (most recent call last): File "/home/rpdock/mc/MC_DNA.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_DNA.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_DNA.py", line 297, in all_atom pro_ch, rna_ch = check_chains(plik, pars) File "/home/rpdock/mc/MC_DNA.py", line 103, 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 Mon Apr 27 22:02:35 2026 ['na-prot_9760.pdb'] msg Refinement of #1 /home/rpdock/web/media/jobs/deb82bf2-cc38-4464-8ae9-3ce758cd0b27/na-prot_9760.pdb dir: /home/rpdock/web/media/jobs/deb82bf2-cc38-4464-8ae9-3ce758cd0b27/ file: na-prot_9760.pdb find `pwd` -iname na-prot_9760.pdb copy /home/rpdock/web/media/jobs/deb82bf2-cc38-4464-8ae9-3ce758cd0b27/prot-na_30/na-prot_9760.pdb to /home/rpdock/web/media/jobs/deb82bf2-cc38-4464-8ae9-3ce758cd0b27//ref_struc/na-prot_9760/na-prot_9760.pdb cmd: python /home/rpdock/mc/MC_DNA.py -s 1000 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/deb82bf2-cc38-4464-8ae9-3ce758cd0b27//ref_struc/na-prot_9760/na-prot_9760.pdb msg python /home/rpdock/mc/MC_DNA.py -s 1000 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/deb82bf2-cc38-4464-8ae9-3ce758cd0b27//ref_struc/na-prot_9760/na-prot_9760.pdb msg run_mc::stderr:Traceback (most recent call last): File "/home/rpdock/mc/MC_DNA.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_DNA.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_DNA.py", line 297, in all_atom pro_ch, rna_ch = check_chains(plik, pars) File "/home/rpdock/mc/MC_DNA.py", line 103, 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 2026-04-27 22:06:16 npdock::MC (refinement) end 2026-04-27 22:06:16 npdock::OK 2026-04-27 22:06:16 Set finished status of deb82bf2-cc38-4464-8ae9-3ce758cd0b27