null Mon 24 Dec 08:08:40 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 2ffj-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2ffj-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2ffj-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ffj-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/2ffj-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ffj-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 08:08:45 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/2ffj-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ffj-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 437 and 0 Target number of residues in the AU: 437 Target solvent content: 0.6475 Checking the provided sequence file Detected sequence length: 300 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 600 Adjusted target solvent content: 0.52 Input MTZ file: 2ffj-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: 19 Cell parameters: 68.806 80.677 120.868 90.000 90.000 90.000 Input sequence file: 2ffj-3.4-parrot-noncs.fasta_lf Building free atoms model in initial map for 4800 target number of atoms Had to go as low as 0.55 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: 29.898 3.400 Wilson plot Bfac: 76.26 9629 reflections ( 99.03 % complete ) and 0 restraints for refining 5325 atoms. Observations/parameters ratio is 0.45 ------------------------------------------------------ Starting model: R = 0.3368 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3501 (Rfree = 0.000) for 5325 atoms. Found 40 (40 requested) and removed 51 (20 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.44 3.35 Search for helices and strands: 0 residues in 0 chains, 5464 seeds are put forward NCS extension: 0 residues added, 5464 seeds are put forward Round 1: 260 peptides, 47 chains. Longest chain 17 peptides. Score 0.364 Round 2: 312 peptides, 49 chains. Longest chain 14 peptides. Score 0.466 Round 3: 351 peptides, 49 chains. Longest chain 34 peptides. Score 0.547 Round 4: 350 peptides, 46 chains. Longest chain 23 peptides. Score 0.570 Round 5: 350 peptides, 46 chains. Longest chain 23 peptides. Score 0.570 Taking the results from Round 5 Chains 46, Residues 304, Estimated correctness of the model 18.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9629 reflections ( 99.03 % complete ) and 9529 restraints for refining 4230 atoms. 8359 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2888 (Rfree = 0.000) for 4230 atoms. Found 31 (31 requested) and removed 48 (15 requested) atoms. Cycle 2: After refmac, R = 0.2787 (Rfree = 0.000) for 4141 atoms. Found 26 (31 requested) and removed 49 (15 requested) atoms. Cycle 3: After refmac, R = 0.2478 (Rfree = 0.000) for 4085 atoms. Found 20 (31 requested) and removed 34 (15 requested) atoms. Cycle 4: After refmac, R = 0.2458 (Rfree = 0.000) for 4057 atoms. Found 11 (30 requested) and removed 31 (15 requested) atoms. Cycle 5: After refmac, R = 0.2344 (Rfree = 0.000) for 4033 atoms. Found 10 (30 requested) and removed 19 (15 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.39 3.30 Search for helices and strands: 0 residues in 0 chains, 4243 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 4260 seeds are put forward Round 1: 291 peptides, 45 chains. Longest chain 16 peptides. Score 0.458 Round 2: 329 peptides, 49 chains. Longest chain 14 peptides. Score 0.502 Round 3: 332 peptides, 41 chains. Longest chain 25 peptides. Score 0.579 Round 4: 354 peptides, 44 chains. Longest chain 25 peptides. Score 0.594 Round 5: 344 peptides, 48 chains. Longest chain 22 peptides. Score 0.542 Taking the results from Round 4 Chains 46, Residues 310, Estimated correctness of the model 26.7 % 2 chains (29 residues) have been docked in sequence ------------------------------------------------------ 9629 reflections ( 99.03 % complete ) and 9305 restraints for refining 4305 atoms. 7999 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2775 (Rfree = 0.000) for 4305 atoms. Found 23 (32 requested) and removed 53 (16 requested) atoms. Cycle 7: After refmac, R = 0.2601 (Rfree = 0.000) for 4242 atoms. Found 22 (32 requested) and removed 31 (16 requested) atoms. Cycle 8: After refmac, R = 0.2507 (Rfree = 0.000) for 4217 atoms. Found 15 (31 requested) and removed 34 (15 requested) atoms. Cycle 9: After refmac, R = 0.2420 (Rfree = 0.000) for 4187 atoms. Found 16 (31 requested) and removed 33 (15 requested) atoms. Cycle 10: After refmac, R = 0.2422 (Rfree = 0.000) for 4157 atoms. Found 13 (31 requested) and removed 24 (15 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.39 3.30 Search for helices and strands: 0 residues in 0 chains, 4316 seeds are put forward NCS extension: 21 residues added (5 deleted due to clashes), 4337 seeds are put forward Round 1: 295 peptides, 48 chains. Longest chain 17 peptides. Score 0.437 Round 2: 321 peptides, 41 chains. Longest chain 20 peptides. Score 0.558 Round 3: 336 peptides, 50 chains. Longest chain 23 peptides. Score 0.508 Round 4: 344 peptides, 41 chains. Longest chain 24 peptides. Score 0.601 Round 5: 329 peptides, 47 chains. Longest chain 15 peptides. Score 0.520 Taking the results from Round 4 Chains 44, Residues 303, Estimated correctness of the model 29.0 % 3 chains (29 residues) have been docked in sequence ------------------------------------------------------ 9629 reflections ( 99.03 % complete ) and 9606 restraints for refining 4342 atoms. 8341 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2702 (Rfree = 0.000) for 4342 atoms. Found 21 (32 requested) and removed 58 (16 requested) atoms. Cycle 12: After refmac, R = 0.2477 (Rfree = 0.000) for 4277 atoms. Found 17 (32 requested) and removed 29 (16 requested) atoms. Cycle 13: After refmac, R = 0.2391 (Rfree = 0.000) for 4246 atoms. Found 13 (32 requested) and removed 29 (16 requested) atoms. Cycle 14: After refmac, R = 0.2365 (Rfree = 0.000) for 4218 atoms. Found 20 (31 requested) and removed 25 (15 requested) atoms. Cycle 15: After refmac, R = 0.2264 (Rfree = 0.000) for 4204 atoms. Found 18 (31 requested) and removed 21 (15 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.41 3.32 Search for helices and strands: 0 residues in 0 chains, 4379 seeds are put forward NCS extension: 30 residues added (0 deleted due to clashes), 4409 seeds are put forward Round 1: 301 peptides, 47 chains. Longest chain 15 peptides. Score 0.461 Round 2: 320 peptides, 45 chains. Longest chain 15 peptides. Score 0.520 Round 3: 332 peptides, 42 chains. Longest chain 29 peptides. Score 0.570 Round 4: 325 peptides, 45 chains. Longest chain 15 peptides. Score 0.530 Round 5: 324 peptides, 41 chains. Longest chain 21 peptides. Score 0.564 Taking the results from Round 3 Chains 42, Residues 290, Estimated correctness of the model 18.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9629 reflections ( 99.03 % complete ) and 10038 restraints for refining 4365 atoms. 8920 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2513 (Rfree = 0.000) for 4365 atoms. Found 24 (32 requested) and removed 44 (16 requested) atoms. Cycle 17: After refmac, R = 0.2348 (Rfree = 0.000) for 4327 atoms. Found 22 (32 requested) and removed 35 (16 requested) atoms. Cycle 18: After refmac, R = 0.2268 (Rfree = 0.000) for 4308 atoms. Found 20 (32 requested) and removed 30 (16 requested) atoms. Cycle 19: After refmac, R = 0.2257 (Rfree = 0.000) for 4295 atoms. Found 10 (32 requested) and removed 21 (16 requested) atoms. Cycle 20: After refmac, R = 0.2194 (Rfree = 0.000) for 4281 atoms. Found 10 (32 requested) and removed 20 (16 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.43 3.34 Search for helices and strands: 0 residues in 0 chains, 4457 seeds are put forward NCS extension: 35 residues added (4 deleted due to clashes), 4492 seeds are put forward Round 1: 288 peptides, 51 chains. Longest chain 20 peptides. Score 0.391 Round 2: 305 peptides, 47 chains. Longest chain 23 peptides. Score 0.470 Round 3: 319 peptides, 49 chains. Longest chain 20 peptides. Score 0.481 Round 4: 312 peptides, 46 chains. Longest chain 22 peptides. Score 0.494 Round 5: 315 peptides, 48 chains. Longest chain 21 peptides. Score 0.482 Taking the results from Round 4 Chains 46, Residues 266, Estimated correctness of the model 0.0 % 3 chains (41 residues) have been docked in sequence ------------------------------------------------------ 9629 reflections ( 99.03 % complete ) and 9687 restraints for refining 4362 atoms. 8515 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2683 (Rfree = 0.000) for 4362 atoms. Found 21 (32 requested) and removed 32 (16 requested) atoms. Cycle 22: After refmac, R = 0.2562 (Rfree = 0.000) for 4324 atoms. Found 22 (32 requested) and removed 33 (16 requested) atoms. Cycle 23: After refmac, R = 0.2463 (Rfree = 0.000) for 4298 atoms. Found 18 (32 requested) and removed 29 (16 requested) atoms. Cycle 24: After refmac, R = 0.2422 (Rfree = 0.000) for 4280 atoms. Found 17 (32 requested) and removed 22 (16 requested) atoms. Cycle 25: After refmac, R = 0.2350 (Rfree = 0.000) for 4269 atoms. Found 16 (32 requested) and removed 20 (16 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.42 3.33 Search for helices and strands: 0 residues in 0 chains, 4463 seeds are put forward NCS extension: 33 residues added (7 deleted due to clashes), 4496 seeds are put forward Round 1: 293 peptides, 50 chains. Longest chain 19 peptides. Score 0.413 Round 2: 308 peptides, 49 chains. Longest chain 14 peptides. Score 0.457 Round 3: 316 peptides, 46 chains. Longest chain 19 peptides. Score 0.503 Round 4: 335 peptides, 48 chains. Longest chain 23 peptides. Score 0.524 Round 5: 310 peptides, 46 chains. Longest chain 27 peptides. Score 0.490 Taking the results from Round 4 Chains 48, Residues 287, Estimated correctness of the model 1.9 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 9629 reflections ( 99.03 % complete ) and 9986 restraints for refining 4362 atoms. 8857 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2687 (Rfree = 0.000) for 4362 atoms. Found 19 (32 requested) and removed 28 (16 requested) atoms. Cycle 27: After refmac, R = 0.2635 (Rfree = 0.000) for 4333 atoms. Found 31 (32 requested) and removed 28 (16 requested) atoms. Cycle 28: After refmac, R = 0.2515 (Rfree = 0.000) for 4323 atoms. Found 19 (32 requested) and removed 29 (16 requested) atoms. Cycle 29: After refmac, R = 0.2422 (Rfree = 0.000) for 4296 atoms. Found 19 (32 requested) and removed 26 (16 requested) atoms. Cycle 30: After refmac, R = 0.2352 (Rfree = 0.000) for 4281 atoms. Found 18 (32 requested) and removed 24 (16 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.41 3.32 Search for helices and strands: 0 residues in 0 chains, 4471 seeds are put forward NCS extension: 30 residues added (2 deleted due to clashes), 4501 seeds are put forward Round 1: 278 peptides, 52 chains. Longest chain 16 peptides. Score 0.356 Round 2: 289 peptides, 45 chains. Longest chain 15 peptides. Score 0.453 Round 3: 290 peptides, 42 chains. Longest chain 16 peptides. Score 0.485 Round 4: 294 peptides, 42 chains. Longest chain 17 peptides. Score 0.494 Round 5: 295 peptides, 43 chains. Longest chain 24 peptides. Score 0.486 Taking the results from Round 4 Chains 42, Residues 252, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 9629 reflections ( 99.03 % complete ) and 10152 restraints for refining 4365 atoms. 9162 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2598 (Rfree = 0.000) for 4365 atoms. Found 32 (32 requested) and removed 26 (16 requested) atoms. Cycle 32: After refmac, R = 0.2476 (Rfree = 0.000) for 4354 atoms. Found 33 (33 requested) and removed 27 (16 requested) atoms. Cycle 33: After refmac, R = 0.2413 (Rfree = 0.000) for 4342 atoms. Found 22 (32 requested) and removed 27 (16 requested) atoms. Cycle 34: After refmac, R = 0.2077 (Rfree = 0.000) for 4329 atoms. Found 5 (32 requested) and removed 19 (16 requested) atoms. Cycle 35: After refmac, R = 0.2039 (Rfree = 0.000) for 4307 atoms. Found 11 (32 requested) and removed 18 (16 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.41 3.32 Search for helices and strands: 0 residues in 0 chains, 4467 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 4486 seeds are put forward Round 1: 235 peptides, 43 chains. Longest chain 13 peptides. Score 0.344 Round 2: 275 peptides, 47 chains. Longest chain 16 peptides. Score 0.401 Round 3: 276 peptides, 46 chains. Longest chain 22 peptides. Score 0.413 Round 4: 290 peptides, 43 chains. Longest chain 23 peptides. Score 0.475 Round 5: 276 peptides, 43 chains. Longest chain 17 peptides. Score 0.444 Taking the results from Round 4 Chains 44, Residues 247, Estimated correctness of the model 0.0 % 2 chains (19 residues) have been docked in sequence ------------------------------------------------------ 9629 reflections ( 99.03 % complete ) and 9952 restraints for refining 4361 atoms. 8945 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2542 (Rfree = 0.000) for 4361 atoms. Found 25 (32 requested) and removed 33 (16 requested) atoms. Cycle 37: After refmac, R = 0.2481 (Rfree = 0.000) for 4332 atoms. Found 25 (32 requested) and removed 31 (16 requested) atoms. Cycle 38: After refmac, R = 0.2341 (Rfree = 0.000) for 4308 atoms. Found 20 (32 requested) and removed 22 (16 requested) atoms. Cycle 39: After refmac, R = 0.2264 (Rfree = 0.000) for 4301 atoms. Found 14 (32 requested) and removed 23 (16 requested) atoms. Cycle 40: After refmac, R = 0.2210 (Rfree = 0.000) for 4289 atoms. Found 10 (32 requested) and removed 24 (16 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.45 3.36 Search for helices and strands: 0 residues in 0 chains, 4421 seeds are put forward NCS extension: 41 residues added (1 deleted due to clashes), 4462 seeds are put forward Round 1: 253 peptides, 44 chains. Longest chain 16 peptides. Score 0.379 Round 2: 271 peptides, 41 chains. Longest chain 17 peptides. Score 0.453 Round 3: 285 peptides, 44 chains. Longest chain 18 peptides. Score 0.454 Round 4: 273 peptides, 44 chains. Longest chain 15 peptides. Score 0.427 Round 5: 261 peptides, 42 chains. Longest chain 20 peptides. Score 0.419 Taking the results from Round 3 Chains 45, Residues 241, Estimated correctness of the model 0.0 % 3 chains (37 residues) have been docked in sequence ------------------------------------------------------ 9629 reflections ( 99.03 % complete ) and 9739 restraints for refining 4364 atoms. 8688 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2433 (Rfree = 0.000) for 4364 atoms. Found 17 (32 requested) and removed 30 (16 requested) atoms. Cycle 42: After refmac, R = 0.2385 (Rfree = 0.000) for 4338 atoms. Found 14 (32 requested) and removed 24 (16 requested) atoms. Cycle 43: After refmac, R = 0.2339 (Rfree = 0.000) for 4319 atoms. Found 14 (32 requested) and removed 27 (16 requested) atoms. Cycle 44: After refmac, R = 0.2305 (Rfree = 0.000) for 4302 atoms. Found 11 (32 requested) and removed 22 (16 requested) atoms. Cycle 45: After refmac, R = 0.2302 (Rfree = 0.000) for 4286 atoms. Found 10 (32 requested) and removed 19 (16 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.42 3.33 Search for helices and strands: 0 residues in 0 chains, 4408 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 4430 seeds are put forward Round 1: 237 peptides, 45 chains. Longest chain 12 peptides. Score 0.327 Round 2: 270 peptides, 46 chains. Longest chain 13 peptides. Score 0.399 Round 3: 282 peptides, 43 chains. Longest chain 16 peptides. Score 0.457 Round 4: 285 peptides, 47 chains. Longest chain 16 peptides. Score 0.424 Round 5: 284 peptides, 44 chains. Longest chain 15 peptides. Score 0.452 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 44, Residues 239, Estimated correctness of the model 0.0 % 2 chains (18 residues) have been docked in sequence Sequence coverage is 7 % Consider running further cycles of model building using 2ffj-3_warpNtrace.pdb as input Building loops using Loopy2018 44 chains (239 residues) following loop building 2 chains (18 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 9629 reflections ( 99.03 % complete ) and 9893 restraints for refining 4365 atoms. 8908 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2476 (Rfree = 0.000) for 4365 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 47: After refmac, R = 0.2484 (Rfree = 0.000) for 4337 atoms. Found 0 (32 requested) and removed 11 (16 requested) atoms. Cycle 48: After refmac, R = 0.2441 (Rfree = 0.000) for 4319 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 49: After refmac, R = 0.2388 (Rfree = 0.000) for 4300 atoms. Found 0 (32 requested) and removed 13 (16 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:54:21 GMT 2018 Job finished. TimeTaking 45.67 Used memory is bytes: 5489712