null 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 2ppv-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ppv-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ppv-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ppv-3.6-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/2ppv-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ppv-3.6-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/2ppv-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ppv-3.6-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 295 and 0 Target number of residues in the AU: 295 Target solvent content: 0.6881 Checking the provided sequence file Detected sequence length: 332 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 332 Adjusted target solvent content: 0.65 Input MTZ file: 2ppv-3.6-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: 20 Cell parameters: 133.390 136.620 56.180 90.000 90.000 90.000 Input sequence file: 2ppv-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 2656 target number of atoms Had to go as low as 0.90 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: 29.185 3.601 Wilson plot Bfac: 108.94 6210 reflections ( 99.36 % complete ) and 0 restraints for refining 2947 atoms. Observations/parameters ratio is 0.53 ------------------------------------------------------ Starting model: R = 0.3561 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3806 (Rfree = 0.000) for 2947 atoms. Found 18 (18 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.99 3.25 Search for helices and strands: 0 residues in 0 chains, 3008 seeds are put forward Round 1: 133 peptides, 23 chains. Longest chain 10 peptides. Score 0.332 Round 2: 176 peptides, 27 chains. Longest chain 14 peptides. Score 0.417 Round 3: 197 peptides, 25 chains. Longest chain 24 peptides. Score 0.506 Round 4: 207 peptides, 22 chains. Longest chain 22 peptides. Score 0.571 Round 5: 193 peptides, 23 chains. Longest chain 23 peptides. Score 0.521 Taking the results from Round 4 Chains 23, Residues 185, Estimated correctness of the model 2.9 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 6210 reflections ( 99.36 % complete ) and 5214 restraints for refining 2403 atoms. 4453 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2975 (Rfree = 0.000) for 2403 atoms. Found 15 (15 requested) and removed 16 (7 requested) atoms. Cycle 2: After refmac, R = 0.2745 (Rfree = 0.000) for 2326 atoms. Found 10 (15 requested) and removed 16 (7 requested) atoms. Cycle 3: After refmac, R = 0.2656 (Rfree = 0.000) for 2277 atoms. Found 14 (14 requested) and removed 14 (7 requested) atoms. Cycle 4: After refmac, R = 0.2526 (Rfree = 0.000) for 2249 atoms. Found 4 (14 requested) and removed 11 (7 requested) atoms. Cycle 5: After refmac, R = 0.2509 (Rfree = 0.000) for 2217 atoms. Found 13 (14 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.83 3.12 Search for helices and strands: 0 residues in 0 chains, 2306 seeds are put forward Round 1: 186 peptides, 26 chains. Longest chain 15 peptides. Score 0.461 Round 2: 212 peptides, 22 chains. Longest chain 20 peptides. Score 0.583 Round 3: 207 peptides, 25 chains. Longest chain 27 peptides. Score 0.534 Round 4: 199 peptides, 21 chains. Longest chain 21 peptides. Score 0.562 Round 5: 214 peptides, 24 chains. Longest chain 19 peptides. Score 0.564 Taking the results from Round 2 Chains 24, Residues 190, Estimated correctness of the model 7.8 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 6210 reflections ( 99.36 % complete ) and 4699 restraints for refining 2237 atoms. 3940 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3125 (Rfree = 0.000) for 2237 atoms. Found 14 (14 requested) and removed 21 (7 requested) atoms. Cycle 7: After refmac, R = 0.2885 (Rfree = 0.000) for 2186 atoms. Found 14 (14 requested) and removed 11 (7 requested) atoms. Cycle 8: After refmac, R = 0.2753 (Rfree = 0.000) for 2174 atoms. Found 14 (14 requested) and removed 12 (7 requested) atoms. Cycle 9: After refmac, R = 0.2791 (Rfree = 0.000) for 2161 atoms. Found 13 (13 requested) and removed 8 (6 requested) atoms. Cycle 10: After refmac, R = 0.2621 (Rfree = 0.000) for 2151 atoms. Found 11 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.88 3.16 Search for helices and strands: 0 residues in 0 chains, 2294 seeds are put forward Round 1: 192 peptides, 29 chains. Longest chain 17 peptides. Score 0.439 Round 2: 210 peptides, 25 chains. Longest chain 23 peptides. Score 0.542 Round 3: 208 peptides, 24 chains. Longest chain 23 peptides. Score 0.549 Round 4: 207 peptides, 23 chains. Longest chain 17 peptides. Score 0.558 Round 5: 203 peptides, 22 chains. Longest chain 18 peptides. Score 0.560 Taking the results from Round 5 Chains 24, Residues 181, Estimated correctness of the model 0.0 % 4 chains (43 residues) have been docked in sequence ------------------------------------------------------ 6210 reflections ( 99.36 % complete ) and 4875 restraints for refining 2406 atoms. 4032 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3119 (Rfree = 0.000) for 2406 atoms. Found 15 (15 requested) and removed 19 (7 requested) atoms. Cycle 12: After refmac, R = 0.2862 (Rfree = 0.000) for 2360 atoms. Found 12 (15 requested) and removed 23 (7 requested) atoms. Cycle 13: After refmac, R = 0.2865 (Rfree = 0.000) for 2319 atoms. Found 14 (15 requested) and removed 15 (7 requested) atoms. Cycle 14: After refmac, R = 0.2695 (Rfree = 0.000) for 2302 atoms. Found 11 (14 requested) and removed 10 (7 requested) atoms. Cycle 15: After refmac, R = 0.2880 (Rfree = 0.000) for 2279 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.92 3.19 Search for helices and strands: 0 residues in 0 chains, 2389 seeds are put forward Round 1: 173 peptides, 28 chains. Longest chain 13 peptides. Score 0.393 Round 2: 193 peptides, 24 chains. Longest chain 27 peptides. Score 0.508 Round 3: 202 peptides, 25 chains. Longest chain 21 peptides. Score 0.520 Round 4: 206 peptides, 24 chains. Longest chain 23 peptides. Score 0.544 Round 5: 208 peptides, 26 chains. Longest chain 20 peptides. Score 0.524 Taking the results from Round 4 Chains 26, Residues 182, Estimated correctness of the model 0.0 % 2 chains (25 residues) have been docked in sequence ------------------------------------------------------ 6210 reflections ( 99.36 % complete ) and 5141 restraints for refining 2408 atoms. 4362 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3065 (Rfree = 0.000) for 2408 atoms. Found 15 (15 requested) and removed 23 (7 requested) atoms. Cycle 17: After refmac, R = 0.2566 (Rfree = 0.000) for 2355 atoms. Found 12 (15 requested) and removed 14 (7 requested) atoms. Cycle 18: After refmac, R = 0.2557 (Rfree = 0.000) for 2340 atoms. Found 4 (15 requested) and removed 13 (7 requested) atoms. Cycle 19: After refmac, R = 0.2381 (Rfree = 0.000) for 2323 atoms. Found 5 (14 requested) and removed 10 (7 requested) atoms. Cycle 20: After refmac, R = 0.2478 (Rfree = 0.000) for 2308 atoms. Found 11 (14 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.88 3.16 Search for helices and strands: 0 residues in 0 chains, 2453 seeds are put forward Round 1: 172 peptides, 24 chains. Longest chain 16 peptides. Score 0.446 Round 2: 185 peptides, 22 chains. Longest chain 25 peptides. Score 0.512 Round 3: 188 peptides, 22 chains. Longest chain 22 peptides. Score 0.520 Round 4: 187 peptides, 20 chains. Longest chain 24 peptides. Score 0.543 Round 5: 196 peptides, 23 chains. Longest chain 22 peptides. Score 0.529 Taking the results from Round 4 Chains 21, Residues 167, Estimated correctness of the model 0.0 % 1 chains (22 residues) have been docked in sequence ------------------------------------------------------ 6210 reflections ( 99.36 % complete ) and 5273 restraints for refining 2408 atoms. 4530 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2823 (Rfree = 0.000) for 2408 atoms. Found 15 (15 requested) and removed 11 (7 requested) atoms. Cycle 22: After refmac, R = 0.2526 (Rfree = 0.000) for 2388 atoms. Found 12 (15 requested) and removed 13 (7 requested) atoms. Cycle 23: After refmac, R = 0.2467 (Rfree = 0.000) for 2371 atoms. Found 10 (15 requested) and removed 13 (7 requested) atoms. Cycle 24: After refmac, R = 0.2653 (Rfree = 0.000) for 2358 atoms. Found 15 (15 requested) and removed 20 (7 requested) atoms. Cycle 25: After refmac, R = 0.2331 (Rfree = 0.000) for 2333 atoms. Found 7 (15 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.83 3.12 Search for helices and strands: 0 residues in 0 chains, 2424 seeds are put forward Round 1: 176 peptides, 24 chains. Longest chain 16 peptides. Score 0.458 Round 2: 191 peptides, 19 chains. Longest chain 24 peptides. Score 0.566 Round 3: 196 peptides, 22 chains. Longest chain 25 peptides. Score 0.542 Round 4: 194 peptides, 22 chains. Longest chain 24 peptides. Score 0.536 Round 5: 194 peptides, 22 chains. Longest chain 30 peptides. Score 0.536 Taking the results from Round 2 Chains 19, Residues 172, Estimated correctness of the model 0.8 % 1 chains (21 residues) have been docked in sequence ------------------------------------------------------ 6210 reflections ( 99.36 % complete ) and 5155 restraints for refining 2408 atoms. 4402 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2639 (Rfree = 0.000) for 2408 atoms. Found 14 (15 requested) and removed 17 (7 requested) atoms. Cycle 27: After refmac, R = 0.2441 (Rfree = 0.000) for 2387 atoms. Found 7 (15 requested) and removed 8 (7 requested) atoms. Cycle 28: After refmac, R = 0.2340 (Rfree = 0.000) for 2377 atoms. Found 5 (15 requested) and removed 10 (7 requested) atoms. Cycle 29: After refmac, R = 0.2299 (Rfree = 0.000) for 2363 atoms. Found 6 (15 requested) and removed 11 (7 requested) atoms. Cycle 30: After refmac, R = 0.2488 (Rfree = 0.000) for 2350 atoms. Found 15 (15 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.83 3.12 Search for helices and strands: 0 residues in 0 chains, 2431 seeds are put forward Round 1: 177 peptides, 26 chains. Longest chain 14 peptides. Score 0.434 Round 2: 199 peptides, 25 chains. Longest chain 22 peptides. Score 0.512 Round 3: 198 peptides, 22 chains. Longest chain 23 peptides. Score 0.547 Round 4: 195 peptides, 22 chains. Longest chain 24 peptides. Score 0.539 Round 5: 195 peptides, 18 chains. Longest chain 28 peptides. Score 0.589 Taking the results from Round 5 Chains 19, Residues 177, Estimated correctness of the model 10.2 % 2 chains (41 residues) have been docked in sequence ------------------------------------------------------ 6210 reflections ( 99.36 % complete ) and 4926 restraints for refining 2407 atoms. 4069 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2701 (Rfree = 0.000) for 2407 atoms. Found 15 (15 requested) and removed 18 (7 requested) atoms. Cycle 32: After refmac, R = 0.2404 (Rfree = 0.000) for 2387 atoms. Found 10 (15 requested) and removed 13 (7 requested) atoms. Cycle 33: After refmac, R = 0.2499 (Rfree = 0.000) for 2374 atoms. Found 13 (15 requested) and removed 14 (7 requested) atoms. Cycle 34: After refmac, R = 0.2638 (Rfree = 0.000) for 2365 atoms. Found 15 (15 requested) and removed 14 (7 requested) atoms. Cycle 35: After refmac, R = 0.2330 (Rfree = 0.000) for 2357 atoms. Found 9 (15 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.78 3.08 Search for helices and strands: 0 residues in 0 chains, 2426 seeds are put forward Round 1: 156 peptides, 26 chains. Longest chain 20 peptides. Score 0.366 Round 2: 183 peptides, 23 chains. Longest chain 20 peptides. Score 0.493 Round 3: 188 peptides, 26 chains. Longest chain 15 peptides. Score 0.467 Round 4: 200 peptides, 27 chains. Longest chain 15 peptides. Score 0.489 Round 5: 196 peptides, 27 chains. Longest chain 16 peptides. Score 0.477 Taking the results from Round 2 Chains 23, Residues 160, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6210 reflections ( 99.36 % complete ) and 5347 restraints for refining 2407 atoms. 4730 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2545 (Rfree = 0.000) for 2407 atoms. Found 15 (15 requested) and removed 16 (7 requested) atoms. Cycle 37: After refmac, R = 0.2496 (Rfree = 0.000) for 2394 atoms. Found 15 (15 requested) and removed 11 (7 requested) atoms. Cycle 38: After refmac, R = 0.2353 (Rfree = 0.000) for 2384 atoms. Found 8 (15 requested) and removed 11 (7 requested) atoms. Cycle 39: After refmac, R = 0.2558 (Rfree = 0.000) for 2376 atoms. Found 15 (15 requested) and removed 9 (7 requested) atoms. Cycle 40: After refmac, R = 0.2376 (Rfree = 0.000) for 2372 atoms. Found 8 (15 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.80 3.09 Search for helices and strands: 0 residues in 0 chains, 2458 seeds are put forward Round 1: 150 peptides, 30 chains. Longest chain 10 peptides. Score 0.284 Round 2: 187 peptides, 29 chains. Longest chain 13 peptides. Score 0.423 Round 3: 173 peptides, 24 chains. Longest chain 21 peptides. Score 0.449 Round 4: 170 peptides, 25 chains. Longest chain 12 peptides. Score 0.426 Round 5: 179 peptides, 23 chains. Longest chain 25 peptides. Score 0.481 Taking the results from Round 5 Chains 24, Residues 156, Estimated correctness of the model 0.0 % 1 chains (17 residues) have been docked in sequence ------------------------------------------------------ 6210 reflections ( 99.36 % complete ) and 5213 restraints for refining 2408 atoms. 4555 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2500 (Rfree = 0.000) for 2408 atoms. Found 15 (15 requested) and removed 11 (7 requested) atoms. Cycle 42: After refmac, R = 0.2343 (Rfree = 0.000) for 2393 atoms. Found 10 (15 requested) and removed 7 (7 requested) atoms. Cycle 43: After refmac, R = 0.2254 (Rfree = 0.000) for 2384 atoms. Found 5 (15 requested) and removed 8 (7 requested) atoms. Cycle 44: After refmac, R = 0.2435 (Rfree = 0.000) for 2377 atoms. Found 15 (15 requested) and removed 12 (7 requested) atoms. Cycle 45: After refmac, R = 0.2135 (Rfree = 0.000) for 2365 atoms. Found 9 (15 requested) and removed 15 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.82 3.11 Search for helices and strands: 0 residues in 0 chains, 2475 seeds are put forward Round 1: 136 peptides, 27 chains. Longest chain 9 peptides. Score 0.279 Round 2: 179 peptides, 26 chains. Longest chain 27 peptides. Score 0.440 Round 3: 171 peptides, 21 chains. Longest chain 24 peptides. Score 0.485 Round 4: 176 peptides, 22 chains. Longest chain 27 peptides. Score 0.486 Round 5: 177 peptides, 20 chains. Longest chain 15 peptides. Score 0.516 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 20, Residues 157, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2ppv-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6210 reflections ( 99.36 % complete ) and 5255 restraints for refining 2408 atoms. 4647 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2472 (Rfree = 0.000) for 2408 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.2916 (Rfree = 0.000) for 2375 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.2753 (Rfree = 0.000) for 2347 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.2457 (Rfree = 0.000) for 2330 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:17:52 GMT 2018 Job finished. TimeTaking 49.92 Used memory is bytes: 4551088