null Sun 23 Dec 22:22:46 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 2aj7-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2aj7-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2aj7-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2aj7-4.0-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/2aj7-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2aj7-4.0-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 ============================================================ Sun 23 Dec 22:22:56 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/2aj7-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2aj7-4.0-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 357 and 0 Target number of residues in the AU: 357 Target solvent content: 0.6586 Checking the provided sequence file Detected sequence length: 163 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 326 Adjusted target solvent content: 0.69 Input MTZ file: 2aj7-4.0-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: 173 Cell parameters: 108.801 108.801 82.811 90.000 90.000 120.000 Input sequence file: 2aj7-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 2608 target number of atoms Had to go as low as 1.15 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 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: 94.224 4.000 Wilson plot Bfac: 83.62 4804 reflections ( 99.90 % complete ) and 0 restraints for refining 2922 atoms. Observations/parameters ratio is 0.41 ------------------------------------------------------ Starting model: R = 0.3433 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2558 (Rfree = 0.000) for 2922 atoms. Found 13 (13 requested) and removed 22 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.76 2.88 Search for helices and strands: 0 residues in 0 chains, 2943 seeds are put forward NCS extension: 0 residues added, 2943 seeds are put forward Round 1: 174 peptides, 31 chains. Longest chain 11 peptides. Score 0.340 Round 2: 213 peptides, 25 chains. Longest chain 17 peptides. Score 0.525 Round 3: 217 peptides, 24 chains. Longest chain 19 peptides. Score 0.546 Round 4: 219 peptides, 23 chains. Longest chain 20 peptides. Score 0.562 Round 5: 217 peptides, 22 chains. Longest chain 18 peptides. Score 0.569 Taking the results from Round 5 Chains 24, Residues 195, Estimated correctness of the model 0.0 % 2 chains (21 residues) have been docked in sequence ------------------------------------------------------ 4804 reflections ( 99.90 % complete ) and 5099 restraints for refining 2352 atoms. 4275 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2848 (Rfree = 0.000) for 2352 atoms. Found 11 (11 requested) and removed 15 (5 requested) atoms. Cycle 2: After refmac, R = 0.2676 (Rfree = 0.000) for 2342 atoms. Found 8 (11 requested) and removed 8 (5 requested) atoms. Cycle 3: After refmac, R = 0.2543 (Rfree = 0.000) for 2329 atoms. Found 1 (11 requested) and removed 9 (5 requested) atoms. Cycle 4: After refmac, R = 0.2527 (Rfree = 0.000) for 2310 atoms. Found 1 (11 requested) and removed 25 (5 requested) atoms. Cycle 5: After refmac, R = 0.2446 (Rfree = 0.000) for 2278 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.75 2.87 Search for helices and strands: 0 residues in 0 chains, 2346 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 2358 seeds are put forward Round 1: 218 peptides, 28 chains. Longest chain 19 peptides. Score 0.503 Round 2: 219 peptides, 24 chains. Longest chain 25 peptides. Score 0.551 Round 3: 226 peptides, 23 chains. Longest chain 23 peptides. Score 0.579 Round 4: 209 peptides, 22 chains. Longest chain 21 peptides. Score 0.550 Round 5: 210 peptides, 22 chains. Longest chain 20 peptides. Score 0.552 Taking the results from Round 3 Chains 23, Residues 203, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4804 reflections ( 99.90 % complete ) and 5200 restraints for refining 2355 atoms. 4411 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2885 (Rfree = 0.000) for 2355 atoms. Found 11 (11 requested) and removed 17 (5 requested) atoms. Cycle 7: After refmac, R = 0.2741 (Rfree = 0.000) for 2336 atoms. Found 4 (11 requested) and removed 9 (5 requested) atoms. Cycle 8: After refmac, R = 0.2591 (Rfree = 0.000) for 2326 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 9: After refmac, R = 0.2436 (Rfree = 0.000) for 2324 atoms. Found 7 (11 requested) and removed 21 (5 requested) atoms. Cycle 10: After refmac, R = 0.2388 (Rfree = 0.000) for 2306 atoms. Found 3 (10 requested) and removed 12 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.77 2.89 Search for helices and strands: 0 residues in 0 chains, 2357 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 2380 seeds are put forward Round 1: 213 peptides, 26 chains. Longest chain 18 peptides. Score 0.513 Round 2: 217 peptides, 22 chains. Longest chain 23 peptides. Score 0.569 Round 3: 214 peptides, 22 chains. Longest chain 21 peptides. Score 0.562 Round 4: 211 peptides, 22 chains. Longest chain 20 peptides. Score 0.555 Round 5: 228 peptides, 24 chains. Longest chain 23 peptides. Score 0.572 Taking the results from Round 5 Chains 24, Residues 204, Estimated correctness of the model 0.0 % 1 chains (22 residues) have been docked in sequence ------------------------------------------------------ 4804 reflections ( 99.90 % complete ) and 4919 restraints for refining 2355 atoms. 4034 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3045 (Rfree = 0.000) for 2355 atoms. Found 11 (11 requested) and removed 14 (5 requested) atoms. Cycle 12: After refmac, R = 0.2846 (Rfree = 0.000) for 2322 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 13: After refmac, R = 0.2762 (Rfree = 0.000) for 2315 atoms. Found 4 (11 requested) and removed 21 (5 requested) atoms. Cycle 14: After refmac, R = 0.2716 (Rfree = 0.000) for 2292 atoms. Found 2 (10 requested) and removed 11 (5 requested) atoms. Cycle 15: After refmac, R = 0.2640 (Rfree = 0.000) for 2275 atoms. Found 2 (10 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.77 2.89 Search for helices and strands: 0 residues in 0 chains, 2339 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 2364 seeds are put forward Round 1: 205 peptides, 27 chains. Longest chain 20 peptides. Score 0.481 Round 2: 217 peptides, 23 chains. Longest chain 22 peptides. Score 0.558 Round 3: 218 peptides, 22 chains. Longest chain 31 peptides. Score 0.571 Round 4: 224 peptides, 20 chains. Longest chain 32 peptides. Score 0.606 Round 5: 215 peptides, 20 chains. Longest chain 29 peptides. Score 0.586 Taking the results from Round 4 Chains 24, Residues 204, Estimated correctness of the model 0.0 % 2 chains (26 residues) have been docked in sequence ------------------------------------------------------ 4804 reflections ( 99.90 % complete ) and 4982 restraints for refining 2355 atoms. 4094 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3058 (Rfree = 0.000) for 2355 atoms. Found 7 (11 requested) and removed 7 (5 requested) atoms. Cycle 17: After refmac, R = 0.2709 (Rfree = 0.000) for 2345 atoms. Found 4 (11 requested) and removed 7 (5 requested) atoms. Cycle 18: After refmac, R = 0.2643 (Rfree = 0.000) for 2322 atoms. Found 4 (11 requested) and removed 10 (5 requested) atoms. Cycle 19: After refmac, R = 0.2546 (Rfree = 0.000) for 2309 atoms. Found 4 (11 requested) and removed 5 (5 requested) atoms. Cycle 20: After refmac, R = 0.2546 (Rfree = 0.000) for 2305 atoms. Found 2 (10 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.78 2.90 Search for helices and strands: 0 residues in 0 chains, 2350 seeds are put forward NCS extension: 39 residues added (3 deleted due to clashes), 2389 seeds are put forward Round 1: 192 peptides, 28 chains. Longest chain 16 peptides. Score 0.433 Round 2: 219 peptides, 25 chains. Longest chain 29 peptides. Score 0.540 Round 3: 217 peptides, 24 chains. Longest chain 24 peptides. Score 0.546 Round 4: 207 peptides, 24 chains. Longest chain 21 peptides. Score 0.522 Round 5: 210 peptides, 19 chains. Longest chain 22 peptides. Score 0.586 Taking the results from Round 5 Chains 19, Residues 191, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4804 reflections ( 99.90 % complete ) and 5310 restraints for refining 2354 atoms. 4565 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2733 (Rfree = 0.000) for 2354 atoms. Found 11 (11 requested) and removed 5 (5 requested) atoms. Cycle 22: After refmac, R = 0.2567 (Rfree = 0.000) for 2349 atoms. Found 2 (11 requested) and removed 9 (5 requested) atoms. Cycle 23: After refmac, R = 0.2567 (Rfree = 0.000) for 2324 atoms. Found 4 (11 requested) and removed 11 (5 requested) atoms. Cycle 24: After refmac, R = 0.2434 (Rfree = 0.000) for 2309 atoms. Found 1 (11 requested) and removed 6 (5 requested) atoms. Cycle 25: After refmac, R = 0.2436 (Rfree = 0.000) for 2287 atoms. Found 1 (10 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.78 2.90 Search for helices and strands: 0 residues in 0 chains, 2333 seeds are put forward NCS extension: 22 residues added (3 deleted due to clashes), 2355 seeds are put forward Round 1: 178 peptides, 27 chains. Longest chain 13 peptides. Score 0.406 Round 2: 207 peptides, 25 chains. Longest chain 19 peptides. Score 0.510 Round 3: 208 peptides, 26 chains. Longest chain 19 peptides. Score 0.501 Round 4: 214 peptides, 23 chains. Longest chain 30 peptides. Score 0.550 Round 5: 214 peptides, 24 chains. Longest chain 28 peptides. Score 0.539 Taking the results from Round 4 Chains 23, Residues 191, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4804 reflections ( 99.90 % complete ) and 5268 restraints for refining 2355 atoms. 4527 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2784 (Rfree = 0.000) for 2355 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 27: After refmac, R = 0.2582 (Rfree = 0.000) for 2345 atoms. Found 5 (11 requested) and removed 8 (5 requested) atoms. Cycle 28: After refmac, R = 0.2537 (Rfree = 0.000) for 2337 atoms. Found 3 (11 requested) and removed 13 (5 requested) atoms. Cycle 29: After refmac, R = 0.2434 (Rfree = 0.000) for 2319 atoms. Found 3 (11 requested) and removed 10 (5 requested) atoms. Cycle 30: After refmac, R = 0.2462 (Rfree = 0.000) for 2306 atoms. Found 2 (10 requested) and removed 12 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.93 3.01 Search for helices and strands: 0 residues in 0 chains, 2340 seeds are put forward NCS extension: 52 residues added (2 deleted due to clashes), 2392 seeds are put forward Round 1: 168 peptides, 29 chains. Longest chain 12 peptides. Score 0.348 Round 2: 191 peptides, 26 chains. Longest chain 13 peptides. Score 0.455 Round 3: 194 peptides, 26 chains. Longest chain 14 peptides. Score 0.464 Round 4: 200 peptides, 25 chains. Longest chain 16 peptides. Score 0.492 Round 5: 207 peptides, 26 chains. Longest chain 21 peptides. Score 0.498 Taking the results from Round 5 Chains 27, Residues 181, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 4804 reflections ( 99.90 % complete ) and 5150 restraints for refining 2353 atoms. 4407 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3188 (Rfree = 0.000) for 2353 atoms. Found 11 (11 requested) and removed 5 (5 requested) atoms. Cycle 32: After refmac, R = 0.2834 (Rfree = 0.000) for 2343 atoms. Found 10 (11 requested) and removed 7 (5 requested) atoms. Cycle 33: After refmac, R = 0.3031 (Rfree = 0.000) for 2334 atoms. Found 11 (11 requested) and removed 33 (5 requested) atoms. Cycle 34: After refmac, R = 0.2743 (Rfree = 0.000) for 2303 atoms. Found 6 (10 requested) and removed 33 (5 requested) atoms. Cycle 35: After refmac, R = 0.2605 (Rfree = 0.000) for 2270 atoms. Found 8 (10 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.84 2.94 Search for helices and strands: 0 residues in 0 chains, 2321 seeds are put forward NCS extension: 37 residues added (0 deleted due to clashes), 2358 seeds are put forward Round 1: 190 peptides, 29 chains. Longest chain 23 peptides. Score 0.414 Round 2: 200 peptides, 26 chains. Longest chain 23 peptides. Score 0.480 Round 3: 198 peptides, 28 chains. Longest chain 22 peptides. Score 0.450 Round 4: 187 peptides, 25 chains. Longest chain 14 peptides. Score 0.457 Round 5: 192 peptides, 23 chains. Longest chain 20 peptides. Score 0.495 Taking the results from Round 5 Chains 23, Residues 169, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4804 reflections ( 99.90 % complete ) and 5290 restraints for refining 2355 atoms. 4637 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2899 (Rfree = 0.000) for 2355 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 37: After refmac, R = 0.2916 (Rfree = 0.000) for 2353 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 38: After refmac, R = 0.2715 (Rfree = 0.000) for 2347 atoms. Found 11 (11 requested) and removed 7 (5 requested) atoms. Cycle 39: After refmac, R = 0.2649 (Rfree = 0.000) for 2335 atoms. Found 2 (11 requested) and removed 8 (5 requested) atoms. Cycle 40: After refmac, R = 0.2619 (Rfree = 0.000) for 2320 atoms. Found 6 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.85 2.95 Search for helices and strands: 0 residues in 0 chains, 2369 seeds are put forward NCS extension: 22 residues added (4 deleted due to clashes), 2391 seeds are put forward Round 1: 177 peptides, 30 chains. Longest chain 15 peptides. Score 0.363 Round 2: 173 peptides, 19 chains. Longest chain 26 peptides. Score 0.495 Round 3: 185 peptides, 25 chains. Longest chain 18 peptides. Score 0.452 Round 4: 175 peptides, 22 chains. Longest chain 21 peptides. Score 0.462 Round 5: 174 peptides, 24 chains. Longest chain 21 peptides. Score 0.433 Taking the results from Round 2 Chains 19, Residues 154, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4804 reflections ( 99.90 % complete ) and 5424 restraints for refining 2355 atoms. 4827 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2732 (Rfree = 0.000) for 2355 atoms. Found 11 (11 requested) and removed 14 (5 requested) atoms. Cycle 42: After refmac, R = 0.2665 (Rfree = 0.000) for 2346 atoms. Found 6 (11 requested) and removed 8 (5 requested) atoms. Cycle 43: After refmac, R = 0.2601 (Rfree = 0.000) for 2340 atoms. Found 5 (11 requested) and removed 9 (5 requested) atoms. Cycle 44: After refmac, R = 0.2468 (Rfree = 0.000) for 2327 atoms. Found 3 (11 requested) and removed 6 (5 requested) atoms. Cycle 45: After refmac, R = 0.2409 (Rfree = 0.000) for 2318 atoms. Found 2 (11 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.86 2.96 Search for helices and strands: 0 residues in 0 chains, 2361 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 2373 seeds are put forward Round 1: 165 peptides, 30 chains. Longest chain 16 peptides. Score 0.325 Round 2: 192 peptides, 27 chains. Longest chain 20 peptides. Score 0.446 Round 3: 185 peptides, 24 chains. Longest chain 16 peptides. Score 0.464 Round 4: 197 peptides, 23 chains. Longest chain 20 peptides. Score 0.508 Round 5: 193 peptides, 25 chains. Longest chain 23 peptides. Score 0.473 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 24, Residues 174, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 2aj7-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4804 reflections ( 99.90 % complete ) and 5192 restraints for refining 2355 atoms. 4474 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2809 (Rfree = 0.000) for 2355 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.2634 (Rfree = 0.000) for 2327 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.2594 (Rfree = 0.000) for 2311 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.2551 (Rfree = 0.000) for 2295 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:17:51 GMT 2018 Job finished. TimeTaking 55.08 Used memory is bytes: 10390592