2026-07-22 10:23:02 NPdock start 2026-07-22 10:23:02 ver: server 2026-07-22 10:23:02 mode: 11111 2026-07-22 10:23:02 is RNA? 0 2026-07-22 10:23:02 Interface: prot: '' na: '' 2026-07-22 10:23:02 Curr dir:/home/rpdock/web/media/jobs/1a4e97f7-4e09-4089-b51a-64727243428a/ 2026-07-22 10:23:02 GRAMM in progress... 2026-07-22 10:23:02 python /home/rpdock/run_gramm//run_gramm1.py -d 20000 -p prot.pdb -r na.pdb -pi '' -ri '' -n 1 -pf '*' -rf '*' 2026-07-22 11:32:45 GRAMM done 2026-07-22 11:32:45 DNP scoring in progress... 2026-07-22 11:32:45 time python /home/rpdock/run_gramm//DNP/laczony/QUASI-DNP-QDV_potential_1.0.py -m 100 -f list.txt -o dnp_out.txt 2026-07-22 11:32:45 QDV-DNP starts 2026-07-22 11:32:45 Show log every 100 structures 2026-07-22 11:32:45 QUASI-DNP starts 2026-07-22 11:32:46 na-prot_1000.pdb -620842.07566 2026-07-22 11:33:11 na-prot_94.pdb -913260.935709 2026-07-22 11:33:36 na-prot_194.pdb -825613.665694 2026-07-22 11:34:02 na-prot_294.pdb -876880.393292 2026-07-22 11:34:28 na-prot_394.pdb -748225.396179 2026-07-22 11:34:54 na-prot_494.pdb -713723.076607 2026-07-22 11:35:20 na-prot_594.pdb -905190.764555 2026-07-22 11:35:47 na-prot_694.pdb -784876.426772 2026-07-22 11:36:14 na-prot_794.pdb -703180.656122 2026-07-22 11:36:41 na-prot_894.pdb -684792.52363 2026-07-22 11:37:08 na-prot_994.pdb -739282.050194 2026-07-22 11:37:35 na-prot_1100.pdb -633423.71171 2026-07-22 11:38:01 na-prot_1200.pdb -823804.340126 2026-07-22 11:38:29 na-prot_1300.pdb -604874.647902 2026-07-22 11:38:55 na-prot_1400.pdb -1022251.5819 2026-07-22 11:39:23 na-prot_1500.pdb -652591.347976 2026-07-22 11:39:50 na-prot_1600.pdb -615592.837027 2026-07-22 11:40:17 na-prot_1700.pdb -1083910.15043 2026-07-22 11:40:45 na-prot_1800.pdb -557946.527292 2026-07-22 11:41:12 na-prot_1900.pdb -976917.234664 2026-07-22 11:41:40 na-prot_2000.pdb -683271.041942 2026-07-22 11:42:07 na-prot_2100.pdb -655032.135796 2026-07-22 11:42:34 na-prot_2200.pdb -965596.512244 2026-07-22 11:43:02 na-prot_2300.pdb -736747.140722 2026-07-22 11:43:29 na-prot_2400.pdb -544049.139426 2026-07-22 11:43:57 na-prot_2500.pdb -742217.884371 2026-07-22 11:44:24 na-prot_2600.pdb -761783.876961 2026-07-22 11:44:52 na-prot_2700.pdb -860355.30014 2026-07-22 11:45:19 na-prot_2800.pdb -796453.168509 2026-07-22 11:45:47 na-prot_2900.pdb -635999.779107 2026-07-22 11:46:14 na-prot_3000.pdb -694947.274366 2026-07-22 11:46:42 na-prot_3100.pdb -461508.332378 2026-07-22 11:47:09 na-prot_3200.pdb -729970.911184 2026-07-22 11:47:37 na-prot_3300.pdb -837047.780181 2026-07-22 11:48:05 na-prot_3400.pdb -561482.166117 2026-07-22 11:48:32 na-prot_3500.pdb -966231.679599 2026-07-22 11:49:00 na-prot_3600.pdb -579809.80633 2026-07-22 11:49:27 na-prot_3700.pdb -789930.094838 2026-07-22 11:49:55 na-prot_3800.pdb -641848.417887 2026-07-22 11:50:22 na-prot_3900.pdb -354912.946918 2026-07-22 11:50:50 na-prot_4000.pdb -652830.813984 2026-07-22 11:51:16 na-prot_4100.pdb -570330.275054 2026-07-22 11:51:43 na-prot_4200.pdb -774035.187196 2026-07-22 11:52:10 na-prot_4300.pdb -589154.964273 2026-07-22 11:52:37 na-prot_4400.pdb -601454.29083 2026-07-22 11:53:04 na-prot_4500.pdb -550255.00234 2026-07-22 11:53:31 na-prot_4600.pdb -441152.51784 2026-07-22 11:53:59 na-prot_4700.pdb -677996.545841 2026-07-22 11:54:26 na-prot_4800.pdb -733480.814156 2026-07-22 11:54:53 na-prot_4900.pdb -524685.824536 2026-07-22 11:55:20 na-prot_5000.pdb -520770.075115 2026-07-22 11:55:46 na-prot_5100.pdb -799176.539238 2026-07-22 11:56:13 na-prot_5200.pdb -644755.172814 2026-07-22 11:56:40 na-prot_5300.pdb -513135.615869 2026-07-22 11:57:08 na-prot_5400.pdb -777468.50857 2026-07-22 11:57:35 na-prot_5500.pdb -655417.866558 2026-07-22 11:58:02 na-prot_5600.pdb -562031.26328 2026-07-22 11:58:29 na-prot_5700.pdb -728141.531646 2026-07-22 11:58:56 na-prot_5800.pdb -816785.90425 2026-07-22 11:59:22 na-prot_5900.pdb -645852.017423 2026-07-22 11:59:49 na-prot_6000.pdb -862852.321244 2026-07-22 12:00:16 na-prot_6100.pdb -555947.056675 2026-07-22 12:00:43 na-prot_6200.pdb -801997.891737 2026-07-22 12:01:10 na-prot_6300.pdb -414089.908297 2026-07-22 12:01:37 na-prot_6400.pdb -575089.318567 2026-07-22 12:02:04 na-prot_6500.pdb -429144.838766 2026-07-22 12:02:31 na-prot_6600.pdb -872014.361992 2026-07-22 12:02:58 na-prot_6700.pdb -584583.926721 2026-07-22 12:03:25 na-prot_6800.pdb -396574.85902 2026-07-22 12:03:51 na-prot_6900.pdb -610274.535666 2026-07-22 12:04:17 na-prot_7000.pdb -408795.948422 2026-07-22 12:04:44 na-prot_7100.pdb -547329.241444 2026-07-22 12:05:11 na-prot_7200.pdb -579835.196607 2026-07-22 12:05:38 na-prot_7300.pdb -805113.613976 2026-07-22 12:06:05 na-prot_7400.pdb -483434.113035 2026-07-22 12:06:32 na-prot_7500.pdb -740624.466296 2026-07-22 12:06:59 na-prot_7600.pdb -720914.075968 2026-07-22 12:07:26 na-prot_7700.pdb -707708.717519 2026-07-22 12:07:53 na-prot_7800.pdb -792176.972788 2026-07-22 12:08:19 na-prot_7900.pdb -594638.571964 2026-07-22 12:08:46 na-prot_8000.pdb -394050.159831 2026-07-22 12:09:12 na-prot_8100.pdb -811870.961164 2026-07-22 12:09:39 na-prot_8200.pdb -603139.442092 2026-07-22 12:10:06 na-prot_8300.pdb -691646.041644 2026-07-22 12:10:33 na-prot_8400.pdb -445816.648485 2026-07-22 12:11:00 na-prot_8500.pdb -661159.292453 2026-07-22 12:11:27 na-prot_8600.pdb -392643.262796 2026-07-22 12:11:53 na-prot_8700.pdb -1134010.20492 2026-07-22 12:12:20 na-prot_8800.pdb -462696.536028 2026-07-22 12:12:46 na-prot_8900.pdb -921455.476081 2026-07-22 12:13:13 na-prot_9000.pdb -477211.006793 2026-07-22 12:13:40 na-prot_9100.pdb -441172.164666 2026-07-22 12:14:07 na-prot_9200.pdb -537279.521831 2026-07-22 12:14:34 na-prot_9300.pdb -1001037.2533 2026-07-22 12:15:01 na-prot_9400.pdb -528962.835925 2026-07-22 12:15:28 na-prot_9500.pdb -804128.326909 2026-07-22 12:15:55 na-prot_9600.pdb -492257.981527 2026-07-22 12:16:21 na-prot_9700.pdb -812273.913689 2026-07-22 12:16:48 na-prot_9800.pdb -628920.911526 2026-07-22 12:17:15 na-prot_9900.pdb -532547.017246 2026-07-22 12:17:41 na-prot_10000.pdb -755871.055125 2026-07-22 12:18:08 na-prot_10100.pdb -727811.109334 2026-07-22 12:18:36 na-prot_10200.pdb -704490.750245 2026-07-22 12:19:03 na-prot_10300.pdb -675143.792677 2026-07-22 12:19:30 na-prot_10400.pdb -614105.688145 2026-07-22 12:19:57 na-prot_10500.pdb -600643.36881 2026-07-22 12:20:23 na-prot_10600.pdb -741302.706281 2026-07-22 12:20:50 na-prot_10700.pdb -526217.266023 2026-07-22 12:21:17 na-prot_10800.pdb -655606.159142 2026-07-22 12:21:44 na-prot_10900.pdb -385426.7704 2026-07-22 12:22:11 na-prot_11000.pdb -520870.549516 2026-07-22 12:22:38 na-prot_11100.pdb -474389.498678 2026-07-22 12:23:05 na-prot_11200.pdb -645492.363856 2026-07-22 12:23:32 na-prot_11300.pdb -510586.572918 2026-07-22 12:24:00 na-prot_11400.pdb -493993.061385 2026-07-22 12:24:26 na-prot_11500.pdb -775266.563231 2026-07-22 12:24:53 na-prot_11600.pdb -772738.245597 2026-07-22 12:25:20 na-prot_11700.pdb -658683.540867 2026-07-22 12:25:46 na-prot_11800.pdb -799521.51288 2026-07-22 12:26:13 na-prot_11900.pdb -708177.888046 2026-07-22 12:26:40 na-prot_12000.pdb -551485.843123 2026-07-22 12:27:07 na-prot_12100.pdb -367996.466368 2026-07-22 12:27:34 na-prot_12200.pdb -474740.950144 2026-07-22 12:28:02 na-prot_12300.pdb -546658.907799 2026-07-22 12:28:29 na-prot_12400.pdb -677498.715283 2026-07-22 12:28:56 na-prot_12500.pdb -519687.66008 2026-07-22 12:29:24 na-prot_12600.pdb -654843.444329 2026-07-22 12:29:53 na-prot_12700.pdb -531153.826807 2026-07-22 12:30:19 na-prot_12800.pdb -339875.699405 2026-07-22 12:30:46 na-prot_12900.pdb -629356.107363 2026-07-22 12:31:14 na-prot_13000.pdb -521738.895966 2026-07-22 12:31:41 na-prot_13100.pdb -1097469.80068 2026-07-22 12:32:08 na-prot_13200.pdb -406160.477073 2026-07-22 12:32:35 na-prot_13300.pdb -486926.319762 2026-07-22 12:33:04 na-prot_13400.pdb -711539.572997 2026-07-22 12:33:31 na-prot_13500.pdb -555299.752444 2026-07-22 12:33:59 na-prot_13600.pdb -693655.429173 2026-07-22 12:34:26 na-prot_13700.pdb -378062.061966 2026-07-22 12:34:53 na-prot_13800.pdb -517224.349735 2026-07-22 12:35:20 na-prot_13900.pdb -499340.405802 2026-07-22 12:35:47 na-prot_14000.pdb -431705.15154 2026-07-22 12:36:14 na-prot_14100.pdb -619148.744307 2026-07-22 12:36:41 na-prot_14200.pdb -591785.280936 2026-07-22 12:37:09 na-prot_14300.pdb -429427.507602 2026-07-22 12:37:36 na-prot_14400.pdb -542862.470799 2026-07-22 12:38:03 na-prot_14500.pdb -705820.150864 2026-07-22 12:38:30 na-prot_14600.pdb -586149.079732 2026-07-22 12:38:57 na-prot_14700.pdb -374933.966013 2026-07-22 12:39:24 na-prot_14800.pdb -605722.460324 2026-07-22 12:39:51 na-prot_14900.pdb -348291.800154 2026-07-22 12:40:18 na-prot_15000.pdb -457251.47006 2026-07-22 12:40:45 na-prot_15100.pdb -612016.421919 2026-07-22 12:41:12 na-prot_15200.pdb -377989.269647 2026-07-22 12:41:40 na-prot_15300.pdb -870359.038043 2026-07-22 12:42:07 na-prot_15400.pdb -757905.25477 2026-07-22 12:42:34 na-prot_15500.pdb -361843.858004 2026-07-22 12:43:01 na-prot_15600.pdb -695702.231146 2026-07-22 12:43:29 na-prot_15700.pdb -540537.433281 2026-07-22 12:43:56 na-prot_15800.pdb -460287.779485 2026-07-22 12:44:23 na-prot_15900.pdb -492890.102394 2026-07-22 12:44:50 na-prot_16000.pdb -648062.609217 2026-07-22 12:45:17 na-prot_16100.pdb -663437.346511 2026-07-22 12:45:44 na-prot_16200.pdb -734900.665938 2026-07-22 12:46:12 na-prot_16300.pdb -533524.124444 2026-07-22 12:46:39 na-prot_16400.pdb -637821.80506 2026-07-22 12:47:07 na-prot_16500.pdb -652786.33453 2026-07-22 12:47:34 na-prot_16600.pdb -440937.198554 2026-07-22 12:48:01 na-prot_16700.pdb -374699.516346 2026-07-22 12:48:28 na-prot_16800.pdb -472877.33229 2026-07-22 12:48:55 na-prot_16900.pdb -574049.433583 2026-07-22 12:49:21 na-prot_17000.pdb -653839.103816 2026-07-22 12:49:49 na-prot_17100.pdb -721884.598271 2026-07-22 12:50:16 na-prot_17200.pdb -778766.223502 2026-07-22 12:50:43 na-prot_17300.pdb -692029.461835 2026-07-22 12:51:11 na-prot_17400.pdb -477951.805751 2026-07-22 12:51:38 na-prot_17500.pdb -529842.92134 2026-07-22 12:52:06 na-prot_17600.pdb -424174.112761 2026-07-22 12:52:33 na-prot_17700.pdb -413631.346737 2026-07-22 12:53:01 na-prot_17800.pdb -892468.072892 2026-07-22 12:53:28 na-prot_17900.pdb -816075.625941 2026-07-22 12:53:55 na-prot_18000.pdb -673078.064843 2026-07-22 12:54:22 na-prot_18100.pdb -777454.718328 2026-07-22 12:54:49 na-prot_18200.pdb -432152.525112 2026-07-22 12:55:16 na-prot_18300.pdb -681994.760257 2026-07-22 12:55:43 na-prot_18400.pdb -468074.454917 2026-07-22 12:56:11 na-prot_18500.pdb -349407.906346 2026-07-22 12:56:38 na-prot_18600.pdb -776031.208673 2026-07-22 12:57:05 na-prot_18700.pdb -441914.764835 2026-07-22 12:57:32 na-prot_18800.pdb -762014.443149 2026-07-22 12:57:59 na-prot_18900.pdb -624010.605685 2026-07-22 12:58:26 na-prot_19000.pdb -493162.303666 2026-07-22 12:58:53 na-prot_19100.pdb -682054.747188 2026-07-22 12:59:21 na-prot_19200.pdb -593841.320496 2026-07-22 12:59:48 na-prot_19300.pdb -503608.488222 2026-07-22 13:00:15 na-prot_19400.pdb -563275.807103 2026-07-22 13:00:42 na-prot_19500.pdb -299346.510456 2026-07-22 13:01:09 na-prot_19600.pdb -772549.669894 2026-07-22 13:01:36 na-prot_19700.pdb -731208.304008 2026-07-22 13:02:03 na-prot_19800.pdb -351686.525911 2026-07-22 13:02:30 na-prot_19900.pdb -721865.088615 2026-07-22 13:02:56 na-prot_20000.pdb -722087.559845 2026-07-22 13:02:56 Varani starts 2026-07-22 13:02:57 na-prot_1000.pdb 91.611 2026-07-22 13:03:38 na-prot_94.pdb 20.527 2026-07-22 13:04:19 na-prot_194.pdb 237.187 2026-07-22 13:05:00 na-prot_294.pdb 198.847 2026-07-22 13:05:42 na-prot_394.pdb 93.544 2026-07-22 13:06:23 na-prot_494.pdb 202.485 2026-07-22 13:07:05 na-prot_594.pdb 271.314 2026-07-22 13:07:46 na-prot_694.pdb 219.314 2026-07-22 13:08:27 na-prot_794.pdb 97.635 2026-07-22 13:09:08 na-prot_894.pdb 10.806 2026-07-22 13:09:49 na-prot_994.pdb 60.628 2026-07-22 13:10:30 na-prot_1100.pdb 294.878 2026-07-22 13:11:12 na-prot_1200.pdb 137.006 2026-07-22 13:11:53 na-prot_1300.pdb 56.531 2026-07-22 13:12:34 na-prot_1400.pdb 426.013 2026-07-22 13:13:16 na-prot_1500.pdb 170.958 2026-07-22 13:13:57 na-prot_1600.pdb 243.274 2026-07-22 13:14:38 na-prot_1700.pdb 611.635 2026-07-22 13:15:19 na-prot_1800.pdb 193.996 2026-07-22 13:16:00 na-prot_1900.pdb 345.03 2026-07-22 13:16:41 na-prot_2000.pdb 178.69 2026-07-22 13:17:22 na-prot_2100.pdb 237.878 2026-07-22 13:18:03 na-prot_2200.pdb 164.808 2026-07-22 13:18:44 na-prot_2300.pdb 172.428 2026-07-22 13:19:25 na-prot_2400.pdb 143.349 2026-07-22 13:20:06 na-prot_2500.pdb 396.444 2026-07-22 13:20:47 na-prot_2600.pdb 170.396 2026-07-22 13:21:28 na-prot_2700.pdb 146.984 2026-07-22 13:22:09 na-prot_2800.pdb 16.405 2026-07-22 13:22:50 na-prot_2900.pdb 243.859 2026-07-22 13:23:31 na-prot_3000.pdb 130.196 2026-07-22 13:24:12 na-prot_3100.pdb 65.766 2026-07-22 13:24:53 na-prot_3200.pdb 328.059 2026-07-22 13:25:34 na-prot_3300.pdb 388.658 2026-07-22 13:26:15 na-prot_3400.pdb 230.244 2026-07-22 13:26:56 na-prot_3500.pdb 321.553 2026-07-22 13:27:37 na-prot_3600.pdb 221.646 2026-07-22 13:28:18 na-prot_3700.pdb 342.583 2026-07-22 13:28:59 na-prot_3800.pdb 132.111 2026-07-22 13:29:41 na-prot_3900.pdb 194.54 2026-07-22 13:30:22 na-prot_4000.pdb 199.531 2026-07-22 13:31:03 na-prot_4100.pdb 157.507 2026-07-22 13:31:45 na-prot_4200.pdb 192.74 2026-07-22 13:32:26 na-prot_4300.pdb 118.856 2026-07-22 13:33:08 na-prot_4400.pdb 133.781 2026-07-22 13:33:49 na-prot_4500.pdb 20.948 2026-07-22 13:34:31 na-prot_4600.pdb -26.331 2026-07-22 13:35:12 na-prot_4700.pdb 299.893 2026-07-22 13:35:53 na-prot_4800.pdb 129.187 2026-07-22 13:36:34 na-prot_4900.pdb 162.075 2026-07-22 13:37:16 na-prot_5000.pdb 221.11 2026-07-22 13:37:57 na-prot_5100.pdb 336.087 2026-07-22 13:38:38 na-prot_5200.pdb 51.065 2026-07-22 13:39:19 na-prot_5300.pdb 131.42 2026-07-22 13:40:00 na-prot_5400.pdb 308.202 2026-07-22 13:40:41 na-prot_5500.pdb 51.651 2026-07-22 13:41:22 na-prot_5600.pdb -18.023 2026-07-22 13:42:03 na-prot_5700.pdb 311.127 2026-07-22 13:42:44 na-prot_5800.pdb 270.08 2026-07-22 13:43:25 na-prot_5900.pdb 111.507 2026-07-22 13:44:06 na-prot_6000.pdb 151.839 2026-07-22 13:44:46 na-prot_6100.pdb 8.433 2026-07-22 13:45:28 na-prot_6200.pdb 90.431 2026-07-22 13:46:09 na-prot_6300.pdb 32.7 2026-07-22 13:46:50 na-prot_6400.pdb 257.615 2026-07-22 13:47:31 na-prot_6500.pdb -24.505 2026-07-22 13:48:12 na-prot_6600.pdb 482.995 2026-07-22 13:48:54 na-prot_6700.pdb 205.248 2026-07-22 13:49:35 na-prot_6800.pdb 68.644 2026-07-22 13:50:16 na-prot_6900.pdb 92.596 2026-07-22 13:50:57 na-prot_7000.pdb -1.653 2026-07-22 13:51:38 na-prot_7100.pdb 51.848 2026-07-22 13:52:19 na-prot_7200.pdb 143.314 2026-07-22 13:53:00 na-prot_7300.pdb 145.845 2026-07-22 13:53:42 na-prot_7400.pdb 116.097 2026-07-22 13:54:22 na-prot_7500.pdb 190.193 2026-07-22 13:55:04 na-prot_7600.pdb 297.042 2026-07-22 13:55:45 na-prot_7700.pdb 193.96 2026-07-22 13:56:26 na-prot_7800.pdb 246.965 2026-07-22 13:57:07 na-prot_7900.pdb 15.199 2026-07-22 13:57:48 na-prot_8000.pdb 184.943 2026-07-22 13:58:29 na-prot_8100.pdb 207.382 2026-07-22 13:59:11 na-prot_8200.pdb 64.454 2026-07-22 13:59:51 na-prot_8300.pdb 159.118 2026-07-22 14:00:32 na-prot_8400.pdb 110.674 2026-07-22 14:01:13 na-prot_8500.pdb 141.748 2026-07-22 14:01:55 na-prot_8600.pdb 79.59 2026-07-22 14:02:37 na-prot_8700.pdb 391.398 2026-07-22 14:03:18 na-prot_8800.pdb 135.356 2026-07-22 14:04:00 na-prot_8900.pdb 355.708 2026-07-22 14:04:41 na-prot_9000.pdb 27.564 2026-07-22 14:05:23 na-prot_9100.pdb 61.805 2026-07-22 14:06:04 na-prot_9200.pdb 184.945 2026-07-22 14:06:45 na-prot_9300.pdb 318.548 2026-07-22 14:07:26 na-prot_9400.pdb 77.032 2026-07-22 14:08:07 na-prot_9500.pdb 107.032 2026-07-22 14:08:48 na-prot_9600.pdb -5.055 2026-07-22 14:09:29 na-prot_9700.pdb 251.646 2026-07-22 14:10:11 na-prot_9800.pdb 55.765 2026-07-22 14:10:51 na-prot_9900.pdb 156.618 2026-07-22 14:11:33 na-prot_10000.pdb 317.27 2026-07-22 14:12:14 na-prot_10100.pdb 86.029 2026-07-22 14:12:55 na-prot_10200.pdb 306.256 2026-07-22 14:13:37 na-prot_10300.pdb 25.226 2026-07-22 14:14:19 na-prot_10400.pdb 122.745 2026-07-22 14:15:00 na-prot_10500.pdb 61.387 2026-07-22 14:15:41 na-prot_10600.pdb 294.288 2026-07-22 14:16:22 na-prot_10700.pdb 14.279 2026-07-22 14:17:04 na-prot_10800.pdb 42.345 2026-07-22 14:17:46 na-prot_10900.pdb -33.309 2026-07-22 14:18:27 na-prot_11000.pdb 143.068 2026-07-22 14:19:09 na-prot_11100.pdb 70.636 2026-07-22 14:19:50 na-prot_11200.pdb 173.426 2026-07-22 14:20:30 na-prot_11300.pdb 113.33 2026-07-22 14:21:12 na-prot_11400.pdb 178.702 2026-07-22 14:21:53 na-prot_11500.pdb -4.109 2026-07-22 14:22:34 na-prot_11600.pdb 286.006 2026-07-22 14:23:15 na-prot_11700.pdb 255.773 2026-07-22 14:23:57 na-prot_11800.pdb 115.708 2026-07-22 14:24:38 na-prot_11900.pdb 178.303 2026-07-22 14:25:19 na-prot_12000.pdb 222.408 2026-07-22 14:26:00 na-prot_12100.pdb 36.622 2026-07-22 14:26:41 na-prot_12200.pdb 104.805 2026-07-22 14:27:23 na-prot_12300.pdb -5.654 2026-07-22 14:28:04 na-prot_12400.pdb 153.533 2026-07-22 14:28:45 na-prot_12500.pdb 101.077 2026-07-22 14:29:26 na-prot_12600.pdb 101.618 2026-07-22 14:30:07 na-prot_12700.pdb 89.879 2026-07-22 14:30:50 na-prot_12800.pdb 60.268 2026-07-22 14:31:32 na-prot_12900.pdb 195.454 2026-07-22 14:32:14 na-prot_13000.pdb 130.336 2026-07-22 14:32:55 na-prot_13100.pdb 483.653 2026-07-22 14:33:37 na-prot_13200.pdb 69.502 2026-07-22 14:34:18 na-prot_13300.pdb 246.931 2026-07-22 14:35:00 na-prot_13400.pdb 286.094 2026-07-22 14:35:42 na-prot_13500.pdb 41.715 2026-07-22 14:36:24 na-prot_13600.pdb 103.151 2026-07-22 14:37:06 na-prot_13700.pdb 135.511 2026-07-22 14:37:48 na-prot_13800.pdb -13.159 2026-07-22 14:38:30 na-prot_13900.pdb 60.518 2026-07-22 14:39:12 na-prot_14000.pdb 145.284 2026-07-22 14:39:53 na-prot_14100.pdb 320.674 2026-07-22 14:40:35 na-prot_14200.pdb 151.791 2026-07-22 14:41:17 na-prot_14300.pdb 63.527 2026-07-22 14:41:59 na-prot_14400.pdb 62.037 2026-07-22 14:42:41 na-prot_14500.pdb 129.951 2026-07-22 14:43:23 na-prot_14600.pdb 308.453 2026-07-22 14:44:05 na-prot_14700.pdb 81.035 2026-07-22 14:44:47 na-prot_14800.pdb 206.595 2026-07-22 14:45:28 na-prot_14900.pdb -9.122 2026-07-22 14:46:10 na-prot_15000.pdb 13.568 2026-07-22 14:46:51 na-prot_15100.pdb 425.899 2026-07-22 14:47:33 na-prot_15200.pdb 81.624 2026-07-22 14:48:15 na-prot_15300.pdb 194.537 2026-07-22 14:48:56 na-prot_15400.pdb 135.344 2026-07-22 14:49:38 na-prot_15500.pdb 95.302 2026-07-22 14:50:20 na-prot_15600.pdb 179.966 2026-07-22 14:51:01 na-prot_15700.pdb 188.788 2026-07-22 14:51:44 na-prot_15800.pdb 147.571 2026-07-22 14:52:26 na-prot_15900.pdb 149.685 2026-07-22 14:53:08 na-prot_16000.pdb 247.4 2026-07-22 14:53:50 na-prot_16100.pdb 181.709 2026-07-22 14:54:32 na-prot_16200.pdb 271.972 2026-07-22 14:55:13 na-prot_16300.pdb 4.851 2026-07-22 14:55:55 na-prot_16400.pdb 112.757 2026-07-22 14:56:37 na-prot_16500.pdb 107.74 2026-07-22 14:57:20 na-prot_16600.pdb 8.203 2026-07-22 14:58:01 na-prot_16700.pdb 52.486 2026-07-22 14:58:43 na-prot_16800.pdb 41.802 2026-07-22 14:59:25 na-prot_16900.pdb 27.57 2026-07-22 15:00:07 na-prot_17000.pdb 222.551 2026-07-22 15:00:48 na-prot_17100.pdb 353.794 2026-07-22 15:01:30 na-prot_17200.pdb 194.581 2026-07-22 15:02:12 na-prot_17300.pdb 158.46 2026-07-22 15:02:54 na-prot_17400.pdb 67.857 2026-07-22 15:03:37 na-prot_17500.pdb 67.866 2026-07-22 15:04:19 na-prot_17600.pdb 45.205 2026-07-22 15:05:01 na-prot_17700.pdb 35.841 2026-07-22 15:05:43 na-prot_17800.pdb 233.559 2026-07-22 15:06:25 na-prot_17900.pdb 40.581 2026-07-22 15:07:07 na-prot_18000.pdb 80.722 2026-07-22 15:07:49 na-prot_18100.pdb 83.173 2026-07-22 15:08:30 na-prot_18200.pdb 160.201 2026-07-22 15:09:12 na-prot_18300.pdb 431.857 2026-07-22 15:09:53 na-prot_18400.pdb 30.059 2026-07-22 15:10:35 na-prot_18500.pdb 221.377 2026-07-22 15:11:17 na-prot_18600.pdb 383.795 2026-07-22 15:11:59 na-prot_18700.pdb 92.812 2026-07-22 15:12:41 na-prot_18800.pdb 128.855 2026-07-22 15:13:22 na-prot_18900.pdb -14.405 2026-07-22 15:14:04 na-prot_19000.pdb 100.448 2026-07-22 15:14:45 na-prot_19100.pdb 129.72 2026-07-22 15:15:26 na-prot_19200.pdb 53.852 2026-07-22 15:16:09 na-prot_19300.pdb 39.945 2026-07-22 15:16:51 na-prot_19400.pdb 197.111 2026-07-22 15:17:33 na-prot_19500.pdb 69.506 2026-07-22 15:18:15 na-prot_19600.pdb 131.906 2026-07-22 15:18:56 na-prot_19700.pdb 31.824 2026-07-22 15:19:38 na-prot_19800.pdb -11.907 2026-07-22 15:20:19 na-prot_19900.pdb 272.506 2026-07-22 15:21:00 na-prot_20000.pdb 195.866 2026-07-22 15:21:00 DFIRE starts 2026-07-22 15:21:01 na-prot_1000.pdb -62.344175 2026-07-22 15:21:44 na-prot_94.pdb -97.490232 2026-07-22 15:22:28 na-prot_194.pdb -85.325756 2026-07-22 15:23:12 na-prot_294.pdb -88.828542 2026-07-22 15:23:55 na-prot_394.pdb -74.239279 2026-07-22 15:24:38 na-prot_494.pdb -80.322957 2026-07-22 15:25:21 na-prot_594.pdb -94.735335 2026-07-22 15:26:03 na-prot_694.pdb -80.214657 2026-07-22 15:26:46 na-prot_794.pdb -86.597942 2026-07-22 15:27:30 na-prot_894.pdb -81.328928 2026-07-22 15:28:13 na-prot_994.pdb -79.328580 2026-07-22 15:28:56 na-prot_1100.pdb -67.930598 2026-07-22 15:29:39 na-prot_1200.pdb -93.334981 2026-07-22 15:30:22 na-prot_1300.pdb -84.373089 2026-07-22 15:31:04 na-prot_1400.pdb -111.705065 2026-07-22 15:31:46 na-prot_1500.pdb -69.027376 2026-07-22 15:32:29 na-prot_1600.pdb -84.482924 2026-07-22 15:33:13 na-prot_1700.pdb -118.424018 2026-07-22 15:33:56 na-prot_1800.pdb -69.582761 2026-07-22 15:34:39 na-prot_1900.pdb -109.457281 2026-07-22 15:35:22 na-prot_2000.pdb -63.472412 2026-07-22 15:36:05 na-prot_2100.pdb -76.168675 2026-07-22 15:36:48 na-prot_2200.pdb -93.219779 2026-07-22 15:37:31 na-prot_2300.pdb -73.740690 2026-07-22 15:38:15 na-prot_2400.pdb -64.804308 2026-07-22 15:38:58 na-prot_2500.pdb -77.096212 2026-07-22 15:39:42 na-prot_2600.pdb -75.985702 2026-07-22 15:40:25 na-prot_2700.pdb -84.885902 2026-07-22 15:41:07 na-prot_2800.pdb -80.586186 2026-07-22 15:41:50 na-prot_2900.pdb -75.368481 2026-07-22 15:42:33 na-prot_3000.pdb 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na-prot_5100.pdb -88.148092 2026-07-22 15:58:11 na-prot_5200.pdb -73.647783 2026-07-22 15:58:53 na-prot_5300.pdb -61.765919 2026-07-22 15:59:35 na-prot_5400.pdb -85.286234 2026-07-22 16:00:17 na-prot_5500.pdb -67.968713 2026-07-22 16:01:00 na-prot_5600.pdb -64.493110 2026-07-22 16:01:42 na-prot_5700.pdb -67.926622 2026-07-22 16:02:25 na-prot_5800.pdb -82.642881 2026-07-22 16:03:08 na-prot_5900.pdb -69.185203 2026-07-22 16:03:50 na-prot_6000.pdb -79.188718 2026-07-22 16:04:32 na-prot_6100.pdb -56.856921 2026-07-22 16:05:15 na-prot_6200.pdb -78.075493 2026-07-22 16:05:57 na-prot_6300.pdb -53.100059 2026-07-22 16:06:40 na-prot_6400.pdb -64.828771 2026-07-22 16:07:23 na-prot_6500.pdb -47.674581 2026-07-22 16:08:06 na-prot_6600.pdb -102.916874 2026-07-22 16:08:49 na-prot_6700.pdb -67.787599 2026-07-22 16:09:32 na-prot_6800.pdb -63.116998 2026-07-22 16:10:14 na-prot_6900.pdb -61.769205 2026-07-22 16:10:57 na-prot_7000.pdb -46.132445 2026-07-22 16:11:39 na-prot_7100.pdb -61.265612 2026-07-22 16:12:22 na-prot_7200.pdb -64.834064 2026-07-22 16:13:05 na-prot_7300.pdb -75.837934 2026-07-22 16:13:48 na-prot_7400.pdb -55.461985 2026-07-22 16:14:32 na-prot_7500.pdb -81.151049 2026-07-22 16:15:15 na-prot_7600.pdb -76.448337 2026-07-22 16:15:58 na-prot_7700.pdb -79.309826 2026-07-22 16:16:41 na-prot_7800.pdb -83.210270 2026-07-22 16:17:24 na-prot_7900.pdb -70.380725 2026-07-22 16:18:07 na-prot_8000.pdb -55.609486 2026-07-22 16:18:51 na-prot_8100.pdb -76.245443 2026-07-22 16:19:33 na-prot_8200.pdb -64.626745 2026-07-22 16:20:16 na-prot_8300.pdb -62.796728 2026-07-22 16:20:58 na-prot_8400.pdb -65.113931 2026-07-22 16:21:42 na-prot_8500.pdb -76.722884 2026-07-22 16:22:25 na-prot_8600.pdb -52.836611 2026-07-22 16:23:07 na-prot_8700.pdb -97.077382 2026-07-22 16:23:51 na-prot_8800.pdb -49.171571 2026-07-22 16:24:34 na-prot_8900.pdb -109.411757 2026-07-22 16:25:17 na-prot_9000.pdb -59.590527 2026-07-22 16:25:59 na-prot_9100.pdb -58.790309 2026-07-22 16:26:43 na-prot_9200.pdb -59.854366 2026-07-22 16:27:26 na-prot_9300.pdb -91.019466 2026-07-22 16:28:08 na-prot_9400.pdb -52.332579 2026-07-22 16:28:51 na-prot_9500.pdb -76.104595 2026-07-22 16:29:33 na-prot_9600.pdb -58.333763 2026-07-22 16:30:16 na-prot_9700.pdb -76.515459 2026-07-22 16:30:59 na-prot_9800.pdb -60.748055 2026-07-22 16:31:42 na-prot_9900.pdb -81.233098 2026-07-22 16:32:25 na-prot_10000.pdb -90.085797 2026-07-22 16:33:07 na-prot_10100.pdb -80.717390 2026-07-22 16:33:49 na-prot_10200.pdb -73.817528 2026-07-22 16:34:32 na-prot_10300.pdb -73.672878 2026-07-22 16:35:15 na-prot_10400.pdb -74.611685 2026-07-22 16:35:58 na-prot_10500.pdb -62.769273 2026-07-22 16:36:41 na-prot_10600.pdb -87.054018 2026-07-22 16:37:23 na-prot_10700.pdb -62.242224 2026-07-22 16:38:06 na-prot_10800.pdb -55.226346 2026-07-22 16:38:48 na-prot_10900.pdb -56.778140 2026-07-22 16:39:31 na-prot_11000.pdb -55.018286 2026-07-22 16:40:14 na-prot_11100.pdb -48.533448 2026-07-22 16:40:56 na-prot_11200.pdb -76.593822 2026-07-22 16:41:40 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/home/rpdock/web/media/jobs/1a4e97f7-4e09-4089-b51a-64727243428a/prot-na_10/na-prot_17100.pdb -2.18053872989 2026-07-22 17:43:34 /home/rpdock/web/media/jobs/1a4e97f7-4e09-4089-b51a-64727243428a/prot-na_10/na-prot_17200.pdb -3.85466085417 2026-07-22 17:43:34 /home/rpdock/web/media/jobs/1a4e97f7-4e09-4089-b51a-64727243428a/prot-na_10/na-prot_17300.pdb -3.16547186323 2026-07-22 17:43:34 /home/rpdock/web/media/jobs/1a4e97f7-4e09-4089-b51a-64727243428a/prot-na_10/na-prot_17400.pdb -1.4925551917 2026-07-22 17:43:34 /home/rpdock/web/media/jobs/1a4e97f7-4e09-4089-b51a-64727243428a/prot-na_10/na-prot_17500.pdb -2.20100833883 2026-07-22 17:43:34 /home/rpdock/web/media/jobs/1a4e97f7-4e09-4089-b51a-64727243428a/prot-na_10/na-prot_17600.pdb -1.06008251486 2026-07-22 17:43:34 /home/rpdock/web/media/jobs/1a4e97f7-4e09-4089-b51a-64727243428a/prot-na_10/na-prot_17700.pdb -1.6570617666 2026-07-22 17:43:34 /home/rpdock/web/media/jobs/1a4e97f7-4e09-4089-b51a-64727243428a/prot-na_10/na-prot_17800.pdb -3.92088699637 2026-07-22 17:43:34 /home/rpdock/web/media/jobs/1a4e97f7-4e09-4089-b51a-64727243428a/prot-na_10/na-prot_17900.pdb -3.70401400437 2026-07-22 17:43:34 /home/rpdock/web/media/jobs/1a4e97f7-4e09-4089-b51a-64727243428a/prot-na_10/na-prot_18000.pdb -2.73137695981 2026-07-22 17:43:34 /home/rpdock/web/media/jobs/1a4e97f7-4e09-4089-b51a-64727243428a/prot-na_10/na-prot_18100.pdb -3.30584490882 2026-07-22 17:43:34 /home/rpdock/web/media/jobs/1a4e97f7-4e09-4089-b51a-64727243428a/prot-na_10/na-prot_18200.pdb -1.2659851185 2026-07-22 17:43:34 /home/rpdock/web/media/jobs/1a4e97f7-4e09-4089-b51a-64727243428a/prot-na_10/na-prot_18300.pdb -2.93915584612 2026-07-22 17:43:34 /home/rpdock/web/media/jobs/1a4e97f7-4e09-4089-b51a-64727243428a/prot-na_10/na-prot_18400.pdb -1.73465048669 2026-07-22 17:43:34 /home/rpdock/web/media/jobs/1a4e97f7-4e09-4089-b51a-64727243428a/prot-na_10/na-prot_18500.pdb -0.580739304872 2026-07-22 17:43:34 /home/rpdock/web/media/jobs/1a4e97f7-4e09-4089-b51a-64727243428a/prot-na_10/na-prot_18600.pdb -3.76410151087 2026-07-22 17:43:34 /home/rpdock/web/media/jobs/1a4e97f7-4e09-4089-b51a-64727243428a/prot-na_10/na-prot_18700.pdb -1.61080616929 2026-07-22 17:43:34 /home/rpdock/web/media/jobs/1a4e97f7-4e09-4089-b51a-64727243428a/prot-na_10/na-prot_18800.pdb -2.51847245208 2026-07-22 17:43:34 /home/rpdock/web/media/jobs/1a4e97f7-4e09-4089-b51a-64727243428a/prot-na_10/na-prot_18900.pdb -2.12807965839 2026-07-22 17:43:34 /home/rpdock/web/media/jobs/1a4e97f7-4e09-4089-b51a-64727243428a/prot-na_10/na-prot_19000.pdb -1.32473427702 2026-07-22 17:43:34 /home/rpdock/web/media/jobs/1a4e97f7-4e09-4089-b51a-64727243428a/prot-na_10/na-prot_19100.pdb -2.45765130504 2026-07-22 17:43:34 /home/rpdock/web/media/jobs/1a4e97f7-4e09-4089-b51a-64727243428a/prot-na_10/na-prot_19200.pdb -2.42389903762 2026-07-22 17:43:34 /home/rpdock/web/media/jobs/1a4e97f7-4e09-4089-b51a-64727243428a/prot-na_10/na-prot_19300.pdb -2.11033311046 2026-07-22 17:43:34 /home/rpdock/web/media/jobs/1a4e97f7-4e09-4089-b51a-64727243428a/prot-na_10/na-prot_19400.pdb -2.33066079991 2026-07-22 17:43:34 /home/rpdock/web/media/jobs/1a4e97f7-4e09-4089-b51a-64727243428a/prot-na_10/na-prot_19500.pdb -0.57535536747 2026-07-22 17:43:34 /home/rpdock/web/media/jobs/1a4e97f7-4e09-4089-b51a-64727243428a/prot-na_10/na-prot_19600.pdb -2.94211839886 2026-07-22 17:43:34 /home/rpdock/web/media/jobs/1a4e97f7-4e09-4089-b51a-64727243428a/prot-na_10/na-prot_19700.pdb -2.64748227246 2026-07-22 17:43:34 /home/rpdock/web/media/jobs/1a4e97f7-4e09-4089-b51a-64727243428a/prot-na_10/na-prot_19800.pdb -1.24275348276 2026-07-22 17:43:34 /home/rpdock/web/media/jobs/1a4e97f7-4e09-4089-b51a-64727243428a/prot-na_10/na-prot_19900.pdb -2.61878941791 2026-07-22 17:43:34 /home/rpdock/web/media/jobs/1a4e97f7-4e09-4089-b51a-64727243428a/prot-na_10/na-prot_20000.pdb -2.10663926494 2026-07-22 17:43:34 [..]1009641) ('/home/rpdock/web/media/jobs/1a4e97f7-4e09-4089-b51a-64727243428a/prot-na_10/na-prot_19994.pdb', -1.9207653000584062) ('/home/rpdock/web/media/jobs/1a4e97f7-4e09-4089-b51a-64727243428a/prot-na_10/na-prot_19995.pdb', -1.5673080080169068) ('/home/rpdock/web/media/jobs/1a4e97f7-4e09-4089-b51a-64727243428a/prot-na_10/na-prot_19996.pdb', -4.1576900805110535) ('/home/rpdock/web/media/jobs/1a4e97f7-4e09-4089-b51a-64727243428a/prot-na_10/na-prot_19997.pdb', -1.8924332106510937) ('/home/rpdock/web/media/jobs/1a4e97f7-4e09-4089-b51a-64727243428a/prot-na_10/na-prot_19998.pdb', -1.9938513029278375) ('/home/rpdock/web/media/jobs/1a4e97f7-4e09-4089-b51a-64727243428a/prot-na_10/na-prot_19999.pdb', -2.340293045747993) ('/home/rpdock/web/media/jobs/1a4e97f7-4e09-4089-b51a-64727243428a/prot-na_10/na-prot_20000.pdb', -2.1066392649402124) 20930.10user 1150.23system 6:10:49elapsed 99%CPU (0avgtext+0avgdata 262456maxresident)k 9617088inputs+13445448outputs (43major+196320134minor)pagefaults 0swaps 2026-07-22 17:43:34 Clustering (cuttoff: 5, nr_clust: 100 ) in progress... 2026-07-22 17:43:34 time python /home/rpdock/run_gramm//clustering_v4.py dars_out.txt list.txt 5 100 2026-07-22 17:43:34 100 best scored structures 2026-07-22 17:43:34 1 na-prot_7162.pdb -8.00958319437 2026-07-22 17:43:34 2 na-prot_14480.pdb -7.67686882036 2026-07-22 17:43:34 3 na-prot_12042.pdb -7.66940052842 2026-07-22 17:43:34 4 na-prot_2136.pdb -7.60210534776 2026-07-22 17:43:34 5 na-prot_14642.pdb -7.3793882429 2026-07-22 17:43:34 6 na-prot_19220.pdb -7.25851035667 2026-07-22 17:43:34 7 na-prot_3467.pdb -7.24836251852 2026-07-22 17:43:34 8 na-prot_4097.pdb -7.22561799433 2026-07-22 17:43:34 9 na-prot_1173.pdb -7.22467634215 2026-07-22 17:43:34 10 na-prot_7421.pdb -7.22428188864 2026-07-22 17:43:34 11 na-prot_4730.pdb -7.01094174014 2026-07-22 17:43:34 12 na-prot_2210.pdb -6.92991005101 2026-07-22 17:43:34 13 na-prot_502.pdb -6.87501362688 2026-07-22 17:43:34 14 na-prot_1375.pdb -6.86454181877 2026-07-22 17:43:34 15 na-prot_6162.pdb -6.83224078219 2026-07-22 17:43:34 16 na-prot_4135.pdb -6.79787212015 2026-07-22 17:43:34 17 na-prot_19202.pdb -6.79502482137 2026-07-22 17:43:34 18 na-prot_472.pdb -6.74669942222 2026-07-22 17:43:34 19 na-prot_11001.pdb -6.73536988748 2026-07-22 17:43:34 20 na-prot_888.pdb -6.71337308572 2026-07-22 17:43:34 21 na-prot_5927.pdb -6.70565636265 2026-07-22 17:43:34 22 na-prot_112.pdb -6.68718188669 2026-07-22 17:43:34 23 na-prot_173.pdb -6.68327311001 2026-07-22 17:43:34 24 na-prot_9902.pdb -6.63910710154 2026-07-22 17:43:34 25 na-prot_10113.pdb -6.63131919554 2026-07-22 17:43:34 26 na-prot_21.pdb -6.62239254898 2026-07-22 17:43:34 27 na-prot_6970.pdb -6.61262072981 2026-07-22 17:43:34 28 na-prot_15217.pdb -6.59590678639 2026-07-22 17:43:34 29 na-prot_15593.pdb -6.52286649209 2026-07-22 17:43:34 30 na-prot_6431.pdb -6.49699093856 2026-07-22 17:43:34 31 na-prot_11519.pdb -6.44689203021 2026-07-22 17:43:34 32 na-prot_26.pdb -6.43884062675 2026-07-22 17:43:34 33 na-prot_1694.pdb -6.42603496407 2026-07-22 17:43:34 34 na-prot_303.pdb -6.40172839526 2026-07-22 17:43:34 35 na-prot_14316.pdb -6.39628516138 2026-07-22 17:43:34 36 na-prot_13631.pdb -6.35714845576 2026-07-22 17:43:34 37 na-prot_2689.pdb -6.31679672881 2026-07-22 17:43:34 38 na-prot_37.pdb -6.31557766828 2026-07-22 17:43:34 39 na-prot_3459.pdb -6.31339264397 2026-07-22 17:43:34 40 na-prot_1327.pdb -6.28048212112 2026-07-22 17:43:34 41 na-prot_687.pdb -6.25698595481 2026-07-22 17:43:34 42 na-prot_7328.pdb -6.25392502213 2026-07-22 17:43:34 43 na-prot_292.pdb -6.23679873865 2026-07-22 17:43:34 44 na-prot_5449.pdb -6.23194003141 2026-07-22 17:43:34 45 na-prot_11166.pdb -6.2247767162 2026-07-22 17:43:34 46 na-prot_11430.pdb -6.21988786486 2026-07-22 17:43:34 47 na-prot_12190.pdb -6.18899267914 2026-07-22 17:43:34 48 na-prot_2694.pdb -6.18373587566 2026-07-22 17:43:34 49 na-prot_4624.pdb -6.16631094041 2026-07-22 17:43:34 50 na-prot_169.pdb -6.158974633 2026-07-22 17:43:34 51 na-prot_13851.pdb -6.15191756863 2026-07-22 17:43:34 52 na-prot_3352.pdb -6.14809330758 2026-07-22 17:43:34 53 na-prot_223.pdb -6.121753844 2026-07-22 17:43:34 54 na-prot_49.pdb -6.11936512093 2026-07-22 17:43:34 55 na-prot_9909.pdb -6.10696059744 2026-07-22 17:43:34 56 na-prot_5.pdb -6.08662422499 2026-07-22 17:43:34 57 na-prot_7274.pdb -6.08363965614 2026-07-22 17:43:34 58 na-prot_412.pdb -6.07773665462 2026-07-22 17:43:34 59 na-prot_6779.pdb -6.06194852871 2026-07-22 17:43:34 60 na-prot_1827.pdb -6.05984829924 2026-07-22 17:43:34 61 na-prot_9622.pdb -6.05688365949 2026-07-22 17:43:34 62 na-prot_2655.pdb -6.04423350203 2026-07-22 17:43:34 63 na-prot_945.pdb -6.04350107219 2026-07-22 17:43:34 64 na-prot_6645.pdb -6.03791830295 2026-07-22 17:43:34 65 na-prot_8134.pdb -6.03538391325 2026-07-22 17:43:34 66 na-prot_19212.pdb -6.03074288651 2026-07-22 17:43:34 67 na-prot_3507.pdb -6.02970911915 2026-07-22 17:43:34 68 na-prot_219.pdb -6.02959629269 2026-07-22 17:43:34 69 na-prot_7307.pdb -6.02957143477 2026-07-22 17:43:34 70 na-prot_53.pdb -6.00492067453 2026-07-22 17:43:34 71 na-prot_9413.pdb -5.99169389737 2026-07-22 17:43:34 72 na-prot_16365.pdb -5.98451332511 2026-07-22 17:43:34 73 na-prot_461.pdb -5.97863089591 2026-07-22 17:43:34 74 na-prot_13647.pdb -5.96008690898 2026-07-22 17:43:34 75 na-prot_11560.pdb -5.95712352226 2026-07-22 17:43:34 76 na-prot_9102.pdb -5.93377671024 2026-07-22 17:43:34 77 na-prot_1.pdb -5.92142448271 2026-07-22 17:43:34 78 na-prot_2604.pdb -5.91817577142 2026-07-22 17:43:34 79 na-prot_17007.pdb -5.91344420341 2026-07-22 17:43:34 80 na-prot_15518.pdb -5.90645861702 2026-07-22 17:43:34 81 na-prot_13259.pdb -5.90625471181 2026-07-22 17:43:34 82 na-prot_1802.pdb -5.89666800805 2026-07-22 17:43:34 83 na-prot_1469.pdb -5.87628822353 2026-07-22 17:43:34 84 na-prot_48.pdb -5.87324761408 2026-07-22 17:43:34 85 na-prot_7262.pdb -5.87229140815 2026-07-22 17:43:34 86 na-prot_10512.pdb -5.87152470945 2026-07-22 17:43:34 87 na-prot_1645.pdb -5.86871490048 2026-07-22 17:43:34 88 na-prot_2756.pdb -5.86281072405 2026-07-22 17:43:34 89 na-prot_9181.pdb -5.85750883485 2026-07-22 17:43:34 90 na-prot_4174.pdb -5.85201277667 2026-07-22 17:43:34 91 na-prot_17835.pdb -5.8512608869 2026-07-22 17:43:34 92 na-prot_1119.pdb -5.84607992645 2026-07-22 17:43:34 93 na-prot_923.pdb -5.83956000742 2026-07-22 17:43:34 94 na-prot_413.pdb -5.83619632413 2026-07-22 17:43:34 95 na-prot_2896.pdb -5.82818859124 2026-07-22 17:43:34 96 na-prot_3071.pdb -5.81319890008 2026-07-22 17:43:34 97 na-prot_19861.pdb -5.8128058143 2026-07-22 17:43:34 98 na-prot_68.pdb -5.81063964756 2026-07-22 17:43:34 99 na-prot_16861.pdb -5.80817467619 2026-07-22 17:43:34 100 na-prot_14177.pdb -5.80384729182 2026-07-22 17:43:34 Chains: A 2026-07-22 17:44:00 100 best scored structures 2026-07-22 17:44:00 GRAMM analysis selected for further analysis: prot-na_10 2026-07-22 17:44:00 Cluster #1 with 100 structures 2026-07-22 17:44:00 1 na-prot_7162.pdb -8.00958319437 2026-07-22 17:44:00 2 na-prot_14480.pdb -7.67686882036 2026-07-22 17:44:00 3 na-prot_12042.pdb -7.66940052842 2026-07-22 17:44:00 4 na-prot_2136.pdb -7.60210534776 2026-07-22 17:44:00 5 na-prot_14642.pdb -7.3793882429 2026-07-22 17:44:00 6 na-prot_19220.pdb -7.25851035667 2026-07-22 17:44:00 7 na-prot_3467.pdb -7.24836251852 2026-07-22 17:44:00 8 na-prot_4097.pdb -7.22561799433 2026-07-22 17:44:00 9 na-prot_1173.pdb -7.22467634215 2026-07-22 17:44:00 10 na-prot_7421.pdb -7.22428188864 2026-07-22 17:44:00 11 na-prot_4730.pdb -7.01094174014 2026-07-22 17:44:00 12 na-prot_2210.pdb -6.92991005101 2026-07-22 17:44:00 13 na-prot_502.pdb -6.87501362688 2026-07-22 17:44:00 14 na-prot_1375.pdb -6.86454181877 2026-07-22 17:44:00 15 na-prot_6162.pdb -6.83224078219 2026-07-22 17:44:00 16 na-prot_4135.pdb -6.79787212015 2026-07-22 17:44:00 17 na-prot_19202.pdb -6.79502482137 2026-07-22 17:44:00 18 na-prot_472.pdb -6.74669942222 2026-07-22 17:44:00 19 na-prot_11001.pdb -6.73536988748 2026-07-22 17:44:00 20 na-prot_888.pdb -6.71337308572 2026-07-22 17:44:00 21 na-prot_5927.pdb -6.70565636265 2026-07-22 17:44:00 22 na-prot_112.pdb -6.68718188669 2026-07-22 17:44:00 23 na-prot_173.pdb -6.68327311001 2026-07-22 17:44:00 24 na-prot_9902.pdb -6.63910710154 2026-07-22 17:44:00 25 na-prot_10113.pdb -6.63131919554 2026-07-22 17:44:00 26 na-prot_21.pdb -6.62239254898 2026-07-22 17:44:00 27 na-prot_6970.pdb -6.61262072981 2026-07-22 17:44:00 28 na-prot_15217.pdb -6.59590678639 2026-07-22 17:44:00 29 na-prot_15593.pdb -6.52286649209 2026-07-22 17:44:00 30 na-prot_6431.pdb -6.49699093856 2026-07-22 17:44:00 31 na-prot_11519.pdb -6.44689203021 2026-07-22 17:44:00 32 na-prot_26.pdb -6.43884062675 2026-07-22 17:44:00 33 na-prot_1694.pdb -6.42603496407 2026-07-22 17:44:00 34 na-prot_303.pdb -6.40172839526 2026-07-22 17:44:00 35 na-prot_14316.pdb -6.39628516138 2026-07-22 17:44:00 36 na-prot_13631.pdb -6.35714845576 2026-07-22 17:44:00 37 na-prot_2689.pdb -6.31679672881 2026-07-22 17:44:00 38 na-prot_37.pdb -6.31557766828 2026-07-22 17:44:00 39 na-prot_3459.pdb -6.31339264397 2026-07-22 17:44:00 40 na-prot_1327.pdb -6.28048212112 2026-07-22 17:44:00 41 na-prot_687.pdb -6.25698595481 2026-07-22 17:44:00 42 na-prot_7328.pdb -6.25392502213 2026-07-22 17:44:00 43 na-prot_292.pdb -6.23679873865 2026-07-22 17:44:00 44 na-prot_5449.pdb -6.23194003141 2026-07-22 17:44:00 45 na-prot_11166.pdb -6.2247767162 2026-07-22 17:44:00 46 na-prot_11430.pdb -6.21988786486 2026-07-22 17:44:00 47 na-prot_12190.pdb -6.18899267914 2026-07-22 17:44:00 48 na-prot_2694.pdb -6.18373587566 2026-07-22 17:44:00 49 na-prot_4624.pdb -6.16631094041 2026-07-22 17:44:00 50 na-prot_169.pdb -6.158974633 2026-07-22 17:44:00 51 na-prot_13851.pdb -6.15191756863 2026-07-22 17:44:00 52 na-prot_3352.pdb -6.14809330758 2026-07-22 17:44:00 53 na-prot_223.pdb -6.121753844 2026-07-22 17:44:00 54 na-prot_49.pdb -6.11936512093 2026-07-22 17:44:00 55 na-prot_9909.pdb -6.10696059744 2026-07-22 17:44:00 56 na-prot_5.pdb -6.08662422499 2026-07-22 17:44:00 57 na-prot_7274.pdb -6.08363965614 2026-07-22 17:44:00 58 na-prot_412.pdb -6.07773665462 2026-07-22 17:44:00 59 na-prot_6779.pdb -6.06194852871 2026-07-22 17:44:00 60 na-prot_1827.pdb -6.05984829924 2026-07-22 17:44:00 61 na-prot_9622.pdb -6.05688365949 2026-07-22 17:44:00 62 na-prot_2655.pdb -6.04423350203 2026-07-22 17:44:00 63 na-prot_945.pdb -6.04350107219 2026-07-22 17:44:00 64 na-prot_6645.pdb -6.03791830295 2026-07-22 17:44:00 65 na-prot_8134.pdb -6.03538391325 2026-07-22 17:44:00 66 na-prot_19212.pdb -6.03074288651 2026-07-22 17:44:00 67 na-prot_3507.pdb -6.02970911915 2026-07-22 17:44:00 68 na-prot_219.pdb -6.02959629269 2026-07-22 17:44:00 69 na-prot_7307.pdb -6.02957143477 2026-07-22 17:44:00 70 na-prot_53.pdb -6.00492067453 2026-07-22 17:44:00 71 na-prot_9413.pdb -5.99169389737 2026-07-22 17:44:00 72 na-prot_16365.pdb -5.98451332511 2026-07-22 17:44:00 73 na-prot_461.pdb -5.97863089591 2026-07-22 17:44:00 74 na-prot_13647.pdb -5.96008690898 2026-07-22 17:44:00 75 na-prot_11560.pdb -5.95712352226 2026-07-22 17:44:00 76 na-prot_9102.pdb -5.93377671024 2026-07-22 17:44:00 77 na-prot_1.pdb -5.92142448271 2026-07-22 17:44:00 78 na-prot_2604.pdb -5.91817577142 2026-07-22 17:44:00 79 na-prot_17007.pdb -5.91344420341 2026-07-22 17:44:00 80 na-prot_15518.pdb -5.90645861702 2026-07-22 17:44:00 81 na-prot_13259.pdb -5.90625471181 2026-07-22 17:44:00 82 na-prot_1802.pdb -5.89666800805 2026-07-22 17:44:00 83 na-prot_1469.pdb -5.87628822353 2026-07-22 17:44:00 84 na-prot_48.pdb -5.87324761408 2026-07-22 17:44:00 85 na-prot_7262.pdb -5.87229140815 2026-07-22 17:44:00 86 na-prot_10512.pdb -5.87152470945 2026-07-22 17:44:00 87 na-prot_1645.pdb -5.86871490048 2026-07-22 17:44:00 88 na-prot_2756.pdb -5.86281072405 2026-07-22 17:44:00 89 na-prot_9181.pdb -5.85750883485 2026-07-22 17:44:00 90 na-prot_4174.pdb -5.85201277667 2026-07-22 17:44:00 91 na-prot_17835.pdb -5.8512608869 2026-07-22 17:44:00 92 na-prot_1119.pdb -5.84607992645 2026-07-22 17:44:00 93 na-prot_923.pdb -5.83956000742 2026-07-22 17:44:00 94 na-prot_413.pdb -5.83619632413 2026-07-22 17:44:00 95 na-prot_2896.pdb -5.82818859124 2026-07-22 17:44:00 96 na-prot_3071.pdb -5.81319890008 2026-07-22 17:44:00 97 na-prot_19861.pdb -5.8128058143 2026-07-22 17:44:00 98 na-prot_68.pdb -5.81063964756 2026-07-22 17:44:00 99 na-prot_16861.pdb -5.80817467619 2026-07-22 17:44:00 100 na-prot_14177.pdb -5.80384729182 2026-07-22 17:44:00 Sent to refinement: clusters_found|na-prot_7162.pdb 2026-07-22 17:44:00 Sent to refinement: clusters_found|na-prot_7162.pdb 2026-07-22 17:44:00 DARS clustering end 2026-07-22 17:44:00 MC (refinement) init 2026-07-22 17:44:00 python /home/rpdock/run_gramm//run_mc.py -f dars_to_mc.txt -d /home/rpdock/web/media/jobs/1a4e97f7-4e09-4089-b51a-64727243428a/ 2026-07-22 17:44:00 Refinement of #1 /home/rpdock/web/media/jobs/1a4e97f7-4e09-4089-b51a-64727243428a/na-prot_7162.pdb 2026-07-22 17:44:00 python /home/rpdock/mc/MC_DNA.py -s 1000 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/1a4e97f7-4e09-4089-b51a-64727243428a//ref_struc/na-prot_7162/na-prot_7162.pdb 2026-07-22 17:47:16 run_mc::stderr:Traceback (most recent call last): File "/home/rpdock/mc/MC_DNA.py", line 628, in s, datas = write_all_atoms (datas, step_real, cal.split()[0], plik, pars, historyT, historyR,rna) File "/home/rpdock/mc/MC_DNA.py", line 360, in write_all_atoms all_at_ch_rna, all_at_ch_prot = all_atom (plik, pars, transl, rotation, rna) File "/home/rpdock/mc/MC_DNA.py", line 297, in all_atom pro_ch, rna_ch = check_chains(plik, pars) File "/home/rpdock/mc/MC_DNA.py", line 103, in check_chains struc = pars.get_structure('native', plik) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py", line 83, in get_structure self._parse(handle.readlines()) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py", line 109, in _parse self.trailer = self._parse_coordinates(coords_trailer) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py", line 219, in _parse_coordinates structure_builder.init_residue(resname, hetero_flag, resseq, icode) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/StructureBuilder.py", line 156, in init_residue residue=Residue(res_id, resname, self.segid) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/Residue.py", line 30, in __init__ Entity.__init__(self, id) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/Entity.py", line 23, in __init__ self.full_id=None MemoryError 2026-07-22 17:47:16 start - parameters: File name /home/rpdock/web/media/jobs/1a4e97f7-4e09-4089-b51a-64727243428a//ref_struc/na-prot_7162/na-prot_7162.pdb Steps 1000 Temp. start 15000.0 Temp. end 295.0 False msg start - parameters: File name /home/rpdock/web/media/jobs/1a4e97f7-4e09-4089-b51a-64727243428a//ref_struc/na-prot_7162/na-prot_7162.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 - 948994.86 -885797.13 -285208.01 2120000.00 1 T 460319.91 -919876.87 -299803.22 1680000.00 T= 15000.0 K progress 0.1 2 R 330354.10 -900085.51 -289560.39 1520000.00 T= 14955.885 K progress 0.2 3 R 570341.17 -875319.65 -274339.18 1720000.00 T= 14941.18 K progress 0.3 4 T 443200.21 -817807.68 -258992.10 1520000.00 T= 14911.77 K progress 0.4 5 T 42168.59 -833799.56 -244031.85 1120000.00 T= 14897.065 K progress 0.5 6 R -73076.80 -796543.26 -236533.54 960000.00 T= 14882.36 K progress 0.6 7 R -514742.78 -764675.86 -230066.92 480000.00 T= 14852.95 K progress 0.7 8 T -603739.53 -728862.66 -234876.87 360000.00 T= 14808.835 K progress 0.8 9 T -713820.02 -663885.20 -209934.82 160000.00 T= 14794.13 K progress 0.9 10 T -550814.55 -646979.41 -183835.13 280000.00 T= 14779.425 K progress 1.0 11 R -587408.33 -677611.57 -189796.76 280000.00 T= 14750.015 K progress 1.1 12 R -433821.41 -704528.19 -209293.22 480000.00 T= 14735.31 K progress 1.2 13 T -629741.03 -648009.85 -181731.18 200000.00 T= 14720.605 K progress 1.3 14 R -610923.95 -530756.02 -160167.93 80000.00 T= 14705.9 K progress 1.4 15 R -607382.84 -527649.34 -159733.49 80000.00 T= 14691.195 K progress 1.5 16 T -666883.91 -544507.28 -162376.62 40000.00 T= 14661.785 K progress 1.6 17 T -687013.15 -561479.09 -165534.06 40000.00 T= 14647.08 K progress 1.7 18 T -622931.54 -513011.86 -149919.68 40000.00 T= 14632.375 K progress 1.8 19 R -759618.07 -619946.53 -179671.54 40000.00 T= 14617.67 K progress 1.9 20 T -659848.74 -533686.54 -166162.20 40000.00 T= 14602.965 K progress 2.0 21 R -701901.04 -544354.81 -197546.22 40000.00 T= 14588.26 K progress 2.1 22 T -676372.19 -562151.64 -194220.55 80000.00 T= 14573.555 K progress 2.2 23 T -724870.37 -576081.44 -188788.93 40000.00 T= 14558.85 K progress 2.3 24 T -720305.41 -565260.73 -195044.67 40000.00 T= 14544.145 K progress 2.4 25 R -685772.90 -549170.67 -176602.23 40000.00 T= 14529.44 K progress 2.5 26 R -679392.29 -712436.30 -246955.99 280000.00 T= 14441.21 K progress 2.6 27 T -521132.70 -747291.14 -253841.56 480000.00 T= 14426.505 K progress 2.7 28 T -548074.34 -715119.88 -232954.46 400000.00 T= 14323.57 K progress 2.8 29 T -322205.61 -727801.51 -234404.10 640000.00 T= 14308.865 K progress 2.9 30 T -462395.32 -744598.77 -237796.55 520000.00 T= 14264.75 K progress 3.0 31 R -568731.48 -527319.70 -161411.78 120000.00 T= 14250.045 K progress 3.1 32 T -610529.15 -494232.61 -156296.54 40000.00 T= 14235.34 K progress 3.2 33 R -363113.74 -392884.37 -130229.37 160000.00 T= 14205.93 K progress 3.3 34 R -422640.56 -483236.48 -139404.09 200000.00 T= 14191.225 K progress 3.4 35 R -565101.47 -783257.17 -261844.30 480000.00 T= 14176.52 K progress 3.5 36 R -436334.71 -455786.49 -140548.22 160000.00 T= 14161.815 K progress 3.6 37 R -516485.13 -517891.46 -158593.67 160000.00 T= 14073.585 K progress 3.7 38 T -505188.89 -587953.77 -197235.12 280000.00 T= 14029.47 K progress 3.8 39 T -584555.33 -576589.04 -207966.29 200000.00 T= 14014.765 K progress 3.9 40 T -584269.85 -582438.50 -201831.35 200000.00 T= 13970.65 K progress 4.0 41 R -570435.90 -545063.13 -185372.77 160000.00 T= 13941.24 K progress 4.1 42 R -554529.00 -506615.05 -167913.95 120000.00 T= 13926.535 K progress 4.2 43 T -667465.54 -580121.83 -207343.71 120000.00 T= 13911.83 K progress 4.3 44 T -695968.50 -573599.26 -202369.24 80000.00 T= 13853.01 K progress 4.4 45 T -671790.00 -590733.21 -201056.79 120000.00 T= 13838.305 K progress 4.5 46 T -690296.16 -613364.23 -196931.94 120000.00 T= 13808.895 K progress 4.6 47 T -711924.83 -624208.48 -207716.36 120000.00 T= 13779.485 K progress 4.7 48 T -742111.55 -612632.28 -209479.27 80000.00 T= 13764.78 K progress 4.8 49 T -625191.78 -624481.30 -200710.48 200000.00 T= 13750.075 K progress 4.9 50 T -646732.30 -637862.62 -208869.68 200000.00 T= 13720.665 K progress 5.0 51 R -682837.77 -636610.39 -206227.38 160000.00 T= 13705.96 K progress 5.1 52 T -733625.28 -612245.24 -201380.03 80000.00 T= 13661.845 K progress 5.2 53 T -673752.45 -560461.14 -193291.32 80000.00 T= 13647.14 K progress 5.3 54 T -669565.53 -539105.60 -210459.93 80000.00 T= 13632.435 K progress 5.4 55 T -665450.13 -616684.77 -208765.37 160000.00 T= 13603.025 K progress 5.5 56 R -629338.99 -623333.65 -206005.34 200000.00 T= 13588.32 K progress 5.6 57 T -656131.61 -579784.32 -196347.29 120000.00 T= 13544.205 K progress 5.7 58 T -540457.98 -499789.79 -200668.19 160000.00 T= 13529.5 K progress 5.8 59 T -636016.15 -592628.72 -203387.43 160000.00 T= 13514.795 K progress 5.9 60 R -634921.77 -590499.64 -204422.12 160000.00 T= 13500.09 K progress 6.0 61 T -602395.50 -563490.12 -198905.38 160000.00 T= 13470.68 K progress 6.1 62 R -678752.60 -525388.36 -193364.23 40000.00 T= 13455.975 K progress 6.2 63 R -687640.33 -533336.31 -194304.02 40000.00 T= 13367.745 K progress 6.3 64 T -652364.81 -547966.09 -184398.72 80000.00 T= 13338.335 K progress 6.4 65 R -673389.30 -525470.70 -187918.59 40000.00 T= 13323.63 K progress 6.5 66 T -637151.46 -499804.66 -177346.81 40000.00 T= 13294.22 K progress 6.6 67 T -630349.65 -538844.00 -171505.65 80000.00 T= 13279.515 K progress 6.7 68 R -632588.15 -542415.25 -170172.90 80000.00 T= 13264.81 K progress 6.8 69 R -603817.33 -547629.81 -176187.52 120000.00 T= 13235.4 K progress 6.9 70 T -707734.98 -615846.27 -211888.71 120000.00 T= 13220.695 K progress 7.0 71 T -636045.32 -574641.83 -181403.49 120000.00 T= 13205.99 K progress 7.1 72 R -613280.52 -556377.78 -176902.74 120000.00 T= 13191.285 K progress 7.2 73 R -549987.12 -532854.19 -177132.93 160000.00 T= 13176.58 K progress 7.3 74 R -604668.84 -577276.13 -187392.72 160000.00 T= 13147.17 K progress 7.4 75 T -663054.06 -634893.94 -188160.11 160000.00 T= 13103.055 K progress 7.5 76 T -753297.85 -711381.25 -201916.60 160000.00 T= 13088.35 K progress 7.6 77 R -749412.40 -684221.01 -225191.38 160000.00 T= 12985.415 K progress 7.7 78 T -648140.01 -749347.75 -218792.26 320000.00 T= 12956.005 K progress 7.8 79 R -611286.04 -710616.77 -220669.28 320000.00 T= 12941.3 K progress 7.9 80 R -635547.26 -547095.87 -168451.39 80000.00 T= 12867.775 K progress 8.0 81 R -711643.61 -629460.77 -202182.84 120000.00 T= 12808.955 K progress 8.1 82 T -605745.67 -680733.50 -205012.17 280000.00 T= 12735.43 K progress 8.2 83 R -427212.87 -743076.76 -244136.11 560000.00 T= 12706.02 K progress 8.3 84 R -633324.61 -542441.35 -170883.26 80000.00 T= 12632.495 K progress 8.4 85 T -609198.05 -603225.30 -165972.75 160000.00 T= 12617.79 K progress 8.5 86 R -541808.56 -527561.84 -174246.72 160000.00 T= 12573.675 K progress 8.6 87 R -460219.61 -469268.81 -150950.80 160000.00 T= 12558.97 K progress 8.7 88 T -587245.59 -511440.80 -155804.79 80000.00 T= 12544.265 K progress 8.8 89 T -603319.40 -519994.98 -163324.43 80000.00 T= 12529.56 K progress 8.9 90 R -619533.34 -533501.18 -166032.16 80000.00 T= 12500.15 K progress 9.0 91 R -539296.92 -651827.89 -207469.03 320000.00 T= 12485.445 K progress 9.1 92 R -503463.34 -567387.29 -176076.05 240000.00 T= 12470.74 K progress 9.2 93 R -513003.08 -572580.98 -180422.10 240000.00 T= 12456.035 K progress 9.3 94 T -736492.43 -589878.69 -186613.74 40000.00 T= 12441.33 K progress 9.4 95 R -493541.08 -388419.60 -145121.48 40000.00 T= 12426.625 K progress 9.5 96 R -601852.51 -440207.09 -161645.41 0.00 T= 12411.92 K progress 9.6 97 R -597491.39 -520480.06 -157011.33 80000.00 T= 12397.215 K progress 9.7 98 R -605242.12 -522144.35 -163097.76 80000.00 T= 12382.51 K progress 9.8 99 T -586383.13 -511352.50 -155030.63 80000.00 T= 12367.805 K progress 9.9 100 R -588403.10 -512330.94 -156072.16 80000.00 T= 12353.1 K progress 10.0 101 T -655247.45 -536884.82 -158362.63 40000.00 T= 12338.395 K progress 10.1 102 R -627197.15 -540960.38 -166236.77 80000.00 T= 12323.69 K progress 10.2 103 T -598291.97 -570459.69 -187832.28 160000.00 T= 12308.985 K progress 10.3 104 R -607229.56 -578582.34 -188647.22 160000.00 T= 12294.28 K progress 10.4 105 R -667397.19 -570808.07 -176589.12 80000.00 T= 12279.575 K progress 10.5 106 T -675422.05 -575412.20 -180009.85 80000.00 T= 12264.87 K progress 10.6 107 R -615384.35 -494082.75 -161301.60 40000.00 T= 12250.165 K progress 10.7 108 R -756458.57 -702991.60 -213466.96 160000.00 T= 12235.46 K progress 10.8 109 T -538319.67 -555958.68 -182360.99 200000.00 T= 12220.755 K progress 10.9 110 T -693816.97 -647894.46 -205922.51 160000.00 T= 12206.05 K progress 11.0 111 R -699286.95 -558449.07 -180837.89 40000.00 T= 12161.935 K progress 11.1 112 R -705196.64 -561181.48 -184015.16 40000.00 T= 12117.82 K progress 11.2 113 T -662006.15 -592297.81 -189708.34 120000.00 T= 12088.41 K progress 11.3 114 T -685208.91 -564401.41 -200807.50 80000.00 T= 12014.885 K progress 11.4 115 R -700937.92 -579012.29 -201925.63 80000.00 T= 12000.18 K progress 11.5 116 T -736165.68 -630959.79 -225205.89 120000.00 T= 11985.475 K progress 11.6 117 T -575271.87 -590106.53 -225165.34 240000.00 T= 11941.36 K progress 11.7 118 R -615502.57 -594164.00 -221338.57 200000.00 T= 11926.655 K progress 11.8 119 R -585263.24 -488914.46 -176348.78 80000.00 T= 11867.835 K progress 11.9 120 R -615502.57 -594164.00 -221338.57 200000.00 T= 11838.425 K progress 12.0 121 R -526681.96 -566590.57 -200091.39 240000.00 T= 11823.72 K progress 12.1 122 T -458046.43 -629359.53 -228686.90 400000.00 T= 11735.49 K progress 12.2 123 R -471669.78 -596209.88 -235459.89 360000.00 T= 11647.26 K progress 12.3 124 T -649801.91 -619192.25 -230609.67 200000.00 T= 11617.85 K progress 12.4 125 R -750989.94 -636379.34 -234610.60 120000.00 T= 11588.44 K progress 12.5 126 T -712841.77 -590231.52 -202610.25 80000.00 T= 11559.03 K progress 12.6 127 T -713667.34 -598876.77 -194790.57 80000.00 T= 11485.505 K progress 12.7 128 R -674040.72 -560701.23 -193339.49 80000.00 T= 11441.39 K progress 12.8 129 T -730673.59 -587637.60 -223035.99 80000.00 T= 11426.685 K progress 12.9 130 R -455821.66 -405829.61 -129992.04 80000.00 T= 11382.57 K progress 13.0 131 T -451636.07 -402479.65 -129156.43 80000.00 T= 11367.865 K progress 13.1 132 T -428586.11 -392662.84 -115923.26 80000.00 T= 11338.455 K progress 13.2 133 T -521192.08 -419403.87 -141788.21 40000.00 T= 11323.75 K progress 13.3 134 R -532213.83 -427469.83 -144743.99 40000.00 T= 11309.045 K progress 13.4 135 T -439447.69 -393015.66 -126432.03 80000.00 T= 11294.34 K progress 13.5 136 T -333921.73 -304315.40 -109606.33 80000.00 T= 11279.635 K progress 13.6 137 T -249946.03 -339065.51 -110880.52 200000.00 T= 11220.815 K progress 13.7 138 T -338544.96 -312936.37 -105608.60 80000.00 T= 11191.405 K progress 13.8 139 R -323994.09 -297927.87 -106066.23 80000.00 T= 11176.7 K progress 13.9 140 T -356491.67 -324850.92 -111640.75 80000.00 T= 11147.29 K progress 14.0 141 R -376825.39 -338653.35 -118172.04 80000.00 T= 11132.585 K progress 14.1 142 T -397258.38 -342630.55 -134627.83 80000.00 T= 11103.175 K progress 14.2 143 T -431311.58 -374584.22 -136727.36 80000.00 T= 11088.47 K progress 14.3 144 R -483017.85 -519861.26 -163156.59 200000.00 T= 11073.765 K progress 14.4 145 T -344806.39 -558380.75 -186425.64 400000.00 T= 11029.65 K progress 14.5 146 R -347168.22 -413334.32 -133833.90 200000.00 T= 11014.945 K progress 14.6 147 R -330286.84 -403109.14 -127177.71 200000.00 T= 10985.535 K progress 14.7 148 T -352020.85 -406630.62 -145390.24 200000.00 T= 10970.83 K progress 14.8 149 R -311362.21 -374639.64 -136722.58 200000.00 T= 10956.125 K progress 14.9 150 T -566788.36 -455770.30 -151018.06 40000.00 T= 10941.42 K progress 15.0 151 T -573156.53 -461279.80 -151876.73 40000.00 T= 10897.305 K progress 15.1 152 R -627335.28 -538650.41 -168684.86 80000.00 T= 10882.6 K progress 15.2 153 T -592003.81 -546355.41 -165648.40 120000.00 T= 10853.19 K progress 15.3 154 T -624528.05 -633184.44 -191343.61 200000.00 T= 10838.485 K progress 15.4 155 T -660463.09 -654881.06 -205582.03 200000.00 T= 10823.78 K progress 15.5 156 R -713424.59 -595652.22 -197772.38 80000.00 T= 10809.075 K progress 15.6 157 R -721365.06 -599521.60 -201843.46 80000.00 T= 10764.96 K progress 15.7 158 T -763525.58 -649520.37 -234005.20 120000.00 T= 10750.255 K progress 15.8 159 R -720994.86 -620724.61 -220270.24 120000.00 T= 10735.55 K progress 15.9 160 T -795758.26 -696607.87 -219150.40 120000.00 T= 10676.73 K progress 16.0 161 R -770815.81 -670585.12 -220230.69 120000.00 T= 10662.025 K progress 16.1 162 T -749808.61 -611237.71 -218570.90 80000.00 T= 10632.615 K progress 16.2 163 T -720821.51 -598979.65 -201841.86 80000.00 T= 10617.91 K progress 16.3 164 R -729298.77 -603807.08 -205491.69 80000.00 T= 10603.205 K progress 16.4 165 T -663669.54 -565026.18 -218643.37 120000.00 T= 10588.5 K progress 16.5 166 R -625155.59 -678426.71 -226728.88 280000.00 T= 10559.09 K progress 16.6 167 R -759532.00 -645291.53 -234240.48 120000.00 T= 10544.385 K progress 16.7 168 T -775267.98 -677144.60 -218123.38 120000.00 T= 10500.27 K progress 16.8 169 R -777332.77 -679511.99 -217820.78 120000.00 T= 10485.565 K progress 16.9 170 T -676077.48 -685962.81 -230114.67 240000.00 T= 10456.155 K progress 17.0 171 T -655722.84 -708482.94 -227239.90 280000.00 T= 10441.45 K progress 17.1 172 T -594282.07 -721428.62 -232853.45 360000.00 T= 10382.63 K progress 17.2 173 R -645110.18 -753233.96 -211876.22 320000.00 T= 10353.22 K progress 17.3 174 T -753732.67 -768052.10 -225680.57 240000.00 T= 10338.515 K progress 17.4 175 R -702257.89 -693248.99 -209008.91 200000.00 T= 10323.81 K progress 17.5 176 R -745345.20 -757488.32 -227856.88 240000.00 T= 10279.695 K progress 17.6 177 R -755839.93 -770220.74 -225619.18 240000.00 T= 10264.99 K progress 17.7 178 T -707837.09 -705994.50 -201842.58 200000.00 T= 10235.58 K progress 17.8 179 T -712964.88 -814627.36 -218337.52 320000.00 T= 10220.875 K progress 17.9 180 T -889686.08 -939846.80 -269839.27 320000.00 T= 10206.17 K progress 18.0 181 R -665875.31 -897721.24 -248154.07 480000.00 T= 10015.005 K progress 18.1 182 T -467682.67 -836377.07 -271305.60 640000.00 T= 9970.89 K progress 18.2 183 R -625894.58 -565127.53 -180767.05 120000.00 T= 9926.775 K progress 18.3 184 R -696166.61 -615143.43 -201023.19 120000.00 T= 9912.07 K progress 18.4 185 T -634517.78 -596938.88 -197578.91 160000.00 T= 9867.955 K progress 18.5 186 T -661005.52 -627193.18 -193812.35 160000.00 T= 9853.25 K progress 18.6 187 T -508116.17 -631590.16 -196526.01 320000.00 T= 9823.84 K progress 18.7 188 R -634137.02 -959573.95 -274563.07 600000.00 T= 9794.43 K progress 18.8 189 T -748034.16 -887220.30 -260813.85 400000.00 T= 9706.2 K progress 18.9 190 R -689984.51 -618490.46 -191494.05 120000.00 T= 9676.79 K progress 19.0 191 R -698277.42 -610542.17 -207735.26 120000.00 T= 9588.56 K progress 19.1 192 R -690250.44 -605870.59 -204379.86 120000.00 T= 9573.855 K progress 19.2 193 R -669663.76 -604573.01 -185090.74 120000.00 T= 9559.15 K progress 19.3 194 T -648442.30 -611181.67 -197260.64 160000.00 T= 9515.035 K progress 19.4 195 T -708591.86 -672711.51 -195880.36 160000.00 T= 9500.33 K progress 19.5 196 T -665133.40 -714841.20 -230292.20 280000.00 T= 9485.625 K progress 19.6 197 R -539071.31 -890110.31 -248961.00 600000.00 T= 9397.395 K progress 19.7 198 R -519693.16 -901579.12 -258114.04 640000.00 T= 9382.69 K progress 19.8 199 T -746594.20 -813761.13 -212833.08 280000.00 T= 9367.985 K progress 19.9 200 R -762733.68 -870327.53 -252406.15 360000.00 T= 9353.28 K progress 20.0 Long traj 201 R -753252.90 -752863.46 -200389.44 200000.00 T= 9338.575 K progress 20.1 202 T -694652.80 -683213.35 -211439.45 200000.00 T= 9309.165 K progress 20.2 203 T -744245.78 -746094.64 -198151.14 200000.00 T= 9294.46 K progress 20.3 204 R -747559.76 -749250.18 -198309.58 200000.00 T= 9265.05 K progress 20.4 205 R -729621.12 -734971.35 -194649.77 200000.00 T= 9250.345 K progress 20.5 206 R -643212.60 -727813.08 -195399.52 280000.00 T= 9235.64 K progress 20.6 207 R -678727.82 -752691.90 -206035.92 280000.00 T= 9206.23 K progress 20.7 208 R -773879.63 -774419.07 -199460.56 200000.00 T= 9191.525 K progress 20.8 209 T -618285.81 -636152.24 -182133.57 200000.00 T= 9176.82 K progress 20.9 210 T -606862.54 -597967.20 -168895.34 160000.00 T= 9162.115 K progress 21.0 211 T -489125.66 -601468.52 -167657.14 280000.00 T= 9132.705 K progress 21.1 212 T -475842.13 -591311.13 -204531.00 320000.00 T= 9103.295 K progress 21.2 213 R -528931.70 -543015.00 -185916.71 200000.00 T= 9088.59 K progress 21.3 214 T -532956.60 -553217.68 -179738.93 200000.00 T= 9073.885 K progress 21.4 215 R -528265.01 -544135.25 -184129.76 200000.00 T= 9059.18 K progress 21.5 216 T -639575.14 -610254.50 -189320.64 160000.00 T= 9044.475 K progress 21.6 217 T -601330.80 -549828.15 -171502.65 120000.00 T= 9015.065 K progress 21.7 218 T -581278.99 -517389.67 -183889.32 120000.00 T= 8956.245 K progress 21.8 219 T -587303.94 -604562.55 -182741.39 200000.00 T= 8926.835 K progress 21.9 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 193, in deepcopy _keep_alive(x, memo) # Make sure x lives at least as long as d File "/usr/lib/python2.7/copy.py", line 278, in _keep_alive memo[id(memo)].append(x) 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 219, in _parse_coordinates structure_builder.init_residue(resname, hetero_flag, resseq, icode) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/StructureBuilder.py", line 156, in init_residue residue=Residue(res_id, resname, self.segid) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/Residue.py", line 30, in __init__ Entity.__init__(self, id) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/Entity.py", line 23, in __init__ self.full_id=None MemoryError Wed Jul 22 17:44:00 2026 ['na-prot_7162.pdb'] msg Refinement of #1 /home/rpdock/web/media/jobs/1a4e97f7-4e09-4089-b51a-64727243428a/na-prot_7162.pdb dir: /home/rpdock/web/media/jobs/1a4e97f7-4e09-4089-b51a-64727243428a/ file: na-prot_7162.pdb find `pwd` -iname na-prot_7162.pdb copy /home/rpdock/web/media/jobs/1a4e97f7-4e09-4089-b51a-64727243428a/prot-na_10/na-prot_7162.pdb to /home/rpdock/web/media/jobs/1a4e97f7-4e09-4089-b51a-64727243428a//ref_struc/na-prot_7162/na-prot_7162.pdb cmd: python /home/rpdock/mc/MC_DNA.py -s 1000 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/1a4e97f7-4e09-4089-b51a-64727243428a//ref_struc/na-prot_7162/na-prot_7162.pdb msg python /home/rpdock/mc/MC_DNA.py -s 1000 -a 15000 -t 295 -f /home/rpdock/web/media/jobs/1a4e97f7-4e09-4089-b51a-64727243428a//ref_struc/na-prot_7162/na-prot_7162.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 219, in _parse_coordinates structure_builder.init_residue(resname, hetero_flag, resseq, icode) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/StructureBuilder.py", line 156, in init_residue residue=Residue(res_id, resname, self.segid) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/Residue.py", line 30, in __init__ Entity.__init__(self, id) File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/Entity.py", line 23, in __init__ self.full_id=None MemoryError 2026-07-22 17:47:16 npdock::MC (refinement) end 2026-07-22 17:47:16 npdock::OK 2026-07-22 17:47:16 Set finished status of 1a4e97f7-4e09-4089-b51a-64727243428a