null Tue 25 Dec 19:27:55 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 2pn1-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2pn1-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2pn1-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pn1-3.8-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/2pn1-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pn1-3.8-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 19:28:05 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/2pn1-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pn1-3.8-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 236 and 0 Target number of residues in the AU: 236 Target solvent content: 0.6410 Checking the provided sequence file Detected sequence length: 331 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 331 Adjusted target solvent content: 0.50 Input MTZ file: 2pn1-3.8-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: 91.460 61.130 76.770 90.000 124.022 90.000 Input sequence file: 2pn1-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 2648 target number of atoms Had to go as low as 0.70 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. Conditional restraints will be used 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 Loops will be built when appropriate and at the last cycle Resolution range: 63.629 3.800 Wilson plot Bfac: 72.18 3397 reflections ( 95.47 % complete ) and 0 restraints for refining 2934 atoms. Observations/parameters ratio is 0.29 ------------------------------------------------------ Starting model: R = 0.3381 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2986 (Rfree = 0.000) for 2934 atoms. Found 14 (16 requested) and removed 32 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.51 3.51 Search for helices and strands: 0 residues in 0 chains, 2963 seeds are put forward Round 1: 106 peptides, 21 chains. Longest chain 8 peptides. Score 0.289 Round 2: 135 peptides, 24 chains. Longest chain 13 peptides. Score 0.369 Round 3: 137 peptides, 22 chains. Longest chain 15 peptides. Score 0.418 Round 4: 142 peptides, 24 chains. Longest chain 13 peptides. Score 0.401 Round 5: 144 peptides, 25 chains. Longest chain 15 peptides. Score 0.391 Taking the results from Round 3 Chains 23, Residues 115, Estimated correctness of the model 0.0 % 3 chains (17 residues) have been docked in sequence ------------------------------------------------------ 3397 reflections ( 95.47 % complete ) and 5593 restraints for refining 2394 atoms. 5100 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2527 (Rfree = 0.000) for 2394 atoms. Found 13 (13 requested) and removed 20 (6 requested) atoms. Cycle 2: After refmac, R = 0.2400 (Rfree = 0.000) for 2344 atoms. Found 8 (13 requested) and removed 13 (6 requested) atoms. Cycle 3: After refmac, R = 0.2244 (Rfree = 0.000) for 2316 atoms. Found 12 (12 requested) and removed 18 (6 requested) atoms. Cycle 4: After refmac, R = 0.2101 (Rfree = 0.000) for 2297 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 5: After refmac, R = 0.2065 (Rfree = 0.000) for 2277 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.61 3.61 Search for helices and strands: 0 residues in 0 chains, 2341 seeds are put forward Round 1: 128 peptides, 25 chains. Longest chain 9 peptides. Score 0.315 Round 2: 154 peptides, 24 chains. Longest chain 13 peptides. Score 0.454 Round 3: 162 peptides, 27 chains. Longest chain 13 peptides. Score 0.432 Round 4: 159 peptides, 24 chains. Longest chain 12 peptides. Score 0.475 Round 5: 167 peptides, 24 chains. Longest chain 15 peptides. Score 0.507 Taking the results from Round 5 Chains 24, Residues 143, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 3397 reflections ( 95.47 % complete ) and 5264 restraints for refining 2319 atoms. 4697 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2246 (Rfree = 0.000) for 2319 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. Cycle 7: After refmac, R = 0.2067 (Rfree = 0.000) for 2291 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 8: After refmac, R = 0.1863 (Rfree = 0.000) for 2267 atoms. Found 7 (12 requested) and removed 7 (6 requested) atoms. Cycle 9: After refmac, R = 0.1897 (Rfree = 0.000) for 2262 atoms. Found 10 (12 requested) and removed 9 (6 requested) atoms. Cycle 10: After refmac, R = 0.2161 (Rfree = 0.000) for 2259 atoms. Found 12 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.51 3.51 Search for helices and strands: 0 residues in 0 chains, 2349 seeds are put forward Round 1: 147 peptides, 28 chains. Longest chain 10 peptides. Score 0.345 Round 2: 156 peptides, 23 chains. Longest chain 14 peptides. Score 0.481 Round 3: 155 peptides, 24 chains. Longest chain 12 peptides. Score 0.458 Round 4: 155 peptides, 24 chains. Longest chain 13 peptides. Score 0.458 Round 5: 151 peptides, 23 chains. Longest chain 12 peptides. Score 0.460 Taking the results from Round 2 Chains 23, Residues 133, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3397 reflections ( 95.47 % complete ) and 5162 restraints for refining 2290 atoms. 4653 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2219 (Rfree = 0.000) for 2290 atoms. Found 11 (12 requested) and removed 11 (6 requested) atoms. Cycle 12: After refmac, R = 0.1979 (Rfree = 0.000) for 2274 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 13: After refmac, R = 0.1878 (Rfree = 0.000) for 2253 atoms. Found 10 (12 requested) and removed 10 (6 requested) atoms. Cycle 14: After refmac, R = 0.1917 (Rfree = 0.000) for 2239 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 15: After refmac, R = 0.1920 (Rfree = 0.000) for 2234 atoms. Found 11 (12 requested) and removed 11 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.52 3.52 Search for helices and strands: 0 residues in 0 chains, 2305 seeds are put forward Round 1: 129 peptides, 27 chains. Longest chain 8 peptides. Score 0.278 Round 2: 143 peptides, 24 chains. Longest chain 15 peptides. Score 0.406 Round 3: 151 peptides, 23 chains. Longest chain 17 peptides. Score 0.460 Round 4: 148 peptides, 22 chains. Longest chain 17 peptides. Score 0.466 Round 5: 154 peptides, 25 chains. Longest chain 17 peptides. Score 0.435 Taking the results from Round 4 Chains 23, Residues 126, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 3397 reflections ( 95.47 % complete ) and 5175 restraints for refining 2353 atoms. 4657 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1958 (Rfree = 0.000) for 2353 atoms. Found 12 (12 requested) and removed 22 (6 requested) atoms. Cycle 17: After refmac, R = 0.1917 (Rfree = 0.000) for 2319 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. Cycle 18: After refmac, R = 0.1777 (Rfree = 0.000) for 2307 atoms. Found 12 (12 requested) and removed 7 (6 requested) atoms. Cycle 19: After refmac, R = 0.1620 (Rfree = 0.000) for 2303 atoms. Found 8 (12 requested) and removed 7 (6 requested) atoms. Cycle 20: After refmac, R = 0.1661 (Rfree = 0.000) for 2299 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.43 3.43 Search for helices and strands: 0 residues in 0 chains, 2360 seeds are put forward Round 1: 122 peptides, 25 chains. Longest chain 10 peptides. Score 0.285 Round 2: 139 peptides, 26 chains. Longest chain 10 peptides. Score 0.348 Round 3: 153 peptides, 27 chains. Longest chain 13 peptides. Score 0.393 Round 4: 163 peptides, 29 chains. Longest chain 10 peptides. Score 0.399 Round 5: 144 peptides, 24 chains. Longest chain 14 peptides. Score 0.410 Taking the results from Round 5 Chains 24, Residues 120, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3397 reflections ( 95.47 % complete ) and 5510 restraints for refining 2394 atoms. 5054 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1990 (Rfree = 0.000) for 2394 atoms. Found 13 (13 requested) and removed 15 (6 requested) atoms. Cycle 22: After refmac, R = 0.1732 (Rfree = 0.000) for 2371 atoms. Found 12 (13 requested) and removed 11 (6 requested) atoms. Cycle 23: After refmac, R = 0.1798 (Rfree = 0.000) for 2356 atoms. Found 13 (13 requested) and removed 8 (6 requested) atoms. Cycle 24: After refmac, R = 0.1832 (Rfree = 0.000) for 2355 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 25: After refmac, R = 0.1648 (Rfree = 0.000) for 2345 atoms. Found 11 (12 requested) and removed 12 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.49 3.49 Search for helices and strands: 0 residues in 0 chains, 2407 seeds are put forward Round 1: 118 peptides, 25 chains. Longest chain 11 peptides. Score 0.264 Round 2: 126 peptides, 22 chains. Longest chain 11 peptides. Score 0.367 Round 3: 132 peptides, 23 chains. Longest chain 11 peptides. Score 0.375 Round 4: 138 peptides, 25 chains. Longest chain 11 peptides. Score 0.363 Round 5: 139 peptides, 23 chains. Longest chain 11 peptides. Score 0.407 Taking the results from Round 5 Chains 23, Residues 116, Estimated correctness of the model 0.0 % 2 chains (11 residues) have been docked in sequence ------------------------------------------------------ 3397 reflections ( 95.47 % complete ) and 5360 restraints for refining 2385 atoms. 4884 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1978 (Rfree = 0.000) for 2385 atoms. Found 9 (13 requested) and removed 18 (6 requested) atoms. Cycle 27: After refmac, R = 0.1811 (Rfree = 0.000) for 2358 atoms. Found 13 (13 requested) and removed 17 (6 requested) atoms. Cycle 28: After refmac, R = 0.1348 (Rfree = 0.000) for 2341 atoms. Found 5 (12 requested) and removed 13 (6 requested) atoms. Cycle 29: After refmac, R = 0.1268 (Rfree = 0.000) for 2329 atoms. Found 4 (12 requested) and removed 7 (6 requested) atoms. Cycle 30: After refmac, R = 0.1607 (Rfree = 0.000) for 2321 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.41 3.41 Search for helices and strands: 0 residues in 0 chains, 2384 seeds are put forward Round 1: 112 peptides, 25 chains. Longest chain 6 peptides. Score 0.233 Round 2: 130 peptides, 26 chains. Longest chain 8 peptides. Score 0.304 Round 3: 130 peptides, 26 chains. Longest chain 9 peptides. Score 0.304 Round 4: 140 peptides, 26 chains. Longest chain 9 peptides. Score 0.352 Round 5: 143 peptides, 24 chains. Longest chain 18 peptides. Score 0.406 Taking the results from Round 5 Chains 25, Residues 119, Estimated correctness of the model 0.0 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ 3397 reflections ( 95.47 % complete ) and 5417 restraints for refining 2395 atoms. 4908 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2008 (Rfree = 0.000) for 2395 atoms. Found 13 (13 requested) and removed 25 (6 requested) atoms. Cycle 32: After refmac, R = 0.1705 (Rfree = 0.000) for 2368 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. Cycle 33: After refmac, R = 0.1793 (Rfree = 0.000) for 2366 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. Cycle 34: After refmac, R = 0.1692 (Rfree = 0.000) for 2359 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. Cycle 35: After refmac, R = 0.1730 (Rfree = 0.000) for 2351 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.45 3.45 Search for helices and strands: 0 residues in 0 chains, 2403 seeds are put forward Round 1: 103 peptides, 22 chains. Longest chain 8 peptides. Score 0.251 Round 2: 117 peptides, 22 chains. Longest chain 10 peptides. Score 0.324 Round 3: 114 peptides, 21 chains. Longest chain 9 peptides. Score 0.330 Round 4: 119 peptides, 20 chains. Longest chain 10 peptides. Score 0.376 Round 5: 123 peptides, 21 chains. Longest chain 11 peptides. Score 0.374 Taking the results from Round 4 Chains 20, Residues 99, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3397 reflections ( 95.47 % complete ) and 5735 restraints for refining 2395 atoms. 5359 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1684 (Rfree = 0.000) for 2395 atoms. Found 12 (13 requested) and removed 14 (6 requested) atoms. Cycle 37: After refmac, R = 0.2012 (Rfree = 0.000) for 2383 atoms. Found 13 (13 requested) and removed 13 (6 requested) atoms. Cycle 38: After refmac, R = 0.1778 (Rfree = 0.000) for 2367 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. Cycle 39: After refmac, R = 0.1353 (Rfree = 0.000) for 2360 atoms. Found 8 (13 requested) and removed 11 (6 requested) atoms. Cycle 40: After refmac, R = 0.1235 (Rfree = 0.000) for 2351 atoms. Found 2 (12 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.47 3.47 Search for helices and strands: 0 residues in 0 chains, 2395 seeds are put forward Round 1: 89 peptides, 21 chains. Longest chain 7 peptides. Score 0.196 Round 2: 112 peptides, 23 chains. Longest chain 10 peptides. Score 0.277 Round 3: 125 peptides, 26 chains. Longest chain 8 peptides. Score 0.279 Round 4: 112 peptides, 24 chains. Longest chain 8 peptides. Score 0.255 Round 5: 115 peptides, 23 chains. Longest chain 10 peptides. Score 0.292 Taking the results from Round 5 Chains 23, Residues 92, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3397 reflections ( 95.47 % complete ) and 5609 restraints for refining 2376 atoms. 5264 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1743 (Rfree = 0.000) for 2376 atoms. Found 11 (13 requested) and removed 25 (6 requested) atoms. Cycle 42: After refmac, R = 0.1594 (Rfree = 0.000) for 2358 atoms. Found 9 (12 requested) and removed 11 (6 requested) atoms. Cycle 43: After refmac, R = 0.1722 (Rfree = 0.000) for 2352 atoms. Found 12 (12 requested) and removed 16 (6 requested) atoms. Cycle 44: After refmac, R = 0.1908 (Rfree = 0.000) for 2342 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 45: After refmac, R = 0.1360 (Rfree = 0.000) for 2334 atoms. Found 4 (12 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.42 3.42 Search for helices and strands: 0 residues in 0 chains, 2379 seeds are put forward Round 1: 117 peptides, 27 chains. Longest chain 6 peptides. Score 0.216 Round 2: 115 peptides, 25 chains. Longest chain 8 peptides. Score 0.249 Round 3: 128 peptides, 26 chains. Longest chain 7 peptides. Score 0.294 Round 4: 131 peptides, 25 chains. Longest chain 8 peptides. Score 0.330 Round 5: 121 peptides, 24 chains. Longest chain 9 peptides. Score 0.301 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 25, Residues 106, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence Sequence coverage is 5 % Consider running further cycles of model building using 2pn1-3_warpNtrace.pdb as input Building loops using Loopy2018 25 chains (106 residues) following loop building 2 chains (6 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3397 reflections ( 95.47 % complete ) and 5583 restraints for refining 2390 atoms. 5179 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1736 (Rfree = 0.000) for 2390 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.1552 (Rfree = 0.000) for 2381 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.1492 (Rfree = 0.000) for 2373 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.1476 (Rfree = 0.000) for 2366 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:13:58 GMT 2018 Job finished. TimeTaking 46.06 Used memory is bytes: 3912816