2026-07-06 08:50:02 NPdock start 2026-07-06 08:50:02 ver: server 2026-07-06 08:50:02 mode: 11111 2026-07-06 08:50:02 is RNA? 0 2026-07-06 08:50:02 Interface: prot: '' na: '' 2026-07-06 08:50:02 Curr dir:/home/rpdock/web/media/jobs/28bf50a6-d532-41dc-9a0e-e75cbbfb5a03/ 2026-07-06 08:50:02 GRAMM in progress... 2026-07-06 08:50:02 python /home/rpdock/run_gramm//run_gramm1.py -d 20000 -p prot.pdb -r na.pdb -pi '' -ri '' -n 1 -pf '*' -rf '*' 2026-07-06 09:58:50 GRAMM done 2026-07-06 09:58:50 DNP scoring in progress... 2026-07-06 09:58:50 time python /home/rpdock/run_gramm//DNP/laczony/QUASI-DNP-QDV_potential_1.0.py -m 100 -f list.txt -o dnp_out.txt 2026-07-06 09:58:51 QDV-DNP starts 2026-07-06 09:58:51 Show log every 100 structures 2026-07-06 09:58:51 QUASI-DNP starts 2026-07-06 09:58:51 na-prot_1000.pdb -776039.457786 2026-07-06 09:59:10 na-prot_94.pdb -625963.762062 2026-07-06 09:59:29 na-prot_194.pdb -568948.274391 2026-07-06 09:59:47 na-prot_294.pdb -925134.937764 2026-07-06 10:00:06 na-prot_394.pdb -566508.464206 2026-07-06 10:00:25 na-prot_494.pdb -653669.022356 2026-07-06 10:00:44 na-prot_594.pdb -566046.297232 2026-07-06 10:01:03 na-prot_694.pdb -718078.377656 2026-07-06 10:01:22 na-prot_794.pdb -489878.386133 2026-07-06 10:01:41 na-prot_894.pdb -655905.125042 2026-07-06 10:02:00 na-prot_994.pdb -586304.459888 2026-07-06 10:02:19 na-prot_1100.pdb -730718.800133 2026-07-06 10:02:38 na-prot_1200.pdb -817515.655105 2026-07-06 10:02:58 na-prot_1300.pdb -531832.42045 2026-07-06 10:03:18 na-prot_1400.pdb -661908.150437 2026-07-06 10:03:37 na-prot_1500.pdb -967868.469639 2026-07-06 10:03:57 na-prot_1600.pdb -424246.461047 2026-07-06 10:04:17 na-prot_1700.pdb -622613.252242 2026-07-06 10:04:40 na-prot_1800.pdb -677941.224549 2026-07-06 10:05:00 na-prot_1900.pdb -694672.820356 2026-07-06 10:05:20 na-prot_2000.pdb -669847.834807 2026-07-06 10:05:39 na-prot_2100.pdb -586511.677725 2026-07-06 10:05:59 na-prot_2200.pdb -646334.977237 2026-07-06 10:06:18 na-prot_2300.pdb -804908.553871 2026-07-06 10:06:38 na-prot_2400.pdb -453807.971789 2026-07-06 10:06:57 na-prot_2500.pdb -758339.083558 2026-07-06 10:07:17 na-prot_2600.pdb -404037.326071 2026-07-06 10:07:36 na-prot_2700.pdb -922041.900095 2026-07-06 10:07:56 na-prot_2800.pdb -680996.802079 2026-07-06 10:08:16 na-prot_2900.pdb -337545.316534 2026-07-06 10:08:35 na-prot_3000.pdb -887435.834342 2026-07-06 10:08:55 na-prot_3100.pdb -349618.320753 2026-07-06 10:09:14 na-prot_3200.pdb -675506.626914 2026-07-06 10:09:33 na-prot_3300.pdb -476715.069552 2026-07-06 10:09:52 na-prot_3400.pdb -570956.651249 2026-07-06 10:10:11 na-prot_3500.pdb -508558.128591 2026-07-06 10:10:31 na-prot_3600.pdb -644999.119931 2026-07-06 10:10:50 na-prot_3700.pdb -459820.388841 2026-07-06 10:11:10 na-prot_3800.pdb -692708.374023 2026-07-06 10:11:29 na-prot_3900.pdb -534093.930721 2026-07-06 10:11:49 na-prot_4000.pdb -505047.1154 2026-07-06 10:12:09 na-prot_4100.pdb -643773.206433 2026-07-06 10:12:28 na-prot_4200.pdb -508368.077437 2026-07-06 10:12:48 na-prot_4300.pdb -486834.28834 2026-07-06 10:13:08 na-prot_4400.pdb -642365.317926 2026-07-06 10:13:27 na-prot_4500.pdb -427639.449535 2026-07-06 10:13:47 na-prot_4600.pdb -492023.04178 2026-07-06 10:14:06 na-prot_4700.pdb -631444.850595 2026-07-06 10:14:26 na-prot_4800.pdb -717856.161482 2026-07-06 10:14:46 na-prot_4900.pdb -502907.095281 2026-07-06 10:15:05 na-prot_5000.pdb -503876.066648 2026-07-06 10:15:25 na-prot_5100.pdb -537005.361282 2026-07-06 10:15:45 na-prot_5200.pdb -603040.391716 2026-07-06 10:16:05 na-prot_5300.pdb -680060.863366 2026-07-06 10:16:24 na-prot_5400.pdb -671761.97337 2026-07-06 10:16:44 na-prot_5500.pdb -370434.160114 2026-07-06 10:17:03 na-prot_5600.pdb -639136.456428 2026-07-06 10:17:23 na-prot_5700.pdb -546155.623419 2026-07-06 10:17:42 na-prot_5800.pdb -348375.367254 2026-07-06 10:18:02 na-prot_5900.pdb -519762.388436 2026-07-06 10:18:22 na-prot_6000.pdb -454954.846945 2026-07-06 10:18:41 na-prot_6100.pdb -508583.414764 2026-07-06 10:19:01 na-prot_6200.pdb -459560.371897 2026-07-06 10:19:21 na-prot_6300.pdb -847531.784483 2026-07-06 10:19:40 na-prot_6400.pdb -428032.172403 2026-07-06 10:19:59 na-prot_6500.pdb -546629.5734 2026-07-06 10:20:19 na-prot_6600.pdb -528488.135168 2026-07-06 10:20:38 na-prot_6700.pdb -875472.90057 2026-07-06 10:20:58 na-prot_6800.pdb -578090.251439 2026-07-06 10:21:17 na-prot_6900.pdb -463519.023285 2026-07-06 10:21:37 na-prot_7000.pdb -605707.353163 2026-07-06 10:21:56 na-prot_7100.pdb -1022067.98239 2026-07-06 10:22:16 na-prot_7200.pdb -655275.364955 2026-07-06 10:22:36 na-prot_7300.pdb -449804.278241 2026-07-06 10:22:55 na-prot_7400.pdb -450249.764957 2026-07-06 10:23:15 na-prot_7500.pdb -633536.975585 2026-07-06 10:23:34 na-prot_7600.pdb -376289.408116 2026-07-06 10:23:54 na-prot_7700.pdb -427979.743894 2026-07-06 10:24:13 na-prot_7800.pdb -520632.516281 2026-07-06 10:24:32 na-prot_7900.pdb -628849.904398 2026-07-06 10:24:52 na-prot_8000.pdb -486390.257243 2026-07-06 10:25:11 na-prot_8100.pdb -555510.339295 2026-07-06 10:25:31 na-prot_8200.pdb -576499.885676 2026-07-06 10:25:50 na-prot_8300.pdb -479550.483355 2026-07-06 10:26:10 na-prot_8400.pdb -461859.139345 2026-07-06 10:26:29 na-prot_8500.pdb -605417.598842 2026-07-06 10:26:49 na-prot_8600.pdb -334623.084664 2026-07-06 10:27:09 na-prot_8700.pdb -572098.759227 2026-07-06 10:27:29 na-prot_8800.pdb -564786.414292 2026-07-06 10:27:48 na-prot_8900.pdb -477952.230183 2026-07-06 10:28:08 na-prot_9000.pdb -580499.81483 2026-07-06 10:28:27 na-prot_9100.pdb -379904.367376 2026-07-06 10:28:47 na-prot_9200.pdb -551631.274413 2026-07-06 10:29:07 na-prot_9300.pdb -672617.291479 2026-07-06 10:29:27 na-prot_9400.pdb -570037.346265 2026-07-06 10:29:47 na-prot_9500.pdb -578992.055608 2026-07-06 10:30:06 na-prot_9600.pdb -563580.752191 2026-07-06 10:30:25 na-prot_9700.pdb -354343.467118 2026-07-06 10:30:45 na-prot_9800.pdb -436536.854164 2026-07-06 10:31:04 na-prot_9900.pdb -451391.114886 2026-07-06 10:31:23 na-prot_10000.pdb -646289.737807 2026-07-06 10:31:42 na-prot_10100.pdb -726617.910896 2026-07-06 10:32:02 na-prot_10200.pdb -500411.74985 2026-07-06 10:32:21 na-prot_10300.pdb -467612.840737 2026-07-06 10:32:40 na-prot_10400.pdb -589070.292965 2026-07-06 10:32:59 na-prot_10500.pdb -429983.142865 2026-07-06 10:33:19 na-prot_10600.pdb -561435.690882 2026-07-06 10:33:38 na-prot_10700.pdb -556493.647083 2026-07-06 10:33:57 na-prot_10800.pdb -358821.515985 2026-07-06 10:34:17 na-prot_10900.pdb -603225.389916 2026-07-06 10:34:36 na-prot_11000.pdb -553082.318441 2026-07-06 10:34:56 na-prot_11100.pdb -451899.149458 2026-07-06 10:35:15 na-prot_11200.pdb -487097.700766 2026-07-06 10:35:35 na-prot_11300.pdb -497012.461422 2026-07-06 10:35:55 na-prot_11400.pdb -602904.569323 2026-07-06 10:36:14 na-prot_11500.pdb -476231.010316 2026-07-06 10:36:34 na-prot_11600.pdb -341161.005586 2026-07-06 10:36:53 na-prot_11700.pdb -244066.600883 2026-07-06 10:37:12 na-prot_11800.pdb -564714.874225 2026-07-06 10:37:32 na-prot_11900.pdb -861128.459764 2026-07-06 10:37:51 na-prot_12000.pdb -436394.714954 2026-07-06 10:38:11 na-prot_12100.pdb -679680.37943 2026-07-06 10:38:30 na-prot_12200.pdb -507632.403111 2026-07-06 10:38:50 na-prot_12300.pdb -448365.55739 2026-07-06 10:39:10 na-prot_12400.pdb -630736.301447 2026-07-06 10:39:29 na-prot_12500.pdb -516285.104149 2026-07-06 10:39:49 na-prot_12600.pdb -705835.093648 2026-07-06 10:40:08 na-prot_12700.pdb -456372.929856 2026-07-06 10:40:28 na-prot_12800.pdb -475007.029508 2026-07-06 10:40:47 na-prot_12900.pdb -525949.332632 2026-07-06 10:41:06 na-prot_13000.pdb -562566.310275 2026-07-06 10:41:26 na-prot_13100.pdb -493836.226101 2026-07-06 10:41:46 na-prot_13200.pdb -420476.954926 2026-07-06 10:42:06 na-prot_13300.pdb -788265.32228 2026-07-06 10:42:25 na-prot_13400.pdb -434056.407686 2026-07-06 10:42:45 na-prot_13500.pdb -462699.819735 2026-07-06 10:43:04 na-prot_13600.pdb -359055.075699 2026-07-06 10:43:24 na-prot_13700.pdb -542894.21384 2026-07-06 10:43:44 na-prot_13800.pdb -412538.359965 2026-07-06 10:44:03 na-prot_13900.pdb -699407.036895 2026-07-06 10:44:23 na-prot_14000.pdb -415151.789968 2026-07-06 10:44:43 na-prot_14100.pdb -665267.341827 2026-07-06 10:45:03 na-prot_14200.pdb -426873.061693 2026-07-06 10:45:22 na-prot_14300.pdb -468130.116221 2026-07-06 10:45:42 na-prot_14400.pdb -537509.865928 2026-07-06 10:46:03 na-prot_14500.pdb -441433.465184 2026-07-06 10:46:23 na-prot_14600.pdb -454704.155013 2026-07-06 10:46:42 na-prot_14700.pdb -549137.148924 2026-07-06 10:47:02 na-prot_14800.pdb -808204.535186 2026-07-06 10:47:21 na-prot_14900.pdb -405539.056184 2026-07-06 10:47:41 na-prot_15000.pdb -714539.820409 2026-07-06 10:48:00 na-prot_15100.pdb -623233.512821 2026-07-06 10:48:20 na-prot_15200.pdb -455144.68985 2026-07-06 10:48:39 na-prot_15300.pdb -364786.013004 2026-07-06 10:48:59 na-prot_15400.pdb -537586.164416 2026-07-06 10:49:19 na-prot_15500.pdb -346469.755125 2026-07-06 10:49:39 na-prot_15600.pdb -668887.008865 2026-07-06 10:49:58 na-prot_15700.pdb -540905.879695 2026-07-06 10:50:18 na-prot_15800.pdb -596670.588322 2026-07-06 10:50:37 na-prot_15900.pdb -483017.632496 2026-07-06 10:50:57 na-prot_16000.pdb -605071.147476 2026-07-06 10:51:17 na-prot_16100.pdb -544168.903327 2026-07-06 10:51:36 na-prot_16200.pdb -589068.147583 2026-07-06 10:51:56 na-prot_16300.pdb -485518.006923 2026-07-06 10:52:16 na-prot_16400.pdb -664760.273228 2026-07-06 10:52:35 na-prot_16500.pdb -573075.577237 2026-07-06 10:52:55 na-prot_16600.pdb -395777.980916 2026-07-06 10:53:14 na-prot_16700.pdb -879460.512654 2026-07-06 10:53:34 na-prot_16800.pdb -591659.720808 2026-07-06 10:53:54 na-prot_16900.pdb -385399.104047 2026-07-06 10:54:13 na-prot_17000.pdb -462046.81049 2026-07-06 10:54:33 na-prot_17100.pdb -518946.173008 2026-07-06 10:54:52 na-prot_17200.pdb -615291.308632 2026-07-06 10:55:12 na-prot_17300.pdb -388936.553018 2026-07-06 10:55:32 na-prot_17400.pdb -515739.343781 2026-07-06 10:55:51 na-prot_17500.pdb -533135.812326 2026-07-06 10:56:11 na-prot_17600.pdb -391578.621243 2026-07-06 10:56:30 na-prot_17700.pdb -376769.048371 2026-07-06 10:56:50 na-prot_17800.pdb -457112.318907 2026-07-06 10:57:10 na-prot_17900.pdb -415480.094283 2026-07-06 10:57:29 na-prot_18000.pdb -634431.68113 2026-07-06 10:57:49 na-prot_18100.pdb -386528.848997 2026-07-06 10:58:08 na-prot_18200.pdb -845449.776379 2026-07-06 10:58:28 na-prot_18300.pdb -644801.089448 2026-07-06 10:58:48 na-prot_18400.pdb -655221.196508 2026-07-06 10:59:08 na-prot_18500.pdb -430891.497715 2026-07-06 10:59:27 na-prot_18600.pdb -906220.30965 2026-07-06 10:59:46 na-prot_18700.pdb -385812.778914 2026-07-06 11:00:05 na-prot_18800.pdb -827332.326904 2026-07-06 11:00:25 na-prot_18900.pdb -533025.415898 2026-07-06 11:00:45 na-prot_19000.pdb -628256.465727 2026-07-06 11:01:07 na-prot_19100.pdb -637777.055024 2026-07-06 11:01:27 na-prot_19200.pdb -448305.405852 2026-07-06 11:01:47 na-prot_19300.pdb -531433.582137 2026-07-06 11:02:06 na-prot_19400.pdb -618421.304764 2026-07-06 11:02:26 na-prot_19500.pdb -441011.243355 2026-07-06 11:02:46 na-prot_19600.pdb -386138.242188 2026-07-06 11:03:05 na-prot_19700.pdb -488527.224689 2026-07-06 11:03:25 na-prot_19800.pdb -463692.023767 2026-07-06 11:03:45 na-prot_19900.pdb -444680.78803 2026-07-06 11:04:04 na-prot_20000.pdb -457873.193218 2026-07-06 11:04:04 Varani starts 2026-07-06 11:04:05 na-prot_1000.pdb 66.695 2026-07-06 11:04:35 na-prot_94.pdb 147.003 2026-07-06 11:05:06 na-prot_194.pdb 61.771 2026-07-06 11:05:37 na-prot_294.pdb 184.908 2026-07-06 11:06:08 na-prot_394.pdb 35.748 2026-07-06 11:06:39 na-prot_494.pdb 182.791 2026-07-06 11:07:10 na-prot_594.pdb 139.129 2026-07-06 11:07:41 na-prot_694.pdb 212.569 2026-07-06 11:08:12 na-prot_794.pdb 126.241 2026-07-06 11:08:43 na-prot_894.pdb 204.897 2026-07-06 11:09:14 na-prot_994.pdb 20.981 2026-07-06 11:09:45 na-prot_1100.pdb 290.516 2026-07-06 11:10:16 na-prot_1200.pdb 336.649 2026-07-06 11:10:46 na-prot_1300.pdb 114.403 2026-07-06 11:11:17 na-prot_1400.pdb 158.251 2026-07-06 11:11:48 na-prot_1500.pdb 184.563 2026-07-06 11:12:19 na-prot_1600.pdb 93.905 2026-07-06 11:12:50 na-prot_1700.pdb 25.351 2026-07-06 11:13:22 na-prot_1800.pdb 279.677 2026-07-06 11:13:53 na-prot_1900.pdb 74.689 2026-07-06 11:14:24 na-prot_2000.pdb -79.931 2026-07-06 11:14:55 na-prot_2100.pdb 179.291 2026-07-06 11:15:26 na-prot_2200.pdb 138.315 2026-07-06 11:15:57 na-prot_2300.pdb -8.4 2026-07-06 11:16:28 na-prot_2400.pdb 127.617 2026-07-06 11:16:59 na-prot_2500.pdb 39.307 2026-07-06 11:17:30 na-prot_2600.pdb 100.409 2026-07-06 11:18:01 na-prot_2700.pdb 58.363 2026-07-06 11:18:32 na-prot_2800.pdb 409.841 2026-07-06 11:19:03 na-prot_2900.pdb 186.933 2026-07-06 11:19:34 na-prot_3000.pdb 301.512 2026-07-06 11:20:05 na-prot_3100.pdb 108.141 2026-07-06 11:20:36 na-prot_3200.pdb 57.289 2026-07-06 11:21:07 na-prot_3300.pdb 98.788 2026-07-06 11:21:37 na-prot_3400.pdb 161.105 2026-07-06 11:22:08 na-prot_3500.pdb 201.316 2026-07-06 11:22:39 na-prot_3600.pdb -45.227 2026-07-06 11:23:10 na-prot_3700.pdb 4.397 2026-07-06 11:23:41 na-prot_3800.pdb 99.908 2026-07-06 11:24:12 na-prot_3900.pdb 119.707 2026-07-06 11:24:42 na-prot_4000.pdb 50.896 2026-07-06 11:25:13 na-prot_4100.pdb 80.878 2026-07-06 11:25:44 na-prot_4200.pdb -7.302 2026-07-06 11:26:15 na-prot_4300.pdb -56.029 2026-07-06 11:26:46 na-prot_4400.pdb 73.763 2026-07-06 11:27:17 na-prot_4500.pdb 193.033 2026-07-06 11:27:48 na-prot_4600.pdb 192.557 2026-07-06 11:28:18 na-prot_4700.pdb -35.318 2026-07-06 11:28:49 na-prot_4800.pdb 226.536 2026-07-06 11:29:20 na-prot_4900.pdb 57.928 2026-07-06 11:29:51 na-prot_5000.pdb 72.464 2026-07-06 11:30:22 na-prot_5100.pdb 6.019 2026-07-06 11:30:53 na-prot_5200.pdb 110.151 2026-07-06 11:31:24 na-prot_5300.pdb 176.494 2026-07-06 11:31:55 na-prot_5400.pdb 99.498 2026-07-06 11:32:26 na-prot_5500.pdb 118.838 2026-07-06 11:32:56 na-prot_5600.pdb 134.86 2026-07-06 11:33:27 na-prot_5700.pdb 156.715 2026-07-06 11:33:57 na-prot_5800.pdb 22.242 2026-07-06 11:34:29 na-prot_5900.pdb 32.26 2026-07-06 11:34:59 na-prot_6000.pdb 96.977 2026-07-06 11:35:30 na-prot_6100.pdb 167.642 2026-07-06 11:36:00 na-prot_6200.pdb 154.571 2026-07-06 11:36:32 na-prot_6300.pdb 280.132 2026-07-06 11:37:03 na-prot_6400.pdb 317.074 2026-07-06 11:37:34 na-prot_6500.pdb 135.221 2026-07-06 11:38:04 na-prot_6600.pdb 177.376 2026-07-06 11:38:35 na-prot_6700.pdb 261.019 2026-07-06 11:39:06 na-prot_6800.pdb -25.692 2026-07-06 11:39:37 na-prot_6900.pdb 188.687 2026-07-06 11:40:08 na-prot_7000.pdb -8.62 2026-07-06 11:40:39 na-prot_7100.pdb 449.601 2026-07-06 11:41:10 na-prot_7200.pdb 249.834 2026-07-06 11:41:41 na-prot_7300.pdb 34.909 2026-07-06 11:42:12 na-prot_7400.pdb -82.22 2026-07-06 11:42:43 na-prot_7500.pdb 94.214 2026-07-06 11:43:14 na-prot_7600.pdb 123.122 2026-07-06 11:43:45 na-prot_7700.pdb 131.013 2026-07-06 11:44:16 na-prot_7800.pdb 175.79 2026-07-06 11:44:47 na-prot_7900.pdb 137.914 2026-07-06 11:45:17 na-prot_8000.pdb 153.08 2026-07-06 11:45:48 na-prot_8100.pdb 194.038 2026-07-06 11:46:18 na-prot_8200.pdb 97.096 2026-07-06 11:46:49 na-prot_8300.pdb 273.898 2026-07-06 11:47:19 na-prot_8400.pdb -29.045 2026-07-06 11:47:50 na-prot_8500.pdb 108.547 2026-07-06 11:48:21 na-prot_8600.pdb 179.642 2026-07-06 11:48:51 na-prot_8700.pdb -10.904 2026-07-06 11:49:22 na-prot_8800.pdb 95.979 2026-07-06 11:49:53 na-prot_8900.pdb 62.971 2026-07-06 11:50:24 na-prot_9000.pdb 20.151 2026-07-06 11:50:55 na-prot_9100.pdb 199.465 2026-07-06 11:51:26 na-prot_9200.pdb -19.462 2026-07-06 11:51:57 na-prot_9300.pdb 89.355 2026-07-06 11:52:28 na-prot_9400.pdb 70.34 2026-07-06 11:52:59 na-prot_9500.pdb 147.896 2026-07-06 11:53:30 na-prot_9600.pdb 46.939 2026-07-06 11:54:01 na-prot_9700.pdb 78.095 2026-07-06 11:54:32 na-prot_9800.pdb 16.693 2026-07-06 11:55:03 na-prot_9900.pdb 119.358 2026-07-06 11:55:34 na-prot_10000.pdb 245.137 2026-07-06 11:56:05 na-prot_10100.pdb 188.774 2026-07-06 11:56:35 na-prot_10200.pdb 131.115 2026-07-06 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12:08:27 na-prot_12500.pdb 26.874 2026-07-06 12:08:58 na-prot_12600.pdb 80.585 2026-07-06 12:09:28 na-prot_12700.pdb 69.023 2026-07-06 12:09:59 na-prot_12800.pdb 19.781 2026-07-06 12:10:30 na-prot_12900.pdb 157.379 2026-07-06 12:11:00 na-prot_13000.pdb 57.436 2026-07-06 12:11:31 na-prot_13100.pdb 83.801 2026-07-06 12:12:02 na-prot_13200.pdb 38.467 2026-07-06 12:12:33 na-prot_13300.pdb 742.021 2026-07-06 12:13:03 na-prot_13400.pdb -58.29 2026-07-06 12:13:34 na-prot_13500.pdb 172.562 2026-07-06 12:14:05 na-prot_13600.pdb 41.589 2026-07-06 12:14:36 na-prot_13700.pdb 170.619 2026-07-06 12:15:06 na-prot_13800.pdb 61.198 2026-07-06 12:15:37 na-prot_13900.pdb 268.388 2026-07-06 12:16:08 na-prot_14000.pdb 168.304 2026-07-06 12:16:38 na-prot_14100.pdb 332.972 2026-07-06 12:17:09 na-prot_14200.pdb 137.362 2026-07-06 12:17:40 na-prot_14300.pdb 163.401 2026-07-06 12:18:10 na-prot_14400.pdb 64.525 2026-07-06 12:18:41 na-prot_14500.pdb 233.328 2026-07-06 12:19:12 na-prot_14600.pdb 111.487 2026-07-06 12:19:43 na-prot_14700.pdb 231.269 2026-07-06 12:20:14 na-prot_14800.pdb 324.917 2026-07-06 12:20:45 na-prot_14900.pdb 45.942 2026-07-06 12:21:16 na-prot_15000.pdb 57.55 2026-07-06 12:21:47 na-prot_15100.pdb 176.179 2026-07-06 12:22:18 na-prot_15200.pdb 66.076 2026-07-06 12:22:49 na-prot_15300.pdb 215.927 2026-07-06 12:23:20 na-prot_15400.pdb 239.884 2026-07-06 12:23:50 na-prot_15500.pdb -42.135 2026-07-06 12:24:21 na-prot_15600.pdb 129.685 2026-07-06 12:24:52 na-prot_15700.pdb 112.732 2026-07-06 12:25:22 na-prot_15800.pdb 197.365 2026-07-06 12:25:53 na-prot_15900.pdb 26.247 2026-07-06 12:26:24 na-prot_16000.pdb 198.27 2026-07-06 12:26:55 na-prot_16100.pdb 139.741 2026-07-06 12:27:26 na-prot_16200.pdb 158.33 2026-07-06 12:27:56 na-prot_16300.pdb 286.744 2026-07-06 12:28:27 na-prot_16400.pdb 184.806 2026-07-06 12:28:57 na-prot_16500.pdb 129.06 2026-07-06 12:29:28 na-prot_16600.pdb 91.138 2026-07-06 12:29:59 na-prot_16700.pdb 176.4 2026-07-06 12:30:30 na-prot_16800.pdb 193.752 2026-07-06 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12:42:17 na-prot_19100.pdb 80.672 2026-07-06 12:42:48 na-prot_19200.pdb 18.732 2026-07-06 12:43:19 na-prot_19300.pdb 159.564 2026-07-06 12:43:50 na-prot_19400.pdb 159.654 2026-07-06 12:44:21 na-prot_19500.pdb 43.178 2026-07-06 12:44:51 na-prot_19600.pdb 146.603 2026-07-06 12:45:22 na-prot_19700.pdb -18.418 2026-07-06 12:45:53 na-prot_19800.pdb 86.351 2026-07-06 12:46:23 na-prot_19900.pdb -59.067 2026-07-06 12:46:54 na-prot_20000.pdb 41.779 2026-07-06 12:46:54 DFIRE starts 2026-07-06 12:46:54 na-prot_1000.pdb -73.865253 2026-07-06 12:47:34 na-prot_94.pdb -63.262119 2026-07-06 12:48:14 na-prot_194.pdb -59.575671 2026-07-06 12:48:54 na-prot_294.pdb -93.307277 2026-07-06 12:49:35 na-prot_394.pdb -59.755703 2026-07-06 12:50:16 na-prot_494.pdb -64.615739 2026-07-06 12:50:56 na-prot_594.pdb -61.321563 2026-07-06 12:51:37 na-prot_694.pdb -77.669935 2026-07-06 12:52:17 na-prot_794.pdb -53.870965 2026-07-06 12:52:57 na-prot_894.pdb -59.499239 2026-07-06 12:53:38 na-prot_994.pdb -56.543882 2026-07-06 12:54:18 na-prot_1100.pdb -64.805851 2026-07-06 12:54:58 na-prot_1200.pdb -71.935749 2026-07-06 12:55:38 na-prot_1300.pdb -54.188782 2026-07-06 12:56:17 na-prot_1400.pdb -65.283879 2026-07-06 12:56:57 na-prot_1500.pdb -85.726096 2026-07-06 12:57:36 na-prot_1600.pdb -49.355347 2026-07-06 12:58:16 na-prot_1700.pdb -61.830027 2026-07-06 12:58:55 na-prot_1800.pdb -79.408370 2026-07-06 12:59:35 na-prot_1900.pdb -72.053870 2026-07-06 13:00:15 na-prot_2000.pdb -68.926651 2026-07-06 13:00:56 na-prot_2100.pdb -56.847270 2026-07-06 13:01:37 na-prot_2200.pdb -66.813028 2026-07-06 13:02:18 na-prot_2300.pdb -80.194810 2026-07-06 13:02:58 na-prot_2400.pdb -57.838807 2026-07-06 13:03:39 na-prot_2500.pdb -62.369999 2026-07-06 13:04:19 na-prot_2600.pdb -46.340562 2026-07-06 13:04:59 na-prot_2700.pdb -86.423524 2026-07-06 13:05:39 na-prot_2800.pdb -69.254145 2026-07-06 13:06:18 na-prot_2900.pdb -44.403313 2026-07-06 13:06:57 na-prot_3000.pdb -85.426364 2026-07-06 13:07:37 na-prot_3100.pdb 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na-prot_5200.pdb -72.804286 2026-07-06 13:22:18 na-prot_5300.pdb -65.607840 2026-07-06 13:22:58 na-prot_5400.pdb -51.196106 2026-07-06 13:23:38 na-prot_5500.pdb -44.988731 2026-07-06 13:24:18 na-prot_5600.pdb -63.398842 2026-07-06 13:24:59 na-prot_5700.pdb -45.622879 2026-07-06 13:25:39 na-prot_5800.pdb -35.846089 2026-07-06 13:26:19 na-prot_5900.pdb -58.834984 2026-07-06 13:26:59 na-prot_6000.pdb -47.890909 2026-07-06 13:27:39 na-prot_6100.pdb -64.018867 2026-07-06 13:28:19 na-prot_6200.pdb -46.017067 2026-07-06 13:28:59 na-prot_6300.pdb -77.759550 2026-07-06 13:29:39 na-prot_6400.pdb -48.062356 2026-07-06 13:30:20 na-prot_6500.pdb -42.560625 2026-07-06 13:30:59 na-prot_6600.pdb -59.753320 2026-07-06 13:31:38 na-prot_6700.pdb -74.355010 2026-07-06 13:32:18 na-prot_6800.pdb -56.353885 2026-07-06 13:32:58 na-prot_6900.pdb -52.579870 2026-07-06 13:33:39 na-prot_7000.pdb -56.932607 2026-07-06 13:34:19 na-prot_7100.pdb -90.702727 2026-07-06 13:34:59 na-prot_7200.pdb -73.898675 2026-07-06 13:35:38 na-prot_7300.pdb -48.593469 2026-07-06 13:36:18 na-prot_7400.pdb -56.121173 2026-07-06 13:36:57 na-prot_7500.pdb -60.538576 2026-07-06 13:37:37 na-prot_7600.pdb -33.331644 2026-07-06 13:38:17 na-prot_7700.pdb -51.429884 2026-07-06 13:38:57 na-prot_7800.pdb -56.790290 2026-07-06 13:39:37 na-prot_7900.pdb -52.045500 2026-07-06 13:40:17 na-prot_8000.pdb -58.920577 2026-07-06 13:40:57 na-prot_8100.pdb -56.641164 2026-07-06 13:41:38 na-prot_8200.pdb -53.313663 2026-07-06 13:42:18 na-prot_8300.pdb -58.489908 2026-07-06 13:42:57 na-prot_8400.pdb -56.421532 2026-07-06 13:43:37 na-prot_8500.pdb -57.253696 2026-07-06 13:44:18 na-prot_8600.pdb -33.954738 2026-07-06 13:44:58 na-prot_8700.pdb -56.736654 2026-07-06 13:45:37 na-prot_8800.pdb -60.015442 2026-07-06 13:46:17 na-prot_8900.pdb -48.419173 2026-07-06 13:46:57 na-prot_9000.pdb -58.640396 2026-07-06 13:47:37 na-prot_9100.pdb -35.117231 2026-07-06 13:48:17 na-prot_9200.pdb -62.868414 2026-07-06 13:48:57 na-prot_9300.pdb -71.492708 2026-07-06 13:49:36 na-prot_9400.pdb -49.944938 2026-07-06 13:50:16 na-prot_9500.pdb -64.011873 2026-07-06 13:50:56 na-prot_9600.pdb -50.305179 2026-07-06 13:51:37 na-prot_9700.pdb -43.219380 2026-07-06 13:52:17 na-prot_9800.pdb -47.787084 2026-07-06 13:52:57 na-prot_9900.pdb -52.707778 2026-07-06 13:53:37 na-prot_10000.pdb -69.923487 2026-07-06 13:54:17 na-prot_10100.pdb -64.581883 2026-07-06 13:54:58 na-prot_10200.pdb -44.498765 2026-07-06 13:55:38 na-prot_10300.pdb -44.251930 2026-07-06 13:56:18 na-prot_10400.pdb -49.502238 2026-07-06 13:56:59 na-prot_10500.pdb -43.857290 2026-07-06 13:57:39 na-prot_10600.pdb -43.664656 2026-07-06 13:58:20 na-prot_10700.pdb -50.183834 2026-07-06 13:58:59 na-prot_10800.pdb -47.914126 2026-07-06 13:59:39 na-prot_10900.pdb -60.506298 2026-07-06 14:00:18 na-prot_11000.pdb -48.216650 2026-07-06 14:00:59 na-prot_11100.pdb -45.471765 2026-07-06 14:01:39 na-prot_11200.pdb -43.871503 2026-07-06 14:02:19 na-prot_11300.pdb -56.835491 2026-07-06 14:02:59 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/home/rpdock/web/media/jobs/28bf50a6-d532-41dc-9a0e-e75cbbfb5a03/prot-na_10/na-prot_17100.pdb -1.1545456039 2026-07-06 15:00:15 /home/rpdock/web/media/jobs/28bf50a6-d532-41dc-9a0e-e75cbbfb5a03/prot-na_10/na-prot_17200.pdb -2.04577615554 2026-07-06 15:00:15 /home/rpdock/web/media/jobs/28bf50a6-d532-41dc-9a0e-e75cbbfb5a03/prot-na_10/na-prot_17300.pdb -0.00710060694723 2026-07-06 15:00:15 /home/rpdock/web/media/jobs/28bf50a6-d532-41dc-9a0e-e75cbbfb5a03/prot-na_10/na-prot_17400.pdb -1.31963640228 2026-07-06 15:00:15 /home/rpdock/web/media/jobs/28bf50a6-d532-41dc-9a0e-e75cbbfb5a03/prot-na_10/na-prot_17500.pdb -1.21858493458 2026-07-06 15:00:15 /home/rpdock/web/media/jobs/28bf50a6-d532-41dc-9a0e-e75cbbfb5a03/prot-na_10/na-prot_17600.pdb -0.36362807567 2026-07-06 15:00:15 /home/rpdock/web/media/jobs/28bf50a6-d532-41dc-9a0e-e75cbbfb5a03/prot-na_10/na-prot_17700.pdb -0.59914696021 2026-07-06 15:00:15 /home/rpdock/web/media/jobs/28bf50a6-d532-41dc-9a0e-e75cbbfb5a03/prot-na_10/na-prot_17800.pdb -1.55638434637 2026-07-06 15:00:15 /home/rpdock/web/media/jobs/28bf50a6-d532-41dc-9a0e-e75cbbfb5a03/prot-na_10/na-prot_17900.pdb -0.757413659406 2026-07-06 15:00:15 /home/rpdock/web/media/jobs/28bf50a6-d532-41dc-9a0e-e75cbbfb5a03/prot-na_10/na-prot_18000.pdb -1.8524962995 2026-07-06 15:00:15 /home/rpdock/web/media/jobs/28bf50a6-d532-41dc-9a0e-e75cbbfb5a03/prot-na_10/na-prot_18100.pdb -0.718862344304 2026-07-06 15:00:15 /home/rpdock/web/media/jobs/28bf50a6-d532-41dc-9a0e-e75cbbfb5a03/prot-na_10/na-prot_18200.pdb -3.10690221042 2026-07-06 15:00:15 /home/rpdock/web/media/jobs/28bf50a6-d532-41dc-9a0e-e75cbbfb5a03/prot-na_10/na-prot_18300.pdb -1.88191017454 2026-07-06 15:00:15 /home/rpdock/web/media/jobs/28bf50a6-d532-41dc-9a0e-e75cbbfb5a03/prot-na_10/na-prot_18400.pdb -2.05836132167 2026-07-06 15:00:15 /home/rpdock/web/media/jobs/28bf50a6-d532-41dc-9a0e-e75cbbfb5a03/prot-na_10/na-prot_18500.pdb -0.547276916213 2026-07-06 15:00:15 /home/rpdock/web/media/jobs/28bf50a6-d532-41dc-9a0e-e75cbbfb5a03/prot-na_10/na-prot_18600.pdb -3.50592494431 2026-07-06 15:00:15 /home/rpdock/web/media/jobs/28bf50a6-d532-41dc-9a0e-e75cbbfb5a03/prot-na_10/na-prot_18700.pdb -0.149864576166 2026-07-06 15:00:15 /home/rpdock/web/media/jobs/28bf50a6-d532-41dc-9a0e-e75cbbfb5a03/prot-na_10/na-prot_18800.pdb -2.91964983411 2026-07-06 15:00:15 /home/rpdock/web/media/jobs/28bf50a6-d532-41dc-9a0e-e75cbbfb5a03/prot-na_10/na-prot_18900.pdb -1.07608162498 2026-07-06 15:00:15 /home/rpdock/web/media/jobs/28bf50a6-d532-41dc-9a0e-e75cbbfb5a03/prot-na_10/na-prot_19000.pdb -1.8258171849 2026-07-06 15:00:15 /home/rpdock/web/media/jobs/28bf50a6-d532-41dc-9a0e-e75cbbfb5a03/prot-na_10/na-prot_19100.pdb -2.18387837444 2026-07-06 15:00:15 /home/rpdock/web/media/jobs/28bf50a6-d532-41dc-9a0e-e75cbbfb5a03/prot-na_10/na-prot_19200.pdb -0.704712566751 2026-07-06 15:00:15 /home/rpdock/web/media/jobs/28bf50a6-d532-41dc-9a0e-e75cbbfb5a03/prot-na_10/na-prot_19300.pdb -0.814252944839 2026-07-06 15:00:15 /home/rpdock/web/media/jobs/28bf50a6-d532-41dc-9a0e-e75cbbfb5a03/prot-na_10/na-prot_19400.pdb -1.53622798943 2026-07-06 15:00:15 /home/rpdock/web/media/jobs/28bf50a6-d532-41dc-9a0e-e75cbbfb5a03/prot-na_10/na-prot_19500.pdb -1.81862656774 2026-07-06 15:00:15 /home/rpdock/web/media/jobs/28bf50a6-d532-41dc-9a0e-e75cbbfb5a03/prot-na_10/na-prot_19600.pdb -0.47110774637 2026-07-06 15:00:15 /home/rpdock/web/media/jobs/28bf50a6-d532-41dc-9a0e-e75cbbfb5a03/prot-na_10/na-prot_19700.pdb -0.844817483338 2026-07-06 15:00:15 /home/rpdock/web/media/jobs/28bf50a6-d532-41dc-9a0e-e75cbbfb5a03/prot-na_10/na-prot_19800.pdb -0.530667069833 2026-07-06 15:00:15 /home/rpdock/web/media/jobs/28bf50a6-d532-41dc-9a0e-e75cbbfb5a03/prot-na_10/na-prot_19900.pdb -2.05121415016 2026-07-06 15:00:15 /home/rpdock/web/media/jobs/28bf50a6-d532-41dc-9a0e-e75cbbfb5a03/prot-na_10/na-prot_20000.pdb -1.10581133118 2026-07-06 15:00:15 [..]0095321) ('/home/rpdock/web/media/jobs/28bf50a6-d532-41dc-9a0e-e75cbbfb5a03/prot-na_10/na-prot_19994.pdb', -1.0970491496516372) ('/home/rpdock/web/media/jobs/28bf50a6-d532-41dc-9a0e-e75cbbfb5a03/prot-na_10/na-prot_19995.pdb', -1.3738056249448776) ('/home/rpdock/web/media/jobs/28bf50a6-d532-41dc-9a0e-e75cbbfb5a03/prot-na_10/na-prot_19996.pdb', -0.9375569084944052) ('/home/rpdock/web/media/jobs/28bf50a6-d532-41dc-9a0e-e75cbbfb5a03/prot-na_10/na-prot_19997.pdb', -1.7794178274944694) ('/home/rpdock/web/media/jobs/28bf50a6-d532-41dc-9a0e-e75cbbfb5a03/prot-na_10/na-prot_19998.pdb', -1.8738144724342103) ('/home/rpdock/web/media/jobs/28bf50a6-d532-41dc-9a0e-e75cbbfb5a03/prot-na_10/na-prot_19999.pdb', -1.5863923569383975) ('/home/rpdock/web/media/jobs/28bf50a6-d532-41dc-9a0e-e75cbbfb5a03/prot-na_10/na-prot_20000.pdb', -1.105811331178576) 16880.40user 1053.42system 5:01:24elapsed 99%CPU (0avgtext+0avgdata 234328maxresident)k 5505184inputs+11204720outputs (40major+194315363minor)pagefaults 0swaps 2026-07-06 15:00:15 Clustering (cuttoff: 5, nr_clust: 100 ) in progress... 2026-07-06 15:00:15 time python /home/rpdock/run_gramm//clustering_v4.py dars_out.txt list.txt 5 100 2026-07-06 15:00:15 100 best scored structures 2026-07-06 15:00:15 1 na-prot_3327.pdb -5.72679309267 2026-07-06 15:00:15 2 na-prot_17447.pdb -5.67553412962 2026-07-06 15:00:15 3 na-prot_302.pdb -5.66440087588 2026-07-06 15:00:15 4 na-prot_3562.pdb -5.65154821032 2026-07-06 15:00:15 5 na-prot_11339.pdb -5.61663024339 2026-07-06 15:00:15 6 na-prot_326.pdb -5.61460042088 2026-07-06 15:00:15 7 na-prot_208.pdb -5.50768783536 2026-07-06 15:00:15 8 na-prot_895.pdb -5.50488747161 2026-07-06 15:00:15 9 na-prot_4890.pdb -5.46725432479 2026-07-06 15:00:15 10 na-prot_9805.pdb -5.4634542221 2026-07-06 15:00:15 11 na-prot_84.pdb -5.46179320762 2026-07-06 15:00:15 12 na-prot_688.pdb -5.44677300076 2026-07-06 15:00:15 13 na-prot_1595.pdb -5.4273627919 2026-07-06 15:00:15 14 na-prot_8569.pdb -5.3911312228 2026-07-06 15:00:15 15 na-prot_17.pdb -5.37771716778 2026-07-06 15:00:15 16 na-prot_1937.pdb -5.37448518488 2026-07-06 15:00:15 17 na-prot_4598.pdb -5.37347105155 2026-07-06 15:00:15 18 na-prot_1.pdb -5.37074030562 2026-07-06 15:00:15 19 na-prot_383.pdb -5.33104257976 2026-07-06 15:00:15 20 na-prot_12450.pdb -5.31466522797 2026-07-06 15:00:15 21 na-prot_78.pdb -5.27110847984 2026-07-06 15:00:15 22 na-prot_10014.pdb -5.26806616111 2026-07-06 15:00:15 23 na-prot_12144.pdb -5.24553185589 2026-07-06 15:00:15 24 na-prot_8685.pdb -5.21118103471 2026-07-06 15:00:15 25 na-prot_2759.pdb -5.20268413104 2026-07-06 15:00:15 26 na-prot_303.pdb -5.17972856087 2026-07-06 15:00:15 27 na-prot_2735.pdb -5.17768182631 2026-07-06 15:00:15 28 na-prot_2.pdb -5.17285766569 2026-07-06 15:00:15 29 na-prot_12962.pdb -5.16786359637 2026-07-06 15:00:15 30 na-prot_669.pdb -5.15418533688 2026-07-06 15:00:15 31 na-prot_5071.pdb -5.13307244604 2026-07-06 15:00:15 32 na-prot_4306.pdb -5.10735865493 2026-07-06 15:00:15 33 na-prot_1087.pdb -5.10480965792 2026-07-06 15:00:15 34 na-prot_4848.pdb -5.08272850262 2026-07-06 15:00:15 35 na-prot_371.pdb -5.07932139355 2026-07-06 15:00:15 36 na-prot_24.pdb -5.07216257584 2026-07-06 15:00:15 37 na-prot_17373.pdb -5.05593666461 2026-07-06 15:00:15 38 na-prot_5.pdb -5.05312700659 2026-07-06 15:00:15 39 na-prot_498.pdb -5.04219339565 2026-07-06 15:00:15 40 na-prot_2037.pdb -5.03179114024 2026-07-06 15:00:15 41 na-prot_205.pdb -5.02826655695 2026-07-06 15:00:15 42 na-prot_49.pdb -5.00871275636 2026-07-06 15:00:15 43 na-prot_18584.pdb -4.98528922159 2026-07-06 15:00:15 44 na-prot_285.pdb -4.98042095951 2026-07-06 15:00:15 45 na-prot_1995.pdb -4.96565264592 2026-07-06 15:00:15 46 na-prot_12528.pdb -4.95711765574 2026-07-06 15:00:15 47 na-prot_4832.pdb -4.95072453894 2026-07-06 15:00:15 48 na-prot_608.pdb -4.95024650386 2026-07-06 15:00:15 49 na-prot_10887.pdb -4.94169690255 2026-07-06 15:00:15 50 na-prot_143.pdb -4.93827631641 2026-07-06 15:00:15 51 na-prot_10567.pdb -4.93483180334 2026-07-06 15:00:15 52 na-prot_4024.pdb -4.93156746926 2026-07-06 15:00:15 53 na-prot_8010.pdb -4.93133651491 2026-07-06 15:00:15 54 na-prot_130.pdb -4.92415866779 2026-07-06 15:00:15 55 na-prot_1264.pdb -4.9190769919 2026-07-06 15:00:15 56 na-prot_5864.pdb -4.91896012668 2026-07-06 15:00:15 57 na-prot_13278.pdb -4.91030030008 2026-07-06 15:00:15 58 na-prot_14211.pdb -4.90863957343 2026-07-06 15:00:15 59 na-prot_548.pdb -4.90088647419 2026-07-06 15:00:15 60 na-prot_2430.pdb -4.8924023809 2026-07-06 15:00:15 61 na-prot_15789.pdb -4.88437090486 2026-07-06 15:00:15 62 na-prot_1734.pdb -4.87836676412 2026-07-06 15:00:15 63 na-prot_6124.pdb -4.87668565702 2026-07-06 15:00:15 64 na-prot_39.pdb -4.87668532909 2026-07-06 15:00:15 65 na-prot_718.pdb -4.8717111219 2026-07-06 15:00:15 66 na-prot_904.pdb -4.87085685825 2026-07-06 15:00:15 67 na-prot_6972.pdb -4.87046868832 2026-07-06 15:00:15 68 na-prot_16692.pdb -4.86299404748 2026-07-06 15:00:15 69 na-prot_425.pdb -4.85936127719 2026-07-06 15:00:15 70 na-prot_4.pdb -4.85744751097 2026-07-06 15:00:15 71 na-prot_1676.pdb -4.85658345391 2026-07-06 15:00:15 72 na-prot_5830.pdb -4.85069471404 2026-07-06 15:00:15 73 na-prot_319.pdb -4.84892255154 2026-07-06 15:00:15 74 na-prot_162.pdb -4.84652280601 2026-07-06 15:00:15 75 na-prot_61.pdb -4.83731086819 2026-07-06 15:00:15 76 na-prot_6180.pdb -4.83213493703 2026-07-06 15:00:15 77 na-prot_514.pdb -4.82198267733 2026-07-06 15:00:15 78 na-prot_13843.pdb -4.81849015438 2026-07-06 15:00:15 79 na-prot_4125.pdb -4.81336468474 2026-07-06 15:00:15 80 na-prot_153.pdb -4.81295974345 2026-07-06 15:00:15 81 na-prot_13981.pdb -4.80995738139 2026-07-06 15:00:15 82 na-prot_184.pdb -4.8088961161 2026-07-06 15:00:15 83 na-prot_6054.pdb -4.79994121207 2026-07-06 15:00:15 84 na-prot_1237.pdb -4.7977489025 2026-07-06 15:00:15 85 na-prot_7032.pdb -4.79562217857 2026-07-06 15:00:15 86 na-prot_152.pdb -4.79553560476 2026-07-06 15:00:15 87 na-prot_1031.pdb -4.78678893918 2026-07-06 15:00:15 88 na-prot_5150.pdb -4.78625981067 2026-07-06 15:00:15 89 na-prot_69.pdb -4.7858270361 2026-07-06 15:00:15 90 na-prot_407.pdb -4.7853724632 2026-07-06 15:00:15 91 na-prot_11593.pdb -4.7712312486 2026-07-06 15:00:15 92 na-prot_2819.pdb -4.76652728296 2026-07-06 15:00:15 93 na-prot_884.pdb -4.7532642015 2026-07-06 15:00:15 94 na-prot_3618.pdb -4.74348318466 2026-07-06 15:00:15 95 na-prot_66.pdb -4.74205920652 2026-07-06 15:00:15 96 na-prot_389.pdb -4.72951538112 2026-07-06 15:00:15 97 na-prot_993.pdb -4.71685320448 2026-07-06 15:00:15 98 na-prot_25.pdb -4.71230799545 2026-07-06 15:00:15 99 na-prot_2473.pdb -4.70896483641 2026-07-06 15:00:15 100 na-prot_2634.pdb -4.70121469474 2026-07-06 15:00:15 Chains: A 2026-07-06 15:00:41 100 best scored structures 2026-07-06 15:00:41 GRAMM analysis selected for further analysis: prot-na_10 2026-07-06 15:00:41 Cluster #1 with 100 structures 2026-07-06 15:00:41 1 na-prot_3327.pdb -5.72679309267 2026-07-06 15:00:41 2 na-prot_17447.pdb -5.67553412962 2026-07-06 15:00:41 3 na-prot_302.pdb -5.66440087588 2026-07-06 15:00:41 4 na-prot_3562.pdb -5.65154821032 2026-07-06 15:00:41 5 na-prot_11339.pdb -5.61663024339 2026-07-06 15:00:41 6 na-prot_326.pdb -5.61460042088 2026-07-06 15:00:41 7 na-prot_208.pdb -5.50768783536 2026-07-06 15:00:41 8 na-prot_895.pdb -5.50488747161 2026-07-06 15:00:41 9 na-prot_4890.pdb -5.46725432479 2026-07-06 15:00:41 10 na-prot_9805.pdb -5.4634542221 2026-07-06 15:00:41 11 na-prot_84.pdb -5.46179320762 2026-07-06 15:00:41 12 na-prot_688.pdb -5.44677300076 2026-07-06 15:00:41 13 na-prot_1595.pdb -5.4273627919 2026-07-06 15:00:41 14 na-prot_8569.pdb -5.3911312228 2026-07-06 15:00:41 15 na-prot_17.pdb -5.37771716778 2026-07-06 15:00:41 16 na-prot_1937.pdb -5.37448518488 2026-07-06 15:00:41 17 na-prot_4598.pdb -5.37347105155 2026-07-06 15:00:41 18 na-prot_1.pdb -5.37074030562 2026-07-06 15:00:41 19 na-prot_383.pdb -5.33104257976 2026-07-06 15:00:41 20 na-prot_12450.pdb -5.31466522797 2026-07-06 15:00:41 21 na-prot_78.pdb -5.27110847984 2026-07-06 15:00:41 22 na-prot_10014.pdb -5.26806616111 2026-07-06 15:00:41 23 na-prot_12144.pdb -5.24553185589 2026-07-06 15:00:41 24 na-prot_8685.pdb -5.21118103471 2026-07-06 15:00:41 25 na-prot_2759.pdb -5.20268413104 2026-07-06 15:00:41 26 na-prot_303.pdb -5.17972856087 2026-07-06 15:00:41 27 na-prot_2735.pdb -5.17768182631 2026-07-06 15:00:41 28 na-prot_2.pdb -5.17285766569 2026-07-06 15:00:41 29 na-prot_12962.pdb -5.16786359637 2026-07-06 15:00:41 30 na-prot_669.pdb -5.15418533688 2026-07-06 15:00:41 31 na-prot_5071.pdb -5.13307244604 2026-07-06 15:00:41 32 na-prot_4306.pdb -5.10735865493 2026-07-06 15:00:41 33 na-prot_1087.pdb -5.10480965792 2026-07-06 15:00:41 34 na-prot_4848.pdb -5.08272850262 2026-07-06 15:00:41 35 na-prot_371.pdb -5.07932139355 2026-07-06 15:00:41 36 na-prot_24.pdb -5.07216257584 2026-07-06 15:00:41 37 na-prot_17373.pdb -5.05593666461 2026-07-06 15:00:41 38 na-prot_5.pdb -5.05312700659 2026-07-06 15:00:41 39 na-prot_498.pdb -5.04219339565 2026-07-06 15:00:41 40 na-prot_2037.pdb -5.03179114024 2026-07-06 15:00:41 41 na-prot_205.pdb -5.02826655695 2026-07-06 15:00:41 42 na-prot_49.pdb -5.00871275636 2026-07-06 15:00:41 43 na-prot_18584.pdb -4.98528922159 2026-07-06 15:00:41 44 na-prot_285.pdb -4.98042095951 2026-07-06 15:00:41 45 na-prot_1995.pdb -4.96565264592 2026-07-06 15:00:41 46 na-prot_12528.pdb -4.95711765574 2026-07-06 15:00:41 47 na-prot_4832.pdb -4.95072453894 2026-07-06 15:00:41 48 na-prot_608.pdb -4.95024650386 2026-07-06 15:00:41 49 na-prot_10887.pdb -4.94169690255 2026-07-06 15:00:41 50 na-prot_143.pdb -4.93827631641 2026-07-06 15:00:41 51 na-prot_10567.pdb -4.93483180334 2026-07-06 15:00:41 52 na-prot_4024.pdb -4.93156746926 2026-07-06 15:00:41 53 na-prot_8010.pdb -4.93133651491 2026-07-06 15:00:41 54 na-prot_130.pdb -4.92415866779 2026-07-06 15:00:41 55 na-prot_1264.pdb -4.9190769919 2026-07-06 15:00:41 56 na-prot_5864.pdb -4.91896012668 2026-07-06 15:00:41 57 na-prot_13278.pdb -4.91030030008 2026-07-06 15:00:41 58 na-prot_14211.pdb -4.90863957343 2026-07-06 15:00:41 59 na-prot_548.pdb -4.90088647419 2026-07-06 15:00:41 60 na-prot_2430.pdb -4.8924023809 2026-07-06 15:00:41 61 na-prot_15789.pdb -4.88437090486 2026-07-06 15:00:41 62 na-prot_1734.pdb -4.87836676412 2026-07-06 15:00:41 63 na-prot_6124.pdb -4.87668565702 2026-07-06 15:00:41 64 na-prot_39.pdb -4.87668532909 2026-07-06 15:00:41 65 na-prot_718.pdb -4.8717111219 2026-07-06 15:00:41 66 na-prot_904.pdb -4.87085685825 2026-07-06 15:00:41 67 na-prot_6972.pdb -4.87046868832 2026-07-06 15:00:41 68 na-prot_16692.pdb -4.86299404748 2026-07-06 15:00:41 69 na-prot_425.pdb -4.85936127719 2026-07-06 15:00:41 70 na-prot_4.pdb -4.85744751097 2026-07-06 15:00:41 71 na-prot_1676.pdb -4.85658345391 2026-07-06 15:00:41 72 na-prot_5830.pdb -4.85069471404 2026-07-06 15:00:41 73 na-prot_319.pdb -4.84892255154 2026-07-06 15:00:41 74 na-prot_162.pdb -4.84652280601 2026-07-06 15:00:41 75 na-prot_61.pdb -4.83731086819 2026-07-06 15:00:41 76 na-prot_6180.pdb -4.83213493703 2026-07-06 15:00:41 77 na-prot_514.pdb -4.82198267733 2026-07-06 15:00:41 78 na-prot_13843.pdb -4.81849015438 2026-07-06 15:00:41 79 na-prot_4125.pdb -4.81336468474 2026-07-06 15:00:41 80 na-prot_153.pdb -4.81295974345 2026-07-06 15:00:41 81 na-prot_13981.pdb -4.80995738139 2026-07-06 15:00:41 82 na-prot_184.pdb -4.8088961161 2026-07-06 15:00:41 83 na-prot_6054.pdb -4.79994121207 2026-07-06 15:00:41 84 na-prot_1237.pdb -4.7977489025 2026-07-06 15:00:41 85 na-prot_7032.pdb -4.79562217857 2026-07-06 15:00:41 86 na-prot_152.pdb -4.79553560476 2026-07-06 15:00:41 87 na-prot_1031.pdb -4.78678893918 2026-07-06 15:00:41 88 na-prot_5150.pdb -4.78625981067 2026-07-06 15:00:41 89 na-prot_69.pdb -4.7858270361 2026-07-06 15:00:41 90 na-prot_407.pdb -4.7853724632 2026-07-06 15:00:41 91 na-prot_11593.pdb -4.7712312486 2026-07-06 15:00:41 92 na-prot_2819.pdb -4.76652728296 2026-07-06 15:00:41 93 na-prot_884.pdb -4.7532642015 2026-07-06 15:00:41 94 na-prot_3618.pdb -4.74348318466 2026-07-06 15:00:41 95 na-prot_66.pdb -4.74205920652 2026-07-06 15:00:41 96 na-prot_389.pdb -4.72951538112 2026-07-06 15:00:41 97 na-prot_993.pdb -4.71685320448 2026-07-06 15:00:41 98 na-prot_25.pdb -4.71230799545 2026-07-06 15:00:41 99 na-prot_2473.pdb -4.70896483641 2026-07-06 15:00:41 100 na-prot_2634.pdb -4.70121469474 2026-07-06 15:00:41 Sent to refinement: clusters_found|na-prot_3327.pdb 2026-07-06 15:00:41 Sent to refinement: clusters_found|na-prot_3327.pdb 2026-07-06 15:00:41 DARS clustering end 2026-07-06 15:00:41 MC (refinement) init 2026-07-06 15:00:41 python /home/rpdock/run_gramm//run_mc.py -f dars_to_mc.txt -d /home/rpdock/web/media/jobs/28bf50a6-d532-41dc-9a0e-e75cbbfb5a03/ 2026-07-06 15:00:41 Refinement of #1 /home/rpdock/web/media/jobs/28bf50a6-d532-41dc-9a0e-e75cbbfb5a03/na-prot_3327.pdb 2026-07-06 15:00:41 python /home/rpdock/mc/MC_DNA.py -s 1000 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/28bf50a6-d532-41dc-9a0e-e75cbbfb5a03//ref_struc/na-prot_3327/na-prot_3327.pdb 2026-07-06 15:03:50 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 2026-07-06 15:03:50 start - parameters: File name /home/rpdock/web/media/jobs/28bf50a6-d532-41dc-9a0e-e75cbbfb5a03//ref_struc/na-prot_3327/na-prot_3327.pdb Steps 1000 Temp. start 15000.0 Temp. end 295.0 False msg start - parameters: File name /home/rpdock/web/media/jobs/28bf50a6-d532-41dc-9a0e-e75cbbfb5a03//ref_struc/na-prot_3327/na-prot_3327.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 0 - -520970.45 -769706.34 -191264.11 440000.00 1 R -663993.62 -724594.17 -179399.45 240000.00 T= 14985.295 K progress 0.1 2 T -759854.36 -728914.10 -190940.26 160000.00 T= 14970.59 K progress 0.2 3 T -842206.97 -714446.92 -207760.04 80000.00 T= 14955.885 K progress 0.3 4 T -830692.71 -758468.16 -192224.55 120000.00 T= 14897.065 K progress 0.4 5 R -748371.31 -693964.55 -174406.76 120000.00 T= 14882.36 K progress 0.5 6 R -750126.63 -695719.87 -174406.76 120000.00 T= 14867.655 K progress 0.6 7 T -737648.06 -703538.23 -194109.82 160000.00 T= 14852.95 K progress 0.7 8 T -656775.87 -760353.14 -216422.73 320000.00 T= 14838.245 K progress 0.8 9 T -488546.72 -765338.62 -203208.10 480000.00 T= 14823.54 K progress 0.9 10 R -352049.01 -744771.72 -207277.29 600000.00 T= 14808.835 K progress 1.0 11 T -414883.38 -765372.45 -209510.92 560000.00 T= 14794.13 K progress 1.1 12 T -502110.53 -704947.50 -197163.03 400000.00 T= 14750.015 K progress 1.2 13 T -377756.47 -659928.02 -157828.46 440000.00 T= 14735.31 K progress 1.3 14 T -462331.80 -679725.55 -182606.25 400000.00 T= 14720.605 K progress 1.4 15 R -294387.93 -650465.66 -163922.27 520000.00 T= 14691.195 K progress 1.5 16 R -298417.78 -654425.47 -163992.31 520000.00 T= 14661.785 K progress 1.6 17 R -288657.09 -644528.13 -164128.96 520000.00 T= 14647.08 K progress 1.7 18 T -460986.97 -606190.85 -134796.12 280000.00 T= 14632.375 K progress 1.8 19 R -684911.97 -684690.36 -160221.60 160000.00 T= 14617.67 K progress 1.9 20 R -767369.36 -742250.78 -185118.58 160000.00 T= 14588.26 K progress 2.0 21 T -690350.39 -722834.31 -167516.09 200000.00 T= 14544.145 K progress 2.1 22 R -676994.04 -676363.36 -160630.67 160000.00 T= 14529.44 K progress 2.2 23 T -771116.16 -684194.73 -166921.43 80000.00 T= 14397.095 K progress 2.3 24 R -760954.33 -710391.22 -170563.11 120000.00 T= 14382.39 K progress 2.4 25 T -842444.21 -725887.69 -196556.51 80000.00 T= 14367.685 K progress 2.5 26 R -859648.76 -738328.96 -201319.79 80000.00 T= 14338.275 K progress 2.6 27 T -870812.67 -749010.42 -201802.25 80000.00 T= 14323.57 K progress 2.7 28 R -794781.40 -726570.70 -188210.69 120000.00 T= 14308.865 K progress 2.8 29 T -926066.30 -728458.31 -197607.98 0.00 T= 14294.16 K progress 2.9 30 R -875104.26 -696716.58 -178387.68 0.00 T= 14279.455 K progress 3.0 31 R -844968.42 -672009.87 -172958.55 0.00 T= 14235.34 K progress 3.1 32 R -867557.72 -690582.88 -176974.84 0.00 T= 14220.635 K progress 3.2 33 T -679534.81 -568081.98 -151452.82 40000.00 T= 14191.225 K progress 3.3 34 T -721286.47 -627257.64 -174028.83 80000.00 T= 14176.52 K progress 3.4 35 R -666064.54 -619867.90 -166196.65 120000.00 T= 14147.11 K progress 3.5 36 R -635606.68 -635997.52 -159609.16 160000.00 T= 14132.405 K progress 3.6 37 R -622732.04 -624592.99 -158139.04 160000.00 T= 14117.7 K progress 3.7 38 T -541698.46 -558165.93 -143532.53 160000.00 T= 14102.995 K progress 3.8 39 T -676346.49 -631115.66 -165230.83 120000.00 T= 14073.585 K progress 3.9 40 T -906013.87 -719934.45 -186079.43 0.00 T= 14058.88 K progress 4.0 41 R -905541.17 -719186.35 -186354.82 0.00 T= 14014.765 K progress 4.1 42 R -923907.92 -772060.42 -191847.50 40000.00 T= 14000.06 K progress 4.2 43 R -919876.70 -731592.26 -188284.43 0.00 T= 13955.945 K progress 4.3 44 T -843329.12 -760348.53 -202980.59 120000.00 T= 13941.24 K progress 4.4 45 T -910912.25 -787688.79 -203223.46 80000.00 T= 13926.535 K progress 4.5 46 R -795390.37 -704687.68 -170702.69 80000.00 T= 13911.83 K progress 4.6 47 R -896966.58 -743874.82 -193091.76 40000.00 T= 13897.125 K progress 4.7 48 T -901498.63 -710120.00 -191378.63 0.00 T= 13882.42 K progress 4.8 49 R -900572.66 -712976.98 -187595.69 0.00 T= 13867.715 K progress 4.9 50 R -934326.81 -745851.90 -188474.91 0.00 T= 13838.305 K progress 5.0 51 R -894364.27 -744085.91 -190278.36 40000.00 T= 13823.6 K progress 5.1 52 R -939987.23 -746911.52 -193075.71 0.00 T= 13808.895 K progress 5.2 53 R -915173.72 -761578.56 -193595.16 40000.00 T= 13779.485 K progress 5.3 54 R -910627.96 -756415.20 -194212.77 40000.00 T= 13764.78 K progress 5.4 55 R -883407.34 -733048.87 -190358.46 40000.00 T= 13750.075 K progress 5.5 56 T -905404.09 -755336.86 -190067.23 40000.00 T= 13735.37 K progress 5.6 57 R -902452.98 -712711.74 -189741.24 0.00 T= 13720.665 K progress 5.7 58 R -948052.39 -757869.23 -190183.15 0.00 T= 13705.96 K progress 5.8 59 R -913625.51 -763685.56 -189939.95 40000.00 T= 13647.14 K progress 5.9 60 T -896380.83 -778170.28 -198210.55 80000.00 T= 13632.435 K progress 6.0 61 R -888284.41 -774153.89 -194130.53 80000.00 T= 13573.615 K progress 6.1 62 R -908424.31 -781582.83 -206841.48 80000.00 T= 13558.91 K progress 6.2 63 T -875936.31 -762889.09 -193047.22 80000.00 T= 13544.205 K progress 6.3 64 T -906257.81 -752037.72 -194220.09 40000.00 T= 13514.795 K progress 6.4 65 R -914382.01 -757366.77 -197015.24 40000.00 T= 13500.09 K progress 6.5 66 T -919541.61 -764168.04 -195373.57 40000.00 T= 13455.975 K progress 6.6 67 T -930210.75 -768493.57 -201717.18 40000.00 T= 13441.27 K progress 6.7 68 R -918285.59 -754225.85 -204059.74 40000.00 T= 13397.155 K progress 6.8 69 R -918965.54 -758144.76 -200820.78 40000.00 T= 13382.45 K progress 6.9 70 T -890069.23 -743626.35 -186442.88 40000.00 T= 13367.745 K progress 7.0 71 T -670821.14 -636062.13 -154759.00 120000.00 T= 13353.04 K progress 7.1 72 R -598354.98 -566252.38 -152102.60 120000.00 T= 13308.925 K progress 7.2 73 T -642538.97 -573092.29 -149446.68 80000.00 T= 13279.515 K progress 7.3 74 R -556357.93 -493193.45 -143164.48 80000.00 T= 13250.105 K progress 7.4 75 R -620736.18 -554031.54 -146704.64 80000.00 T= 13220.695 K progress 7.5 76 R -629850.33 -598058.88 -151791.45 120000.00 T= 13205.99 K progress 7.6 77 T -640365.17 -610180.22 -150184.95 120000.00 T= 13191.285 K progress 7.7 78 T -881156.15 -727700.74 -193455.41 40000.00 T= 13147.17 K progress 7.8 79 R -911684.82 -755221.52 -196463.30 40000.00 T= 13029.53 K progress 7.9 80 R -803731.12 -636648.88 -167082.24 0.00 T= 13014.825 K progress 8.0 81 T -633981.94 -528292.34 -145689.59 40000.00 T= 12985.415 K progress 8.1 82 T -641033.58 -538040.47 -142993.11 40000.00 T= 12970.71 K progress 8.2 83 R -652818.51 -546288.48 -146530.03 40000.00 T= 12941.3 K progress 8.3 84 R -777256.01 -617561.32 -159694.70 0.00 T= 12911.89 K progress 8.4 85 T -876006.13 -708202.39 -167803.73 0.00 T= 12897.185 K progress 8.5 86 R -879068.67 -716875.22 -162193.45 0.00 T= 12882.48 K progress 8.6 87 R -882318.49 -716301.64 -166016.86 0.00 T= 12867.775 K progress 8.7 88 T -817508.08 -655663.65 -161844.44 0.00 T= 12838.365 K progress 8.8 89 T -839611.71 -669706.15 -169905.55 0.00 T= 12823.66 K progress 8.9 90 R -827349.87 -661963.81 -165386.07 0.00 T= 12779.545 K progress 9.0 91 T -829714.95 -664591.41 -165123.54 0.00 T= 12764.84 K progress 9.1 92 R -767078.73 -682027.55 -165051.18 80000.00 T= 12750.135 K progress 9.2 93 R -651429.57 -572638.63 -158790.94 80000.00 T= 12720.725 K progress 9.3 94 R -681483.54 -602278.72 -159204.81 80000.00 T= 12706.02 K progress 9.4 95 T -622746.71 -559479.39 -143267.31 80000.00 T= 12691.315 K progress 9.5 96 R -571379.76 -523111.62 -128268.14 80000.00 T= 12676.61 K progress 9.6 97 R -579473.37 -528248.60 -131224.77 80000.00 T= 12647.2 K progress 9.7 98 T -391030.71 -537721.80 -133308.92 280000.00 T= 12632.495 K progress 9.8 99 R -392146.54 -538757.07 -133389.47 280000.00 T= 12617.79 K progress 9.9 100 R -388620.20 -535218.86 -133401.33 280000.00 T= 12603.085 K progress 10.0 101 T -352705.00 -480003.50 -112701.50 240000.00 T= 12558.97 K progress 10.1 102 R -395689.46 -499814.27 -135875.19 240000.00 T= 12514.855 K progress 10.2 103 T -613329.44 -560288.09 -133041.36 80000.00 T= 12500.15 K progress 10.3 104 T -552703.47 -504411.99 -128291.48 80000.00 T= 12470.74 K progress 10.4 105 T -518058.24 -505035.96 -133022.28 120000.00 T= 12441.33 K progress 10.5 106 R -516457.88 -504981.02 -131476.86 120000.00 T= 12397.215 K progress 10.6 107 T -606574.40 -552053.36 -134521.04 80000.00 T= 12367.805 K progress 10.7 108 R -602810.08 -544653.24 -138156.84 80000.00 T= 12353.1 K progress 10.8 109 R -631758.50 -537113.50 -134645.01 40000.00 T= 12338.395 K progress 10.9 110 T -628067.13 -536013.31 -132053.82 40000.00 T= 12308.985 K progress 11.0 111 R -630168.24 -534924.94 -135243.29 40000.00 T= 12294.28 K progress 11.1 112 R -628009.38 -535268.29 -132741.09 40000.00 T= 12279.575 K progress 11.2 113 T -576195.49 -491526.38 -124669.11 40000.00 T= 12264.87 K progress 11.3 114 R -593452.25 -560567.91 -152884.34 120000.00 T= 12250.165 K progress 11.4 115 R -585480.40 -552669.35 -152811.06 120000.00 T= 12235.46 K progress 11.5 116 R -546620.37 -648036.17 -178584.20 280000.00 T= 12220.755 K progress 11.6 117 R -673419.25 -713645.54 -199773.71 240000.00 T= 12206.05 K progress 11.7 118 R -697717.04 -695088.40 -202628.64 200000.00 T= 12117.82 K progress 11.8 119 R -638298.85 -650774.74 -187524.11 200000.00 T= 12029.59 K progress 11.9 120 R -701826.05 -704576.75 -197249.30 200000.00 T= 12000.18 K progress 12.0 121 T -595498.86 -586887.67 -168611.18 160000.00 T= 11956.065 K progress 12.1 122 R -589083.60 -588921.00 -160162.61 160000.00 T= 11911.95 K progress 12.2 123 R -590861.35 -554841.56 -156019.78 120000.00 T= 11897.245 K progress 12.3 124 T -515895.68 -543671.89 -132223.79 160000.00 T= 11882.54 K progress 12.4 125 R -542790.80 -528515.38 -134275.43 120000.00 T= 11823.72 K progress 12.5 126 R -513531.68 -538296.82 -135234.86 160000.00 T= 11809.015 K progress 12.6 127 T -623722.12 -605344.79 -178377.34 160000.00 T= 11794.31 K progress 12.7 128 R -579562.15 -576497.77 -163064.38 160000.00 T= 11779.605 K progress 12.8 129 T -473008.23 -557622.69 -155385.55 240000.00 T= 11691.375 K progress 12.9 130 R -527994.45 -562080.17 -165914.28 200000.00 T= 11676.67 K progress 13.0 131 R -571655.05 -604111.32 -167543.73 200000.00 T= 11661.965 K progress 13.1 132 R -462863.74 -581707.14 -161156.61 280000.00 T= 11647.26 K progress 13.2 133 R -463395.26 -584410.94 -158984.32 280000.00 T= 11632.555 K progress 13.3 134 T -434932.26 -604168.38 -150763.88 320000.00 T= 11617.85 K progress 13.4 135 T -490080.97 -603722.38 -166358.59 280000.00 T= 11603.145 K progress 13.5 136 T -471876.81 -589045.81 -162831.00 280000.00 T= 11588.44 K progress 13.6 137 R -578285.10 -642264.34 -176020.76 240000.00 T= 11573.735 K progress 13.7 138 T -607956.07 -611238.10 -156717.97 160000.00 T= 11544.325 K progress 13.8 139 R -621064.03 -587498.74 -153565.29 120000.00 T= 11529.62 K progress 13.9 140 R -657065.54 -544078.68 -152986.86 40000.00 T= 11514.915 K progress 14.0 141 T -715888.58 -560682.41 -155206.17 0.00 T= 11485.505 K progress 14.1 142 T -697722.69 -604635.88 -173086.81 80000.00 T= 11456.095 K progress 14.2 143 T -708757.01 -563972.91 -144784.10 0.00 T= 11441.39 K progress 14.3 144 T -611643.10 -521543.01 -130100.09 40000.00 T= 11426.685 K progress 14.4 145 R -618222.70 -526273.53 -131949.16 40000.00 T= 11367.865 K progress 14.5 146 R -586364.92 -533091.55 -133273.37 80000.00 T= 11353.16 K progress 14.6 147 R -579429.11 -530865.71 -128563.41 80000.00 T= 11338.455 K progress 14.7 148 T -560896.66 -481810.24 -119086.42 40000.00 T= 11309.045 K progress 14.8 149 R -540380.52 -460060.81 -120319.70 40000.00 T= 11294.34 K progress 14.9 150 T -525836.39 -444786.30 -121050.09 40000.00 T= 11264.93 K progress 15.0 151 T -455710.02 -386050.50 -109659.52 40000.00 T= 11250.225 K progress 15.1 152 R -516892.03 -441928.50 -114963.52 40000.00 T= 11235.52 K progress 15.2 153 R -548699.16 -469560.84 -119138.33 40000.00 T= 11220.815 K progress 15.3 154 R -535614.10 -462449.92 -113164.18 40000.00 T= 11161.995 K progress 15.4 155 R -517813.70 -449390.93 -108422.77 40000.00 T= 11147.29 K progress 15.5 156 T -548332.54 -507870.40 -120462.14 80000.00 T= 11132.585 K progress 15.6 157 T -588369.62 -533565.31 -134804.31 80000.00 T= 11117.88 K progress 15.7 158 R -603416.48 -511542.79 -131873.70 40000.00 T= 11103.175 K progress 15.8 159 R -478786.75 -449476.41 -109310.34 80000.00 T= 11073.765 K progress 15.9 160 R -517247.91 -483992.08 -113255.83 80000.00 T= 11059.06 K progress 16.0 161 R -599340.54 -510148.72 -129191.82 40000.00 T= 11029.65 K progress 16.1 162 T -516979.64 -446010.16 -110969.48 40000.00 T= 11014.945 K progress 16.2 163 R -491010.89 -427595.00 -103415.89 40000.00 T= 11000.24 K progress 16.3 164 T -438819.85 -406287.32 -112532.52 80000.00 T= 10985.535 K progress 16.4 165 T -501412.58 -424487.21 -116925.37 40000.00 T= 10970.83 K progress 16.5 166 R -522088.02 -443782.19 -118305.83 40000.00 T= 10956.125 K progress 16.6 167 R -617731.76 -482406.40 -135325.36 0.00 T= 10941.42 K progress 16.7 168 R -604546.54 -538658.24 -145888.30 80000.00 T= 10853.19 K progress 16.8 169 R -605770.86 -537700.98 -148069.88 80000.00 T= 10779.665 K progress 16.9 170 R -633959.24 -525875.94 -148083.30 40000.00 T= 10750.255 K progress 17.0 171 R -542285.26 -500474.77 -121810.48 80000.00 T= 10735.55 K progress 17.1 172 R -542453.57 -502109.07 -120344.49 80000.00 T= 10720.845 K progress 17.2 173 T -651134.87 -574438.72 -156696.15 80000.00 T= 10676.73 K progress 17.3 174 T -705442.60 -585352.40 -160090.20 40000.00 T= 10647.32 K progress 17.4 175 T -713699.56 -585198.02 -168501.54 40000.00 T= 10617.91 K progress 17.5 176 R -733699.33 -577806.60 -155892.73 0.00 T= 10603.205 K progress 17.6 177 R -730664.39 -574801.77 -155862.61 0.00 T= 10588.5 K progress 17.7 178 R -706344.70 -560733.85 -145610.86 0.00 T= 10559.09 K progress 17.8 179 R -712730.23 -559604.10 -153126.14 0.00 T= 10529.68 K progress 17.9 180 R -712730.23 -559604.10 -153126.14 0.00 T= 10500.27 K progress 18.0 181 T -692187.65 -580019.44 -152168.21 40000.00 T= 10470.86 K progress 18.1 182 T -794548.18 -688773.94 -185774.25 80000.00 T= 10456.155 K progress 18.2 183 T -698473.84 -651509.76 -166964.08 120000.00 T= 10426.745 K progress 18.3 184 T -690418.74 -612496.96 -157921.78 80000.00 T= 10412.04 K progress 18.4 185 R -713056.82 -602285.46 -150771.36 40000.00 T= 10353.22 K progress 18.5 186 T -695895.26 -593415.14 -142480.12 40000.00 T= 10338.515 K progress 18.6 187 T -722073.16 -570582.36 -151490.80 0.00 T= 10294.4 K progress 18.7 188 R -720456.61 -569310.07 -151146.54 0.00 T= 10279.695 K progress 18.8 189 T -732638.79 -600253.14 -172385.66 40000.00 T= 10264.99 K progress 18.9 190 T -772005.36 -631251.39 -180753.97 40000.00 T= 10250.285 K progress 19.0 191 T -738786.33 -611226.91 -167559.43 40000.00 T= 10220.875 K progress 19.1 192 R -784725.89 -653023.06 -171702.83 40000.00 T= 10191.465 K progress 19.2 193 T -820923.59 -714666.20 -186257.38 80000.00 T= 10176.76 K progress 19.3 194 T -826439.07 -717472.84 -188966.23 80000.00 T= 10162.055 K progress 19.4 195 R -807240.30 -703867.62 -183372.68 80000.00 T= 10147.35 K progress 19.5 196 R -803145.98 -696885.91 -186260.07 80000.00 T= 10132.645 K progress 19.6 197 T -830542.73 -761236.35 -189306.38 120000.00 T= 10117.94 K progress 19.7 198 R -811386.11 -805097.06 -206289.05 200000.00 T= 10088.53 K progress 19.8 199 T -787574.16 -702331.93 -205242.23 120000.00 T= 10073.825 K progress 19.9 200 R -787661.30 -702427.88 -205233.41 120000.00 T= 10044.415 K progress 20.0 Long traj 201 T -615328.17 -644931.80 -170396.36 200000.00 T= 10029.71 K progress 20.1 202 R -602593.28 -599545.10 -163048.18 160000.00 T= 10015.005 K progress 20.2 203 T -691951.31 -750444.88 -181506.43 240000.00 T= 10000.3 K progress 20.3 204 T -678310.13 -734084.30 -184225.83 240000.00 T= 9941.48 K progress 20.4 205 R -632618.46 -735649.54 -176968.92 280000.00 T= 9926.775 K progress 20.5 206 R -623539.09 -725786.43 -177752.66 280000.00 T= 9853.25 K progress 20.6 207 R -567987.12 -703934.92 -184052.20 320000.00 T= 9838.545 K progress 20.7 208 T -653640.55 -743356.88 -190283.67 280000.00 T= 9765.02 K progress 20.8 209 R -706126.98 -731060.25 -175066.73 200000.00 T= 9750.315 K progress 20.9 210 R -706095.43 -730316.61 -175778.82 200000.00 T= 9691.495 K progress 21.0 211 T -676774.84 -777635.46 -179139.37 280000.00 T= 9676.79 K progress 21.1 212 T -702444.69 -779032.33 -203412.36 280000.00 T= 9662.085 K progress 21.2 213 R -710470.19 -788695.58 -201774.61 280000.00 T= 9647.38 K progress 21.3 214 R -621626.00 -773505.83 -208120.17 360000.00 T= 9632.675 K progress 21.4 215 R -852277.11 -766121.04 -206156.07 120000.00 T= 9603.265 K progress 21.5 216 T -903274.27 -751851.62 -191422.64 40000.00 T= 9588.56 K progress 21.6 217 R -937627.13 -749057.47 -188569.65 0.00 T= 9544.445 K progress 21.7 218 R -857145.27 -667673.78 -189471.49 0.00 T= 9529.74 K progress 21.8 219 T -860359.33 -680804.01 -179555.32 0.00 T= 9515.035 K progress 21.9 220 T -822645.90 -656149.00 -166496.90 0.00 T= 9500.33 K progress 22.0 221 T -663859.30 -549929.18 -153930.11 40000.00 T= 9485.625 K progress 22.1 222 R -732911.11 -566929.47 -165981.64 0.00 T= 9456.215 K progress 22.2 223 T -772469.96 -593537.28 -178932.68 0.00 T= 9426.805 K progress 22.3 224 T -677651.85 -606330.67 -151321.18 80000.00 T= 9382.69 K progress 22.4 225 R -555606.36 -538055.65 -137550.71 120000.00 T= 9367.985 K progress 22.5 226 R -539620.93 -527968.55 -131652.37 120000.00 T= 9338.575 K progress 22.6 227 T -666712.60 -638216.31 -148496.29 120000.00 T= 9309.165 K progress 22.7 228 R -636062.68 -604450.03 -151612.65 120000.00 T= 9279.755 K progress 22.8 229 R -642388.69 -610949.05 -151439.64 120000.00 T= 9265.05 K progress 22.9 230 T -726769.66 -652495.27 -154274.39 80000.00 T= 9235.64 K progress 23.0 231 T -903274.49 -716622.45 -186652.04 0.00 T= 9103.295 K progress 23.1 232 T -884716.34 -732378.99 -192337.35 40000.00 T= 9059.18 K progress 23.2 233 R -912897.38 -754016.37 -198881.01 40000.00 T= 9000.36 K progress 23.3 234 T -827284.27 -713513.74 -193770.52 80000.00 T= 8985.655 K progress 23.4 235 R -687084.83 -642230.70 -164854.13 120000.00 T= 8970.95 K progress 23.5 236 T -659989.74 -688177.38 -171812.36 200000.00 T= 8926.835 K progress 23.6 237 T -706853.48 -680146.18 -146707.30 120000.00 T= 8897.425 K progress 23.7 238 T -886900.62 -699494.99 -187405.63 0.00 T= 8882.72 K progress 23.8 239 T -767277.07 -684545.88 -162731.19 80000.00 T= 8838.605 K progress 23.9 240 T -786569.41 -651727.62 -174841.80 40000.00 T= 8823.9 K progress 24.0 241 T -870397.11 -680986.60 -189410.50 0.00 T= 8809.195 K progress 24.1 242 R -871784.92 -682406.33 -189378.60 0.00 T= 8750.375 K progress 24.2 243 R -891646.18 -704292.69 -187353.49 0.00 T= 8706.26 K progress 24.3 244 R -890614.57 -706555.31 -184059.26 0.00 T= 8676.85 K progress 24.4 245 T -869507.13 -680225.76 -189281.37 0.00 T= 8544.505 K progress 24.5 246 R -866456.99 -676074.55 -190382.44 0.00 T= 8529.8 K progress 24.6 247 R -897143.05 -711489.61 -185653.44 0.00 T= 8515.095 K progress 24.7 248 R -937015.30 -744083.23 -192932.07 0.00 T= 8485.685 K progress 24.8 249 R -926337.50 -731923.56 -194413.95 0.00 T= 8456.275 K progress 24.9 250 R -942555.06 -749422.43 -193132.63 0.00 T= 8441.57 K progress 25.0 251 R -957085.20 -764719.35 -192365.85 0.00 T= 8426.865 K progress 25.1 252 T -890195.26 -768822.70 -201372.55 80000.00 T= 8353.34 K progress 25.2 253 T -754746.11 -672241.29 -162504.82 80000.00 T= 8338.635 K progress 25.3 254 T -689995.62 -727439.42 -162556.20 200000.00 T= 8294.52 K progress 25.4 255 R -692407.49 -729844.81 -162562.68 200000.00 T= 8279.815 K progress 25.5 256 T -663701.12 -730300.75 -173400.37 240000.00 T= 8265.11 K progress 25.6 257 T -796251.20 -736044.36 -180206.84 120000.00 T= 8235.7 K progress 25.7 258 T -874316.39 -753695.66 -200620.73 80000.00 T= 8220.995 K progress 25.8 259 T -931512.21 -760469.10 -211043.11 40000.00 T= 8191.585 K progress 25.9 260 R -903768.82 -736984.57 -206784.25 40000.00 T= 8132.765 K progress 26.0 261 T -910694.91 -753990.03 -196704.88 40000.00 T= 8059.24 K progress 26.1 262 R -844504.90 -750137.84 -174367.06 80000.00 T= 8044.535 K progress 26.2 263 R -825187.87 -731128.95 -174058.92 80000.00 T= 8015.125 K progress 26.3 264 T -942095.25 -751593.73 -190501.52 0.00 T= 7985.715 K progress 26.4 265 T -984095.74 -782924.58 -201171.16 0.00 T= 7971.01 K progress 26.5 266 R -951506.74 -794075.65 -197431.09 40000.00 T= 7779.845 K progress 26.6 267 T -845989.72 -754958.53 -211031.18 120000.00 T= 7765.14 K progress 26.7 268 T -977659.39 -782043.20 -195616.19 0.00 T= 7735.73 K progress 26.8 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 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 228, in _deepcopy_list memo[id(x)] = 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 Jul 6 15:00:41 2026 ['na-prot_3327.pdb'] msg Refinement of #1 /home/rpdock/web/media/jobs/28bf50a6-d532-41dc-9a0e-e75cbbfb5a03/na-prot_3327.pdb dir: /home/rpdock/web/media/jobs/28bf50a6-d532-41dc-9a0e-e75cbbfb5a03/ file: na-prot_3327.pdb find `pwd` -iname na-prot_3327.pdb copy /home/rpdock/web/media/jobs/28bf50a6-d532-41dc-9a0e-e75cbbfb5a03/prot-na_10/na-prot_3327.pdb to /home/rpdock/web/media/jobs/28bf50a6-d532-41dc-9a0e-e75cbbfb5a03//ref_struc/na-prot_3327/na-prot_3327.pdb cmd: python /home/rpdock/mc/MC_DNA.py -s 1000 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/28bf50a6-d532-41dc-9a0e-e75cbbfb5a03//ref_struc/na-prot_3327/na-prot_3327.pdb msg python /home/rpdock/mc/MC_DNA.py -s 1000 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/28bf50a6-d532-41dc-9a0e-e75cbbfb5a03//ref_struc/na-prot_3327/na-prot_3327.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 2026-07-06 15:03:50 npdock::MC (refinement) end 2026-07-06 15:03:50 npdock::OK 2026-07-06 15:03:50 Set finished status of 28bf50a6-d532-41dc-9a0e-e75cbbfb5a03