null Tue 25 Dec 19:27:57 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 1vr0-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vr0-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vr0-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vr0-3.4-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/1vr0-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vr0-3.4-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 ============================================================ Tue 25 Dec 19:28:12 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/1vr0-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vr0-3.4-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 510 and 0 Target number of residues in the AU: 510 Target solvent content: 0.6232 Checking the provided sequence file Detected sequence length: 247 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 3 Adjusted target number of residues: 741 Adjusted target solvent content: 0.45 Input MTZ file: 1vr0-3.4-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: 20 Cell parameters: 46.686 69.193 453.518 90.000 90.000 90.000 Input sequence file: 1vr0-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 5928 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: 226.759 3.400 Wilson plot Bfac: 62.77 10631 reflections ( 99.67 % complete ) and 0 restraints for refining 6526 atoms. Observations/parameters ratio is 0.41 ------------------------------------------------------ Starting model: R = 0.3108 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3176 (Rfree = 0.000) for 6526 atoms. Found 49 (49 requested) and removed 134 (24 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.29 3.52 Search for helices and strands: 0 residues in 0 chains, 6568 seeds are put forward NCS extension: 0 residues added, 6568 seeds are put forward Round 1: 291 peptides, 60 chains. Longest chain 9 peptides. Score 0.295 Round 2: 374 peptides, 64 chains. Longest chain 15 peptides. Score 0.441 Round 3: 371 peptides, 56 chains. Longest chain 18 peptides. Score 0.504 Round 4: 385 peptides, 55 chains. Longest chain 18 peptides. Score 0.538 Round 5: 394 peptides, 55 chains. Longest chain 18 peptides. Score 0.554 Taking the results from Round 5 Chains 56, Residues 339, Estimated correctness of the model 13.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 10631 reflections ( 99.67 % complete ) and 12186 restraints for refining 5387 atoms. 10851 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2523 (Rfree = 0.000) for 5387 atoms. Found 29 (40 requested) and removed 56 (20 requested) atoms. Cycle 2: After refmac, R = 0.2345 (Rfree = 0.000) for 5304 atoms. Found 22 (40 requested) and removed 40 (20 requested) atoms. Cycle 3: After refmac, R = 0.2140 (Rfree = 0.000) for 5269 atoms. Found 14 (39 requested) and removed 28 (19 requested) atoms. Cycle 4: After refmac, R = 0.2083 (Rfree = 0.000) for 5246 atoms. Found 16 (39 requested) and removed 28 (19 requested) atoms. Cycle 5: After refmac, R = 0.2084 (Rfree = 0.000) for 5230 atoms. Found 10 (39 requested) and removed 29 (19 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.24 3.46 Search for helices and strands: 0 residues in 0 chains, 5420 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 5438 seeds are put forward Round 1: 362 peptides, 63 chains. Longest chain 15 peptides. Score 0.425 Round 2: 388 peptides, 59 chains. Longest chain 19 peptides. Score 0.511 Round 3: 427 peptides, 59 chains. Longest chain 17 peptides. Score 0.580 Round 4: 414 peptides, 57 chains. Longest chain 17 peptides. Score 0.573 Round 5: 405 peptides, 57 chains. Longest chain 17 peptides. Score 0.558 Taking the results from Round 3 Chains 59, Residues 368, Estimated correctness of the model 22.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10631 reflections ( 99.67 % complete ) and 12099 restraints for refining 5390 atoms. 10686 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2246 (Rfree = 0.000) for 5390 atoms. Found 31 (40 requested) and removed 39 (20 requested) atoms. Cycle 7: After refmac, R = 0.2089 (Rfree = 0.000) for 5371 atoms. Found 9 (40 requested) and removed 28 (20 requested) atoms. Cycle 8: After refmac, R = 0.2045 (Rfree = 0.000) for 5349 atoms. Found 10 (40 requested) and removed 21 (20 requested) atoms. Cycle 9: After refmac, R = 0.2000 (Rfree = 0.000) for 5334 atoms. Found 8 (40 requested) and removed 22 (20 requested) atoms. Cycle 10: After refmac, R = 0.2011 (Rfree = 0.000) for 5320 atoms. Found 11 (40 requested) and removed 21 (20 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.25 3.47 Search for helices and strands: 0 residues in 0 chains, 5533 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 5557 seeds are put forward Round 1: 359 peptides, 61 chains. Longest chain 18 peptides. Score 0.437 Round 2: 418 peptides, 62 chains. Longest chain 16 peptides. Score 0.542 Round 3: 413 peptides, 59 chains. Longest chain 15 peptides. Score 0.557 Round 4: 429 peptides, 57 chains. Longest chain 20 peptides. Score 0.598 Round 5: 409 peptides, 54 chains. Longest chain 20 peptides. Score 0.587 Taking the results from Round 4 Chains 57, Residues 372, Estimated correctness of the model 28.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10631 reflections ( 99.67 % complete ) and 12293 restraints for refining 5390 atoms. 10862 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2314 (Rfree = 0.000) for 5390 atoms. Found 26 (40 requested) and removed 26 (20 requested) atoms. Cycle 12: After refmac, R = 0.2162 (Rfree = 0.000) for 5374 atoms. Found 14 (40 requested) and removed 25 (20 requested) atoms. Cycle 13: After refmac, R = 0.2080 (Rfree = 0.000) for 5355 atoms. Found 7 (40 requested) and removed 23 (20 requested) atoms. Cycle 14: After refmac, R = 0.2097 (Rfree = 0.000) for 5336 atoms. Found 3 (40 requested) and removed 24 (20 requested) atoms. Cycle 15: After refmac, R = 0.2003 (Rfree = 0.000) for 5313 atoms. Found 8 (40 requested) and removed 20 (20 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.23 3.45 Search for helices and strands: 0 residues in 0 chains, 5483 seeds are put forward NCS extension: 25 residues added (4 deleted due to clashes), 5508 seeds are put forward Round 1: 349 peptides, 59 chains. Longest chain 15 peptides. Score 0.434 Round 2: 392 peptides, 58 chains. Longest chain 18 peptides. Score 0.527 Round 3: 392 peptides, 54 chains. Longest chain 17 peptides. Score 0.558 Round 4: 394 peptides, 56 chains. Longest chain 17 peptides. Score 0.546 Round 5: 394 peptides, 54 chains. Longest chain 24 peptides. Score 0.562 Taking the results from Round 5 Chains 57, Residues 340, Estimated correctness of the model 15.8 % 4 chains (39 residues) have been docked in sequence ------------------------------------------------------ 10631 reflections ( 99.67 % complete ) and 12042 restraints for refining 5390 atoms. 10617 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2302 (Rfree = 0.000) for 5390 atoms. Found 18 (40 requested) and removed 38 (20 requested) atoms. Cycle 17: After refmac, R = 0.2176 (Rfree = 0.000) for 5360 atoms. Found 9 (40 requested) and removed 28 (20 requested) atoms. Cycle 18: After refmac, R = 0.2126 (Rfree = 0.000) for 5339 atoms. Found 11 (40 requested) and removed 22 (20 requested) atoms. Cycle 19: After refmac, R = 0.2078 (Rfree = 0.000) for 5326 atoms. Found 5 (40 requested) and removed 20 (20 requested) atoms. Cycle 20: After refmac, R = 0.2065 (Rfree = 0.000) for 5311 atoms. Found 5 (40 requested) and removed 21 (20 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.26 3.49 Search for helices and strands: 0 residues in 0 chains, 5481 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 5499 seeds are put forward Round 1: 340 peptides, 57 chains. Longest chain 22 peptides. Score 0.433 Round 2: 386 peptides, 56 chains. Longest chain 16 peptides. Score 0.532 Round 3: 392 peptides, 53 chains. Longest chain 30 peptides. Score 0.566 Round 4: 387 peptides, 55 chains. Longest chain 25 peptides. Score 0.542 Round 5: 408 peptides, 56 chains. Longest chain 16 peptides. Score 0.571 Taking the results from Round 5 Chains 56, Residues 352, Estimated correctness of the model 18.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10631 reflections ( 99.67 % complete ) and 12412 restraints for refining 5389 atoms. 11060 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2296 (Rfree = 0.000) for 5389 atoms. Found 20 (40 requested) and removed 32 (20 requested) atoms. Cycle 22: After refmac, R = 0.2241 (Rfree = 0.000) for 5363 atoms. Found 15 (40 requested) and removed 38 (20 requested) atoms. Cycle 23: After refmac, R = 0.2029 (Rfree = 0.000) for 5333 atoms. Found 7 (40 requested) and removed 22 (20 requested) atoms. Cycle 24: After refmac, R = 0.1942 (Rfree = 0.000) for 5318 atoms. Found 7 (40 requested) and removed 21 (20 requested) atoms. Cycle 25: After refmac, R = 0.1932 (Rfree = 0.000) for 5302 atoms. Found 9 (40 requested) and removed 22 (20 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.23 3.45 Search for helices and strands: 0 residues in 0 chains, 5504 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 5520 seeds are put forward Round 1: 323 peptides, 56 chains. Longest chain 17 peptides. Score 0.406 Round 2: 365 peptides, 53 chains. Longest chain 26 peptides. Score 0.517 Round 3: 376 peptides, 52 chains. Longest chain 19 peptides. Score 0.546 Round 4: 357 peptides, 50 chains. Longest chain 21 peptides. Score 0.527 Round 5: 370 peptides, 52 chains. Longest chain 25 peptides. Score 0.535 Taking the results from Round 3 Chains 54, Residues 324, Estimated correctness of the model 10.1 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 10631 reflections ( 99.67 % complete ) and 12344 restraints for refining 5390 atoms. 11058 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2146 (Rfree = 0.000) for 5390 atoms. Found 26 (40 requested) and removed 29 (20 requested) atoms. Cycle 27: After refmac, R = 0.1996 (Rfree = 0.000) for 5378 atoms. Found 14 (40 requested) and removed 21 (20 requested) atoms. Cycle 28: After refmac, R = 0.1934 (Rfree = 0.000) for 5367 atoms. Found 8 (40 requested) and removed 22 (20 requested) atoms. Cycle 29: After refmac, R = 0.1902 (Rfree = 0.000) for 5352 atoms. Found 9 (40 requested) and removed 21 (20 requested) atoms. Cycle 30: After refmac, R = 0.1880 (Rfree = 0.000) for 5338 atoms. Found 8 (40 requested) and removed 20 (20 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.23 3.45 Search for helices and strands: 0 residues in 0 chains, 5503 seeds are put forward NCS extension: 12 residues added (4 deleted due to clashes), 5515 seeds are put forward Round 1: 311 peptides, 51 chains. Longest chain 17 peptides. Score 0.427 Round 2: 354 peptides, 52 chains. Longest chain 28 peptides. Score 0.505 Round 3: 363 peptides, 52 chains. Longest chain 25 peptides. Score 0.522 Round 4: 361 peptides, 53 chains. Longest chain 19 peptides. Score 0.510 Round 5: 342 peptides, 52 chains. Longest chain 22 peptides. Score 0.482 Taking the results from Round 3 Chains 53, Residues 311, Estimated correctness of the model 1.2 % 1 chains (17 residues) have been docked in sequence ------------------------------------------------------ 10631 reflections ( 99.67 % complete ) and 12483 restraints for refining 5390 atoms. 11236 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2063 (Rfree = 0.000) for 5390 atoms. Found 23 (40 requested) and removed 24 (20 requested) atoms. Cycle 32: After refmac, R = 0.1874 (Rfree = 0.000) for 5378 atoms. Found 12 (40 requested) and removed 23 (20 requested) atoms. Cycle 33: After refmac, R = 0.1796 (Rfree = 0.000) for 5363 atoms. Found 5 (40 requested) and removed 20 (20 requested) atoms. Cycle 34: After refmac, R = 0.1784 (Rfree = 0.000) for 5348 atoms. Found 7 (40 requested) and removed 23 (20 requested) atoms. Cycle 35: After refmac, R = 0.1795 (Rfree = 0.000) for 5328 atoms. Found 12 (40 requested) and removed 22 (20 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.21 3.43 Search for helices and strands: 0 residues in 0 chains, 5456 seeds are put forward NCS extension: 19 residues added (3 deleted due to clashes), 5475 seeds are put forward Round 1: 308 peptides, 54 chains. Longest chain 18 peptides. Score 0.392 Round 2: 320 peptides, 48 chains. Longest chain 17 peptides. Score 0.473 Round 3: 330 peptides, 49 chains. Longest chain 18 peptides. Score 0.484 Round 4: 327 peptides, 50 chains. Longest chain 17 peptides. Score 0.469 Round 5: 346 peptides, 51 chains. Longest chain 17 peptides. Score 0.498 Taking the results from Round 5 Chains 51, Residues 295, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10631 reflections ( 99.67 % complete ) and 12768 restraints for refining 5390 atoms. 11639 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2086 (Rfree = 0.000) for 5390 atoms. Found 20 (40 requested) and removed 28 (20 requested) atoms. Cycle 37: After refmac, R = 0.1908 (Rfree = 0.000) for 5376 atoms. Found 10 (40 requested) and removed 21 (20 requested) atoms. Cycle 38: After refmac, R = 0.1835 (Rfree = 0.000) for 5364 atoms. Found 7 (40 requested) and removed 22 (20 requested) atoms. Cycle 39: After refmac, R = 0.1849 (Rfree = 0.000) for 5346 atoms. Found 6 (40 requested) and removed 20 (20 requested) atoms. Cycle 40: After refmac, R = 0.1860 (Rfree = 0.000) for 5329 atoms. Found 7 (40 requested) and removed 22 (20 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.23 3.45 Search for helices and strands: 0 residues in 0 chains, 5508 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 5526 seeds are put forward Round 1: 295 peptides, 57 chains. Longest chain 10 peptides. Score 0.334 Round 2: 327 peptides, 54 chains. Longest chain 16 peptides. Score 0.433 Round 3: 316 peptides, 50 chains. Longest chain 16 peptides. Score 0.447 Round 4: 327 peptides, 51 chains. Longest chain 16 peptides. Score 0.460 Round 5: 326 peptides, 49 chains. Longest chain 17 peptides. Score 0.476 Taking the results from Round 5 Chains 50, Residues 277, Estimated correctness of the model 0.0 % 2 chains (26 residues) have been docked in sequence ------------------------------------------------------ 10631 reflections ( 99.67 % complete ) and 12410 restraints for refining 5390 atoms. 11253 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1982 (Rfree = 0.000) for 5390 atoms. Found 23 (40 requested) and removed 29 (20 requested) atoms. Cycle 42: After refmac, R = 0.1870 (Rfree = 0.000) for 5371 atoms. Found 13 (40 requested) and removed 27 (20 requested) atoms. Cycle 43: After refmac, R = 0.1785 (Rfree = 0.000) for 5351 atoms. Found 7 (40 requested) and removed 22 (20 requested) atoms. Cycle 44: After refmac, R = 0.1786 (Rfree = 0.000) for 5331 atoms. Found 10 (40 requested) and removed 20 (20 requested) atoms. Cycle 45: After refmac, R = 0.1720 (Rfree = 0.000) for 5320 atoms. Found 6 (40 requested) and removed 21 (20 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.20 3.42 Search for helices and strands: 0 residues in 0 chains, 5495 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 5509 seeds are put forward Round 1: 283 peptides, 56 chains. Longest chain 10 peptides. Score 0.316 Round 2: 290 peptides, 51 chains. Longest chain 14 peptides. Score 0.381 Round 3: 308 peptides, 52 chains. Longest chain 18 peptides. Score 0.411 Round 4: 322 peptides, 51 chains. Longest chain 20 peptides. Score 0.450 Round 5: 323 peptides, 52 chains. Longest chain 18 peptides. Score 0.443 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 51, Residues 271, 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 1vr0-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 10631 reflections ( 99.67 % complete ) and 12656 restraints for refining 5390 atoms. 11623 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1891 (Rfree = 0.000) for 5390 atoms. Found 0 (40 requested) and removed 20 (20 requested) atoms. Cycle 47: After refmac, R = 0.1847 (Rfree = 0.000) for 5361 atoms. Found 0 (40 requested) and removed 19 (20 requested) atoms. Cycle 48: After refmac, R = 0.1822 (Rfree = 0.000) for 5340 atoms. Found 0 (40 requested) and removed 6 (20 requested) atoms. Cycle 49: After refmac, R = 0.1826 (Rfree = 0.000) for 5333 atoms. Found 0 (40 requested) and removed 6 (20 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 21:07:15 GMT 2018 Job finished. TimeTaking 99.3 Used memory is bytes: 6728176