Tue 25 Dec 19:27:57 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2pnk-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2pnk-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2pnk-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pnk-4.0-parrot-hancs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pnk-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pnk-4.0-parrot-hancs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Tue 25 Dec 19:28:07 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pnk-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pnk-4.0-parrot-hancs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 4422 and 0 Target number of residues in the AU: 4422 Target solvent content: 0.6614 Target number of residues exceeds 1700, conditional restraints are disabled Checking the provided sequence file Detected sequence length: 428 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 12 Adjusted target number of residues: 5136 Adjusted target solvent content: 0.61 Input MTZ file: 2pnk-4.0-parrot-hancs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 5 Cell parameters: 273.720 158.560 181.240 90.000 116.029 90.000 Input sequence file: 2pnk-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 41088 target number of atoms Had to go as low as 1.00 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 3 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 162.857 4.000 Wilson plot Bfac: 85.98 54586 reflections ( 92.59 % complete ) and 0 restraints for refining 45223 atoms. Observations/parameters ratio is 0.30 ------------------------------------------------------ Starting model: R = 0.3216 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2925 (Rfree = 0.000) for 45223 atoms. Found 214 (214 requested) and removed 193 (107 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.80 3.27 Search for helices and strands: 0 residues in 0 chains, 46225 seeds are put forward NCS extension: 0 residues added, 46225 seeds are put forward Round 1: 2129 peptides, 398 chains. Longest chain 16 peptides. Score 0.317 Round 2: 2659 peptides, 396 chains. Longest chain 20 peptides. Score 0.445 Round 3: 2771 peptides, 371 chains. Longest chain 25 peptides. Score 0.493 Round 4: 2859 peptides, 362 chains. Longest chain 26 peptides. Score 0.519 Round 5: 2893 peptides, 353 chains. Longest chain 28 peptides. Score 0.534 Taking the results from Round 5 Chains 358, Residues 2540, Estimated correctness of the model 0.0 % 8 chains (103 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 54586 reflections ( 92.59 % complete ) and 10236 restraints for refining 37106 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2235 (Rfree = 0.000) for 37106 atoms. Found 169 (176 requested) and removed 157 (88 requested) atoms. Failed to save intermediate PDB Cycle 2: After refmac, R = 0.2117 (Rfree = 0.000) for 37118 atoms. Found 176 (176 requested) and removed 138 (88 requested) atoms. Failed to save intermediate PDB Cycle 3: After refmac, R = 0.2001 (Rfree = 0.000) for 37156 atoms. Found 176 (176 requested) and removed 176 (88 requested) atoms. Cycle 4: After refmac, R = 0.1919 (Rfree = 0.000) for 37156 atoms. Found 176 (176 requested) and removed 162 (88 requested) atoms. Failed to save intermediate PDB Cycle 5: After refmac, R = 0.1430 (Rfree = 0.000) for 37170 atoms. Found 32 (176 requested) and removed 133 (88 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.75 3.23 Search for helices and strands: 0 residues in 0 chains, 38554 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 38570 seeds are put forward Round 1: 2448 peptides, 413 chains. Longest chain 21 peptides. Score 0.379 Round 2: 2817 peptides, 376 chains. Longest chain 25 peptides. Score 0.497 Round 3: 2869 peptides, 377 chains. Longest chain 26 peptides. Score 0.507 Round 4: 2920 peptides, 359 chains. Longest chain 25 peptides. Score 0.533 Round 5: 2914 peptides, 366 chains. Longest chain 28 peptides. Score 0.526 Taking the results from Round 4 Chains 367, Residues 2561, Estimated correctness of the model 0.0 % 13 chains (145 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 54586 reflections ( 92.59 % complete ) and 10406 restraints for refining 37106 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2042 (Rfree = 0.000) for 37106 atoms. Found 176 (176 requested) and removed 167 (88 requested) atoms. Failed to save intermediate PDB Cycle 7: After refmac, R = 0.1903 (Rfree = 0.000) for 37115 atoms. Found 176 (176 requested) and removed 154 (88 requested) atoms. Failed to save intermediate PDBFailed to save intermediate PDB Cycle 8: After refmac, R = 0.1445 (Rfree = 0.000) for 37137 atoms. Found 21 (176 requested) and removed 147 (88 requested) atoms. Cycle 9: After refmac, R = 0.1351 (Rfree = 0.000) for 37011 atoms. Found 17 (175 requested) and removed 132 (87 requested) atoms. Cycle 10: After refmac, R = 0.1323 (Rfree = 0.000) for 36896 atoms. Found 19 (175 requested) and removed 115 (87 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.75 3.23 Search for helices and strands: 0 residues in 0 chains, 38136 seeds are put forward NCS extension: 13 residues added (7 deleted due to clashes), 38149 seeds are put forward Round 1: 2481 peptides, 427 chains. Longest chain 17 peptides. Score 0.373 Round 2: 2776 peptides, 386 chains. Longest chain 19 peptides. Score 0.479 Round 3: 2807 peptides, 373 chains. Longest chain 24 peptides. Score 0.498 Round 4: 2852 peptides, 370 chains. Longest chain 30 peptides. Score 0.510 Round 5: 2864 peptides, 359 chains. Longest chain 27 peptides. Score 0.522 Taking the results from Round 5 Chains 370, Residues 2505, Estimated correctness of the model 0.0 % 16 chains (171 residues) have been docked in sequence ------------------------------------------------------ 54586 reflections ( 92.59 % complete ) and 10291 restraints for refining 37106 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1996 (Rfree = 0.000) for 37106 atoms. Found 176 (176 requested) and removed 173 (88 requested) atoms. Failed to save intermediate PDB Cycle 12: After refmac, R = 0.1897 (Rfree = 0.000) for 37109 atoms. Found 176 (176 requested) and removed 174 (88 requested) atoms. Cycle 13: After refmac, R = 0.1810 (Rfree = 0.000) for 37111 atoms. Found 176 (176 requested) and removed 176 (88 requested) atoms. Failed to save intermediate PDB Cycle 14: After refmac, R = 0.1321 (Rfree = 0.000) for 37111 atoms. Found 18 (176 requested) and removed 125 (88 requested) atoms. Cycle 15: After refmac, R = 0.1241 (Rfree = 0.000) for 37004 atoms. Found 21 (175 requested) and removed 130 (87 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.75 3.23 Search for helices and strands: 0 residues in 0 chains, 38239 seeds are put forward NCS extension: 15 residues added (4 deleted due to clashes), 38254 seeds are put forward Round 1: 2409 peptides, 411 chains. Longest chain 18 peptides. Score 0.372 Round 2: 2820 peptides, 395 chains. Longest chain 26 peptides. Score 0.480 Round 3: 2870 peptides, 386 chains. Longest chain 24 peptides. Score 0.499 Round 4: 2853 peptides, 377 chains. Longest chain 23 peptides. Score 0.504 Round 5: 2826 peptides, 382 chains. Longest chain 24 peptides. Score 0.494 Taking the results from Round 4 Chains 379, Residues 2476, Estimated correctness of the model 0.0 % 4 chains (33 residues) have been docked in sequence ------------------------------------------------------ 54586 reflections ( 92.59 % complete ) and 9632 restraints for refining 37106 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1841 (Rfree = 0.000) for 37106 atoms. Found 176 (176 requested) and removed 172 (88 requested) atoms. Failed to save intermediate PDB Cycle 17: After refmac, R = 0.1776 (Rfree = 0.000) for 37110 atoms. Found 176 (176 requested) and removed 169 (88 requested) atoms. Failed to save intermediate PDBFailed to save intermediate PDB Cycle 18: After refmac, R = 0.1726 (Rfree = 0.000) for 37117 atoms. Found 176 (176 requested) and removed 202 (88 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.1694 (Rfree = 0.000) for 37091 atoms. Found 176 (176 requested) and removed 183 (88 requested) atoms. Failed to save intermediate PDB Cycle 20: After refmac, R = 0.1192 (Rfree = 0.000) for 37084 atoms. Found 19 (176 requested) and removed 133 (88 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.74 3.22 Search for helices and strands: 0 residues in 0 chains, 38332 seeds are put forward NCS extension: 0 residues added, 38332 seeds are put forward Round 1: 2373 peptides, 431 chains. Longest chain 20 peptides. Score 0.342 Round 2: 2719 peptides, 418 chains. Longest chain 22 peptides. Score 0.436 Round 3: 2832 peptides, 418 chains. Longest chain 25 peptides. Score 0.461 Round 4: 2782 peptides, 392 chains. Longest chain 32 peptides. Score 0.475 Round 5: 2797 peptides, 390 chains. Longest chain 28 peptides. Score 0.480 Taking the results from Round 5 Chains 397, Residues 2407, Estimated correctness of the model 0.0 % 11 chains (96 residues) have been docked in sequence ------------------------------------------------------ 54586 reflections ( 92.59 % complete ) and 9588 restraints for refining 37106 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1813 (Rfree = 0.000) for 37106 atoms. Found 176 (176 requested) and removed 159 (88 requested) atoms. Failed to save intermediate PDB Cycle 22: After refmac, R = 0.1748 (Rfree = 0.000) for 37123 atoms. Found 176 (176 requested) and removed 171 (88 requested) atoms. Cycle 23: After refmac, R = 0.1250 (Rfree = 0.000) for 37128 atoms. Found 29 (176 requested) and removed 152 (88 requested) atoms. Cycle 24: After refmac, R = 0.1162 (Rfree = 0.000) for 37005 atoms. Found 21 (175 requested) and removed 120 (87 requested) atoms. Failed to save intermediate PDB Cycle 25: After refmac, R = 0.1116 (Rfree = 0.000) for 36906 atoms. Found 11 (175 requested) and removed 114 (87 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.75 3.23 Search for helices and strands: 0 residues in 0 chains, 38094 seeds are put forward NCS extension: 0 residues added, 38094 seeds are put forward Round 1: 2347 peptides, 424 chains. Longest chain 16 peptides. Score 0.343 Round 2: 2611 peptides, 404 chains. Longest chain 30 peptides. Score 0.426 Round 3: 2708 peptides, 398 chains. Longest chain 29 peptides. Score 0.453 Round 4: 2680 peptides, 381 chains. Longest chain 27 peptides. Score 0.464 Round 5: 2697 peptides, 380 chains. Longest chain 28 peptides. Score 0.468 Taking the results from Round 5 Chains 386, Residues 2317, Estimated correctness of the model 0.0 % 10 chains (117 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 54586 reflections ( 92.59 % complete ) and 9353 restraints for refining 37106 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1889 (Rfree = 0.000) for 37106 atoms. Found 176 (176 requested) and removed 155 (88 requested) atoms. Cycle 27: After refmac, R = 0.1770 (Rfree = 0.000) for 37127 atoms. Found 176 (176 requested) and removed 150 (88 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.1254 (Rfree = 0.000) for 37153 atoms. Found 35 (176 requested) and removed 132 (88 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.1155 (Rfree = 0.000) for 37056 atoms. Found 21 (176 requested) and removed 121 (88 requested) atoms. Failed to save intermediate PDB Cycle 30: After refmac, R = 0.1110 (Rfree = 0.000) for 36956 atoms. Found 15 (175 requested) and removed 114 (87 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.75 3.23 Search for helices and strands: 0 residues in 0 chains, 38114 seeds are put forward NCS extension: 0 residues added, 38114 seeds are put forward Round 1: 2196 peptides, 414 chains. Longest chain 16 peptides. Score 0.316 Round 2: 2520 peptides, 405 chains. Longest chain 21 peptides. Score 0.404 Round 3: 2542 peptides, 398 chains. Longest chain 21 peptides. Score 0.416 Round 4: 2585 peptides, 389 chains. Longest chain 27 peptides. Score 0.435 Round 5: 2574 peptides, 379 chains. Longest chain 23 peptides. Score 0.443 Taking the results from Round 5 Chains 384, Residues 2195, Estimated correctness of the model 0.0 % 8 chains (87 residues) have been docked in sequence ------------------------------------------------------ 54586 reflections ( 92.59 % complete ) and 8733 restraints for refining 37106 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1843 (Rfree = 0.000) for 37106 atoms. Found 176 (176 requested) and removed 157 (88 requested) atoms. Cycle 32: After refmac, R = 0.1794 (Rfree = 0.000) for 37125 atoms. Found 176 (176 requested) and removed 162 (88 requested) atoms. Cycle 33: After refmac, R = 0.1697 (Rfree = 0.000) for 37139 atoms. Found 176 (176 requested) and removed 177 (88 requested) atoms. Cycle 34: After refmac, R = 0.1183 (Rfree = 0.000) for 37138 atoms. Found 22 (176 requested) and removed 135 (88 requested) atoms. Cycle 35: After refmac, R = 0.1105 (Rfree = 0.000) for 37025 atoms. Found 26 (175 requested) and removed 121 (87 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.75 3.23 Search for helices and strands: 0 residues in 0 chains, 38130 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 38148 seeds are put forward Round 1: 2067 peptides, 397 chains. Longest chain 14 peptides. Score 0.302 Round 2: 2425 peptides, 399 chains. Longest chain 20 peptides. Score 0.388 Round 3: 2468 peptides, 390 chains. Longest chain 19 peptides. Score 0.408 Round 4: 2483 peptides, 396 chains. Longest chain 19 peptides. Score 0.405 Round 5: 2548 peptides, 397 chains. Longest chain 36 peptides. Score 0.419 Taking the results from Round 5 Chains 399, Residues 2151, Estimated correctness of the model 0.0 % 7 chains (60 residues) have been docked in sequence ------------------------------------------------------ 54586 reflections ( 92.59 % complete ) and 8476 restraints for refining 37106 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1827 (Rfree = 0.000) for 37106 atoms. Found 176 (176 requested) and removed 160 (88 requested) atoms. Cycle 37: After refmac, R = 0.1756 (Rfree = 0.000) for 37122 atoms. Found 176 (176 requested) and removed 163 (88 requested) atoms. Cycle 38: After refmac, R = 0.1708 (Rfree = 0.000) for 37135 atoms. Found 176 (176 requested) and removed 154 (88 requested) atoms. Cycle 39: After refmac, R = 0.1155 (Rfree = 0.000) for 37157 atoms. Found 23 (176 requested) and removed 137 (88 requested) atoms. Cycle 40: After refmac, R = 0.1072 (Rfree = 0.000) for 37043 atoms. Found 13 (176 requested) and removed 127 (88 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.74 3.22 Search for helices and strands: 0 residues in 0 chains, 38190 seeds are put forward NCS extension: 0 residues added, 38190 seeds are put forward Round 1: 1938 peptides, 379 chains. Longest chain 15 peptides. Score 0.288 Round 2: 2366 peptides, 397 chains. Longest chain 17 peptides. Score 0.376 Round 3: 2409 peptides, 390 chains. Longest chain 22 peptides. Score 0.394 Round 4: 2378 peptides, 380 chains. Longest chain 21 peptides. Score 0.397 Round 5: 2458 peptides, 381 chains. Longest chain 23 peptides. Score 0.414 Taking the results from Round 5 Chains 384, Residues 2077, Estimated correctness of the model 0.0 % 5 chains (50 residues) have been docked in sequence ------------------------------------------------------ 54586 reflections ( 92.59 % complete ) and 8132 restraints for refining 37106 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1826 (Rfree = 0.000) for 37106 atoms. Found 176 (176 requested) and removed 174 (88 requested) atoms. Cycle 42: After refmac, R = 0.1755 (Rfree = 0.000) for 37108 atoms. Found 176 (176 requested) and removed 158 (88 requested) atoms. Failed to save intermediate PDB Cycle 43: After refmac, R = 0.1224 (Rfree = 0.000) for 37126 atoms. Found 20 (176 requested) and removed 128 (88 requested) atoms. Cycle 44: After refmac, R = 0.1144 (Rfree = 0.000) for 37018 atoms. Found 31 (175 requested) and removed 128 (87 requested) atoms. Cycle 45: After refmac, R = 0.1111 (Rfree = 0.000) for 36921 atoms. Found 21 (175 requested) and removed 123 (87 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.75 3.23 Search for helices and strands: 0 residues in 0 chains, 38011 seeds are put forward NCS extension: 0 residues added, 38011 seeds are put forward Round 1: 1914 peptides, 375 chains. Longest chain 12 peptides. Score 0.286 Round 2: 2242 peptides, 380 chains. Longest chain 17 peptides. Score 0.364 Round 3: 2242 peptides, 368 chains. Longest chain 18 peptides. Score 0.377 Round 4: 2297 peptides, 366 chains. Longest chain 18 peptides. Score 0.393 Round 5: 2300 peptides, 363 chains. Longest chain 22 peptides. Score 0.396 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 366, Residues 1937, Estimated correctness of the model 0.0 % 8 chains (68 residues) have been docked in sequence Sequence coverage is 3 % Consider running further cycles of model building using 2pnk-4_warpNtrace.pdb as input Building loops using Loopy2018 366 chains (1937 residues) following loop building 8 chains (68 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 54586 reflections ( 92.59 % complete ) and 7661 restraints for refining 37106 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1802 (Rfree = 0.000) for 37106 atoms. Found 0 (176 requested) and removed 88 (88 requested) atoms. Cycle 47: After refmac, R = 0.1773 (Rfree = 0.000) for 37018 atoms. Found 0 (175 requested) and removed 87 (87 requested) atoms. Cycle 48: After refmac, R = 0.1245 (Rfree = 0.000) for 36931 atoms. Found 0 (175 requested) and removed 87 (87 requested) atoms. Cycle 49: After refmac, R = 0.1139 (Rfree = 0.000) for 36844 atoms. Found 0 (175 requested) and removed 87 (87 requested) atoms. Writing output files ... Failed to save intermediate PDB TimeTaking 409.03