Mon 24 Dec 07:29:25 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2nuj-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2nuj-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2nuj-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2nuj-3.8-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2nuj-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2nuj-3.8-parrot-noncs ############### 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 ============================================================ Mon 24 Dec 07:29:29 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/noncs/ArpWArp/wArpResults/WorkingDir/2nuj-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2nuj-3.8-parrot-noncs/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 312 and 0 Target number of residues in the AU: 312 Target solvent content: 0.6372 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: 0.62 Input MTZ file: 2nuj-3.8-parrot-noncs.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: 91 Cell parameters: 78.401 78.401 151.418 90.000 90.000 90.000 Input sequence file: 2nuj-3.8-parrot-noncs.fasta_lf Building free atoms model in initial map for 2608 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 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: 78.401 3.800 Wilson plot Bfac: 70.25 4938 reflections ( 97.42 % complete ) and 0 restraints for refining 2873 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Starting model: R = 0.3673 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3255 (Rfree = 0.000) for 2873 atoms. Found 15 (15 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.52 2.99 Search for helices and strands: 0 residues in 0 chains, 2908 seeds are put forward NCS extension: 0 residues added, 2908 seeds are put forward Round 1: 137 peptides, 29 chains. Longest chain 8 peptides. Score 0.257 Round 2: 175 peptides, 30 chains. Longest chain 12 peptides. Score 0.385 Round 3: 178 peptides, 27 chains. Longest chain 12 peptides. Score 0.441 Round 4: 169 peptides, 24 chains. Longest chain 23 peptides. Score 0.455 Round 5: 179 peptides, 26 chains. Longest chain 16 peptides. Score 0.459 Taking the results from Round 5 Chains 26, Residues 153, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 4938 reflections ( 97.42 % complete ) and 5137 restraints for refining 2357 atoms. 4532 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2869 (Rfree = 0.000) for 2357 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 2: After refmac, R = 0.2725 (Rfree = 0.000) for 2334 atoms. Found 6 (12 requested) and removed 8 (6 requested) atoms. Cycle 3: After refmac, R = 0.2655 (Rfree = 0.000) for 2322 atoms. Found 3 (12 requested) and removed 7 (6 requested) atoms. Cycle 4: After refmac, R = 0.2606 (Rfree = 0.000) for 2313 atoms. Found 3 (12 requested) and removed 7 (6 requested) atoms. Cycle 5: After refmac, R = 0.2557 (Rfree = 0.000) for 2305 atoms. Found 1 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.53 3.00 Search for helices and strands: 0 residues in 0 chains, 2345 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 2369 seeds are put forward Round 1: 155 peptides, 27 chains. Longest chain 12 peptides. Score 0.360 Round 2: 162 peptides, 25 chains. Longest chain 17 peptides. Score 0.416 Round 3: 163 peptides, 24 chains. Longest chain 22 peptides. Score 0.435 Round 4: 170 peptides, 26 chains. Longest chain 16 peptides. Score 0.429 Round 5: 173 peptides, 27 chains. Longest chain 20 peptides. Score 0.424 Taking the results from Round 3 Chains 24, Residues 139, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 4938 reflections ( 97.42 % complete ) and 5309 restraints for refining 2359 atoms. 4763 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2610 (Rfree = 0.000) for 2359 atoms. Found 9 (12 requested) and removed 8 (6 requested) atoms. Cycle 7: After refmac, R = 0.2478 (Rfree = 0.000) for 2346 atoms. Found 4 (12 requested) and removed 9 (6 requested) atoms. Cycle 8: After refmac, R = 0.2455 (Rfree = 0.000) for 2335 atoms. Found 2 (12 requested) and removed 6 (6 requested) atoms. Cycle 9: After refmac, R = 0.2433 (Rfree = 0.000) for 2329 atoms. Found 1 (12 requested) and removed 6 (6 requested) atoms. Cycle 10: After refmac, R = 0.2399 (Rfree = 0.000) for 2322 atoms. Found 1 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.51 2.98 Search for helices and strands: 0 residues in 0 chains, 2339 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 2355 seeds are put forward Round 1: 169 peptides, 30 chains. Longest chain 14 peptides. Score 0.363 Round 2: 188 peptides, 30 chains. Longest chain 16 peptides. Score 0.430 Round 3: 190 peptides, 30 chains. Longest chain 16 peptides. Score 0.436 Round 4: 166 peptides, 24 chains. Longest chain 17 peptides. Score 0.445 Round 5: 170 peptides, 27 chains. Longest chain 16 peptides. Score 0.413 Taking the results from Round 4 Chains 25, Residues 142, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4938 reflections ( 97.42 % complete ) and 5275 restraints for refining 2359 atoms. 4700 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2625 (Rfree = 0.000) for 2359 atoms. Found 8 (12 requested) and removed 8 (6 requested) atoms. Cycle 12: After refmac, R = 0.2511 (Rfree = 0.000) for 2347 atoms. Found 3 (12 requested) and removed 6 (6 requested) atoms. Cycle 13: After refmac, R = 0.2485 (Rfree = 0.000) for 2341 atoms. Found 5 (12 requested) and removed 7 (6 requested) atoms. Cycle 14: After refmac, R = 0.2381 (Rfree = 0.000) for 2333 atoms. Found 1 (12 requested) and removed 7 (6 requested) atoms. Cycle 15: After refmac, R = 0.2401 (Rfree = 0.000) for 2324 atoms. Found 3 (12 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.57 3.03 Search for helices and strands: 0 residues in 0 chains, 2352 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 2373 seeds are put forward Round 1: 148 peptides, 26 chains. Longest chain 12 peptides. Score 0.350 Round 2: 167 peptides, 26 chains. Longest chain 12 peptides. Score 0.418 Round 3: 176 peptides, 29 chains. Longest chain 18 peptides. Score 0.404 Round 4: 178 peptides, 28 chains. Longest chain 11 peptides. Score 0.426 Round 5: 168 peptides, 28 chains. Longest chain 11 peptides. Score 0.391 Taking the results from Round 4 Chains 28, Residues 150, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4938 reflections ( 97.42 % complete ) and 5434 restraints for refining 2359 atoms. 4862 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2590 (Rfree = 0.000) for 2359 atoms. Found 8 (12 requested) and removed 7 (6 requested) atoms. Cycle 17: After refmac, R = 0.2389 (Rfree = 0.000) for 2354 atoms. Found 2 (12 requested) and removed 7 (6 requested) atoms. Cycle 18: After refmac, R = 0.2304 (Rfree = 0.000) for 2344 atoms. Found 2 (12 requested) and removed 7 (6 requested) atoms. Cycle 19: After refmac, R = 0.2362 (Rfree = 0.000) for 2336 atoms. Found 3 (12 requested) and removed 7 (6 requested) atoms. Cycle 20: After refmac, R = 0.2346 (Rfree = 0.000) for 2330 atoms. Found 11 (12 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.51 2.98 Search for helices and strands: 0 residues in 0 chains, 2377 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 2390 seeds are put forward Round 1: 169 peptides, 35 chains. Longest chain 7 peptides. Score 0.284 Round 2: 164 peptides, 30 chains. Longest chain 12 peptides. Score 0.345 Round 3: 179 peptides, 31 chains. Longest chain 14 peptides. Score 0.384 Round 4: 174 peptides, 29 chains. Longest chain 12 peptides. Score 0.397 Round 5: 178 peptides, 25 chains. Longest chain 25 peptides. Score 0.470 Taking the results from Round 5 Chains 25, Residues 153, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4938 reflections ( 97.42 % complete ) and 5414 restraints for refining 2359 atoms. 4827 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2547 (Rfree = 0.000) for 2359 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 22: After refmac, R = 0.2414 (Rfree = 0.000) for 2351 atoms. Found 7 (12 requested) and removed 6 (6 requested) atoms. Cycle 23: After refmac, R = 0.2322 (Rfree = 0.000) for 2342 atoms. Found 6 (12 requested) and removed 7 (6 requested) atoms. Cycle 24: After refmac, R = 0.2273 (Rfree = 0.000) for 2337 atoms. Found 1 (12 requested) and removed 7 (6 requested) atoms. Cycle 25: After refmac, R = 0.2231 (Rfree = 0.000) for 2328 atoms. Found 2 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.53 3.00 Search for helices and strands: 0 residues in 0 chains, 2363 seeds are put forward NCS extension: 28 residues added (2 deleted due to clashes), 2391 seeds are put forward Round 1: 157 peptides, 30 chains. Longest chain 11 peptides. Score 0.319 Round 2: 166 peptides, 29 chains. Longest chain 21 peptides. Score 0.368 Round 3: 163 peptides, 30 chains. Longest chain 9 peptides. Score 0.341 Round 4: 165 peptides, 29 chains. Longest chain 12 peptides. Score 0.364 Round 5: 173 peptides, 32 chains. Longest chain 9 peptides. Score 0.347 Taking the results from Round 2 Chains 31, Residues 137, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 4938 reflections ( 97.42 % complete ) and 5234 restraints for refining 2357 atoms. 4681 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2533 (Rfree = 0.000) for 2357 atoms. Found 9 (12 requested) and removed 6 (6 requested) atoms. Cycle 27: After refmac, R = 0.2427 (Rfree = 0.000) for 2351 atoms. Found 3 (12 requested) and removed 8 (6 requested) atoms. Cycle 28: After refmac, R = 0.2407 (Rfree = 0.000) for 2344 atoms. Found 6 (12 requested) and removed 6 (6 requested) atoms. Cycle 29: After refmac, R = 0.2394 (Rfree = 0.000) for 2342 atoms. Found 5 (12 requested) and removed 6 (6 requested) atoms. Cycle 30: After refmac, R = 0.2345 (Rfree = 0.000) for 2339 atoms. Found 4 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.58 3.04 Search for helices and strands: 0 residues in 0 chains, 2382 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 2396 seeds are put forward Round 1: 157 peptides, 33 chains. Longest chain 8 peptides. Score 0.270 Round 2: 165 peptides, 29 chains. Longest chain 14 peptides. Score 0.364 Round 3: 180 peptides, 31 chains. Longest chain 12 peptides. Score 0.387 Round 4: 175 peptides, 31 chains. Longest chain 11 peptides. Score 0.369 Round 5: 191 peptides, 33 chains. Longest chain 13 peptides. Score 0.396 Taking the results from Round 5 Chains 33, Residues 158, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 4938 reflections ( 97.42 % complete ) and 5208 restraints for refining 2359 atoms. 4586 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2677 (Rfree = 0.000) for 2359 atoms. Found 12 (12 requested) and removed 7 (6 requested) atoms. Cycle 32: After refmac, R = 0.2549 (Rfree = 0.000) for 2354 atoms. Found 5 (13 requested) and removed 6 (6 requested) atoms. Cycle 33: After refmac, R = 0.2483 (Rfree = 0.000) for 2345 atoms. Found 10 (12 requested) and removed 6 (6 requested) atoms. Cycle 34: After refmac, R = 0.2436 (Rfree = 0.000) for 2343 atoms. Found 6 (12 requested) and removed 6 (6 requested) atoms. Cycle 35: After refmac, R = 0.2384 (Rfree = 0.000) for 2338 atoms. Found 2 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.51 2.98 Search for helices and strands: 0 residues in 0 chains, 2378 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 2399 seeds are put forward Round 1: 154 peptides, 28 chains. Longest chain 11 peptides. Score 0.340 Round 2: 178 peptides, 31 chains. Longest chain 16 peptides. Score 0.380 Round 3: 170 peptides, 26 chains. Longest chain 23 peptides. Score 0.429 Round 4: 168 peptides, 27 chains. Longest chain 11 peptides. Score 0.406 Round 5: 156 peptides, 23 chains. Longest chain 16 peptides. Score 0.427 Taking the results from Round 3 Chains 26, Residues 144, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4938 reflections ( 97.42 % complete ) and 5343 restraints for refining 2359 atoms. 4793 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2425 (Rfree = 0.000) for 2359 atoms. Found 9 (12 requested) and removed 8 (6 requested) atoms. Cycle 37: After refmac, R = 0.2314 (Rfree = 0.000) for 2341 atoms. Found 7 (12 requested) and removed 8 (6 requested) atoms. Cycle 38: After refmac, R = 0.2201 (Rfree = 0.000) for 2334 atoms. Found 3 (12 requested) and removed 7 (6 requested) atoms. Cycle 39: After refmac, R = 0.2182 (Rfree = 0.000) for 2329 atoms. Found 4 (12 requested) and removed 8 (6 requested) atoms. Cycle 40: After refmac, R = 0.2170 (Rfree = 0.000) for 2319 atoms. Found 1 (12 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.54 3.01 Search for helices and strands: 0 residues in 0 chains, 2356 seeds are put forward NCS extension: 35 residues added (2 deleted due to clashes), 2391 seeds are put forward Round 1: 139 peptides, 29 chains. Longest chain 13 peptides. Score 0.265 Round 2: 146 peptides, 26 chains. Longest chain 14 peptides. Score 0.342 Round 3: 158 peptides, 27 chains. Longest chain 11 peptides. Score 0.371 Round 4: 150 peptides, 28 chains. Longest chain 12 peptides. Score 0.325 Round 5: 150 peptides, 24 chains. Longest chain 13 peptides. Score 0.390 Taking the results from Round 5 Chains 24, Residues 126, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4938 reflections ( 97.42 % complete ) and 5447 restraints for refining 2359 atoms. 4967 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2591 (Rfree = 0.000) for 2359 atoms. Found 11 (12 requested) and removed 8 (6 requested) atoms. Cycle 42: After refmac, R = 0.2424 (Rfree = 0.000) for 2351 atoms. Found 7 (12 requested) and removed 8 (6 requested) atoms. Cycle 43: After refmac, R = 0.2353 (Rfree = 0.000) for 2346 atoms. Found 3 (12 requested) and removed 8 (6 requested) atoms. Cycle 44: After refmac, R = 0.2387 (Rfree = 0.000) for 2338 atoms. Found 4 (12 requested) and removed 6 (6 requested) atoms. Cycle 45: After refmac, R = 0.2361 (Rfree = 0.000) for 2335 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.56 3.02 Search for helices and strands: 0 residues in 0 chains, 2369 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 2391 seeds are put forward Round 1: 144 peptides, 30 chains. Longest chain 10 peptides. Score 0.268 Round 2: 143 peptides, 26 chains. Longest chain 11 peptides. Score 0.331 Round 3: 159 peptides, 25 chains. Longest chain 15 peptides. Score 0.406 Round 4: 152 peptides, 26 chains. Longest chain 11 peptides. Score 0.365 Round 5: 161 peptides, 23 chains. Longest chain 13 peptides. Score 0.444 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 23, Residues 138, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence Sequence coverage is 4 % Consider running further cycles of model building using 2nuj-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4938 reflections ( 97.42 % complete ) and 5343 restraints for refining 2359 atoms. 4800 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2660 (Rfree = 0.000) for 2359 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.2561 (Rfree = 0.000) for 2345 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.2593 (Rfree = 0.000) for 2339 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.2593 (Rfree = 0.000) for 2331 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Writing output files ... TimeTaking 33.02