Sun 23 Dec 22:22:52 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1z82-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1z82-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1z82-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1z82-3.8-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/1z82-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1z82-3.8-parrot-hancs ############### 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 ============================================================ Sun 23 Dec 22:23:01 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/hancs/ArpWArp/wArpResults/WorkingDir/1z82-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1z82-3.8-parrot-hancs/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 388 and 0 Target number of residues in the AU: 388 Target solvent content: 0.6552 Checking the provided sequence file Detected sequence length: 335 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 670 Adjusted target solvent content: 0.40 Input MTZ file: 1z82-3.8-parrot-hancs.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: 4 Cell parameters: 65.170 67.461 75.617 90.000 113.643 90.000 Input sequence file: 1z82-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 5360 target number of atoms Had to go as low as 0.65 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: 29.850 3.801 Wilson plot Bfac: 81.37 6033 reflections ( 99.55 % complete ) and 0 restraints for refining 5931 atoms. Observations/parameters ratio is 0.25 ------------------------------------------------------ Starting model: R = 0.3161 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3027 (Rfree = 0.000) for 5931 atoms. Found 32 (32 requested) and removed 41 (16 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.58 4.10 Search for helices and strands: 0 residues in 0 chains, 6060 seeds are put forward NCS extension: 0 residues added, 6060 seeds are put forward Round 1: 188 peptides, 41 chains. Longest chain 6 peptides. Score 0.244 Round 2: 244 peptides, 46 chains. Longest chain 22 peptides. Score 0.347 Round 3: 265 peptides, 49 chains. Longest chain 9 peptides. Score 0.369 Round 4: 285 peptides, 51 chains. Longest chain 17 peptides. Score 0.400 Round 5: 279 peptides, 50 chains. Longest chain 10 peptides. Score 0.395 Taking the results from Round 4 Chains 51, Residues 234, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 6033 reflections ( 99.55 % complete ) and 11476 restraints for refining 4848 atoms. 10546 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2366 (Rfree = 0.000) for 4848 atoms. Found 13 (26 requested) and removed 45 (13 requested) atoms. Cycle 2: After refmac, R = 0.2388 (Rfree = 0.000) for 4721 atoms. Found 20 (26 requested) and removed 40 (13 requested) atoms. Cycle 3: After refmac, R = 0.2251 (Rfree = 0.000) for 4660 atoms. Found 21 (25 requested) and removed 25 (12 requested) atoms. Cycle 4: After refmac, R = 0.2183 (Rfree = 0.000) for 4625 atoms. Found 18 (25 requested) and removed 29 (12 requested) atoms. Cycle 5: After refmac, R = 0.2162 (Rfree = 0.000) for 4581 atoms. Found 15 (25 requested) and removed 19 (12 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.65 4.18 Search for helices and strands: 0 residues in 0 chains, 4760 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 4786 seeds are put forward Round 1: 241 peptides, 53 chains. Longest chain 8 peptides. Score 0.255 Round 2: 278 peptides, 50 chains. Longest chain 11 peptides. Score 0.393 Round 3: 282 peptides, 52 chains. Longest chain 9 peptides. Score 0.381 Round 4: 289 peptides, 50 chains. Longest chain 10 peptides. Score 0.421 Round 5: 294 peptides, 50 chains. Longest chain 14 peptides. Score 0.434 Taking the results from Round 5 Chains 50, Residues 244, Estimated correctness of the model 0.0 % 5 chains (33 residues) have been docked in sequence ------------------------------------------------------ 6033 reflections ( 99.55 % complete ) and 10035 restraints for refining 4434 atoms. 8993 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1985 (Rfree = 0.000) for 4434 atoms. Found 24 (24 requested) and removed 39 (12 requested) atoms. Cycle 7: After refmac, R = 0.1907 (Rfree = 0.000) for 4385 atoms. Found 17 (24 requested) and removed 24 (12 requested) atoms. Cycle 8: After refmac, R = 0.1569 (Rfree = 0.000) for 4360 atoms. Found 3 (24 requested) and removed 20 (12 requested) atoms. Cycle 9: After refmac, R = 0.1694 (Rfree = 0.000) for 4328 atoms. Found 13 (23 requested) and removed 15 (11 requested) atoms. Cycle 10: After refmac, R = 0.1865 (Rfree = 0.000) for 4317 atoms. Found 23 (23 requested) and removed 22 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.68 4.21 Search for helices and strands: 0 residues in 0 chains, 4533 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 4549 seeds are put forward Round 1: 256 peptides, 56 chains. Longest chain 8 peptides. Score 0.263 Round 2: 295 peptides, 51 chains. Longest chain 14 peptides. Score 0.425 Round 3: 297 peptides, 50 chains. Longest chain 19 peptides. Score 0.441 Round 4: 304 peptides, 51 chains. Longest chain 13 peptides. Score 0.448 Round 5: 309 peptides, 49 chains. Longest chain 19 peptides. Score 0.480 Taking the results from Round 5 Chains 51, Residues 260, Estimated correctness of the model 0.0 % 3 chains (25 residues) have been docked in sequence ------------------------------------------------------ 6033 reflections ( 99.55 % complete ) and 9961 restraints for refining 4444 atoms. 8886 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1921 (Rfree = 0.000) for 4444 atoms. Found 17 (24 requested) and removed 43 (12 requested) atoms. Cycle 12: After refmac, R = 0.1880 (Rfree = 0.000) for 4387 atoms. Found 24 (24 requested) and removed 25 (12 requested) atoms. Cycle 13: After refmac, R = 0.1912 (Rfree = 0.000) for 4363 atoms. Found 24 (24 requested) and removed 25 (12 requested) atoms. Cycle 14: After refmac, R = 0.1428 (Rfree = 0.000) for 4347 atoms. Found 7 (23 requested) and removed 15 (11 requested) atoms. Cycle 15: After refmac, R = 0.1367 (Rfree = 0.000) for 4329 atoms. Found 2 (23 requested) and removed 14 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.63 4.15 Search for helices and strands: 0 residues in 0 chains, 4523 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 4541 seeds are put forward Round 1: 242 peptides, 51 chains. Longest chain 8 peptides. Score 0.282 Round 2: 256 peptides, 43 chains. Longest chain 11 peptides. Score 0.414 Round 3: 264 peptides, 46 chains. Longest chain 11 peptides. Score 0.401 Round 4: 266 peptides, 42 chains. Longest chain 15 peptides. Score 0.450 Round 5: 268 peptides, 42 chains. Longest chain 17 peptides. Score 0.455 Taking the results from Round 5 Chains 42, Residues 226, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6033 reflections ( 99.55 % complete ) and 10360 restraints for refining 4438 atoms. 9498 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1746 (Rfree = 0.000) for 4438 atoms. Found 22 (24 requested) and removed 35 (12 requested) atoms. Cycle 17: After refmac, R = 0.1744 (Rfree = 0.000) for 4404 atoms. Found 15 (24 requested) and removed 26 (12 requested) atoms. Cycle 18: After refmac, R = 0.1815 (Rfree = 0.000) for 4376 atoms. Found 24 (24 requested) and removed 24 (12 requested) atoms. Cycle 19: After refmac, R = 0.1380 (Rfree = 0.000) for 4363 atoms. Found 6 (24 requested) and removed 16 (12 requested) atoms. Cycle 20: After refmac, R = 0.1252 (Rfree = 0.000) for 4342 atoms. Found 4 (23 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.62 4.14 Search for helices and strands: 0 residues in 0 chains, 4539 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 4563 seeds are put forward Round 1: 226 peptides, 46 chains. Longest chain 10 peptides. Score 0.296 Round 2: 252 peptides, 46 chains. Longest chain 11 peptides. Score 0.369 Round 3: 255 peptides, 45 chains. Longest chain 14 peptides. Score 0.388 Round 4: 274 peptides, 45 chains. Longest chain 15 peptides. Score 0.438 Round 5: 269 peptides, 44 chains. Longest chain 16 peptides. Score 0.436 Taking the results from Round 4 Chains 47, Residues 229, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 6033 reflections ( 99.55 % complete ) and 10330 restraints for refining 4485 atoms. 9417 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1672 (Rfree = 0.000) for 4485 atoms. Found 20 (24 requested) and removed 28 (12 requested) atoms. Cycle 22: After refmac, R = 0.1861 (Rfree = 0.000) for 4450 atoms. Found 24 (24 requested) and removed 22 (12 requested) atoms. Cycle 23: After refmac, R = 0.1749 (Rfree = 0.000) for 4435 atoms. Found 24 (24 requested) and removed 22 (12 requested) atoms. Cycle 24: After refmac, R = 0.1799 (Rfree = 0.000) for 4426 atoms. Found 24 (24 requested) and removed 20 (12 requested) atoms. Cycle 25: After refmac, R = 0.1785 (Rfree = 0.000) for 4414 atoms. Found 24 (24 requested) and removed 20 (12 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.59 4.11 Search for helices and strands: 0 residues in 0 chains, 4606 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 4619 seeds are put forward Round 1: 211 peptides, 44 chains. Longest chain 9 peptides. Score 0.276 Round 2: 220 peptides, 42 chains. Longest chain 10 peptides. Score 0.327 Round 3: 227 peptides, 41 chains. Longest chain 12 peptides. Score 0.359 Round 4: 252 peptides, 45 chains. Longest chain 12 peptides. Score 0.380 Round 5: 238 peptides, 44 chains. Longest chain 10 peptides. Score 0.354 Taking the results from Round 4 Chains 45, Residues 207, Estimated correctness of the model 0.0 % 4 chains (23 residues) have been docked in sequence ------------------------------------------------------ 6033 reflections ( 99.55 % complete ) and 10057 restraints for refining 4412 atoms. 9202 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1764 (Rfree = 0.000) for 4412 atoms. Found 24 (24 requested) and removed 35 (12 requested) atoms. Cycle 27: After refmac, R = 0.1810 (Rfree = 0.000) for 4376 atoms. Found 24 (24 requested) and removed 25 (12 requested) atoms. Cycle 28: After refmac, R = 0.1845 (Rfree = 0.000) for 4364 atoms. Found 24 (24 requested) and removed 21 (12 requested) atoms. Cycle 29: After refmac, R = 0.1810 (Rfree = 0.000) for 4348 atoms. Found 23 (23 requested) and removed 20 (11 requested) atoms. Cycle 30: After refmac, R = 0.1315 (Rfree = 0.000) for 4339 atoms. Found 6 (23 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.64 4.17 Search for helices and strands: 0 residues in 0 chains, 4510 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 4526 seeds are put forward Round 1: 215 peptides, 46 chains. Longest chain 8 peptides. Score 0.263 Round 2: 246 peptides, 46 chains. Longest chain 11 peptides. Score 0.352 Round 3: 263 peptides, 51 chains. Longest chain 11 peptides. Score 0.341 Round 4: 262 peptides, 47 chains. Longest chain 13 peptides. Score 0.384 Round 5: 267 peptides, 49 chains. Longest chain 10 peptides. Score 0.375 Taking the results from Round 4 Chains 47, Residues 215, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 6033 reflections ( 99.55 % complete ) and 9837 restraints for refining 4341 atoms. 8968 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1688 (Rfree = 0.000) for 4341 atoms. Found 16 (23 requested) and removed 38 (11 requested) atoms. Cycle 32: After refmac, R = 0.1500 (Rfree = 0.000) for 4290 atoms. Found 8 (23 requested) and removed 17 (11 requested) atoms. Cycle 33: After refmac, R = 0.1474 (Rfree = 0.000) for 4275 atoms. Found 6 (23 requested) and removed 18 (11 requested) atoms. Cycle 34: After refmac, R = 0.1381 (Rfree = 0.000) for 4260 atoms. Found 4 (23 requested) and removed 15 (11 requested) atoms. Cycle 35: After refmac, R = 0.1326 (Rfree = 0.000) for 4246 atoms. Found 5 (23 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.64 4.17 Search for helices and strands: 0 residues in 0 chains, 4393 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 4409 seeds are put forward Round 1: 207 peptides, 42 chains. Longest chain 10 peptides. Score 0.289 Round 2: 245 peptides, 44 chains. Longest chain 12 peptides. Score 0.373 Round 3: 238 peptides, 43 chains. Longest chain 10 peptides. Score 0.366 Round 4: 252 peptides, 44 chains. Longest chain 15 peptides. Score 0.392 Round 5: 240 peptides, 43 chains. Longest chain 12 peptides. Score 0.371 Taking the results from Round 4 Chains 44, Residues 208, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 6033 reflections ( 99.55 % complete ) and 10375 restraints for refining 4423 atoms. 9556 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1723 (Rfree = 0.000) for 4423 atoms. Found 24 (24 requested) and removed 29 (12 requested) atoms. Cycle 37: After refmac, R = 0.1434 (Rfree = 0.000) for 4406 atoms. Found 14 (24 requested) and removed 24 (12 requested) atoms. Cycle 38: After refmac, R = 0.1350 (Rfree = 0.000) for 4391 atoms. Found 5 (24 requested) and removed 17 (12 requested) atoms. Cycle 39: After refmac, R = 0.1337 (Rfree = 0.000) for 4375 atoms. Found 7 (24 requested) and removed 15 (12 requested) atoms. Cycle 40: After refmac, R = 0.1325 (Rfree = 0.000) for 4364 atoms. Found 7 (23 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.65 4.18 Search for helices and strands: 0 residues in 0 chains, 4516 seeds are put forward NCS extension: 14 residues added (3 deleted due to clashes), 4530 seeds are put forward Round 1: 187 peptides, 39 chains. Longest chain 11 peptides. Score 0.267 Round 2: 233 peptides, 46 chains. Longest chain 9 peptides. Score 0.316 Round 3: 240 peptides, 43 chains. Longest chain 18 peptides. Score 0.371 Round 4: 234 peptides, 40 chains. Longest chain 18 peptides. Score 0.390 Round 5: 232 peptides, 39 chains. Longest chain 12 peptides. Score 0.396 Taking the results from Round 5 Chains 39, Residues 193, Estimated correctness of the model 0.0 % 3 chains (17 residues) have been docked in sequence ------------------------------------------------------ 6033 reflections ( 99.55 % complete ) and 10617 restraints for refining 4508 atoms. 9838 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1860 (Rfree = 0.000) for 4508 atoms. Found 24 (24 requested) and removed 33 (12 requested) atoms. Cycle 42: After refmac, R = 0.1850 (Rfree = 0.000) for 4482 atoms. Found 24 (24 requested) and removed 27 (12 requested) atoms. Cycle 43: After refmac, R = 0.1864 (Rfree = 0.000) for 4456 atoms. Found 24 (24 requested) and removed 23 (12 requested) atoms. Cycle 44: After refmac, R = 0.1823 (Rfree = 0.000) for 4442 atoms. Found 24 (24 requested) and removed 22 (12 requested) atoms. Cycle 45: After refmac, R = 0.1740 (Rfree = 0.000) for 4430 atoms. Found 24 (24 requested) and removed 24 (12 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.62 4.14 Search for helices and strands: 0 residues in 0 chains, 4631 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 4649 seeds are put forward Round 1: 168 peptides, 38 chains. Longest chain 7 peptides. Score 0.220 Round 2: 208 peptides, 41 chains. Longest chain 9 peptides. Score 0.305 Round 3: 202 peptides, 37 chains. Longest chain 10 peptides. Score 0.337 Round 4: 204 peptides, 39 chains. Longest chain 9 peptides. Score 0.318 Round 5: 205 peptides, 38 chains. Longest chain 11 peptides. Score 0.333 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 37, Residues 165, Estimated correctness of the model 0.0 % 3 chains (10 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 1z82-3_warpNtrace.pdb as input Building loops using Loopy2018 37 chains (165 residues) following loop building 3 chains (10 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6033 reflections ( 99.55 % complete ) and 10082 restraints for refining 4320 atoms. 9440 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1809 (Rfree = 0.000) for 4320 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 47: After refmac, R = 0.1855 (Rfree = 0.000) for 4292 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 48: After refmac, R = 0.1715 (Rfree = 0.000) for 4269 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 49: After refmac, R = 0.1674 (Rfree = 0.000) for 4254 atoms. TimeTaking 65.55