Mon 24 Dec 00:56:28 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2nuj-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2nuj-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2nuj-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2nuj-3.8-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2nuj-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2nuj-3.8-parrot-mrncs ############### 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 00:56:33 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/mrncs/ArpWArp/wArpResults/WorkingDir/2nuj-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2nuj-3.8-parrot-mrncs/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-mrncs.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-mrncs.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 2878 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Starting model: R = 0.3397 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2935 (Rfree = 0.000) for 2878 atoms. Found 15 (15 requested) and removed 17 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.50 2.97 Search for helices and strands: 0 residues in 0 chains, 2912 seeds are put forward NCS extension: 0 residues added, 2912 seeds are put forward Round 1: 144 peptides, 26 chains. Longest chain 12 peptides. Score 0.335 Round 2: 187 peptides, 32 chains. Longest chain 11 peptides. Score 0.397 Round 3: 202 peptides, 29 chains. Longest chain 14 peptides. Score 0.489 Round 4: 201 peptides, 27 chains. Longest chain 16 peptides. Score 0.514 Round 5: 212 peptides, 27 chains. Longest chain 26 peptides. Score 0.546 Taking the results from Round 5 Chains 31, Residues 185, Estimated correctness of the model 0.0 % 4 chains (44 residues) have been docked in sequence ------------------------------------------------------ 4938 reflections ( 97.42 % complete ) and 4613 restraints for refining 2359 atoms. 3762 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2850 (Rfree = 0.000) for 2359 atoms. Found 6 (12 requested) and removed 11 (6 requested) atoms. Cycle 2: After refmac, R = 0.2735 (Rfree = 0.000) for 2329 atoms. Found 6 (12 requested) and removed 13 (6 requested) atoms. Cycle 3: After refmac, R = 0.2699 (Rfree = 0.000) for 2305 atoms. Found 6 (12 requested) and removed 8 (6 requested) atoms. Cycle 4: After refmac, R = 0.2663 (Rfree = 0.000) for 2293 atoms. Found 6 (12 requested) and removed 7 (6 requested) atoms. Cycle 5: After refmac, R = 0.2613 (Rfree = 0.000) for 2284 atoms. Found 1 (12 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.49 2.97 Search for helices and strands: 0 residues in 0 chains, 2322 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 2340 seeds are put forward Round 1: 178 peptides, 30 chains. Longest chain 10 peptides. Score 0.395 Round 2: 196 peptides, 28 chains. Longest chain 12 peptides. Score 0.484 Round 3: 197 peptides, 26 chains. Longest chain 21 peptides. Score 0.515 Round 4: 210 peptides, 29 chains. Longest chain 14 peptides. Score 0.514 Round 5: 200 peptides, 26 chains. Longest chain 19 peptides. Score 0.524 Taking the results from Round 5 Chains 28, Residues 174, Estimated correctness of the model 0.0 % 3 chains (24 residues) have been docked in sequence ------------------------------------------------------ 4938 reflections ( 97.42 % complete ) and 4930 restraints for refining 2358 atoms. 4177 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2922 (Rfree = 0.000) for 2358 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 7: After refmac, R = 0.2833 (Rfree = 0.000) for 2340 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 8: After refmac, R = 0.2724 (Rfree = 0.000) for 2334 atoms. Found 5 (12 requested) and removed 9 (6 requested) atoms. Cycle 9: After refmac, R = 0.2666 (Rfree = 0.000) for 2325 atoms. Found 3 (12 requested) and removed 7 (6 requested) atoms. Cycle 10: After refmac, R = 0.2622 (Rfree = 0.000) for 2317 atoms. Found 3 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.54 3.01 Search for helices and strands: 0 residues in 0 chains, 2382 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 2398 seeds are put forward Round 1: 179 peptides, 32 chains. Longest chain 10 peptides. Score 0.368 Round 2: 190 peptides, 30 chains. Longest chain 14 peptides. Score 0.436 Round 3: 199 peptides, 27 chains. Longest chain 14 peptides. Score 0.508 Round 4: 206 peptides, 28 chains. Longest chain 17 peptides. Score 0.515 Round 5: 207 peptides, 29 chains. Longest chain 19 peptides. Score 0.505 Taking the results from Round 4 Chains 28, Residues 178, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4938 reflections ( 97.42 % complete ) and 5197 restraints for refining 2358 atoms. 4513 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2774 (Rfree = 0.000) for 2358 atoms. Found 12 (12 requested) and removed 6 (6 requested) atoms. Cycle 12: After refmac, R = 0.2597 (Rfree = 0.000) for 2350 atoms. Found 5 (13 requested) and removed 9 (6 requested) atoms. Cycle 13: After refmac, R = 0.2529 (Rfree = 0.000) for 2336 atoms. Found 2 (12 requested) and removed 7 (6 requested) atoms. Cycle 14: After refmac, R = 0.2487 (Rfree = 0.000) for 2327 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 15: After refmac, R = 0.2448 (Rfree = 0.000) for 2317 atoms. Found 2 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.47 2.95 Search for helices and strands: 0 residues in 0 chains, 2367 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 2382 seeds are put forward Round 1: 185 peptides, 33 chains. Longest chain 12 peptides. Score 0.374 Round 2: 196 peptides, 30 chains. Longest chain 14 peptides. Score 0.456 Round 3: 201 peptides, 31 chains. Longest chain 14 peptides. Score 0.458 Round 4: 209 peptides, 32 chains. Longest chain 17 peptides. Score 0.470 Round 5: 208 peptides, 31 chains. Longest chain 21 peptides. Score 0.480 Taking the results from Round 5 Chains 31, Residues 177, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4938 reflections ( 97.42 % complete ) and 5217 restraints for refining 2357 atoms. 4540 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2643 (Rfree = 0.000) for 2357 atoms. Found 10 (12 requested) and removed 9 (6 requested) atoms. Cycle 17: After refmac, R = 0.2422 (Rfree = 0.000) for 2341 atoms. Found 4 (12 requested) and removed 7 (6 requested) atoms. Cycle 18: After refmac, R = 0.2358 (Rfree = 0.000) for 2328 atoms. Found 3 (12 requested) and removed 6 (6 requested) atoms. Cycle 19: After refmac, R = 0.2340 (Rfree = 0.000) for 2316 atoms. Found 7 (12 requested) and removed 9 (6 requested) atoms. Cycle 20: After refmac, R = 0.2282 (Rfree = 0.000) for 2309 atoms. Found 2 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.54 3.01 Search for helices and strands: 0 residues in 0 chains, 2399 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 2423 seeds are put forward Round 1: 189 peptides, 37 chains. Longest chain 11 peptides. Score 0.328 Round 2: 205 peptides, 34 chains. Longest chain 14 peptides. Score 0.428 Round 3: 216 peptides, 32 chains. Longest chain 26 peptides. Score 0.492 Round 4: 204 peptides, 32 chains. Longest chain 13 peptides. Score 0.454 Round 5: 220 peptides, 32 chains. Longest chain 20 peptides. Score 0.504 Taking the results from Round 5 Chains 32, Residues 188, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 4938 reflections ( 97.42 % complete ) and 5031 restraints for refining 2359 atoms. 4277 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2605 (Rfree = 0.000) for 2359 atoms. Found 12 (12 requested) and removed 7 (6 requested) atoms. Cycle 22: After refmac, R = 0.2467 (Rfree = 0.000) for 2336 atoms. Found 9 (13 requested) and removed 9 (6 requested) atoms. Cycle 23: After refmac, R = 0.2355 (Rfree = 0.000) for 2326 atoms. Found 6 (12 requested) and removed 9 (6 requested) atoms. Cycle 24: After refmac, R = 0.2405 (Rfree = 0.000) for 2314 atoms. Found 5 (12 requested) and removed 7 (6 requested) atoms. Cycle 25: After refmac, R = 0.2302 (Rfree = 0.000) for 2304 atoms. Found 4 (12 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.52 2.99 Search for helices and strands: 0 residues in 0 chains, 2355 seeds are put forward NCS extension: 33 residues added (0 deleted due to clashes), 2388 seeds are put forward Round 1: 175 peptides, 35 chains. Longest chain 10 peptides. Score 0.307 Round 2: 183 peptides, 32 chains. Longest chain 11 peptides. Score 0.383 Round 3: 194 peptides, 30 chains. Longest chain 14 peptides. Score 0.450 Round 4: 210 peptides, 31 chains. Longest chain 22 peptides. Score 0.487 Round 5: 186 peptides, 27 chains. Longest chain 11 peptides. Score 0.467 Taking the results from Round 4 Chains 33, Residues 179, Estimated correctness of the model 0.0 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 4938 reflections ( 97.42 % complete ) and 5053 restraints for refining 2359 atoms. 4293 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2637 (Rfree = 0.000) for 2359 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 27: After refmac, R = 0.2471 (Rfree = 0.000) for 2352 atoms. Found 3 (12 requested) and removed 10 (6 requested) atoms. Cycle 28: After refmac, R = 0.2420 (Rfree = 0.000) for 2340 atoms. Found 3 (12 requested) and removed 8 (6 requested) atoms. Cycle 29: After refmac, R = 0.2408 (Rfree = 0.000) for 2333 atoms. Found 2 (12 requested) and removed 9 (6 requested) atoms. Cycle 30: After refmac, R = 0.2361 (Rfree = 0.000) for 2321 atoms. Found 4 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.55 3.02 Search for helices and strands: 0 residues in 0 chains, 2379 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 2394 seeds are put forward Round 1: 170 peptides, 34 chains. Longest chain 12 peptides. Score 0.304 Round 2: 175 peptides, 31 chains. Longest chain 15 peptides. Score 0.369 Round 3: 192 peptides, 31 chains. Longest chain 22 peptides. Score 0.429 Round 4: 177 peptides, 26 chains. Longest chain 21 peptides. Score 0.452 Round 5: 181 peptides, 28 chains. Longest chain 16 peptides. Score 0.436 Taking the results from Round 4 Chains 27, Residues 151, Estimated correctness of the model 0.0 % 2 chains (24 residues) have been docked in sequence ------------------------------------------------------ 4938 reflections ( 97.42 % complete ) and 5164 restraints for refining 2358 atoms. 4494 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2657 (Rfree = 0.000) for 2358 atoms. Found 12 (12 requested) and removed 7 (6 requested) atoms. Cycle 32: After refmac, R = 0.2521 (Rfree = 0.000) for 2345 atoms. Found 5 (12 requested) and removed 8 (6 requested) atoms. Cycle 33: After refmac, R = 0.2433 (Rfree = 0.000) for 2336 atoms. Found 5 (12 requested) and removed 7 (6 requested) atoms. Cycle 34: After refmac, R = 0.2365 (Rfree = 0.000) for 2332 atoms. Found 4 (12 requested) and removed 7 (6 requested) atoms. Cycle 35: After refmac, R = 0.2343 (Rfree = 0.000) for 2326 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.49 2.97 Search for helices and strands: 0 residues in 0 chains, 2372 seeds are put forward NCS extension: 29 residues added (0 deleted due to clashes), 2401 seeds are put forward Round 1: 156 peptides, 31 chains. Longest chain 9 peptides. Score 0.299 Round 2: 170 peptides, 32 chains. Longest chain 13 peptides. Score 0.336 Round 3: 168 peptides, 28 chains. Longest chain 10 peptides. Score 0.391 Round 4: 173 peptides, 31 chains. Longest chain 12 peptides. Score 0.362 Round 5: 170 peptides, 28 chains. Longest chain 12 peptides. Score 0.398 Taking the results from Round 5 Chains 29, Residues 142, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 4938 reflections ( 97.42 % complete ) and 5481 restraints for refining 2358 atoms. 4910 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2638 (Rfree = 0.000) for 2358 atoms. Found 10 (12 requested) and removed 8 (6 requested) atoms. Cycle 37: After refmac, R = 0.2527 (Rfree = 0.000) for 2349 atoms. Found 6 (12 requested) and removed 6 (6 requested) atoms. Cycle 38: After refmac, R = 0.2503 (Rfree = 0.000) for 2337 atoms. Found 5 (12 requested) and removed 7 (6 requested) atoms. Cycle 39: After refmac, R = 0.2466 (Rfree = 0.000) for 2332 atoms. Found 1 (12 requested) and removed 6 (6 requested) atoms. Cycle 40: After refmac, R = 0.2443 (Rfree = 0.000) for 2327 atoms. Found 2 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.48 2.96 Search for helices and strands: 0 residues in 0 chains, 2368 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 2381 seeds are put forward Round 1: 146 peptides, 30 chains. Longest chain 8 peptides. Score 0.276 Round 2: 187 peptides, 29 chains. Longest chain 23 peptides. Score 0.441 Round 3: 183 peptides, 32 chains. Longest chain 13 peptides. Score 0.383 Round 4: 190 peptides, 29 chains. Longest chain 21 peptides. Score 0.451 Round 5: 178 peptides, 27 chains. Longest chain 13 peptides. Score 0.441 Taking the results from Round 4 Chains 29, Residues 161, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 4938 reflections ( 97.42 % complete ) and 5321 restraints for refining 2359 atoms. 4698 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2621 (Rfree = 0.000) for 2359 atoms. Found 10 (12 requested) and removed 9 (6 requested) atoms. Cycle 42: After refmac, R = 0.2497 (Rfree = 0.000) for 2353 atoms. Found 2 (12 requested) and removed 7 (6 requested) atoms. Cycle 43: After refmac, R = 0.2444 (Rfree = 0.000) for 2339 atoms. Found 11 (12 requested) and removed 6 (6 requested) atoms. Cycle 44: After refmac, R = 0.2375 (Rfree = 0.000) for 2340 atoms. Found 1 (12 requested) and removed 9 (6 requested) atoms. Cycle 45: After refmac, R = 0.2366 (Rfree = 0.000) for 2327 atoms. Found 1 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.49 2.97 Search for helices and strands: 0 residues in 0 chains, 2369 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 2392 seeds are put forward Round 1: 154 peptides, 31 chains. Longest chain 8 peptides. Score 0.291 Round 2: 171 peptides, 30 chains. Longest chain 14 peptides. Score 0.371 Round 3: 187 peptides, 29 chains. Longest chain 14 peptides. Score 0.441 Round 4: 171 peptides, 28 chains. Longest chain 12 peptides. Score 0.401 Round 5: 166 peptides, 28 chains. Longest chain 13 peptides. Score 0.384 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 29, Residues 158, 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 2nuj-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4938 reflections ( 97.42 % complete ) and 5428 restraints for refining 2359 atoms. 4825 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2522 (Rfree = 0.000) for 2359 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.2479 (Rfree = 0.000) for 2344 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.2436 (Rfree = 0.000) for 2336 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.2409 (Rfree = 0.000) for 2328 atoms. TimeTaking 36.43