Mon 24 Dec 07:48:31 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-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2nuj-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2nuj-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2nuj-3.4-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-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2nuj-3.4-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 07:48:36 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-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2nuj-3.4-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 329 and 0 Target number of residues in the AU: 329 Target solvent content: 0.6174 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-3.4-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-3.4-parrot-noncs.fasta_lf Building free atoms model in initial map for 2608 target number of atoms Had to go as low as 0.85 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 3.400 Wilson plot Bfac: 59.74 6827 reflections ( 97.75 % complete ) and 0 restraints for refining 2917 atoms. Observations/parameters ratio is 0.59 ------------------------------------------------------ Starting model: R = 0.3454 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3136 (Rfree = 0.000) for 2917 atoms. Found 22 (22 requested) and removed 17 (11 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.19 2.71 Search for helices and strands: 0 residues in 0 chains, 2956 seeds are put forward NCS extension: 0 residues added, 2956 seeds are put forward Round 1: 180 peptides, 33 chains. Longest chain 12 peptides. Score 0.356 Round 2: 214 peptides, 34 chains. Longest chain 15 peptides. Score 0.458 Round 3: 228 peptides, 34 chains. Longest chain 18 peptides. Score 0.501 Round 4: 230 peptides, 31 chains. Longest chain 23 peptides. Score 0.546 Round 5: 232 peptides, 32 chains. Longest chain 32 peptides. Score 0.539 Taking the results from Round 4 Chains 32, Residues 199, Estimated correctness of the model 10.1 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 6827 reflections ( 97.75 % complete ) and 4845 restraints for refining 2414 atoms. 4042 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2796 (Rfree = 0.000) for 2414 atoms. Found 17 (18 requested) and removed 12 (9 requested) atoms. Cycle 2: After refmac, R = 0.2648 (Rfree = 0.000) for 2401 atoms. Found 17 (18 requested) and removed 12 (9 requested) atoms. Cycle 3: After refmac, R = 0.2493 (Rfree = 0.000) for 2396 atoms. Found 9 (18 requested) and removed 9 (9 requested) atoms. Cycle 4: After refmac, R = 0.2453 (Rfree = 0.000) for 2389 atoms. Found 8 (18 requested) and removed 11 (9 requested) atoms. Cycle 5: After refmac, R = 0.2438 (Rfree = 0.000) for 2383 atoms. Found 6 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.20 2.72 Search for helices and strands: 0 residues in 0 chains, 2462 seeds are put forward NCS extension: 20 residues added (6 deleted due to clashes), 2482 seeds are put forward Round 1: 201 peptides, 32 chains. Longest chain 15 peptides. Score 0.444 Round 2: 197 peptides, 29 chains. Longest chain 15 peptides. Score 0.474 Round 3: 219 peptides, 27 chains. Longest chain 20 peptides. Score 0.566 Round 4: 200 peptides, 29 chains. Longest chain 15 peptides. Score 0.483 Round 5: 221 peptides, 29 chains. Longest chain 22 peptides. Score 0.546 Taking the results from Round 3 Chains 28, Residues 192, Estimated correctness of the model 17.2 % 3 chains (27 residues) have been docked in sequence ------------------------------------------------------ 6827 reflections ( 97.75 % complete ) and 4744 restraints for refining 2371 atoms. 3896 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2678 (Rfree = 0.000) for 2371 atoms. Found 17 (17 requested) and removed 12 (8 requested) atoms. Cycle 7: After refmac, R = 0.2521 (Rfree = 0.000) for 2366 atoms. Found 6 (17 requested) and removed 10 (8 requested) atoms. Cycle 8: After refmac, R = 0.2491 (Rfree = 0.000) for 2360 atoms. Found 9 (17 requested) and removed 13 (8 requested) atoms. Cycle 9: After refmac, R = 0.2451 (Rfree = 0.000) for 2354 atoms. Found 4 (17 requested) and removed 9 (8 requested) atoms. Cycle 10: After refmac, R = 0.2449 (Rfree = 0.000) for 2347 atoms. Found 6 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.21 2.73 Search for helices and strands: 0 residues in 0 chains, 2400 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 2422 seeds are put forward Round 1: 200 peptides, 33 chains. Longest chain 18 peptides. Score 0.426 Round 2: 188 peptides, 26 chains. Longest chain 18 peptides. Score 0.488 Round 3: 211 peptides, 32 chains. Longest chain 17 peptides. Score 0.476 Round 4: 225 peptides, 30 chains. Longest chain 22 peptides. Score 0.545 Round 5: 213 peptides, 28 chains. Longest chain 18 peptides. Score 0.536 Taking the results from Round 4 Chains 32, Residues 195, Estimated correctness of the model 9.7 % 3 chains (28 residues) have been docked in sequence ------------------------------------------------------ 6827 reflections ( 97.75 % complete ) and 4732 restraints for refining 2371 atoms. 3879 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2782 (Rfree = 0.000) for 2371 atoms. Found 17 (17 requested) and removed 15 (8 requested) atoms. Cycle 12: After refmac, R = 0.2598 (Rfree = 0.000) for 2359 atoms. Found 8 (17 requested) and removed 9 (8 requested) atoms. Cycle 13: After refmac, R = 0.2533 (Rfree = 0.000) for 2356 atoms. Found 3 (17 requested) and removed 9 (8 requested) atoms. Cycle 14: After refmac, R = 0.2493 (Rfree = 0.000) for 2346 atoms. Found 4 (17 requested) and removed 11 (8 requested) atoms. Cycle 15: After refmac, R = 0.2452 (Rfree = 0.000) for 2336 atoms. Found 6 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.19 2.71 Search for helices and strands: 0 residues in 0 chains, 2381 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 2404 seeds are put forward Round 1: 179 peptides, 29 chains. Longest chain 17 peptides. Score 0.414 Round 2: 198 peptides, 25 chains. Longest chain 19 peptides. Score 0.532 Round 3: 204 peptides, 24 chains. Longest chain 17 peptides. Score 0.562 Round 4: 213 peptides, 28 chains. Longest chain 19 peptides. Score 0.536 Round 5: 211 peptides, 28 chains. Longest chain 21 peptides. Score 0.530 Taking the results from Round 3 Chains 24, Residues 180, Estimated correctness of the model 15.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6827 reflections ( 97.75 % complete ) and 5088 restraints for refining 2371 atoms. 4392 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2625 (Rfree = 0.000) for 2371 atoms. Found 9 (17 requested) and removed 8 (8 requested) atoms. Cycle 17: After refmac, R = 0.2558 (Rfree = 0.000) for 2367 atoms. Found 13 (17 requested) and removed 8 (8 requested) atoms. Cycle 18: After refmac, R = 0.2424 (Rfree = 0.000) for 2371 atoms. Found 7 (17 requested) and removed 8 (8 requested) atoms. Cycle 19: After refmac, R = 0.2380 (Rfree = 0.000) for 2368 atoms. Found 1 (17 requested) and removed 8 (8 requested) atoms. Cycle 20: After refmac, R = 0.2336 (Rfree = 0.000) for 2359 atoms. Found 4 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.25 2.76 Search for helices and strands: 0 residues in 0 chains, 2405 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 2422 seeds are put forward Round 1: 194 peptides, 31 chains. Longest chain 14 peptides. Score 0.435 Round 2: 223 peptides, 29 chains. Longest chain 18 peptides. Score 0.552 Round 3: 231 peptides, 32 chains. Longest chain 21 peptides. Score 0.536 Round 4: 227 peptides, 32 chains. Longest chain 19 peptides. Score 0.525 Round 5: 219 peptides, 27 chains. Longest chain 24 peptides. Score 0.566 Taking the results from Round 5 Chains 29, Residues 192, Estimated correctness of the model 17.2 % 4 chains (56 residues) have been docked in sequence ------------------------------------------------------ 6827 reflections ( 97.75 % complete ) and 4503 restraints for refining 2371 atoms. 3567 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2806 (Rfree = 0.000) for 2371 atoms. Found 14 (17 requested) and removed 11 (8 requested) atoms. Cycle 22: After refmac, R = 0.2629 (Rfree = 0.000) for 2357 atoms. Found 8 (17 requested) and removed 10 (8 requested) atoms. Cycle 23: After refmac, R = 0.2573 (Rfree = 0.000) for 2343 atoms. Found 4 (17 requested) and removed 8 (8 requested) atoms. Cycle 24: After refmac, R = 0.2539 (Rfree = 0.000) for 2332 atoms. Found 3 (17 requested) and removed 10 (8 requested) atoms. Cycle 25: After refmac, R = 0.2538 (Rfree = 0.000) for 2324 atoms. Found 7 (17 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.21 2.73 Search for helices and strands: 0 residues in 0 chains, 2376 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 2393 seeds are put forward Round 1: 202 peptides, 31 chains. Longest chain 20 peptides. Score 0.461 Round 2: 218 peptides, 28 chains. Longest chain 31 peptides. Score 0.550 Round 3: 237 peptides, 33 chains. Longest chain 19 peptides. Score 0.541 Round 4: 229 peptides, 29 chains. Longest chain 31 peptides. Score 0.568 Round 5: 204 peptides, 25 chains. Longest chain 19 peptides. Score 0.549 Taking the results from Round 4 Chains 31, Residues 200, Estimated correctness of the model 17.9 % 3 chains (44 residues) have been docked in sequence ------------------------------------------------------ 6827 reflections ( 97.75 % complete ) and 4650 restraints for refining 2371 atoms. 3717 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2758 (Rfree = 0.000) for 2371 atoms. Found 17 (17 requested) and removed 16 (8 requested) atoms. Cycle 27: After refmac, R = 0.2589 (Rfree = 0.000) for 2361 atoms. Found 11 (17 requested) and removed 9 (8 requested) atoms. Cycle 28: After refmac, R = 0.2533 (Rfree = 0.000) for 2357 atoms. Found 6 (17 requested) and removed 8 (8 requested) atoms. Cycle 29: After refmac, R = 0.2451 (Rfree = 0.000) for 2354 atoms. Found 5 (17 requested) and removed 10 (8 requested) atoms. Cycle 30: After refmac, R = 0.2423 (Rfree = 0.000) for 2346 atoms. Found 4 (17 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.22 2.74 Search for helices and strands: 0 residues in 0 chains, 2398 seeds are put forward NCS extension: 33 residues added (2 deleted due to clashes), 2431 seeds are put forward Round 1: 183 peptides, 28 chains. Longest chain 18 peptides. Score 0.442 Round 2: 196 peptides, 27 chains. Longest chain 21 peptides. Score 0.498 Round 3: 215 peptides, 20 chains. Longest chain 28 peptides. Score 0.640 Round 4: 202 peptides, 23 chains. Longest chain 19 peptides. Score 0.570 Round 5: 219 peptides, 23 chains. Longest chain 27 peptides. Score 0.615 Taking the results from Round 3 Chains 23, Residues 195, Estimated correctness of the model 41.2 % 2 chains (26 residues) have been docked in sequence ------------------------------------------------------ 6827 reflections ( 97.75 % complete ) and 4742 restraints for refining 2371 atoms. 3885 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2723 (Rfree = 0.000) for 2371 atoms. Found 17 (17 requested) and removed 12 (8 requested) atoms. Cycle 32: After refmac, R = 0.2610 (Rfree = 0.000) for 2368 atoms. Found 16 (17 requested) and removed 9 (8 requested) atoms. Cycle 33: After refmac, R = 0.2487 (Rfree = 0.000) for 2371 atoms. Found 15 (17 requested) and removed 8 (8 requested) atoms. Cycle 34: After refmac, R = 0.2398 (Rfree = 0.000) for 2372 atoms. Found 5 (17 requested) and removed 10 (8 requested) atoms. Cycle 35: After refmac, R = 0.2359 (Rfree = 0.000) for 2363 atoms. Found 7 (17 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.21 2.73 Search for helices and strands: 0 residues in 0 chains, 2414 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 2435 seeds are put forward Round 1: 193 peptides, 32 chains. Longest chain 17 peptides. Score 0.417 Round 2: 222 peptides, 29 chains. Longest chain 20 peptides. Score 0.549 Round 3: 215 peptides, 29 chains. Longest chain 20 peptides. Score 0.529 Round 4: 206 peptides, 27 chains. Longest chain 19 peptides. Score 0.529 Round 5: 210 peptides, 28 chains. Longest chain 19 peptides. Score 0.527 Taking the results from Round 2 Chains 29, Residues 193, Estimated correctness of the model 11.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6827 reflections ( 97.75 % complete ) and 5051 restraints for refining 2371 atoms. 4308 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2525 (Rfree = 0.000) for 2371 atoms. Found 12 (17 requested) and removed 9 (8 requested) atoms. Cycle 37: After refmac, R = 0.2411 (Rfree = 0.000) for 2368 atoms. Found 6 (17 requested) and removed 8 (8 requested) atoms. Cycle 38: After refmac, R = 0.2359 (Rfree = 0.000) for 2364 atoms. Found 4 (17 requested) and removed 10 (8 requested) atoms. Cycle 39: After refmac, R = 0.2320 (Rfree = 0.000) for 2357 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 40: After refmac, R = 0.2333 (Rfree = 0.000) for 2348 atoms. Found 3 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.22 2.74 Search for helices and strands: 0 residues in 0 chains, 2401 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 2424 seeds are put forward Round 1: 184 peptides, 26 chains. Longest chain 18 peptides. Score 0.475 Round 2: 196 peptides, 28 chains. Longest chain 19 peptides. Score 0.484 Round 3: 203 peptides, 26 chains. Longest chain 17 peptides. Score 0.533 Round 4: 204 peptides, 24 chains. Longest chain 19 peptides. Score 0.562 Round 5: 207 peptides, 26 chains. Longest chain 29 peptides. Score 0.545 Taking the results from Round 4 Chains 24, Residues 180, Estimated correctness of the model 15.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6827 reflections ( 97.75 % complete ) and 5138 restraints for refining 2371 atoms. 4442 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2616 (Rfree = 0.000) for 2371 atoms. Found 11 (17 requested) and removed 8 (8 requested) atoms. Cycle 42: After refmac, R = 0.2560 (Rfree = 0.000) for 2373 atoms. Found 1 (17 requested) and removed 8 (8 requested) atoms. Cycle 43: After refmac, R = 0.2528 (Rfree = 0.000) for 2365 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 44: After refmac, R = 0.2516 (Rfree = 0.000) for 2356 atoms. Found 1 (17 requested) and removed 8 (8 requested) atoms. Cycle 45: After refmac, R = 0.2512 (Rfree = 0.000) for 2349 atoms. Found 3 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.23 2.74 Search for helices and strands: 0 residues in 0 chains, 2402 seeds are put forward NCS extension: 25 residues added (4 deleted due to clashes), 2427 seeds are put forward Round 1: 168 peptides, 26 chains. Longest chain 15 peptides. Score 0.422 Round 2: 196 peptides, 25 chains. Longest chain 14 peptides. Score 0.526 Round 3: 183 peptides, 23 chains. Longest chain 16 peptides. Score 0.514 Round 4: 197 peptides, 28 chains. Longest chain 25 peptides. Score 0.488 Round 5: 201 peptides, 26 chains. Longest chain 21 peptides. Score 0.527 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 27, Residues 175, Estimated correctness of the model 3.1 % 1 chains (9 residues) have been docked in sequence Sequence coverage is 5 % Consider running further cycles of model building using 2nuj-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6827 reflections ( 97.75 % complete ) and 5010 restraints for refining 2371 atoms. 4294 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2780 (Rfree = 0.000) for 2371 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2656 (Rfree = 0.000) for 2355 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.2609 (Rfree = 0.000) for 2345 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.2609 (Rfree = 0.000) for 2336 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Writing output files ... TimeTaking 31.85