null Mon 24 Dec 07:31:26 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-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2ffj-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2ffj-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ffj-3.6-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-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ffj-3.6-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 07:31:30 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-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ffj-3.6-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 430 and 0 Target number of residues in the AU: 430 Target solvent content: 0.6531 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-3.6-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-3.6-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 3.600 Wilson plot Bfac: 80.03 8146 reflections ( 98.92 % complete ) and 0 restraints for refining 5330 atoms. Observations/parameters ratio is 0.38 ------------------------------------------------------ Starting model: R = 0.3423 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3486 (Rfree = 0.000) for 5330 atoms. Found 34 (34 requested) and removed 101 (17 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.61 3.52 Search for helices and strands: 0 residues in 0 chains, 5381 seeds are put forward NCS extension: 0 residues added, 5381 seeds are put forward Round 1: 194 peptides, 42 chains. Longest chain 9 peptides. Score 0.244 Round 2: 253 peptides, 45 chains. Longest chain 9 peptides. Score 0.368 Round 3: 280 peptides, 45 chains. Longest chain 15 peptides. Score 0.433 Round 4: 296 peptides, 43 chains. Longest chain 20 peptides. Score 0.488 Round 5: 317 peptides, 46 chains. Longest chain 17 peptides. Score 0.505 Taking the results from Round 5 Chains 46, Residues 271, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8146 reflections ( 98.92 % complete ) and 10148 restraints for refining 4348 atoms. 9110 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3094 (Rfree = 0.000) for 4348 atoms. Found 26 (27 requested) and removed 61 (13 requested) atoms. Cycle 2: After refmac, R = 0.2777 (Rfree = 0.000) for 4221 atoms. Found 27 (27 requested) and removed 37 (13 requested) atoms. Cycle 3: After refmac, R = 0.2576 (Rfree = 0.000) for 4172 atoms. Found 19 (27 requested) and removed 22 (13 requested) atoms. Cycle 4: After refmac, R = 0.2481 (Rfree = 0.000) for 4142 atoms. Found 19 (26 requested) and removed 25 (13 requested) atoms. Cycle 5: After refmac, R = 0.2470 (Rfree = 0.000) for 4119 atoms. Found 19 (26 requested) and removed 23 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.59 3.50 Search for helices and strands: 0 residues in 0 chains, 4332 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 4350 seeds are put forward Round 1: 246 peptides, 42 chains. Longest chain 14 peptides. Score 0.383 Round 2: 296 peptides, 43 chains. Longest chain 16 peptides. Score 0.488 Round 3: 298 peptides, 41 chains. Longest chain 16 peptides. Score 0.512 Round 4: 299 peptides, 41 chains. Longest chain 17 peptides. Score 0.514 Round 5: 299 peptides, 40 chains. Longest chain 18 peptides. Score 0.523 Taking the results from Round 5 Chains 42, Residues 259, Estimated correctness of the model 0.0 % 2 chains (27 residues) have been docked in sequence ------------------------------------------------------ 8146 reflections ( 98.92 % complete ) and 9356 restraints for refining 4165 atoms. 8259 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2619 (Rfree = 0.000) for 4165 atoms. Found 13 (26 requested) and removed 44 (13 requested) atoms. Cycle 7: After refmac, R = 0.2433 (Rfree = 0.000) for 4094 atoms. Found 11 (26 requested) and removed 28 (13 requested) atoms. Cycle 8: After refmac, R = 0.2463 (Rfree = 0.000) for 4058 atoms. Found 12 (26 requested) and removed 17 (13 requested) atoms. Cycle 9: After refmac, R = 0.2373 (Rfree = 0.000) for 4042 atoms. Found 5 (26 requested) and removed 18 (13 requested) atoms. Cycle 10: After refmac, R = 0.2336 (Rfree = 0.000) for 4020 atoms. Found 8 (25 requested) and removed 20 (12 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.58 3.49 Search for helices and strands: 0 residues in 0 chains, 4163 seeds are put forward NCS extension: 20 residues added (3 deleted due to clashes), 4183 seeds are put forward Round 1: 274 peptides, 50 chains. Longest chain 14 peptides. Score 0.367 Round 2: 302 peptides, 44 chains. Longest chain 16 peptides. Score 0.492 Round 3: 325 peptides, 44 chains. Longest chain 21 peptides. Score 0.539 Round 4: 313 peptides, 45 chains. Longest chain 19 peptides. Score 0.506 Round 5: 322 peptides, 43 chains. Longest chain 20 peptides. Score 0.542 Taking the results from Round 5 Chains 45, Residues 279, Estimated correctness of the model 0.0 % 3 chains (40 residues) have been docked in sequence ------------------------------------------------------ 8146 reflections ( 98.92 % complete ) and 9196 restraints for refining 4250 atoms. 7978 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2746 (Rfree = 0.000) for 4250 atoms. Found 27 (27 requested) and removed 49 (13 requested) atoms. Cycle 12: After refmac, R = 0.2560 (Rfree = 0.000) for 4196 atoms. Found 27 (27 requested) and removed 33 (13 requested) atoms. Cycle 13: After refmac, R = 0.2393 (Rfree = 0.000) for 4172 atoms. Found 13 (26 requested) and removed 34 (13 requested) atoms. Cycle 14: After refmac, R = 0.2350 (Rfree = 0.000) for 4137 atoms. Found 14 (26 requested) and removed 23 (13 requested) atoms. Cycle 15: After refmac, R = 0.2254 (Rfree = 0.000) for 4120 atoms. Found 12 (26 requested) and removed 27 (13 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.60 3.51 Search for helices and strands: 0 residues in 0 chains, 4281 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 4295 seeds are put forward Round 1: 267 peptides, 43 chains. Longest chain 13 peptides. Score 0.423 Round 2: 285 peptides, 41 chains. Longest chain 14 peptides. Score 0.484 Round 3: 287 peptides, 44 chains. Longest chain 15 peptides. Score 0.459 Round 4: 301 peptides, 38 chains. Longest chain 22 peptides. Score 0.545 Round 5: 293 peptides, 40 chains. Longest chain 16 peptides. Score 0.510 Taking the results from Round 4 Chains 39, Residues 263, Estimated correctness of the model 0.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 8146 reflections ( 98.92 % complete ) and 9833 restraints for refining 4301 atoms. 8771 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2527 (Rfree = 0.000) for 4301 atoms. Found 23 (27 requested) and removed 35 (13 requested) atoms. Cycle 17: After refmac, R = 0.2390 (Rfree = 0.000) for 4260 atoms. Found 17 (27 requested) and removed 34 (13 requested) atoms. Cycle 18: After refmac, R = 0.2311 (Rfree = 0.000) for 4230 atoms. Found 6 (27 requested) and removed 22 (13 requested) atoms. Cycle 19: After refmac, R = 0.2202 (Rfree = 0.000) for 4206 atoms. Found 5 (27 requested) and removed 15 (13 requested) atoms. Cycle 20: After refmac, R = 0.2183 (Rfree = 0.000) for 4190 atoms. Found 9 (26 requested) and removed 20 (13 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.62 3.52 Search for helices and strands: 0 residues in 0 chains, 4338 seeds are put forward NCS extension: 24 residues added (5 deleted due to clashes), 4362 seeds are put forward Round 1: 252 peptides, 47 chains. Longest chain 15 peptides. Score 0.344 Round 2: 291 peptides, 44 chains. Longest chain 11 peptides. Score 0.468 Round 3: 286 peptides, 42 chains. Longest chain 13 peptides. Score 0.476 Round 4: 295 peptides, 42 chains. Longest chain 15 peptides. Score 0.496 Round 5: 297 peptides, 46 chains. Longest chain 14 peptides. Score 0.461 Taking the results from Round 4 Chains 42, Residues 253, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8146 reflections ( 98.92 % complete ) and 10011 restraints for refining 4302 atoms. 9041 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2497 (Rfree = 0.000) for 4302 atoms. Found 21 (27 requested) and removed 44 (13 requested) atoms. Cycle 22: After refmac, R = 0.2239 (Rfree = 0.000) for 4263 atoms. Found 6 (27 requested) and removed 20 (13 requested) atoms. Cycle 23: After refmac, R = 0.2143 (Rfree = 0.000) for 4242 atoms. Found 6 (27 requested) and removed 24 (13 requested) atoms. Cycle 24: After refmac, R = 0.2078 (Rfree = 0.000) for 4218 atoms. Found 4 (27 requested) and removed 18 (13 requested) atoms. Cycle 25: After refmac, R = 0.2064 (Rfree = 0.000) for 4201 atoms. Found 3 (26 requested) and removed 16 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.62 3.52 Search for helices and strands: 0 residues in 0 chains, 4348 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 4362 seeds are put forward Round 1: 267 peptides, 49 chains. Longest chain 10 peptides. Score 0.360 Round 2: 289 peptides, 46 chains. Longest chain 12 peptides. Score 0.444 Round 3: 291 peptides, 45 chains. Longest chain 17 peptides. Score 0.458 Round 4: 310 peptides, 44 chains. Longest chain 17 peptides. Score 0.509 Round 5: 298 peptides, 46 chains. Longest chain 19 peptides. Score 0.464 Taking the results from Round 4 Chains 44, Residues 266, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8146 reflections ( 98.92 % complete ) and 9911 restraints for refining 4339 atoms. 8891 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2530 (Rfree = 0.000) for 4339 atoms. Found 24 (27 requested) and removed 36 (13 requested) atoms. Cycle 27: After refmac, R = 0.2393 (Rfree = 0.000) for 4312 atoms. Found 11 (27 requested) and removed 21 (13 requested) atoms. Cycle 28: After refmac, R = 0.2316 (Rfree = 0.000) for 4295 atoms. Found 9 (27 requested) and removed 23 (13 requested) atoms. Cycle 29: After refmac, R = 0.2273 (Rfree = 0.000) for 4275 atoms. Found 9 (27 requested) and removed 18 (13 requested) atoms. Cycle 30: After refmac, R = 0.2226 (Rfree = 0.000) for 4261 atoms. Found 1 (27 requested) and removed 17 (13 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.61 3.52 Search for helices and strands: 0 residues in 0 chains, 4407 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 4424 seeds are put forward Round 1: 243 peptides, 48 chains. Longest chain 11 peptides. Score 0.310 Round 2: 254 peptides, 41 chains. Longest chain 18 peptides. Score 0.413 Round 3: 269 peptides, 41 chains. Longest chain 15 peptides. Score 0.448 Round 4: 266 peptides, 42 chains. Longest chain 15 peptides. Score 0.431 Round 5: 274 peptides, 39 chains. Longest chain 18 peptides. Score 0.479 Taking the results from Round 5 Chains 39, Residues 235, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8146 reflections ( 98.92 % complete ) and 10425 restraints for refining 4350 atoms. 9524 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2673 (Rfree = 0.000) for 4350 atoms. Found 27 (27 requested) and removed 39 (13 requested) atoms. Cycle 32: After refmac, R = 0.2482 (Rfree = 0.000) for 4309 atoms. Found 26 (27 requested) and removed 19 (13 requested) atoms. Cycle 33: After refmac, R = 0.2361 (Rfree = 0.000) for 4295 atoms. Found 7 (27 requested) and removed 19 (13 requested) atoms. Cycle 34: After refmac, R = 0.2348 (Rfree = 0.000) for 4274 atoms. Found 9 (27 requested) and removed 16 (13 requested) atoms. Cycle 35: After refmac, R = 0.2289 (Rfree = 0.000) for 4258 atoms. Found 9 (27 requested) and removed 20 (13 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.59 3.50 Search for helices and strands: 0 residues in 0 chains, 4395 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 4419 seeds are put forward Round 1: 234 peptides, 45 chains. Longest chain 12 peptides. Score 0.319 Round 2: 261 peptides, 42 chains. Longest chain 14 peptides. Score 0.419 Round 3: 262 peptides, 43 chains. Longest chain 20 peptides. Score 0.411 Round 4: 263 peptides, 43 chains. Longest chain 15 peptides. Score 0.413 Round 5: 266 peptides, 41 chains. Longest chain 16 peptides. Score 0.441 Taking the results from Round 5 Chains 41, Residues 225, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 8146 reflections ( 98.92 % complete ) and 10043 restraints for refining 4299 atoms. 9137 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2592 (Rfree = 0.000) for 4299 atoms. Found 23 (27 requested) and removed 40 (13 requested) atoms. Cycle 37: After refmac, R = 0.2482 (Rfree = 0.000) for 4271 atoms. Found 10 (27 requested) and removed 22 (13 requested) atoms. Cycle 38: After refmac, R = 0.2383 (Rfree = 0.000) for 4253 atoms. Found 11 (27 requested) and removed 19 (13 requested) atoms. Cycle 39: After refmac, R = 0.2426 (Rfree = 0.000) for 4242 atoms. Found 6 (27 requested) and removed 19 (13 requested) atoms. Cycle 40: After refmac, R = 0.2378 (Rfree = 0.000) for 4226 atoms. Found 14 (27 requested) and removed 18 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.60 3.51 Search for helices and strands: 0 residues in 0 chains, 4357 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 4377 seeds are put forward Round 1: 211 peptides, 40 chains. Longest chain 13 peptides. Score 0.315 Round 2: 262 peptides, 46 chains. Longest chain 15 peptides. Score 0.380 Round 3: 274 peptides, 47 chains. Longest chain 14 peptides. Score 0.398 Round 4: 280 peptides, 43 chains. Longest chain 23 peptides. Score 0.453 Round 5: 283 peptides, 44 chains. Longest chain 15 peptides. Score 0.450 Taking the results from Round 4 Chains 44, Residues 237, Estimated correctness of the model 0.0 % 1 chains (17 residues) have been docked in sequence ------------------------------------------------------ 8146 reflections ( 98.92 % complete ) and 10095 restraints for refining 4349 atoms. 9128 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2586 (Rfree = 0.000) for 4349 atoms. Found 24 (27 requested) and removed 25 (13 requested) atoms. Cycle 42: After refmac, R = 0.2346 (Rfree = 0.000) for 4325 atoms. Found 13 (27 requested) and removed 20 (13 requested) atoms. Cycle 43: After refmac, R = 0.2217 (Rfree = 0.000) for 4308 atoms. Found 6 (27 requested) and removed 17 (13 requested) atoms. Cycle 44: After refmac, R = 0.2297 (Rfree = 0.000) for 4293 atoms. Found 11 (27 requested) and removed 22 (13 requested) atoms. Cycle 45: After refmac, R = 0.2192 (Rfree = 0.000) for 4279 atoms. Found 4 (27 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.61 3.52 Search for helices and strands: 0 residues in 0 chains, 4410 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 4425 seeds are put forward Round 1: 175 peptides, 35 chains. Longest chain 10 peptides. Score 0.274 Round 2: 222 peptides, 38 chains. Longest chain 15 peptides. Score 0.366 Round 3: 222 peptides, 34 chains. Longest chain 14 peptides. Score 0.411 Round 4: 221 peptides, 37 chains. Longest chain 23 peptides. Score 0.375 Round 5: 229 peptides, 38 chains. Longest chain 12 peptides. Score 0.384 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 34, Residues 188, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence Sequence coverage is 3 % Consider running further cycles of model building using 2ffj-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8146 reflections ( 98.92 % complete ) and 10328 restraints for refining 4337 atoms. 9582 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2406 (Rfree = 0.000) for 4337 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Cycle 47: After refmac, R = 0.2319 (Rfree = 0.000) for 4311 atoms. Found 0 (27 requested) and removed 11 (13 requested) atoms. Cycle 48: After refmac, R = 0.2243 (Rfree = 0.000) for 4296 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Cycle 49: After refmac, R = 0.2222 (Rfree = 0.000) for 4274 atoms. Found 0 (27 requested) and removed 11 (13 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:17:45 GMT 2018 Job finished. TimeTaking 46.32 Used memory is bytes: 3394856