2026-04-30 13:43:03 NPdock start 2026-04-30 13:43:03 ver: server 2026-04-30 13:43:03 mode: 11111 2026-04-30 13:43:03 is RNA? 0 2026-04-30 13:43:03 Interface: prot: '' na: '' 2026-04-30 13:43:03 Curr dir:/home/rpdock/web/media/jobs/19925731-9cf0-49d1-8818-6175660048de/ 2026-04-30 13:43:03 GRAMM in progress... 2026-04-30 13:43:03 python /home/rpdock/run_gramm//run_gramm1.py -d 20000 -p prot.pdb -r na.pdb -pi '' -ri '' -n 1 -pf '*' -rf '*' 2026-04-30 14:18:18 GRAMM done 2026-04-30 14:18:18 DNP scoring in progress... 2026-04-30 14:18:18 time python /home/rpdock/run_gramm//DNP/laczony/QUASI-DNP-QDV_potential_1.0.py -m 100 -f list.txt -o dnp_out.txt 2026-04-30 14:18:19 QDV-DNP starts 2026-04-30 14:18:19 Show log every 100 structures 2026-04-30 14:18:19 QUASI-DNP starts 2026-04-30 14:18:19 na-prot_1000.pdb -567129.438936 2026-04-30 14:18:39 na-prot_94.pdb -563347.659476 2026-04-30 14:18:59 na-prot_194.pdb -397867.416048 2026-04-30 14:19:18 na-prot_294.pdb -693447.099769 2026-04-30 14:19:37 na-prot_394.pdb -627170.307942 2026-04-30 14:19:55 na-prot_494.pdb -743891.600743 2026-04-30 14:20:14 na-prot_594.pdb -444592.670254 2026-04-30 14:20:33 na-prot_694.pdb -698549.489013 2026-04-30 14:20:52 na-prot_794.pdb -459517.807914 2026-04-30 14:21:11 na-prot_894.pdb -177847.917686 2026-04-30 14:21:31 na-prot_994.pdb -192251.650823 2026-04-30 14:21:50 na-prot_1100.pdb -216066.530158 2026-04-30 14:22:09 na-prot_1200.pdb -579704.721391 2026-04-30 14:22:28 na-prot_1300.pdb -544787.517252 2026-04-30 14:22:48 na-prot_1400.pdb -309905.919773 2026-04-30 14:23:08 na-prot_1500.pdb -710929.192147 2026-04-30 14:23:27 na-prot_1600.pdb -739626.309927 2026-04-30 14:23:46 na-prot_1700.pdb -569249.008668 2026-04-30 14:24:06 na-prot_1800.pdb -793781.518495 2026-04-30 14:24:25 na-prot_1900.pdb -805532.358999 2026-04-30 14:24:44 na-prot_2000.pdb -789768.398279 2026-04-30 14:25:04 na-prot_2100.pdb -377688.881667 2026-04-30 14:25:23 na-prot_2200.pdb -327103.265766 2026-04-30 14:25:42 na-prot_2300.pdb -612130.050891 2026-04-30 14:26:01 na-prot_2400.pdb -643481.88516 2026-04-30 14:26:20 na-prot_2500.pdb -97059.243852 2026-04-30 14:26:39 na-prot_2600.pdb -320942.917307 2026-04-30 14:26:59 na-prot_2700.pdb -367361.642215 2026-04-30 14:27:18 na-prot_2800.pdb -431097.20811 2026-04-30 14:27:37 na-prot_2900.pdb -314475.141558 2026-04-30 14:27:56 na-prot_3000.pdb -487487.711615 2026-04-30 14:28:16 na-prot_3100.pdb -448477.305115 2026-04-30 14:28:35 na-prot_3200.pdb -105031.469906 2026-04-30 14:28:54 na-prot_3300.pdb -298691.903145 2026-04-30 14:29:13 na-prot_3400.pdb -490859.794404 2026-04-30 14:29:32 na-prot_3500.pdb -390342.247044 2026-04-30 14:29:51 na-prot_3600.pdb -148758.45563 2026-04-30 14:30:11 na-prot_3700.pdb -510520.965798 2026-04-30 14:30:30 na-prot_3800.pdb -484336.222588 2026-04-30 14:30:49 na-prot_3900.pdb -595705.029924 2026-04-30 14:31:08 na-prot_4000.pdb -227076.764858 2026-04-30 14:31:28 na-prot_4100.pdb -725090.55732 2026-04-30 14:31:47 na-prot_4200.pdb -471768.365494 2026-04-30 14:32:06 na-prot_4300.pdb -753283.764397 2026-04-30 14:32:25 na-prot_4400.pdb -603190.89708 2026-04-30 14:32:44 na-prot_4500.pdb -724242.223607 2026-04-30 14:33:04 na-prot_4600.pdb -640327.919301 2026-04-30 14:33:23 na-prot_4700.pdb -465275.437132 2026-04-30 14:33:42 na-prot_4800.pdb -539566.380578 2026-04-30 14:34:01 na-prot_4900.pdb -623608.087531 2026-04-30 14:34:21 na-prot_5000.pdb -399527.2108 2026-04-30 14:34:40 na-prot_5100.pdb -562782.272078 2026-04-30 14:34:59 na-prot_5200.pdb -749248.089581 2026-04-30 14:35:18 na-prot_5300.pdb -433684.285669 2026-04-30 14:35:38 na-prot_5400.pdb -423894.107205 2026-04-30 14:35:57 na-prot_5500.pdb -447441.472001 2026-04-30 14:36:17 na-prot_5600.pdb -289487.418513 2026-04-30 14:36:36 na-prot_5700.pdb -398128.826667 2026-04-30 14:36:55 na-prot_5800.pdb -523530.068196 2026-04-30 14:37:14 na-prot_5900.pdb -451605.366587 2026-04-30 14:37:34 na-prot_6000.pdb -587647.891894 2026-04-30 14:37:53 na-prot_6100.pdb -425053.20568 2026-04-30 14:38:12 na-prot_6200.pdb -375786.711632 2026-04-30 14:38:31 na-prot_6300.pdb -643701.134908 2026-04-30 14:38:51 na-prot_6400.pdb -268577.05998 2026-04-30 14:39:10 na-prot_6500.pdb -640371.760544 2026-04-30 14:39:29 na-prot_6600.pdb -653728.911407 2026-04-30 14:39:49 na-prot_6700.pdb -635291.088331 2026-04-30 14:40:08 na-prot_6800.pdb -393399.829999 2026-04-30 14:40:27 na-prot_6900.pdb -150821.588725 2026-04-30 14:40:47 na-prot_7000.pdb -482116.730431 2026-04-30 14:41:06 na-prot_7100.pdb -352064.937626 2026-04-30 14:41:26 na-prot_7200.pdb -259079.159098 2026-04-30 14:41:45 na-prot_7300.pdb -369564.701143 2026-04-30 14:42:04 na-prot_7400.pdb -355979.778809 2026-04-30 14:42:24 na-prot_7500.pdb -582673.579544 2026-04-30 14:42:43 na-prot_7600.pdb -149318.270558 2026-04-30 14:43:02 na-prot_7700.pdb -342001.21726 2026-04-30 14:43:21 na-prot_7800.pdb -381783.950943 2026-04-30 14:43:41 na-prot_7900.pdb -608679.142772 2026-04-30 14:44:00 na-prot_8000.pdb -391801.559534 2026-04-30 14:44:20 na-prot_8100.pdb -518882.627188 2026-04-30 14:44:39 na-prot_8200.pdb -380658.433667 2026-04-30 14:44:58 na-prot_8300.pdb -407491.719753 2026-04-30 14:45:17 na-prot_8400.pdb -495068.029992 2026-04-30 14:45:36 na-prot_8500.pdb -432061.452182 2026-04-30 14:45:55 na-prot_8600.pdb -660090.10749 2026-04-30 14:46:15 na-prot_8700.pdb -556176.036565 2026-04-30 14:46:34 na-prot_8800.pdb -656663.569326 2026-04-30 14:46:53 na-prot_8900.pdb -499368.20687 2026-04-30 14:47:12 na-prot_9000.pdb -450607.481488 2026-04-30 14:47:32 na-prot_9100.pdb -712835.477872 2026-04-30 14:47:51 na-prot_9200.pdb -311321.9463 2026-04-30 14:48:10 na-prot_9300.pdb -430641.486479 2026-04-30 14:48:29 na-prot_9400.pdb -351715.299297 2026-04-30 14:48:49 na-prot_9500.pdb -504809.235526 2026-04-30 14:49:08 na-prot_9600.pdb -499439.568086 2026-04-30 14:49:27 na-prot_9700.pdb -295420.294936 2026-04-30 14:49:46 na-prot_9800.pdb -685950.563075 2026-04-30 14:50:05 na-prot_9900.pdb -388728.506183 2026-04-30 14:50:24 na-prot_10000.pdb -477685.115804 2026-04-30 14:50:44 na-prot_10100.pdb -593521.969472 2026-04-30 14:51:03 na-prot_10200.pdb -507054.52334 2026-04-30 14:51:23 na-prot_10300.pdb -434051.714974 2026-04-30 14:51:42 na-prot_10400.pdb -398934.867022 2026-04-30 14:52:01 na-prot_10500.pdb -316684.023605 2026-04-30 14:52:20 na-prot_10600.pdb -259630.738366 2026-04-30 14:52:39 na-prot_10700.pdb -600572.786182 2026-04-30 14:52:59 na-prot_10800.pdb -641289.973989 2026-04-30 14:53:18 na-prot_10900.pdb -133119.223828 2026-04-30 14:53:37 na-prot_11000.pdb -519155.902939 2026-04-30 14:53:56 na-prot_11100.pdb -453549.422018 2026-04-30 14:54:16 na-prot_11200.pdb -830915.654928 2026-04-30 14:54:35 na-prot_11300.pdb -419026.400422 2026-04-30 14:54:54 na-prot_11400.pdb -439696.974751 2026-04-30 14:55:13 na-prot_11500.pdb -404989.854537 2026-04-30 14:55:33 na-prot_11600.pdb -431769.350425 2026-04-30 14:55:52 na-prot_11700.pdb -684117.598555 2026-04-30 14:56:11 na-prot_11800.pdb -200287.971213 2026-04-30 14:56:31 na-prot_11900.pdb -441456.702274 2026-04-30 14:56:50 na-prot_12000.pdb -515965.93325 2026-04-30 14:57:09 na-prot_12100.pdb -740850.432781 2026-04-30 14:57:29 na-prot_12200.pdb -855044.827856 2026-04-30 14:57:48 na-prot_12300.pdb -301059.394216 2026-04-30 14:58:07 na-prot_12400.pdb -231740.935015 2026-04-30 14:58:26 na-prot_12500.pdb -403630.327909 2026-04-30 14:58:45 na-prot_12600.pdb -795717.253554 2026-04-30 14:59:05 na-prot_12700.pdb -136859.567191 2026-04-30 14:59:24 na-prot_12800.pdb -354144.121932 2026-04-30 14:59:43 na-prot_12900.pdb -383748.956512 2026-04-30 15:00:02 na-prot_13000.pdb -422998.483304 2026-04-30 15:00:22 na-prot_13100.pdb -278339.68754 2026-04-30 15:00:41 na-prot_13200.pdb -436788.298553 2026-04-30 15:01:00 na-prot_13300.pdb -438454.142156 2026-04-30 15:01:19 na-prot_13400.pdb -453373.305058 2026-04-30 15:01:38 na-prot_13500.pdb -372815.871416 2026-04-30 15:01:58 na-prot_13600.pdb -317911.206099 2026-04-30 15:02:17 na-prot_13700.pdb -276319.505206 2026-04-30 15:02:36 na-prot_13800.pdb -430950.77303 2026-04-30 15:02:55 na-prot_13900.pdb -519173.211452 2026-04-30 15:03:15 na-prot_14000.pdb -459545.513969 2026-04-30 15:03:34 na-prot_14100.pdb -278973.201618 2026-04-30 15:03:52 na-prot_14200.pdb -558999.367937 2026-04-30 15:04:12 na-prot_14300.pdb -316169.96095 2026-04-30 15:04:31 na-prot_14400.pdb -363133.156262 2026-04-30 15:04:50 na-prot_14500.pdb -333086.720368 2026-04-30 15:05:10 na-prot_14600.pdb -433866.047017 2026-04-30 15:05:29 na-prot_14700.pdb -522288.027934 2026-04-30 15:05:48 na-prot_14800.pdb -411465.911178 2026-04-30 15:06:07 na-prot_14900.pdb -419643.525231 2026-04-30 15:06:27 na-prot_15000.pdb -394161.81779 2026-04-30 15:06:46 na-prot_15100.pdb -212330.788693 2026-04-30 15:07:06 na-prot_15200.pdb -342500.40925 2026-04-30 15:07:25 na-prot_15300.pdb -446088.209868 2026-04-30 15:07:44 na-prot_15400.pdb -677630.619914 2026-04-30 15:08:04 na-prot_15500.pdb -595471.495277 2026-04-30 15:08:23 na-prot_15600.pdb -441081.475174 2026-04-30 15:08:42 na-prot_15700.pdb -464327.415936 2026-04-30 15:09:01 na-prot_15800.pdb -509434.609992 2026-04-30 15:09:21 na-prot_15900.pdb -556369.427126 2026-04-30 15:09:40 na-prot_16000.pdb -614462.073307 2026-04-30 15:09:59 na-prot_16100.pdb -521633.553665 2026-04-30 15:10:18 na-prot_16200.pdb -379918.562738 2026-04-30 15:10:38 na-prot_16300.pdb -683744.64833 2026-04-30 15:10:57 na-prot_16400.pdb -346919.971873 2026-04-30 15:11:16 na-prot_16500.pdb -559948.658168 2026-04-30 15:11:36 na-prot_16600.pdb -139726.243634 2026-04-30 15:11:55 na-prot_16700.pdb -653287.105473 2026-04-30 15:12:14 na-prot_16800.pdb -270824.530907 2026-04-30 15:12:34 na-prot_16900.pdb -481006.721913 2026-04-30 15:12:53 na-prot_17000.pdb -268047.825461 2026-04-30 15:13:12 na-prot_17100.pdb -67376.5368591 2026-04-30 15:13:32 na-prot_17200.pdb -762181.986577 2026-04-30 15:13:51 na-prot_17300.pdb -54520.4258964 2026-04-30 15:14:11 na-prot_17400.pdb -352297.061449 2026-04-30 15:14:30 na-prot_17500.pdb -454143.806369 2026-04-30 15:14:49 na-prot_17600.pdb -406861.953527 2026-04-30 15:15:09 na-prot_17700.pdb -236999.677348 2026-04-30 15:15:28 na-prot_17800.pdb -380129.204094 2026-04-30 15:15:47 na-prot_17900.pdb -677530.538656 2026-04-30 15:16:07 na-prot_18000.pdb -480827.175148 2026-04-30 15:16:26 na-prot_18100.pdb -428719.420998 2026-04-30 15:16:45 na-prot_18200.pdb -397762.752426 2026-04-30 15:17:05 na-prot_18300.pdb -467403.055459 2026-04-30 15:17:24 na-prot_18400.pdb -657668.412313 2026-04-30 15:17:43 na-prot_18500.pdb -444404.343485 2026-04-30 15:18:03 na-prot_18600.pdb -342631.733665 2026-04-30 15:18:22 na-prot_18700.pdb -548941.730596 2026-04-30 15:18:42 na-prot_18800.pdb -576680.044754 2026-04-30 15:19:01 na-prot_18900.pdb -373669.424934 2026-04-30 15:19:20 na-prot_19000.pdb -551852.398895 2026-04-30 15:19:40 na-prot_19100.pdb -470699.37964 2026-04-30 15:19:59 na-prot_19200.pdb -266049.75724 2026-04-30 15:20:18 na-prot_19300.pdb -635702.894207 2026-04-30 15:20:37 na-prot_19400.pdb -318180.717533 2026-04-30 15:20:56 na-prot_19500.pdb -105719.109457 2026-04-30 15:21:16 na-prot_19600.pdb -561542.550722 2026-04-30 15:21:35 na-prot_19700.pdb -456630.586193 2026-04-30 15:21:55 na-prot_19800.pdb -354405.970704 2026-04-30 15:22:14 na-prot_19900.pdb -604199.676726 2026-04-30 15:22:34 na-prot_20000.pdb -294213.052981 2026-04-30 15:22:34 Varani starts 2026-04-30 15:22:34 na-prot_1000.pdb 300.54 2026-04-30 15:23:05 na-prot_94.pdb 206.655 2026-04-30 15:23:37 na-prot_194.pdb 191.965 2026-04-30 15:24:08 na-prot_294.pdb 376.306 2026-04-30 15:24:39 na-prot_394.pdb 213.125 2026-04-30 15:25:11 na-prot_494.pdb 374.574 2026-04-30 15:25:43 na-prot_594.pdb 324.064 2026-04-30 15:26:14 na-prot_694.pdb 132.245 2026-04-30 15:26:46 na-prot_794.pdb 434.869 2026-04-30 15:27:17 na-prot_894.pdb 231.886 2026-04-30 15:27:49 na-prot_994.pdb 388.674 2026-04-30 15:28:20 na-prot_1100.pdb 341.425 2026-04-30 15:28:52 na-prot_1200.pdb 328.969 2026-04-30 15:29:24 na-prot_1300.pdb 145.74 2026-04-30 15:29:55 na-prot_1400.pdb 218.819 2026-04-30 15:30:27 na-prot_1500.pdb 331.207 2026-04-30 15:30:58 na-prot_1600.pdb 316.746 2026-04-30 15:31:30 na-prot_1700.pdb 374.482 2026-04-30 15:32:01 na-prot_1800.pdb -32.153 2026-04-30 15:32:33 na-prot_1900.pdb -69.277 2026-04-30 15:33:04 na-prot_2000.pdb 182.338 2026-04-30 15:33:36 na-prot_2100.pdb 234.549 2026-04-30 15:34:07 na-prot_2200.pdb 302.709 2026-04-30 15:34:38 na-prot_2300.pdb 99.013 2026-04-30 15:35:10 na-prot_2400.pdb 139.985 2026-04-30 15:35:41 na-prot_2500.pdb 231.45 2026-04-30 15:36:13 na-prot_2600.pdb 180.066 2026-04-30 15:36:44 na-prot_2700.pdb 207.019 2026-04-30 15:37:15 na-prot_2800.pdb 202.092 2026-04-30 15:37:46 na-prot_2900.pdb 235.046 2026-04-30 15:38:18 na-prot_3000.pdb 327.972 2026-04-30 15:38:49 na-prot_3100.pdb 111.6 2026-04-30 15:39:21 na-prot_3200.pdb 278.982 2026-04-30 15:39:53 na-prot_3300.pdb 105.15 2026-04-30 15:40:24 na-prot_3400.pdb 227.927 2026-04-30 15:40:55 na-prot_3500.pdb 172.677 2026-04-30 15:41:27 na-prot_3600.pdb 220.081 2026-04-30 15:41:58 na-prot_3700.pdb 245.26 2026-04-30 15:42:29 na-prot_3800.pdb 342.423 2026-04-30 15:43:01 na-prot_3900.pdb 148.534 2026-04-30 15:43:33 na-prot_4000.pdb 290.926 2026-04-30 15:44:04 na-prot_4100.pdb 165.32 2026-04-30 15:44:35 na-prot_4200.pdb 295.769 2026-04-30 15:45:07 na-prot_4300.pdb 224.307 2026-04-30 15:45:38 na-prot_4400.pdb 346.559 2026-04-30 15:46:09 na-prot_4500.pdb 24.155 2026-04-30 15:46:41 na-prot_4600.pdb 137.832 2026-04-30 15:47:12 na-prot_4700.pdb 150.201 2026-04-30 15:47:44 na-prot_4800.pdb 203.389 2026-04-30 15:48:15 na-prot_4900.pdb 271.12 2026-04-30 15:48:46 na-prot_5000.pdb 245.057 2026-04-30 15:49:17 na-prot_5100.pdb 330.224 2026-04-30 15:49:49 na-prot_5200.pdb 350.668 2026-04-30 15:50:20 na-prot_5300.pdb 273.093 2026-04-30 15:50:51 na-prot_5400.pdb 273 2026-04-30 15:51:23 na-prot_5500.pdb 278.009 2026-04-30 15:51:54 na-prot_5600.pdb 198.988 2026-04-30 15:52:26 na-prot_5700.pdb 218.496 2026-04-30 15:52:57 na-prot_5800.pdb 191.566 2026-04-30 15:53:29 na-prot_5900.pdb 244.546 2026-04-30 15:54:00 na-prot_6000.pdb 53.39 2026-04-30 15:54:32 na-prot_6100.pdb 76.395 2026-04-30 15:55:03 na-prot_6200.pdb 426.62 2026-04-30 15:55:35 na-prot_6300.pdb 198.579 2026-04-30 15:56:06 na-prot_6400.pdb 393.071 2026-04-30 15:56:38 na-prot_6500.pdb 247.261 2026-04-30 15:57:10 na-prot_6600.pdb 449.648 2026-04-30 15:57:41 na-prot_6700.pdb 170.59 2026-04-30 15:58:13 na-prot_6800.pdb 191.934 2026-04-30 15:58:45 na-prot_6900.pdb 169.043 2026-04-30 15:59:16 na-prot_7000.pdb 170.186 2026-04-30 15:59:48 na-prot_7100.pdb 380.843 2026-04-30 16:00:19 na-prot_7200.pdb 168.355 2026-04-30 16:00:50 na-prot_7300.pdb 126.308 2026-04-30 16:01:22 na-prot_7400.pdb 207.29 2026-04-30 16:01:54 na-prot_7500.pdb 368.296 2026-04-30 16:02:26 na-prot_7600.pdb 355.463 2026-04-30 16:02:58 na-prot_7700.pdb 111.879 2026-04-30 16:03:29 na-prot_7800.pdb 255.532 2026-04-30 16:04:01 na-prot_7900.pdb 289.668 2026-04-30 16:04:32 na-prot_8000.pdb 307.519 2026-04-30 16:05:04 na-prot_8100.pdb 160.598 2026-04-30 16:05:36 na-prot_8200.pdb 259.437 2026-04-30 16:06:08 na-prot_8300.pdb 276.728 2026-04-30 16:06:39 na-prot_8400.pdb 217.202 2026-04-30 16:07:10 na-prot_8500.pdb 277.521 2026-04-30 16:07:41 na-prot_8600.pdb 213.74 2026-04-30 16:08:13 na-prot_8700.pdb 213.789 2026-04-30 16:08:45 na-prot_8800.pdb 145.011 2026-04-30 16:09:16 na-prot_8900.pdb 190.016 2026-04-30 16:09:48 na-prot_9000.pdb 167.183 2026-04-30 16:10:20 na-prot_9100.pdb 218.979 2026-04-30 16:10:52 na-prot_9200.pdb 89.008 2026-04-30 16:11:23 na-prot_9300.pdb 246.532 2026-04-30 16:11:55 na-prot_9400.pdb 338.066 2026-04-30 16:12:26 na-prot_9500.pdb 327.19 2026-04-30 16:12:57 na-prot_9600.pdb -70.501 2026-04-30 16:13:29 na-prot_9700.pdb 339.134 2026-04-30 16:14:01 na-prot_9800.pdb 292.814 2026-04-30 16:14:33 na-prot_9900.pdb 90.805 2026-04-30 16:15:04 na-prot_10000.pdb 311.132 2026-04-30 16:15:36 na-prot_10100.pdb 102.828 2026-04-30 16:16:08 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16:27:40 na-prot_12400.pdb 197.08 2026-04-30 16:28:12 na-prot_12500.pdb 44.413 2026-04-30 16:28:43 na-prot_12600.pdb 358.332 2026-04-30 16:29:14 na-prot_12700.pdb 224.627 2026-04-30 16:29:46 na-prot_12800.pdb 162.855 2026-04-30 16:30:18 na-prot_12900.pdb 73.515 2026-04-30 16:30:50 na-prot_13000.pdb 298.563 2026-04-30 16:31:22 na-prot_13100.pdb 174.439 2026-04-30 16:31:53 na-prot_13200.pdb 293.289 2026-04-30 16:32:25 na-prot_13300.pdb 301.529 2026-04-30 16:32:56 na-prot_13400.pdb 199.122 2026-04-30 16:33:28 na-prot_13500.pdb 286.981 2026-04-30 16:33:59 na-prot_13600.pdb 170.365 2026-04-30 16:34:31 na-prot_13700.pdb 148.487 2026-04-30 16:35:01 na-prot_13800.pdb 110.677 2026-04-30 16:35:33 na-prot_13900.pdb 296.346 2026-04-30 16:36:04 na-prot_14000.pdb 226.124 2026-04-30 16:36:36 na-prot_14100.pdb 125.108 2026-04-30 16:37:07 na-prot_14200.pdb 472.795 2026-04-30 16:37:38 na-prot_14300.pdb 226.711 2026-04-30 16:38:10 na-prot_14400.pdb 283.453 2026-04-30 16:38:41 na-prot_14500.pdb 257.829 2026-04-30 16:39:12 na-prot_14600.pdb 384.014 2026-04-30 16:39:44 na-prot_14700.pdb 94.418 2026-04-30 16:40:16 na-prot_14800.pdb 302.642 2026-04-30 16:40:47 na-prot_14900.pdb 131.397 2026-04-30 16:41:19 na-prot_15000.pdb 145.77 2026-04-30 16:41:51 na-prot_15100.pdb 167.573 2026-04-30 16:42:23 na-prot_15200.pdb 306.338 2026-04-30 16:42:55 na-prot_15300.pdb 135.677 2026-04-30 16:43:26 na-prot_15400.pdb 273.182 2026-04-30 16:43:58 na-prot_15500.pdb 209.792 2026-04-30 16:44:30 na-prot_15600.pdb 113.547 2026-04-30 16:45:01 na-prot_15700.pdb 113.441 2026-04-30 16:45:33 na-prot_15800.pdb 125.641 2026-04-30 16:46:04 na-prot_15900.pdb 132.056 2026-04-30 16:46:36 na-prot_16000.pdb 101.451 2026-04-30 16:47:07 na-prot_16100.pdb 188.179 2026-04-30 16:47:39 na-prot_16200.pdb 198.919 2026-04-30 16:48:10 na-prot_16300.pdb 270.81 2026-04-30 16:48:42 na-prot_16400.pdb 82.956 2026-04-30 16:49:14 na-prot_16500.pdb 50.828 2026-04-30 16:49:45 na-prot_16600.pdb 159.451 2026-04-30 16:50:16 na-prot_16700.pdb 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-1.39442727588 2026-04-30 19:18:07 /home/rpdock/web/media/jobs/19925731-9cf0-49d1-8818-6175660048de/prot-na_20/na-prot_18500.pdb -0.212176250408 2026-04-30 19:18:07 /home/rpdock/web/media/jobs/19925731-9cf0-49d1-8818-6175660048de/prot-na_20/na-prot_18600.pdb 0.809165681999 2026-04-30 19:18:07 /home/rpdock/web/media/jobs/19925731-9cf0-49d1-8818-6175660048de/prot-na_20/na-prot_18700.pdb -1.32495047343 2026-04-30 19:18:07 /home/rpdock/web/media/jobs/19925731-9cf0-49d1-8818-6175660048de/prot-na_20/na-prot_18800.pdb -1.05846810059 2026-04-30 19:18:07 /home/rpdock/web/media/jobs/19925731-9cf0-49d1-8818-6175660048de/prot-na_20/na-prot_18900.pdb 0.533566148196 2026-04-30 19:18:07 /home/rpdock/web/media/jobs/19925731-9cf0-49d1-8818-6175660048de/prot-na_20/na-prot_19000.pdb -1.11367987055 2026-04-30 19:18:07 /home/rpdock/web/media/jobs/19925731-9cf0-49d1-8818-6175660048de/prot-na_20/na-prot_19100.pdb -0.839724236144 2026-04-30 19:18:07 /home/rpdock/web/media/jobs/19925731-9cf0-49d1-8818-6175660048de/prot-na_20/na-prot_19200.pdb 0.60688919871 2026-04-30 19:18:07 /home/rpdock/web/media/jobs/19925731-9cf0-49d1-8818-6175660048de/prot-na_20/na-prot_19300.pdb -0.985786622734 2026-04-30 19:18:07 /home/rpdock/web/media/jobs/19925731-9cf0-49d1-8818-6175660048de/prot-na_20/na-prot_19400.pdb 0.489834523511 2026-04-30 19:18:07 /home/rpdock/web/media/jobs/19925731-9cf0-49d1-8818-6175660048de/prot-na_20/na-prot_19500.pdb 2.38429309171 2026-04-30 19:18:07 /home/rpdock/web/media/jobs/19925731-9cf0-49d1-8818-6175660048de/prot-na_20/na-prot_19600.pdb -0.438672075847 2026-04-30 19:18:07 /home/rpdock/web/media/jobs/19925731-9cf0-49d1-8818-6175660048de/prot-na_20/na-prot_19700.pdb -0.0298539748177 2026-04-30 19:18:07 /home/rpdock/web/media/jobs/19925731-9cf0-49d1-8818-6175660048de/prot-na_20/na-prot_19800.pdb 0.722703262964 2026-04-30 19:18:07 /home/rpdock/web/media/jobs/19925731-9cf0-49d1-8818-6175660048de/prot-na_20/na-prot_19900.pdb -1.68430644851 2026-04-30 19:18:07 /home/rpdock/web/media/jobs/19925731-9cf0-49d1-8818-6175660048de/prot-na_20/na-prot_20000.pdb 0.795167400651 2026-04-30 19:18:07 [..]316343) ('/home/rpdock/web/media/jobs/19925731-9cf0-49d1-8818-6175660048de/prot-na_20/na-prot_19994.pdb', -0.25659244760067534) ('/home/rpdock/web/media/jobs/19925731-9cf0-49d1-8818-6175660048de/prot-na_20/na-prot_19995.pdb', -2.707518902541884) ('/home/rpdock/web/media/jobs/19925731-9cf0-49d1-8818-6175660048de/prot-na_20/na-prot_19996.pdb', -3.6241362236429073) ('/home/rpdock/web/media/jobs/19925731-9cf0-49d1-8818-6175660048de/prot-na_20/na-prot_19997.pdb', -1.3304537591542043) ('/home/rpdock/web/media/jobs/19925731-9cf0-49d1-8818-6175660048de/prot-na_20/na-prot_19998.pdb', -0.03335719201629783) ('/home/rpdock/web/media/jobs/19925731-9cf0-49d1-8818-6175660048de/prot-na_20/na-prot_19999.pdb', 0.006501433259361658) ('/home/rpdock/web/media/jobs/19925731-9cf0-49d1-8818-6175660048de/prot-na_20/na-prot_20000.pdb', 0.7951674006511331) 16869.45user 992.64system 4:59:48elapsed 99%CPU (0avgtext+0avgdata 217216maxresident)k 2662368inputs+11524896outputs (45major+194844686minor)pagefaults 0swaps 2026-04-30 19:18:07 Clustering (cuttoff: 5, nr_clust: 100 ) in progress... 2026-04-30 19:18:07 time python /home/rpdock/run_gramm//clustering_v4.py dars_out.txt list.txt 5 100 2026-04-30 19:18:07 100 best scored structures 2026-04-30 19:18:07 1 na-prot_8075.pdb -5.38361851599 2026-04-30 19:18:07 2 na-prot_2830.pdb -5.37192506944 2026-04-30 19:18:07 3 na-prot_14033.pdb -5.20737618513 2026-04-30 19:18:07 4 na-prot_11763.pdb -5.07517851163 2026-04-30 19:18:07 5 na-prot_19193.pdb -4.89263010174 2026-04-30 19:18:07 6 na-prot_12736.pdb -4.88647212772 2026-04-30 19:18:07 7 na-prot_14291.pdb -4.87991391331 2026-04-30 19:18:07 8 na-prot_14436.pdb -4.86729264466 2026-04-30 19:18:07 9 na-prot_1169.pdb -4.78919824669 2026-04-30 19:18:07 10 na-prot_13867.pdb -4.7793858239 2026-04-30 19:18:07 11 na-prot_5796.pdb -4.75310222052 2026-04-30 19:18:07 12 na-prot_13699.pdb -4.65418152569 2026-04-30 19:18:07 13 na-prot_781.pdb -4.64582851651 2026-04-30 19:18:07 14 na-prot_401.pdb -4.6117339384 2026-04-30 19:18:07 15 na-prot_2546.pdb -4.59947250684 2026-04-30 19:18:07 16 na-prot_4312.pdb -4.56494959554 2026-04-30 19:18:07 17 na-prot_13177.pdb -4.53859514046 2026-04-30 19:18:07 18 na-prot_313.pdb -4.52951483348 2026-04-30 19:18:07 19 na-prot_8776.pdb -4.49804666123 2026-04-30 19:18:07 20 na-prot_12274.pdb -4.49572081946 2026-04-30 19:18:07 21 na-prot_2519.pdb -4.48768678469 2026-04-30 19:18:07 22 na-prot_11117.pdb -4.46354476015 2026-04-30 19:18:07 23 na-prot_12864.pdb -4.45242500865 2026-04-30 19:18:07 24 na-prot_4198.pdb -4.45139029659 2026-04-30 19:18:07 25 na-prot_1056.pdb -4.44436249558 2026-04-30 19:18:07 26 na-prot_991.pdb -4.43828250807 2026-04-30 19:18:07 27 na-prot_1220.pdb -4.41883858638 2026-04-30 19:18:07 28 na-prot_18848.pdb -4.41424122911 2026-04-30 19:18:07 29 na-prot_6389.pdb -4.39281718521 2026-04-30 19:18:07 30 na-prot_695.pdb -4.39109016096 2026-04-30 19:18:07 31 na-prot_12241.pdb -4.3862754986 2026-04-30 19:18:07 32 na-prot_4063.pdb -4.37027033563 2026-04-30 19:18:07 33 na-prot_5648.pdb -4.34485824906 2026-04-30 19:18:07 34 na-prot_10286.pdb -4.33168953249 2026-04-30 19:18:07 35 na-prot_2077.pdb -4.32484746828 2026-04-30 19:18:07 36 na-prot_4281.pdb -4.32313669074 2026-04-30 19:18:07 37 na-prot_9487.pdb -4.31029594997 2026-04-30 19:18:07 38 na-prot_16238.pdb -4.30737201677 2026-04-30 19:18:07 39 na-prot_3064.pdb -4.2672807546 2026-04-30 19:18:07 40 na-prot_1776.pdb -4.26303291361 2026-04-30 19:18:07 41 na-prot_10067.pdb -4.23076340232 2026-04-30 19:18:07 42 na-prot_18430.pdb -4.22018583412 2026-04-30 19:18:07 43 na-prot_2933.pdb -4.20783020071 2026-04-30 19:18:07 44 na-prot_19049.pdb -4.20711564424 2026-04-30 19:18:07 45 na-prot_4958.pdb -4.18998934368 2026-04-30 19:18:07 46 na-prot_7434.pdb -4.18509341131 2026-04-30 19:18:07 47 na-prot_16431.pdb -4.16852171136 2026-04-30 19:18:07 48 na-prot_1243.pdb -4.15501991686 2026-04-30 19:18:07 49 na-prot_1929.pdb -4.14390811438 2026-04-30 19:18:07 50 na-prot_19983.pdb -4.13819805494 2026-04-30 19:18:07 51 na-prot_1017.pdb -4.13336742936 2026-04-30 19:18:07 52 na-prot_7384.pdb -4.11866298991 2026-04-30 19:18:07 53 na-prot_4779.pdb -4.11132924799 2026-04-30 19:18:07 54 na-prot_2192.pdb -4.10632144855 2026-04-30 19:18:07 55 na-prot_4913.pdb -4.09881996171 2026-04-30 19:18:07 56 na-prot_6768.pdb -4.09845256871 2026-04-30 19:18:07 57 na-prot_17914.pdb -4.08998281517 2026-04-30 19:18:07 58 na-prot_8.pdb -4.08810423685 2026-04-30 19:18:07 59 na-prot_5564.pdb -4.08681945058 2026-04-30 19:18:07 60 na-prot_1738.pdb -4.06354519552 2026-04-30 19:18:07 61 na-prot_5920.pdb -4.06122023583 2026-04-30 19:18:07 62 na-prot_10294.pdb -4.05167028928 2026-04-30 19:18:07 63 na-prot_19283.pdb -4.05067897435 2026-04-30 19:18:07 64 na-prot_9571.pdb -4.04511852959 2026-04-30 19:18:07 65 na-prot_3546.pdb -4.039628726 2026-04-30 19:18:07 66 na-prot_226.pdb -4.03497801759 2026-04-30 19:18:07 67 na-prot_12745.pdb -3.99835703109 2026-04-30 19:18:07 68 na-prot_4020.pdb -3.99589465497 2026-04-30 19:18:07 69 na-prot_17369.pdb -3.99380651317 2026-04-30 19:18:07 70 na-prot_9613.pdb -3.97711452332 2026-04-30 19:18:07 71 na-prot_174.pdb -3.97273731302 2026-04-30 19:18:07 72 na-prot_14675.pdb -3.96560982582 2026-04-30 19:18:07 73 na-prot_8995.pdb -3.95535049793 2026-04-30 19:18:07 74 na-prot_8781.pdb -3.95403908139 2026-04-30 19:18:07 75 na-prot_3317.pdb -3.94255864478 2026-04-30 19:18:07 76 na-prot_1880.pdb -3.94019873291 2026-04-30 19:18:07 77 na-prot_5735.pdb -3.93791362731 2026-04-30 19:18:07 78 na-prot_18234.pdb -3.93601890669 2026-04-30 19:18:07 79 na-prot_10698.pdb -3.92406398981 2026-04-30 19:18:07 80 na-prot_5433.pdb -3.92044263332 2026-04-30 19:18:07 81 na-prot_15728.pdb -3.91661706037 2026-04-30 19:18:07 82 na-prot_2252.pdb -3.913160203 2026-04-30 19:18:07 83 na-prot_1834.pdb -3.90876437804 2026-04-30 19:18:07 84 na-prot_1633.pdb -3.90500472144 2026-04-30 19:18:07 85 na-prot_19105.pdb -3.90422404011 2026-04-30 19:18:07 86 na-prot_443.pdb -3.90086027117 2026-04-30 19:18:07 87 na-prot_4327.pdb -3.88944852037 2026-04-30 19:18:07 88 na-prot_9923.pdb -3.88534748448 2026-04-30 19:18:07 89 na-prot_13220.pdb -3.87252646059 2026-04-30 19:18:07 90 na-prot_9011.pdb -3.86217804341 2026-04-30 19:18:07 91 na-prot_8920.pdb -3.85988599769 2026-04-30 19:18:07 92 na-prot_17168.pdb -3.85887099197 2026-04-30 19:18:07 93 na-prot_15495.pdb -3.85302217951 2026-04-30 19:18:07 94 na-prot_1685.pdb -3.8481118006 2026-04-30 19:18:07 95 na-prot_5879.pdb -3.84693012207 2026-04-30 19:18:07 96 na-prot_3040.pdb -3.84005429051 2026-04-30 19:18:07 97 na-prot_508.pdb -3.82155353278 2026-04-30 19:18:07 98 na-prot_19689.pdb -3.82095722524 2026-04-30 19:18:07 99 na-prot_3165.pdb -3.8180637117 2026-04-30 19:18:07 100 na-prot_10014.pdb -3.81740723156 2026-04-30 19:18:07 Chains: A 2026-04-30 19:18:31 100 best scored structures 2026-04-30 19:18:31 GRAMM analysis selected for further analysis: prot-na_20 2026-04-30 19:18:31 Cluster #1 with 100 structures 2026-04-30 19:18:31 1 na-prot_8075.pdb -5.38361851599 2026-04-30 19:18:31 2 na-prot_2830.pdb -5.37192506944 2026-04-30 19:18:31 3 na-prot_14033.pdb -5.20737618513 2026-04-30 19:18:31 4 na-prot_11763.pdb -5.07517851163 2026-04-30 19:18:31 5 na-prot_19193.pdb -4.89263010174 2026-04-30 19:18:31 6 na-prot_12736.pdb -4.88647212772 2026-04-30 19:18:31 7 na-prot_14291.pdb -4.87991391331 2026-04-30 19:18:31 8 na-prot_14436.pdb -4.86729264466 2026-04-30 19:18:31 9 na-prot_1169.pdb -4.78919824669 2026-04-30 19:18:31 10 na-prot_13867.pdb -4.7793858239 2026-04-30 19:18:31 11 na-prot_5796.pdb -4.75310222052 2026-04-30 19:18:31 12 na-prot_13699.pdb -4.65418152569 2026-04-30 19:18:31 13 na-prot_781.pdb -4.64582851651 2026-04-30 19:18:31 14 na-prot_401.pdb -4.6117339384 2026-04-30 19:18:31 15 na-prot_2546.pdb -4.59947250684 2026-04-30 19:18:31 16 na-prot_4312.pdb -4.56494959554 2026-04-30 19:18:31 17 na-prot_13177.pdb -4.53859514046 2026-04-30 19:18:31 18 na-prot_313.pdb -4.52951483348 2026-04-30 19:18:31 19 na-prot_8776.pdb -4.49804666123 2026-04-30 19:18:31 20 na-prot_12274.pdb -4.49572081946 2026-04-30 19:18:31 21 na-prot_2519.pdb -4.48768678469 2026-04-30 19:18:31 22 na-prot_11117.pdb -4.46354476015 2026-04-30 19:18:31 23 na-prot_12864.pdb -4.45242500865 2026-04-30 19:18:31 24 na-prot_4198.pdb -4.45139029659 2026-04-30 19:18:31 25 na-prot_1056.pdb -4.44436249558 2026-04-30 19:18:31 26 na-prot_991.pdb -4.43828250807 2026-04-30 19:18:31 27 na-prot_1220.pdb -4.41883858638 2026-04-30 19:18:31 28 na-prot_18848.pdb -4.41424122911 2026-04-30 19:18:31 29 na-prot_6389.pdb -4.39281718521 2026-04-30 19:18:31 30 na-prot_695.pdb -4.39109016096 2026-04-30 19:18:31 31 na-prot_12241.pdb -4.3862754986 2026-04-30 19:18:31 32 na-prot_4063.pdb -4.37027033563 2026-04-30 19:18:31 33 na-prot_5648.pdb -4.34485824906 2026-04-30 19:18:31 34 na-prot_10286.pdb -4.33168953249 2026-04-30 19:18:31 35 na-prot_2077.pdb -4.32484746828 2026-04-30 19:18:31 36 na-prot_4281.pdb -4.32313669074 2026-04-30 19:18:31 37 na-prot_9487.pdb -4.31029594997 2026-04-30 19:18:31 38 na-prot_16238.pdb -4.30737201677 2026-04-30 19:18:31 39 na-prot_3064.pdb -4.2672807546 2026-04-30 19:18:31 40 na-prot_1776.pdb -4.26303291361 2026-04-30 19:18:31 41 na-prot_10067.pdb -4.23076340232 2026-04-30 19:18:31 42 na-prot_18430.pdb -4.22018583412 2026-04-30 19:18:31 43 na-prot_2933.pdb -4.20783020071 2026-04-30 19:18:31 44 na-prot_19049.pdb -4.20711564424 2026-04-30 19:18:31 45 na-prot_4958.pdb -4.18998934368 2026-04-30 19:18:31 46 na-prot_7434.pdb -4.18509341131 2026-04-30 19:18:31 47 na-prot_16431.pdb -4.16852171136 2026-04-30 19:18:31 48 na-prot_1243.pdb -4.15501991686 2026-04-30 19:18:31 49 na-prot_1929.pdb -4.14390811438 2026-04-30 19:18:31 50 na-prot_19983.pdb -4.13819805494 2026-04-30 19:18:31 51 na-prot_1017.pdb -4.13336742936 2026-04-30 19:18:31 52 na-prot_7384.pdb -4.11866298991 2026-04-30 19:18:31 53 na-prot_4779.pdb -4.11132924799 2026-04-30 19:18:31 54 na-prot_2192.pdb -4.10632144855 2026-04-30 19:18:31 55 na-prot_4913.pdb -4.09881996171 2026-04-30 19:18:31 56 na-prot_6768.pdb -4.09845256871 2026-04-30 19:18:31 57 na-prot_17914.pdb -4.08998281517 2026-04-30 19:18:31 58 na-prot_8.pdb -4.08810423685 2026-04-30 19:18:31 59 na-prot_5564.pdb -4.08681945058 2026-04-30 19:18:31 60 na-prot_1738.pdb -4.06354519552 2026-04-30 19:18:31 61 na-prot_5920.pdb -4.06122023583 2026-04-30 19:18:31 62 na-prot_10294.pdb -4.05167028928 2026-04-30 19:18:31 63 na-prot_19283.pdb -4.05067897435 2026-04-30 19:18:31 64 na-prot_9571.pdb -4.04511852959 2026-04-30 19:18:31 65 na-prot_3546.pdb -4.039628726 2026-04-30 19:18:31 66 na-prot_226.pdb -4.03497801759 2026-04-30 19:18:31 67 na-prot_12745.pdb -3.99835703109 2026-04-30 19:18:31 68 na-prot_4020.pdb -3.99589465497 2026-04-30 19:18:31 69 na-prot_17369.pdb -3.99380651317 2026-04-30 19:18:31 70 na-prot_9613.pdb -3.97711452332 2026-04-30 19:18:31 71 na-prot_174.pdb -3.97273731302 2026-04-30 19:18:31 72 na-prot_14675.pdb -3.96560982582 2026-04-30 19:18:31 73 na-prot_8995.pdb -3.95535049793 2026-04-30 19:18:31 74 na-prot_8781.pdb -3.95403908139 2026-04-30 19:18:31 75 na-prot_3317.pdb -3.94255864478 2026-04-30 19:18:31 76 na-prot_1880.pdb -3.94019873291 2026-04-30 19:18:31 77 na-prot_5735.pdb -3.93791362731 2026-04-30 19:18:31 78 na-prot_18234.pdb -3.93601890669 2026-04-30 19:18:31 79 na-prot_10698.pdb -3.92406398981 2026-04-30 19:18:31 80 na-prot_5433.pdb -3.92044263332 2026-04-30 19:18:31 81 na-prot_15728.pdb -3.91661706037 2026-04-30 19:18:31 82 na-prot_2252.pdb -3.913160203 2026-04-30 19:18:31 83 na-prot_1834.pdb -3.90876437804 2026-04-30 19:18:31 84 na-prot_1633.pdb -3.90500472144 2026-04-30 19:18:31 85 na-prot_19105.pdb -3.90422404011 2026-04-30 19:18:31 86 na-prot_443.pdb -3.90086027117 2026-04-30 19:18:31 87 na-prot_4327.pdb -3.88944852037 2026-04-30 19:18:31 88 na-prot_9923.pdb -3.88534748448 2026-04-30 19:18:31 89 na-prot_13220.pdb -3.87252646059 2026-04-30 19:18:31 90 na-prot_9011.pdb -3.86217804341 2026-04-30 19:18:31 91 na-prot_8920.pdb -3.85988599769 2026-04-30 19:18:31 92 na-prot_17168.pdb -3.85887099197 2026-04-30 19:18:31 93 na-prot_15495.pdb -3.85302217951 2026-04-30 19:18:31 94 na-prot_1685.pdb -3.8481118006 2026-04-30 19:18:31 95 na-prot_5879.pdb -3.84693012207 2026-04-30 19:18:31 96 na-prot_3040.pdb -3.84005429051 2026-04-30 19:18:31 97 na-prot_508.pdb -3.82155353278 2026-04-30 19:18:31 98 na-prot_19689.pdb -3.82095722524 2026-04-30 19:18:31 99 na-prot_3165.pdb -3.8180637117 2026-04-30 19:18:31 100 na-prot_10014.pdb -3.81740723156 2026-04-30 19:18:31 Sent to refinement: clusters_found|na-prot_8075.pdb 2026-04-30 19:18:31 Sent to refinement: clusters_found|na-prot_8075.pdb 2026-04-30 19:18:31 DARS clustering end 2026-04-30 19:18:31 MC (refinement) init 2026-04-30 19:18:31 python /home/rpdock/run_gramm//run_mc.py -f dars_to_mc.txt -d /home/rpdock/web/media/jobs/19925731-9cf0-49d1-8818-6175660048de/ 2026-04-30 19:18:31 Refinement of #1 /home/rpdock/web/media/jobs/19925731-9cf0-49d1-8818-6175660048de/na-prot_8075.pdb 2026-04-30 19:18:31 python /home/rpdock/mc/MC_DNA.py -s 1000 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/19925731-9cf0-49d1-8818-6175660048de//ref_struc/na-prot_8075/na-prot_8075.pdb 2026-04-30 19:21:55 run_mc::stderr:Traceback (most recent call last): File "/home/rpdock/mc/MC_DNA.py", line 631, in change_atom_list, change_chains, change_chains1, axis, angle = rotation(change_chains) File "/home/rpdock/mc/MC_DNA.py", line 284, in rotation 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 330, in _reconstruct memo[id(x)] = y MemoryError 2026-04-30 19:21:55 start - parameters: File name /home/rpdock/web/media/jobs/19925731-9cf0-49d1-8818-6175660048de//ref_struc/na-prot_8075/na-prot_8075.pdb Steps 1000 Temp. start 15000.0 Temp. end 295.0 False msg start - parameters: File name /home/rpdock/web/media/jobs/19925731-9cf0-49d1-8818-6175660048de//ref_struc/na-prot_8075/na-prot_8075.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 - -346970.49 -872701.03 -274269.45 800000.00 1 T -294040.48 -818961.26 -235079.21 760000.00 T= 15000.0 K progress 0.1 2 R -288860.45 -813781.23 -235079.21 760000.00 T= 14985.295 K progress 0.2 3 T -129710.52 -882825.56 -246884.96 1000000.00 T= 14970.59 K progress 0.3 4 T -235066.20 -866888.38 -248177.83 880000.00 T= 14926.475 K progress 0.4 5 T -344053.11 -891760.89 -252292.21 800000.00 T= 14897.065 K progress 0.5 6 T -261568.87 -762905.17 -218663.70 720000.00 T= 14867.655 K progress 0.6 7 R -531451.00 -751182.59 -220268.42 440000.00 T= 14852.95 K progress 0.7 8 T -496916.79 -658322.26 -198594.53 360000.00 T= 14823.54 K progress 0.8 9 T -646536.27 -594393.64 -172142.63 120000.00 T= 14794.13 K progress 0.9 10 R -658158.45 -597483.54 -180674.92 120000.00 T= 14750.015 K progress 1.0 11 R -648770.54 -596343.49 -172427.05 120000.00 T= 14676.49 K progress 1.1 12 R -636341.54 -582143.97 -174197.57 120000.00 T= 14661.785 K progress 1.2 13 T -616797.98 -538456.17 -158341.81 80000.00 T= 14647.08 K progress 1.3 14 R -616086.07 -537744.26 -158341.81 80000.00 T= 14632.375 K progress 1.4 15 R -628374.53 -548731.12 -159643.42 80000.00 T= 14617.67 K progress 1.5 16 R -621462.59 -544562.78 -156899.82 80000.00 T= 14544.145 K progress 1.6 17 T -612009.83 -685142.86 -206866.97 280000.00 T= 14514.735 K progress 1.7 18 T -681047.58 -642023.71 -199023.86 160000.00 T= 14485.325 K progress 1.8 19 R -674027.54 -633892.17 -200135.37 160000.00 T= 14470.62 K progress 1.9 20 R -662680.92 -650057.49 -212623.42 200000.00 T= 14441.21 K progress 2.0 21 T -701096.09 -747216.53 -233879.57 280000.00 T= 14426.505 K progress 2.1 22 T -736085.43 -688393.79 -207691.64 160000.00 T= 14382.39 K progress 2.2 23 R -725058.04 -745845.92 -219212.11 240000.00 T= 14367.685 K progress 2.3 24 R -847132.29 -773411.69 -233720.60 160000.00 T= 14308.865 K progress 2.4 25 T -604300.56 -793820.80 -250479.76 440000.00 T= 14279.455 K progress 2.5 26 R -476863.24 -767723.87 -229139.38 520000.00 T= 14205.93 K progress 2.6 27 R -499132.96 -801751.00 -257381.96 560000.00 T= 14161.815 K progress 2.7 28 R -492633.22 -774186.57 -238446.65 520000.00 T= 14132.405 K progress 2.8 29 R -687063.32 -770324.39 -236738.93 320000.00 T= 14088.29 K progress 2.9 30 R -669144.74 -752965.56 -236179.18 320000.00 T= 14073.585 K progress 3.0 31 R -678913.58 -769955.58 -228958.00 320000.00 T= 13985.355 K progress 3.1 32 R -668911.74 -758674.53 -230237.21 320000.00 T= 13926.535 K progress 3.2 33 R -654199.23 -752534.05 -221665.18 320000.00 T= 13779.485 K progress 3.3 34 R -675115.40 -768041.64 -227073.77 320000.00 T= 13750.075 K progress 3.4 35 T -265069.51 -686565.61 -218503.90 640000.00 T= 13676.55 K progress 3.5 36 R -414208.88 -723584.06 -210624.82 520000.00 T= 13661.845 K progress 3.6 37 T -436573.67 -701623.27 -214950.41 480000.00 T= 13632.435 K progress 3.7 38 T -279357.15 -785041.85 -214315.30 720000.00 T= 13617.73 K progress 3.8 39 R -348438.01 -734063.90 -214374.11 600000.00 T= 13588.32 K progress 3.9 40 T -319876.84 -729400.79 -230476.05 640000.00 T= 13573.615 K progress 4.0 41 R -457629.96 -775810.18 -241819.78 560000.00 T= 13558.91 K progress 4.1 42 T -566614.35 -712203.10 -214411.25 360000.00 T= 13500.09 K progress 4.2 43 T -518866.10 -735376.15 -223489.96 440000.00 T= 13441.27 K progress 4.3 44 T -499353.56 -665580.67 -193772.90 360000.00 T= 13426.565 K progress 4.4 45 R -453575.60 -653775.84 -199799.76 400000.00 T= 13397.155 K progress 4.5 46 T -360514.38 -695401.99 -225112.39 560000.00 T= 13382.45 K progress 4.6 47 T -497578.66 -715106.05 -222472.62 440000.00 T= 13367.745 K progress 4.7 48 R -439293.75 -668465.67 -210828.08 440000.00 T= 13353.04 K progress 4.8 49 T -530521.55 -651153.33 -199368.22 320000.00 T= 13338.335 K progress 4.9 50 T -482332.16 -630173.05 -172159.11 320000.00 T= 13323.63 K progress 5.0 51 R -513169.70 -655977.68 -177192.02 320000.00 T= 13308.925 K progress 5.1 52 T -412149.51 -748997.36 -223152.15 560000.00 T= 13294.22 K progress 5.2 53 T -125990.73 -631475.55 -174515.18 680000.00 T= 13279.515 K progress 5.3 54 T -452874.93 -637876.95 -174997.98 360000.00 T= 13264.81 K progress 5.4 55 R -472251.83 -651608.96 -180642.87 360000.00 T= 13250.105 K progress 5.5 56 T -701396.80 -684290.02 -217106.78 200000.00 T= 13235.4 K progress 5.6 57 T -670258.60 -648781.17 -181477.44 160000.00 T= 13147.17 K progress 5.7 58 R -636356.26 -651294.26 -185062.01 200000.00 T= 12970.71 K progress 5.8 59 T -641504.36 -620602.43 -180901.93 160000.00 T= 12941.3 K progress 5.9 60 T -611928.13 -631279.96 -180648.18 200000.00 T= 12911.89 K progress 6.0 61 T -641863.47 -615574.91 -186288.57 160000.00 T= 12897.185 K progress 6.1 62 R -663503.81 -630710.43 -192793.38 160000.00 T= 12882.48 K progress 6.2 63 T -475542.86 -649616.62 -185926.25 360000.00 T= 12853.07 K progress 6.3 64 R -435951.32 -681240.27 -194711.05 440000.00 T= 12838.365 K progress 6.4 65 R -473621.80 -614659.80 -178961.99 320000.00 T= 12823.66 K progress 6.5 66 R -485337.02 -620131.17 -185205.85 320000.00 T= 12808.955 K progress 6.6 67 T -485690.24 -626888.90 -178801.34 320000.00 T= 12794.25 K progress 6.7 68 R -481131.47 -625732.21 -175399.26 320000.00 T= 12779.545 K progress 6.8 69 R -272523.21 -591910.32 -160612.89 480000.00 T= 12764.84 K progress 6.9 70 T -350639.64 -646787.10 -183852.54 480000.00 T= 12735.43 K progress 7.0 71 T -443056.66 -566603.01 -156453.65 280000.00 T= 12720.725 K progress 7.1 72 R -492713.61 -609735.22 -162978.40 280000.00 T= 12676.61 K progress 7.2 73 R -501024.95 -616968.44 -164056.51 280000.00 T= 12617.79 K progress 7.3 74 R -481476.28 -599028.74 -162447.54 280000.00 T= 12603.085 K progress 7.4 75 R -421505.67 -550438.68 -151066.99 280000.00 T= 12588.38 K progress 7.5 76 T -388383.77 -520932.26 -147451.51 280000.00 T= 12573.675 K progress 7.6 77 R -388227.80 -525340.40 -142887.41 280000.00 T= 12558.97 K progress 7.7 78 R -527979.63 -599815.37 -168164.26 240000.00 T= 12544.265 K progress 7.8 79 T -530204.79 -562990.66 -167214.13 200000.00 T= 12529.56 K progress 7.9 80 T -512433.45 -644584.68 -187848.76 320000.00 T= 12514.855 K progress 8.0 81 T -375949.14 -749671.67 -226277.47 600000.00 T= 12441.33 K progress 8.1 82 R -561580.69 -739784.19 -221796.50 400000.00 T= 12426.625 K progress 8.2 83 T -511367.05 -635241.91 -196125.14 320000.00 T= 12397.215 K progress 8.3 84 R -513571.13 -641907.21 -191663.92 320000.00 T= 12382.51 K progress 8.4 85 R -509296.76 -610575.20 -178721.57 280000.00 T= 12338.395 K progress 8.5 86 R -382573.66 -547713.87 -154859.80 320000.00 T= 12323.69 K progress 8.6 87 T -507093.27 -650255.42 -216837.85 360000.00 T= 12308.985 K progress 8.7 88 R -485534.25 -631834.20 -213700.05 360000.00 T= 12294.28 K progress 8.8 89 R -518763.12 -659398.35 -219364.77 360000.00 T= 12279.575 K progress 8.9 90 T -534472.55 -654050.91 -200421.64 320000.00 T= 12250.165 K progress 9.0 91 T -703410.81 -677347.09 -226063.72 200000.00 T= 12235.46 K progress 9.1 92 R -712334.72 -685182.82 -227151.90 200000.00 T= 12220.755 K progress 9.2 93 T -690131.29 -671570.15 -218561.13 200000.00 T= 12206.05 K progress 9.3 94 T -691378.45 -655761.04 -195617.41 160000.00 T= 12191.345 K progress 9.4 95 T -687090.03 -628146.98 -178943.05 120000.00 T= 12147.23 K progress 9.5 96 R -715878.45 -617017.64 -178860.80 80000.00 T= 12132.525 K progress 9.6 97 T -714380.18 -580376.01 -174004.16 40000.00 T= 12103.115 K progress 9.7 98 R -647110.86 -634232.18 -172878.68 160000.00 T= 12088.41 K progress 9.8 99 T -707175.42 -633975.57 -193199.84 120000.00 T= 12044.295 K progress 9.9 100 R -764725.18 -654578.91 -190146.28 80000.00 T= 12014.885 K progress 10.0 101 T -677520.69 -693233.01 -184287.68 200000.00 T= 12000.18 K progress 10.1 102 T -552735.38 -643127.20 -189608.18 280000.00 T= 11985.475 K progress 10.2 103 R -476436.10 -610485.35 -185950.75 320000.00 T= 11956.065 K progress 10.3 104 T -778007.77 -666930.87 -191076.91 80000.00 T= 11941.36 K progress 10.4 105 R -792376.73 -668537.87 -203838.85 80000.00 T= 11867.835 K progress 10.5 106 R -806805.62 -672790.52 -214015.10 80000.00 T= 11823.72 K progress 10.6 107 T -764580.45 -674084.54 -210495.91 120000.00 T= 11794.31 K progress 10.7 108 T -721760.72 -684071.20 -197689.52 160000.00 T= 11779.605 K progress 10.8 109 T -500989.98 -595607.54 -185382.44 280000.00 T= 11750.195 K progress 10.9 110 T -477786.26 -550122.36 -167663.90 240000.00 T= 11735.49 K progress 11.0 111 T -626771.40 -639567.81 -187203.59 200000.00 T= 11720.785 K progress 11.1 112 R -738905.75 -632890.40 -186015.35 80000.00 T= 11706.08 K progress 11.2 113 R -741198.66 -635402.76 -185795.90 80000.00 T= 11691.375 K progress 11.3 114 R -739125.58 -635061.83 -184063.75 80000.00 T= 11676.67 K progress 11.4 115 R -756664.52 -646708.90 -189955.61 80000.00 T= 11647.26 K progress 11.5 116 T -528729.35 -617059.82 -191669.54 280000.00 T= 11632.555 K progress 11.6 117 T -678053.76 -645100.20 -192953.56 160000.00 T= 11617.85 K progress 11.7 118 R -603393.71 -625387.76 -178005.95 200000.00 T= 11603.145 K progress 11.8 119 T -529585.21 -689527.64 -200057.57 360000.00 T= 11588.44 K progress 11.9 120 T -645647.09 -655937.72 -189709.37 200000.00 T= 11514.915 K progress 12.0 121 T -654707.45 -559059.98 -175647.47 80000.00 T= 11470.8 K progress 12.1 122 T -664287.28 -611894.66 -172392.62 120000.00 T= 11456.095 K progress 12.2 123 R -674787.35 -578163.59 -176623.76 80000.00 T= 11426.685 K progress 12.3 124 T -825238.78 -630745.20 -194493.58 0.00 T= 11397.275 K progress 12.4 125 T -760421.64 -566944.69 -193476.95 0.00 T= 11367.865 K progress 12.5 126 T -783102.52 -586411.42 -196691.10 0.00 T= 11353.16 K progress 12.6 127 R -813521.75 -604166.28 -209355.47 0.00 T= 11279.635 K progress 12.7 128 T -787653.88 -585270.33 -202383.55 0.00 T= 11264.93 K progress 12.8 129 R -799256.82 -595249.10 -204007.72 0.00 T= 11250.225 K progress 12.9 130 R -733504.14 -578125.94 -195378.21 40000.00 T= 11235.52 K progress 13.0 131 T -662779.48 -627090.89 -195688.59 160000.00 T= 11206.11 K progress 13.1 132 T -817209.24 -679083.83 -218125.41 80000.00 T= 11191.405 K progress 13.2 133 R -724437.25 -644261.53 -200175.72 120000.00 T= 11161.995 K progress 13.3 134 R -810739.30 -673217.78 -217521.53 80000.00 T= 11147.29 K progress 13.4 135 R -800305.24 -661157.53 -219147.71 80000.00 T= 11117.88 K progress 13.5 136 R -793161.37 -656879.65 -216281.72 80000.00 T= 11014.945 K progress 13.6 137 R -802588.85 -667846.90 -214741.95 80000.00 T= 10838.485 K progress 13.7 138 R -731411.53 -647742.17 -203669.36 120000.00 T= 10809.075 K progress 13.8 139 R -712689.40 -630160.54 -202528.86 120000.00 T= 10779.665 K progress 13.9 140 R -695306.94 -611667.39 -203639.55 120000.00 T= 10764.96 K progress 14.0 141 T -660314.36 -639778.90 -180535.46 160000.00 T= 10720.845 K progress 14.1 142 R -729174.01 -691079.76 -198094.26 160000.00 T= 10706.14 K progress 14.2 143 R -765602.10 -643034.03 -202568.07 80000.00 T= 10691.435 K progress 14.3 144 T -824303.46 -723072.88 -221230.57 120000.00 T= 10662.025 K progress 14.4 145 T -576043.02 -783856.55 -232186.47 440000.00 T= 10588.5 K progress 14.5 146 R -551805.28 -760179.85 -231625.43 440000.00 T= 10544.385 K progress 14.6 147 R -587509.27 -761360.32 -226148.96 400000.00 T= 10500.27 K progress 14.7 148 R -586153.17 -762107.22 -224045.95 400000.00 T= 10485.565 K progress 14.8 149 R -555404.54 -761755.45 -233649.09 440000.00 T= 10470.86 K progress 14.9 150 T -609005.97 -722213.08 -206792.89 320000.00 T= 10456.155 K progress 15.0 151 R -618908.97 -727487.99 -211420.98 320000.00 T= 10441.45 K progress 15.1 152 R -603446.84 -711417.44 -212029.40 320000.00 T= 10397.335 K progress 15.2 153 T -693783.42 -623179.75 -190603.67 120000.00 T= 10382.63 K progress 15.3 154 T -726378.33 -564966.87 -201411.45 40000.00 T= 10367.925 K progress 15.4 155 T -755844.03 -558538.83 -197305.20 0.00 T= 10353.22 K progress 15.5 156 R -763253.42 -567076.61 -196176.80 0.00 T= 10338.515 K progress 15.6 157 T -756742.11 -569106.06 -187636.05 0.00 T= 10309.105 K progress 15.7 158 R -719406.77 -560783.87 -198622.91 40000.00 T= 10264.99 K progress 15.8 159 T -572571.41 -450194.73 -162376.68 40000.00 T= 10250.285 K progress 15.9 160 T -591263.79 -463103.85 -168159.94 40000.00 T= 10220.875 K progress 16.0 161 R -619118.97 -464670.19 -154448.78 0.00 T= 10206.17 K progress 16.1 162 T -751915.00 -558503.03 -193411.98 0.00 T= 10191.465 K progress 16.2 163 R -744118.67 -550631.79 -193486.88 0.00 T= 10176.76 K progress 16.3 164 R -756094.36 -562854.32 -193240.04 0.00 T= 10162.055 K progress 16.4 165 T -690335.14 -509212.02 -181123.12 0.00 T= 10132.645 K progress 16.5 166 R -703041.24 -521307.31 -181733.92 0.00 T= 10103.235 K progress 16.6 167 T -656228.07 -586483.59 -189744.48 120000.00 T= 10088.53 K progress 16.7 168 R -681312.30 -569725.43 -191586.87 80000.00 T= 10073.825 K progress 16.8 169 R -678013.00 -617913.17 -180099.83 120000.00 T= 10059.12 K progress 16.9 170 R -667959.52 -595234.81 -192724.71 120000.00 T= 10029.71 K progress 17.0 171 R -719230.74 -609173.27 -190057.48 80000.00 T= 10015.005 K progress 17.1 172 R -653719.96 -617248.55 -196471.41 160000.00 T= 10000.3 K progress 17.2 173 R -658595.17 -619941.84 -198653.33 160000.00 T= 9985.595 K progress 17.3 174 R -698086.57 -591452.94 -186633.63 80000.00 T= 9970.89 K progress 17.4 175 T -646744.30 -749036.91 -217707.39 320000.00 T= 9941.48 K progress 17.5 176 T -544826.39 -633182.61 -191643.78 280000.00 T= 9926.775 K progress 17.6 177 R -574388.11 -617199.81 -197188.30 240000.00 T= 9912.07 K progress 17.7 178 T -701036.48 -554135.09 -186901.39 40000.00 T= 9897.365 K progress 17.8 179 R -701208.23 -551878.99 -189329.24 40000.00 T= 9853.25 K progress 17.9 180 T -695644.60 -552253.77 -183390.84 40000.00 T= 9838.545 K progress 18.0 181 T -753051.29 -598631.44 -194419.84 40000.00 T= 9823.84 K progress 18.1 182 R -718829.48 -578351.86 -180477.62 40000.00 T= 9809.135 K progress 18.2 183 R -733330.24 -589904.83 -183425.41 40000.00 T= 9794.43 K progress 18.3 184 T -715466.25 -573235.45 -182230.81 40000.00 T= 9720.905 K progress 18.4 185 R -692562.84 -544633.72 -187929.12 40000.00 T= 9706.2 K progress 18.5 186 R -681992.61 -537819.62 -184172.99 40000.00 T= 9676.79 K progress 18.6 187 R -708531.29 -566806.58 -181724.71 40000.00 T= 9662.085 K progress 18.7 188 R -544468.57 -559965.87 -184502.70 200000.00 T= 9617.97 K progress 18.8 189 R -527371.94 -543868.16 -183503.78 200000.00 T= 9603.265 K progress 18.9 190 R -530282.43 -543891.62 -186390.81 200000.00 T= 9588.56 K progress 19.0 191 R -533206.61 -550246.05 -182960.56 200000.00 T= 9573.855 K progress 19.1 192 T -521167.09 -543421.59 -177745.50 200000.00 T= 9559.15 K progress 19.2 193 R -531796.20 -548316.04 -183480.16 200000.00 T= 9544.445 K progress 19.3 194 T -518364.64 -540028.94 -178335.70 200000.00 T= 9529.74 K progress 19.4 195 R -524858.60 -473544.89 -171313.71 120000.00 T= 9500.33 K progress 19.5 196 R -522277.70 -473868.23 -168409.47 120000.00 T= 9485.625 K progress 19.6 197 T -710466.60 -568796.03 -181670.58 40000.00 T= 9470.92 K progress 19.7 198 R -672258.40 -533035.69 -179222.71 40000.00 T= 9441.51 K progress 19.8 199 R -675143.47 -541317.03 -173826.44 40000.00 T= 9426.805 K progress 19.9 200 T -676212.75 -541505.79 -174706.96 40000.00 T= 9412.1 K progress 20.0 Long traj 201 R -682089.12 -542928.14 -179160.98 40000.00 T= 9382.69 K progress 20.1 202 R -692002.58 -554441.04 -177561.54 40000.00 T= 9367.985 K progress 20.2 203 R -673336.94 -538225.94 -175111.00 40000.00 T= 9338.575 K progress 20.3 204 R -676981.30 -541870.30 -175111.00 40000.00 T= 9323.87 K progress 20.4 205 R -672759.76 -537580.04 -175179.71 40000.00 T= 9294.46 K progress 20.5 206 T -630035.78 -501865.93 -168169.85 40000.00 T= 9279.755 K progress 20.6 207 R -661113.78 -528127.88 -172985.90 40000.00 T= 9265.05 K progress 20.7 208 T -683852.69 -546131.34 -177721.34 40000.00 T= 9235.64 K progress 20.8 209 T -584768.12 -463738.61 -161029.51 40000.00 T= 9220.935 K progress 20.9 210 T -448174.90 -367279.53 -120895.36 40000.00 T= 9206.23 K progress 21.0 211 R -482801.27 -374885.02 -107916.25 0.00 T= 9176.82 K progress 21.1 212 R -437115.71 -358824.34 -118291.37 40000.00 T= 9162.115 K progress 21.2 213 T -494878.42 -405011.44 -129866.97 40000.00 T= 9147.41 K progress 21.3 214 T -432252.06 -327085.36 -105166.70 0.00 T= 9132.705 K progress 21.4 215 R -413346.61 -316508.69 -96837.92 0.00 T= 9103.295 K progress 21.5 216 R -442878.40 -327260.80 -115617.60 0.00 T= 9088.59 K progress 21.6 217 R -439920.43 -327260.80 -112659.63 0.00 T= 9044.475 K progress 21.7 218 R -438082.63 -326841.62 -111241.01 0.00 T= 9029.77 K progress 21.8 219 T -350520.97 -265169.99 -85350.97 0.00 T= 9015.065 K progress 21.9 220 R -371817.80 -279071.75 -92746.05 0.00 T= 9000.36 K progress 22.0 221 R -348089.96 -262738.98 -85350.97 0.00 T= 8985.655 K progress 22.1 222 T -303270.54 -225600.60 -77669.94 0.00 T= 8970.95 K progress 22.2 223 R -307404.88 -226905.18 -80499.70 0.00 T= 8956.245 K progress 22.3 224 R -303278.29 -225608.35 -77669.94 0.00 T= 8941.54 K progress 22.4 225 R -303883.63 -227811.57 -76072.06 0.00 T= 8926.835 K progress 22.5 226 R -304834.36 -225835.48 -78998.88 0.00 T= 8912.13 K progress 22.6 227 T -343971.91 -255557.31 -88414.59 0.00 T= 8897.425 K progress 22.7 228 T -284513.39 -217559.60 -66953.78 0.00 T= 8882.72 K progress 22.8 229 T -455607.62 -335621.46 -119986.17 0.00 T= 8868.015 K progress 22.9 230 T -503136.61 -367001.74 -136134.87 0.00 T= 8853.31 K progress 23.0 231 R -503049.17 -366893.06 -136156.11 0.00 T= 8838.605 K progress 23.1 232 T -454746.01 -334231.70 -120514.31 0.00 T= 8823.9 K progress 23.2 233 T -326268.61 -254364.19 -71904.43 0.00 T= 8809.195 K progress 23.3 234 T -384479.40 -292732.56 -91746.84 0.00 T= 8794.49 K progress 23.4 235 R -416509.27 -325889.52 -90619.76 0.00 T= 8765.08 K progress 23.5 236 R -378955.81 -319832.80 -99123.01 40000.00 T= 8750.375 K progress 23.6 237 R -395379.43 -331395.41 -103984.02 40000.00 T= 8720.965 K progress 23.7 238 R -322251.24 -296814.47 -105436.77 80000.00 T= 8691.555 K progress 23.8 239 T -422081.39 -353560.19 -108521.19 40000.00 T= 8676.85 K progress 23.9 240 R -362927.84 -340352.30 -102575.53 80000.00 T= 8647.44 K progress 24.0 241 R -353111.71 -327417.07 -105694.64 80000.00 T= 8632.735 K progress 24.1 242 T -388304.53 -322375.57 -105928.96 40000.00 T= 8618.03 K progress 24.2 243 R -405337.90 -334919.50 -110418.40 40000.00 T= 8603.325 K progress 24.3 244 R -434793.37 -335575.29 -99218.09 0.00 T= 8588.62 K progress 24.4 245 T -447027.69 -390681.16 -136346.53 80000.00 T= 8573.915 K progress 24.5 246 T -509892.84 -398140.07 -111752.77 0.00 T= 8559.21 K progress 24.6 247 R -521704.91 -398809.21 -122895.69 0.00 T= 8544.505 K progress 24.7 248 T -496302.38 -387489.10 -108813.28 0.00 T= 8529.8 K progress 24.8 249 R -499566.97 -385995.46 -113571.51 0.00 T= 8515.095 K progress 24.9 250 R -493450.00 -386223.74 -107226.26 0.00 T= 8470.98 K progress 25.0 251 R -439651.29 -378916.87 -100734.42 40000.00 T= 8456.275 K progress 25.1 252 T -439218.78 -425187.78 -134031.00 120000.00 T= 8412.16 K progress 25.2 253 R -435657.50 -412922.24 -142735.26 120000.00 T= 8397.455 K progress 25.3 254 T -502056.46 -419372.75 -162683.71 80000.00 T= 8382.75 K progress 25.4 255 R -401914.48 -435280.46 -126634.02 160000.00 T= 8368.045 K progress 25.5 256 R -407283.06 -437627.32 -129655.74 160000.00 T= 8353.34 K progress 25.6 257 T -455996.69 -515077.28 -140919.41 200000.00 T= 8338.635 K progress 25.7 258 T -445617.26 -469340.57 -136276.69 160000.00 T= 8323.93 K progress 25.8 259 R -423436.80 -482242.39 -141194.42 200000.00 T= 8309.225 K progress 25.9 260 R -429636.84 -485575.85 -144060.99 200000.00 T= 8294.52 K progress 26.0 261 T -426969.32 -482467.15 -144502.17 200000.00 T= 8279.815 K progress 26.1 262 T -528187.91 -511274.50 -136913.41 120000.00 T= 8265.11 K progress 26.2 263 R -555370.12 -523260.86 -152109.26 120000.00 T= 8250.405 K progress 26.3 264 R -602299.44 -531470.00 -150829.44 80000.00 T= 8191.585 K progress 26.4 265 R -595062.34 -525879.02 -149183.32 80000.00 T= 8162.175 K progress 26.5 266 T -582371.64 -452289.72 -130081.93 0.00 T= 8103.355 K progress 26.6 267 R -548000.10 -417245.37 -130754.73 0.00 T= 8088.65 K progress 26.7 268 T -509084.77 -397606.92 -111477.84 0.00 T= 8044.535 K progress 26.8 269 T -549628.83 -426576.69 -123052.13 0.00 T= 8029.83 K progress 26.9 270 R -554201.79 -430787.20 -123414.59 0.00 T= 8015.125 K progress 27.0 271 R -553237.76 -429169.24 -124068.51 0.00 T= 8000.42 K progress 27.1 272 R -539830.98 -414191.28 -125639.71 0.00 T= 7985.715 K progress 27.2 273 R -516710.56 -385558.75 -131151.81 0.00 T= 7956.305 K progress 27.3 274 R -516710.56 -385558.75 -131151.81 0.00 T= 7912.19 K progress 27.4 275 T -547410.81 -403080.56 -144330.25 0.00 T= 7897.485 K progress 27.5 276 R -596163.25 -446431.92 -149731.33 0.00 T= 7882.78 K progress 27.6 277 T -601322.70 -482154.33 -159168.37 40000.00 T= 7868.075 K progress 27.7 278 T -746632.01 -563208.60 -183423.41 0.00 T= 7853.37 K progress 27.8 279 R -705307.07 -585111.21 -200195.86 80000.00 T= 7823.96 K progress 27.9 280 R -720495.70 -568649.31 -191846.39 40000.00 T= 7779.845 K progress 28.0 281 R -690521.85 -519452.75 -171069.11 0.00 T= 7765.14 K progress 28.1 282 T -668262.40 -524711.62 -183550.78 40000.00 T= 7750.435 K progress 28.2 283 T -719151.09 -562796.51 -196354.58 40000.00 T= 7735.73 K progress 28.3 284 R -709025.51 -554094.06 -194931.45 40000.00 T= 7721.025 K progress 28.4 285 T -746362.09 -577180.92 -209181.17 40000.00 T= 7706.32 K progress 28.5 286 R -746223.21 -587570.53 -198652.67 40000.00 T= 7691.615 K progress 28.6 287 R -753315.04 -588050.94 -205264.10 40000.00 T= 7662.205 K progress 28.7 288 T -739618.72 -609149.40 -210469.31 80000.00 T= 7647.5 K progress 28.8 289 R -762145.51 -630196.09 -211949.41 80000.00 T= 7603.385 K progress 28.9 290 T -731845.99 -598094.10 -213751.89 80000.00 T= 7559.27 K progress 29.0 291 R -724485.69 -591423.57 -213062.12 80000.00 T= 7544.565 K progress 29.1 292 R -720517.04 -590546.28 -209970.76 80000.00 T= 7529.86 K progress 29.2 293 R -721962.52 -590546.28 -211416.24 80000.00 T= 7515.155 K progress 29.3 294 R -751781.31 -597573.52 -194207.79 40000.00 T= 7500.45 K progress 29.4 295 R -745883.32 -616335.90 -209547.42 80000.00 T= 7485.745 K progress 29.5 296 T -755011.28 -676659.10 -198352.18 120000.00 T= 7441.63 K progress 29.6 297 T -627518.25 -603330.31 -184187.94 160000.00 T= 7397.515 K progress 29.7 298 T -610994.74 -556366.37 -174628.38 120000.00 T= 7323.99 K progress 29.8 299 T -731125.33 -608554.65 -202570.68 80000.00 T= 7279.875 K progress 29.9 300 T -726379.32 -643652.30 -202727.02 120000.00 T= 7191.645 K progress 30.0 301 T -728688.66 -596083.85 -212604.80 80000.00 T= 7162.235 K progress 30.1 302 T -778791.01 -644322.35 -214468.66 80000.00 T= 7147.53 K progress 30.2 303 R -781656.33 -647457.07 -214199.26 80000.00 T= 7132.825 K progress 30.3 304 R -784811.49 -649193.63 -215617.86 80000.00 T= 7118.12 K progress 30.4 305 R -765676.49 -637428.29 -208248.20 80000.00 T= 7103.415 K progress 30.5 306 R -794907.72 -622904.50 -212003.21 40000.00 T= 7074.005 K progress 30.6 307 R -790372.67 -618825.72 -211546.95 40000.00 T= 7044.595 K progress 30.7 308 R -796367.64 -623402.90 -212964.73 40000.00 T= 7029.89 K progress 30.8 309 T -708886.81 -632350.05 -196536.76 120000.00 T= 7000.48 K progress 30.9 310 R -734276.78 -650159.33 -204117.45 120000.00 T= 6985.775 K progress 31.0 311 R -780561.43 -659077.64 -201483.79 80000.00 T= 6971.07 K progress 31.1 312 R -813539.99 -676350.95 -217189.04 80000.00 T= 6956.365 K progress 31.2 313 T -798275.94 -624826.34 -213449.60 40000.00 T= 6941.66 K progress 31.3 314 R -732854.49 -598127.05 -214727.44 80000.00 T= 6912.25 K progress 31.4 315 R -747542.17 -608418.29 -219123.88 80000.00 T= 6897.545 K progress 31.5 316 R -684161.87 -622100.12 -222061.75 160000.00 T= 6882.84 K progress 31.6 317 R -755020.94 -645101.09 -229919.85 120000.00 T= 6868.135 K progress 31.7 318 R -685397.49 -601322.71 -204074.79 120000.00 T= 6838.725 K progress 31.8 319 R -734337.86 -630299.66 -184038.20 80000.00 T= 6824.02 K progress 31.9 320 R -746790.01 -600439.60 -186350.40 40000.00 T= 6809.315 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 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 230, in _deepcopy_list y.append(deepcopy(a, memo)) File "/usr/lib/python2.7/copy.py", line 192, in deepcopy memo[d] = y MemoryError Error in run_mc Traceback (most recent call last): File "/home/rpdock/mc/MC_DNA.py", line 631, in change_atom_list, change_chains, change_chains1, axis, angle = rotation(change_chains) File "/home/rpdock/mc/MC_DNA.py", line 284, in rotation 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 330, in _reconstruct memo[id(x)] = y MemoryError Thu Apr 30 19:18:31 2026 ['na-prot_8075.pdb'] msg Refinement of #1 /home/rpdock/web/media/jobs/19925731-9cf0-49d1-8818-6175660048de/na-prot_8075.pdb dir: /home/rpdock/web/media/jobs/19925731-9cf0-49d1-8818-6175660048de/ file: na-prot_8075.pdb find `pwd` -iname na-prot_8075.pdb copy /home/rpdock/web/media/jobs/19925731-9cf0-49d1-8818-6175660048de/prot-na_20/na-prot_8075.pdb to /home/rpdock/web/media/jobs/19925731-9cf0-49d1-8818-6175660048de//ref_struc/na-prot_8075/na-prot_8075.pdb cmd: python /home/rpdock/mc/MC_DNA.py -s 1000 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/19925731-9cf0-49d1-8818-6175660048de//ref_struc/na-prot_8075/na-prot_8075.pdb msg python /home/rpdock/mc/MC_DNA.py -s 1000 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/19925731-9cf0-49d1-8818-6175660048de//ref_struc/na-prot_8075/na-prot_8075.pdb msg run_mc::stderr:Traceback (most recent call last): File "/home/rpdock/mc/MC_DNA.py", line 631, in change_atom_list, change_chains, change_chains1, axis, angle = rotation(change_chains) File "/home/rpdock/mc/MC_DNA.py", line 284, in rotation 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 330, in _reconstruct memo[id(x)] = y MemoryError 2026-04-30 19:21:55 npdock::MC (refinement) end 2026-04-30 19:21:55 npdock::OK 2026-04-30 19:21:55 Set finished status of 19925731-9cf0-49d1-8818-6175660048de