null Mon 24 Dec 07:49:49 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 1vr0-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vr0-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vr0-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vr0-3.8-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/1vr0-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vr0-3.8-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 07:49:53 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/1vr0-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vr0-3.8-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 479 and 0 Target number of residues in the AU: 479 Target solvent content: 0.6461 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: 1vr0-3.8-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: 20 Cell parameters: 46.686 69.193 453.518 90.000 90.000 90.000 Input sequence file: 1vr0-3.8-parrot-noncs.fasta_lf Building free atoms model in initial map for 5928 target number of atoms Had to go as low as 0.70 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 3.800 Wilson plot Bfac: 75.70 7656 reflections ( 99.57 % complete ) and 0 restraints for refining 6547 atoms. Observations/parameters ratio is 0.29 ------------------------------------------------------ Starting model: R = 0.3349 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3262 (Rfree = 0.000) for 6547 atoms. Found 36 (36 requested) and removed 48 (18 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.58 3.83 Search for helices and strands: 0 residues in 0 chains, 6662 seeds are put forward NCS extension: 0 residues added, 6662 seeds are put forward Round 1: 264 peptides, 54 chains. Longest chain 10 peptides. Score 0.290 Round 2: 335 peptides, 59 chains. Longest chain 16 peptides. Score 0.404 Round 3: 348 peptides, 50 chains. Longest chain 18 peptides. Score 0.510 Round 4: 356 peptides, 58 chains. Longest chain 15 peptides. Score 0.457 Round 5: 356 peptides, 54 chains. Longest chain 15 peptides. Score 0.492 Taking the results from Round 3 Chains 50, Residues 298, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7656 reflections ( 99.57 % complete ) and 12810 restraints for refining 5362 atoms. 11668 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2785 (Rfree = 0.000) for 5362 atoms. Found 19 (29 requested) and removed 39 (14 requested) atoms. Cycle 2: After refmac, R = 0.2485 (Rfree = 0.000) for 5257 atoms. Found 27 (29 requested) and removed 36 (14 requested) atoms. Cycle 3: After refmac, R = 0.2369 (Rfree = 0.000) for 5193 atoms. Found 28 (28 requested) and removed 33 (14 requested) atoms. Cycle 4: After refmac, R = 0.2285 (Rfree = 0.000) for 5141 atoms. Found 28 (28 requested) and removed 24 (14 requested) atoms. Cycle 5: After refmac, R = 0.2254 (Rfree = 0.000) for 5112 atoms. Found 24 (28 requested) and removed 31 (14 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.56 3.81 Search for helices and strands: 0 residues in 0 chains, 5284 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 5306 seeds are put forward Round 1: 292 peptides, 55 chains. Longest chain 11 peptides. Score 0.347 Round 2: 341 peptides, 52 chains. Longest chain 21 peptides. Score 0.480 Round 3: 347 peptides, 48 chains. Longest chain 18 peptides. Score 0.525 Round 4: 344 peptides, 52 chains. Longest chain 21 peptides. Score 0.486 Round 5: 367 peptides, 52 chains. Longest chain 16 peptides. Score 0.529 Taking the results from Round 5 Chains 52, Residues 315, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7656 reflections ( 99.57 % complete ) and 12160 restraints for refining 5250 atoms. 10952 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2237 (Rfree = 0.000) for 5250 atoms. Found 16 (28 requested) and removed 55 (14 requested) atoms. Cycle 7: After refmac, R = 0.2061 (Rfree = 0.000) for 5169 atoms. Found 20 (28 requested) and removed 29 (14 requested) atoms. Cycle 8: After refmac, R = 0.2033 (Rfree = 0.000) for 5139 atoms. Found 19 (28 requested) and removed 27 (14 requested) atoms. Cycle 9: After refmac, R = 0.1919 (Rfree = 0.000) for 5115 atoms. Found 22 (28 requested) and removed 36 (14 requested) atoms. Cycle 10: After refmac, R = 0.1467 (Rfree = 0.000) for 5095 atoms. Found 3 (28 requested) and removed 21 (14 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.53 3.77 Search for helices and strands: 0 residues in 0 chains, 5303 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 5318 seeds are put forward Round 1: 314 peptides, 62 chains. Longest chain 12 peptides. Score 0.329 Round 2: 345 peptides, 60 chains. Longest chain 13 peptides. Score 0.417 Round 3: 347 peptides, 55 chains. Longest chain 14 peptides. Score 0.465 Round 4: 354 peptides, 54 chains. Longest chain 14 peptides. Score 0.488 Round 5: 357 peptides, 49 chains. Longest chain 15 peptides. Score 0.535 Taking the results from Round 5 Chains 49, Residues 308, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7656 reflections ( 99.57 % complete ) and 12403 restraints for refining 5360 atoms. 11220 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2046 (Rfree = 0.000) for 5360 atoms. Found 17 (29 requested) and removed 34 (14 requested) atoms. Cycle 12: After refmac, R = 0.1916 (Rfree = 0.000) for 5318 atoms. Found 23 (29 requested) and removed 34 (14 requested) atoms. Cycle 13: After refmac, R = 0.1921 (Rfree = 0.000) for 5290 atoms. Found 24 (29 requested) and removed 27 (14 requested) atoms. Cycle 14: After refmac, R = 0.1819 (Rfree = 0.000) for 5276 atoms. Found 21 (29 requested) and removed 32 (14 requested) atoms. Cycle 15: After refmac, R = 0.1851 (Rfree = 0.000) for 5258 atoms. Found 28 (28 requested) and removed 27 (14 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.52 3.76 Search for helices and strands: 0 residues in 0 chains, 5481 seeds are put forward NCS extension: 19 residues added (3 deleted due to clashes), 5500 seeds are put forward Round 1: 316 peptides, 63 chains. Longest chain 10 peptides. Score 0.324 Round 2: 328 peptides, 58 chains. Longest chain 13 peptides. Score 0.399 Round 3: 337 peptides, 57 chains. Longest chain 18 peptides. Score 0.427 Round 4: 358 peptides, 54 chains. Longest chain 18 peptides. Score 0.496 Round 5: 357 peptides, 55 chains. Longest chain 20 peptides. Score 0.485 Taking the results from Round 4 Chains 54, Residues 304, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7656 reflections ( 99.57 % complete ) and 12274 restraints for refining 5362 atoms. 11112 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1998 (Rfree = 0.000) for 5362 atoms. Found 17 (29 requested) and removed 28 (14 requested) atoms. Cycle 17: After refmac, R = 0.1889 (Rfree = 0.000) for 5307 atoms. Found 16 (29 requested) and removed 23 (14 requested) atoms. Cycle 18: After refmac, R = 0.1820 (Rfree = 0.000) for 5281 atoms. Found 15 (29 requested) and removed 29 (14 requested) atoms. Cycle 19: After refmac, R = 0.1855 (Rfree = 0.000) for 5247 atoms. Found 20 (28 requested) and removed 24 (14 requested) atoms. Cycle 20: After refmac, R = 0.1730 (Rfree = 0.000) for 5228 atoms. Found 15 (28 requested) and removed 20 (14 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.52 3.76 Search for helices and strands: 0 residues in 0 chains, 5414 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 5437 seeds are put forward Round 1: 272 peptides, 56 chains. Longest chain 8 peptides. Score 0.289 Round 2: 321 peptides, 59 chains. Longest chain 12 peptides. Score 0.374 Round 3: 334 peptides, 59 chains. Longest chain 13 peptides. Score 0.402 Round 4: 341 peptides, 57 chains. Longest chain 13 peptides. Score 0.435 Round 5: 341 peptides, 55 chains. Longest chain 14 peptides. Score 0.453 Taking the results from Round 5 Chains 55, Residues 286, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7656 reflections ( 99.57 % complete ) and 12699 restraints for refining 5362 atoms. 11610 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2021 (Rfree = 0.000) for 5362 atoms. Found 23 (29 requested) and removed 28 (14 requested) atoms. Cycle 22: After refmac, R = 0.1872 (Rfree = 0.000) for 5322 atoms. Found 18 (29 requested) and removed 21 (14 requested) atoms. Cycle 23: After refmac, R = 0.1791 (Rfree = 0.000) for 5308 atoms. Found 29 (29 requested) and removed 28 (14 requested) atoms. Cycle 24: After refmac, R = 0.1727 (Rfree = 0.000) for 5302 atoms. Found 27 (29 requested) and removed 20 (14 requested) atoms. Cycle 25: After refmac, R = 0.1285 (Rfree = 0.000) for 5306 atoms. Found 7 (29 requested) and removed 17 (14 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.53 3.77 Search for helices and strands: 0 residues in 0 chains, 5499 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 5520 seeds are put forward Round 1: 296 peptides, 64 chains. Longest chain 8 peptides. Score 0.267 Round 2: 336 peptides, 58 chains. Longest chain 14 peptides. Score 0.416 Round 3: 335 peptides, 56 chains. Longest chain 11 peptides. Score 0.432 Round 4: 338 peptides, 59 chains. Longest chain 15 peptides. Score 0.411 Round 5: 320 peptides, 55 chains. Longest chain 11 peptides. Score 0.409 Taking the results from Round 3 Chains 56, Residues 279, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7656 reflections ( 99.57 % complete ) and 12554 restraints for refining 5362 atoms. 11494 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1914 (Rfree = 0.000) for 5362 atoms. Found 29 (29 requested) and removed 24 (14 requested) atoms. Cycle 27: After refmac, R = 0.1713 (Rfree = 0.000) for 5334 atoms. Found 28 (29 requested) and removed 19 (14 requested) atoms. Cycle 28: After refmac, R = 0.1707 (Rfree = 0.000) for 5328 atoms. Found 29 (29 requested) and removed 23 (14 requested) atoms. Cycle 29: After refmac, R = 0.1668 (Rfree = 0.000) for 5324 atoms. Found 29 (29 requested) and removed 20 (14 requested) atoms. Cycle 30: After refmac, R = 0.1280 (Rfree = 0.000) for 5322 atoms. Found 4 (29 requested) and removed 17 (14 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.52 3.76 Search for helices and strands: 0 residues in 0 chains, 5528 seeds are put forward NCS extension: 9 residues added (0 deleted due to clashes), 5537 seeds are put forward Round 1: 252 peptides, 52 chains. Longest chain 13 peptides. Score 0.281 Round 2: 290 peptides, 49 chains. Longest chain 15 peptides. Score 0.400 Round 3: 295 peptides, 51 chains. Longest chain 12 peptides. Score 0.392 Round 4: 297 peptides, 50 chains. Longest chain 13 peptides. Score 0.406 Round 5: 333 peptides, 52 chains. Longest chain 15 peptides. Score 0.464 Taking the results from Round 5 Chains 52, Residues 281, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7656 reflections ( 99.57 % complete ) and 12748 restraints for refining 5361 atoms. 11676 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1945 (Rfree = 0.000) for 5361 atoms. Found 17 (29 requested) and removed 30 (14 requested) atoms. Cycle 32: After refmac, R = 0.1867 (Rfree = 0.000) for 5326 atoms. Found 25 (29 requested) and removed 22 (14 requested) atoms. Cycle 33: After refmac, R = 0.1839 (Rfree = 0.000) for 5312 atoms. Found 29 (29 requested) and removed 27 (14 requested) atoms. Cycle 34: After refmac, R = 0.1783 (Rfree = 0.000) for 5303 atoms. Found 27 (29 requested) and removed 22 (14 requested) atoms. Cycle 35: After refmac, R = 0.1338 (Rfree = 0.000) for 5302 atoms. Found 6 (29 requested) and removed 16 (14 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.53 3.77 Search for helices and strands: 0 residues in 0 chains, 5510 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 5525 seeds are put forward Round 1: 229 peptides, 46 chains. Longest chain 9 peptides. Score 0.287 Round 2: 278 peptides, 53 chains. Longest chain 10 peptides. Score 0.334 Round 3: 264 peptides, 46 chains. Longest chain 15 peptides. Score 0.371 Round 4: 257 peptides, 45 chains. Longest chain 14 peptides. Score 0.365 Round 5: 270 peptides, 46 chains. Longest chain 15 peptides. Score 0.385 Taking the results from Round 5 Chains 46, Residues 224, Estimated correctness of the model 0.0 % 3 chains (21 residues) have been docked in sequence ------------------------------------------------------ 7656 reflections ( 99.57 % complete ) and 12807 restraints for refining 5362 atoms. 11897 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1899 (Rfree = 0.000) for 5362 atoms. Found 14 (29 requested) and removed 33 (14 requested) atoms. Cycle 37: After refmac, R = 0.1660 (Rfree = 0.000) for 5324 atoms. Found 17 (29 requested) and removed 24 (14 requested) atoms. Cycle 38: After refmac, R = 0.1695 (Rfree = 0.000) for 5306 atoms. Found 17 (29 requested) and removed 16 (14 requested) atoms. Cycle 39: After refmac, R = 0.1629 (Rfree = 0.000) for 5298 atoms. Found 26 (29 requested) and removed 17 (14 requested) atoms. Cycle 40: After refmac, R = 0.1592 (Rfree = 0.000) for 5302 atoms. Found 25 (29 requested) and removed 15 (14 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.51 3.75 Search for helices and strands: 0 residues in 0 chains, 5493 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 5506 seeds are put forward Round 1: 225 peptides, 49 chains. Longest chain 7 peptides. Score 0.245 Round 2: 250 peptides, 46 chains. Longest chain 10 peptides. Score 0.338 Round 3: 250 peptides, 41 chains. Longest chain 15 peptides. Score 0.389 Round 4: 239 peptides, 42 chains. Longest chain 13 peptides. Score 0.353 Round 5: 242 peptides, 43 chains. Longest chain 14 peptides. Score 0.350 Taking the results from Round 3 Chains 41, Residues 209, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7656 reflections ( 99.57 % complete ) and 12790 restraints for refining 5362 atoms. 11995 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1758 (Rfree = 0.000) for 5362 atoms. Found 29 (29 requested) and removed 19 (14 requested) atoms. Cycle 42: After refmac, R = 0.1841 (Rfree = 0.000) for 5347 atoms. Found 29 (29 requested) and removed 24 (14 requested) atoms. Cycle 43: After refmac, R = 0.1805 (Rfree = 0.000) for 5335 atoms. Found 29 (29 requested) and removed 24 (14 requested) atoms. Cycle 44: After refmac, R = 0.1267 (Rfree = 0.000) for 5325 atoms. Found 9 (29 requested) and removed 19 (14 requested) atoms. Cycle 45: After refmac, R = 0.1124 (Rfree = 0.000) for 5307 atoms. Found 5 (29 requested) and removed 19 (14 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.54 3.78 Search for helices and strands: 0 residues in 0 chains, 5449 seeds are put forward NCS extension: 28 residues added (2 deleted due to clashes), 5477 seeds are put forward Round 1: 208 peptides, 44 chains. Longest chain 7 peptides. Score 0.255 Round 2: 230 peptides, 44 chains. Longest chain 9 peptides. Score 0.311 Round 3: 254 peptides, 44 chains. Longest chain 10 peptides. Score 0.368 Round 4: 239 peptides, 42 chains. Longest chain 10 peptides. Score 0.353 Round 5: 248 peptides, 40 chains. Longest chain 13 peptides. Score 0.394 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 40, Residues 208, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence Sequence coverage is 3 % Consider running further cycles of model building using 1vr0-3_warpNtrace.pdb as input Building loops using Loopy2018 40 chains (208 residues) following loop building 2 chains (8 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7656 reflections ( 99.57 % complete ) and 12740 restraints for refining 5328 atoms. 11929 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1798 (Rfree = 0.000) for 5328 atoms. Found 0 (29 requested) and removed 14 (14 requested) atoms. Cycle 47: After refmac, R = 0.1935 (Rfree = 0.000) for 5294 atoms. Found 0 (29 requested) and removed 14 (14 requested) atoms. Cycle 48: After refmac, R = 0.1926 (Rfree = 0.000) for 5261 atoms. Found 0 (29 requested) and removed 14 (14 requested) atoms. Cycle 49: After refmac, R = 0.1809 (Rfree = 0.000) for 5241 atoms. Found 0 (28 requested) and removed 14 (14 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:47:15 GMT 2018 Job finished. TimeTaking 57.44 Used memory is bytes: 19307360