/home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3 /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3 /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3 /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3 n_dec 21 Fri Oct 23 16:00:04 2026 Checking of the smallest grid_step Log: ['\n', '*** ERROR: for prot and na molecules the 0.5 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 0.5 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 0.6 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 0.6 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 0.7 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 0.7 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 0.8 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 0.8 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 0.9 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 0.9 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 1.0 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 1.0 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 1.1 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 1.1 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 1.2 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 1.2 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 1.3 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 1.3 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 1.4 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 1.4 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 1.5 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 1.5 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 1.6 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 1.6 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 1.7 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 1.7 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 1.8 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 1.8 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 1.9 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 1.9 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 2.0 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 2.0 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb prepare dir: prot-na_10 0 katalog cp prot-na_5/* prot-na_10 cp from 5 Make rpar... close rpar prepare dir: prot-na_15 0 katalog cp prot-na_5/* prot-na_15 cp from 5 Make rpar... close rpar prepare dir: prot-na_20 0 katal/home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3 /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3 og cp prot-na_5/* prot-na_20 cp from 5 Make rpar... close rpar prepare dir: prot-na_25 0 katalog cp prot-na_5/* prot-na_25 cp from 5 Make rpar... close rpar prepare dir: prot-na_30 0 katalog cp prot-na_5/* prot-na_30 cp from 5 Make rpar... close rpar gramm is running, wait... ['prot-na_1000.pdb', 'prot-na_1001.pdb', 'prot-na_1002.pdb', 'prot-na_1003.pdb', 'prot-na_1004.pdb', 'prot-na_1005.pdb'] Contacts, str_name: 0 350 424 prot-na_1000.pdb Sterical clashes 0.825471698113 Contacts, str_name: 1 336 423 prot-na_1001.pdb Sterical clashes 0.794326241135 Contacts, str_name: 2 310 424 prot-na_1002.pdb Sterical clashes 0.731132075472 Contacts, str_name: 3 311 424 prot-na_1003.pdb Sterical clashes 0.733490566038 Contacts, str_name: 4 320 424 prot-na_1004.pdb Sterical clashes 0.754716981132 Contacts, str_name: 5 318 423 prot-na_1005.pdb Sterical clashes 0.751773049645 There are 0.765151768589 in the file prot-na_5 d_names: ['prot-na_10', 'prot-na_15', 'prot-na_20', 'prot-na_25', 'prot-na_30'] Working directory is prot-na_10 gramm is running, wait... ['prot-na_1000.pdb', 'prot-na_1001.pdb', 'prot-na_1002.pdb', 'prot-na_1003.pdb', 'prot-na_1004.pdb', 'prot-na_1005.pdb'] Contacts, str_name: 0 127 272 prot-na_1000.pdb Sterical clashes 0.466911764706 Contacts, str_name: 1 131 266 prot-na_1001.pdb Sterical clashes 0.492481203008 Contacts, str_name: 2 59 199 prot-na_1002.pdb Sterical clashes 0.29648241206 Contacts, str_name: 3 34 186 prot-na_1003.pdb Sterical clashes 0.182795698925 Contacts, str_name: 4 45 175 prot-na_1004.pdb Sterical clashes 0.257142857143 Contacts, str_name: 5 25 154 prot-na_1005.pdb Sterical clashes 0.162337662338 Working directory is prot-na_15 gramm is running, wait... ['prot-na_1000.pdb', 'prot-na_1001.pdb', 'prot-na_1002.pdb', 'prot-na_1003.pdb', 'prot-na_1004.pdb', 'prot-na_1005.pdb'] Contacts, str_name: 0 4 46 prot-na_1000.pdb Sterical clashes 0.0869565217391 Contacts, str_name: 1 3 47 prot-na_1001.pdb Sterical clashes 0.063829787234 Contacts, str_name: 2 20 95 prot-na_1002.pdb Sterical clashes 0.210526315789 Contacts, str_name: 3 7 70 prot-na_1003.pdb Sterical clashes 0.1 Contacts, str_name: 4 19 85 prot-na_1004.pdb Sterical clashes 0.223529411765 Contacts, str_name: 5 16 102 prot-na_1005.pdb Sterical clashes 0.156862745098 Generating 10000 decoys first: 1 first: 1001 first: 2001 first: 3001 first: 4001 first: 5001 first: 6001 first: 7001 first: 8001 first: 9001 first: 10001 first: 11001 first: 12001 first: 13001 first: 14001 first: 15001 first: 16001 first: 17001 first: 18001 first: 19001 big_first_l, small_first_l, big_int, small_int ['ATOM 1 N PHE A 369 ', 'ATOM 1644 N ASN B 117 '] ['ATOM 1 P G A 1 ', 'ATOM 213 P G D 1 '] {'A': [433, 513]} {'A': [5]} Fri Oct 23 16:35:28 2026 /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/*-*_*.pdb file_pdb prot-na cmd: find /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15 -name prot-na_*.pdb > list1.txt {'A': [433, 513]} {'C': [5]} run_gramm1::run filter Big inter {'A': [433, 513]} Small inter {'C': [5]} accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_22.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_152.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_154.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_411.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_423.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_503.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_505.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_536.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_943.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_953.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_1219.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_1222.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_1248.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_1279.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_1342.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_1400.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_1440.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_1792.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_1958.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_1984.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_2028.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_2203.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_2217.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_2913.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_2958.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_3437.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_3632.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_3697.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_3704.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_3719.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_3741.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_3743.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_3775.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_3806.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_4102.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_4315.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_4498.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_4584.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_5056.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_5171.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_6064.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_6303.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_6347.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_6483.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_6494.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_6666.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_6766.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_7248.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_7519.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_7642.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_7889.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_7918.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_9051.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_9433.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_9440.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_9505.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_9761.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_10073.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_10142.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_10232.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_10254.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_10689.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_11138.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_11448.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_12030.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_12257.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_12277.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_12347.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_12643.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_13028.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_13121.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_13360.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_13824.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_13853.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_14160.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_14629.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_14638.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_14650.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_14680.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_14896.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_15281.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_15322.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_15508.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_15906.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_15966.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_16327.pdb accepted: /home/rpdock/web/media/jobs/73b5fae0-b79c-4fe0-a5ce-93c8cb9bd5c3/prot-na_15/prot-na_16445.pdb accepted: 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