Mon 24 Dec 00:46:38 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vkz-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vkz-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vkz-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkz-3.8-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/1vkz-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkz-3.8-parrot-mrncs ############### 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 00:46:48 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/mrncs/ArpWArp/wArpResults/WorkingDir/1vkz-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkz-3.8-parrot-mrncs/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 627 and 0 Target number of residues in the AU: 627 Target solvent content: 0.5993 Checking the provided sequence file Detected sequence length: 412 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 824 Adjusted target solvent content: 0.47 Input MTZ file: 1vkz-3.8-parrot-mrncs.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: 63.745 78.443 85.018 90.000 95.062 90.000 Input sequence file: 1vkz-3.8-parrot-mrncs.fasta_lf Building free atoms model in initial map for 6592 target number of atoms Had to go as low as 0.60 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: 19.959 3.800 Wilson plot Bfac: 52.34 8080 reflections ( 96.28 % complete ) and 0 restraints for refining 7284 atoms. Observations/parameters ratio is 0.28 ------------------------------------------------------ Starting model: R = 0.2930 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2860 (Rfree = 0.000) for 7284 atoms. Found 40 (40 requested) and removed 39 (20 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.23 3.36 Search for helices and strands: 0 residues in 0 chains, 7407 seeds are put forward NCS extension: 0 residues added, 7407 seeds are put forward Round 1: 239 peptides, 50 chains. Longest chain 9 peptides. Score 0.260 Round 2: 361 peptides, 66 chains. Longest chain 12 peptides. Score 0.372 Round 3: 390 peptides, 65 chains. Longest chain 14 peptides. Score 0.435 Round 4: 418 peptides, 69 chains. Longest chain 13 peptides. Score 0.454 Round 5: 418 peptides, 66 chains. Longest chain 15 peptides. Score 0.476 Taking the results from Round 5 Chains 70, Residues 352, Estimated correctness of the model 0.0 % 9 chains (59 residues) have been docked in sequence ------------------------------------------------------ 8080 reflections ( 96.28 % complete ) and 13246 restraints for refining 5960 atoms. 11689 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2413 (Rfree = 0.000) for 5960 atoms. Found 29 (32 requested) and removed 56 (16 requested) atoms. Cycle 2: After refmac, R = 0.2173 (Rfree = 0.000) for 5823 atoms. Found 25 (32 requested) and removed 36 (16 requested) atoms. Cycle 3: After refmac, R = 0.2019 (Rfree = 0.000) for 5751 atoms. Found 15 (31 requested) and removed 36 (15 requested) atoms. Cycle 4: After refmac, R = 0.1976 (Rfree = 0.000) for 5696 atoms. Found 22 (31 requested) and removed 24 (15 requested) atoms. Cycle 5: After refmac, R = 0.1888 (Rfree = 0.000) for 5673 atoms. Found 10 (31 requested) and removed 26 (15 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.23 3.36 Search for helices and strands: 0 residues in 0 chains, 5848 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 5864 seeds are put forward Round 1: 392 peptides, 71 chains. Longest chain 14 peptides. Score 0.391 Round 2: 459 peptides, 72 chains. Longest chain 20 peptides. Score 0.501 Round 3: 462 peptides, 73 chains. Longest chain 20 peptides. Score 0.499 Round 4: 463 peptides, 63 chains. Longest chain 30 peptides. Score 0.569 Round 5: 458 peptides, 70 chains. Longest chain 18 peptides. Score 0.514 Taking the results from Round 4 Chains 68, Residues 400, Estimated correctness of the model 0.0 % 7 chains (55 residues) have been docked in sequence ------------------------------------------------------ 8080 reflections ( 96.28 % complete ) and 12824 restraints for refining 5878 atoms. 11124 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2121 (Rfree = 0.000) for 5878 atoms. Found 28 (32 requested) and removed 58 (16 requested) atoms. Cycle 7: After refmac, R = 0.1888 (Rfree = 0.000) for 5783 atoms. Found 20 (32 requested) and removed 31 (16 requested) atoms. Cycle 8: After refmac, R = 0.1761 (Rfree = 0.000) for 5747 atoms. Found 5 (31 requested) and removed 31 (15 requested) atoms. Cycle 9: After refmac, R = 0.1777 (Rfree = 0.000) for 5710 atoms. Found 12 (31 requested) and removed 31 (15 requested) atoms. Cycle 10: After refmac, R = 0.1715 (Rfree = 0.000) for 5684 atoms. Found 3 (31 requested) and removed 21 (15 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.29 3.42 Search for helices and strands: 0 residues in 0 chains, 5816 seeds are put forward NCS extension: 32 residues added (3 deleted due to clashes), 5848 seeds are put forward Round 1: 401 peptides, 78 chains. Longest chain 13 peptides. Score 0.352 Round 2: 431 peptides, 68 chains. Longest chain 20 peptides. Score 0.483 Round 3: 459 peptides, 68 chains. Longest chain 22 peptides. Score 0.529 Round 4: 442 peptides, 62 chains. Longest chain 21 peptides. Score 0.544 Round 5: 475 peptides, 64 chains. Longest chain 26 peptides. Score 0.580 Taking the results from Round 5 Chains 67, Residues 411, Estimated correctness of the model 0.0 % 3 chains (30 residues) have been docked in sequence ------------------------------------------------------ 8080 reflections ( 96.28 % complete ) and 13203 restraints for refining 5962 atoms. 11503 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2103 (Rfree = 0.000) for 5962 atoms. Found 30 (32 requested) and removed 51 (16 requested) atoms. Failed to save intermediate PDB Cycle 12: After refmac, R = 0.1917 (Rfree = 0.000) for 5889 atoms. Found 17 (32 requested) and removed 39 (16 requested) atoms. Cycle 13: After refmac, R = 0.1814 (Rfree = 0.000) for 5854 atoms. Found 6 (32 requested) and removed 31 (16 requested) atoms. Cycle 14: After refmac, R = 0.1769 (Rfree = 0.000) for 5817 atoms. Found 7 (32 requested) and removed 28 (16 requested) atoms. Cycle 15: After refmac, R = 0.1743 (Rfree = 0.000) for 5791 atoms. Found 5 (31 requested) and removed 30 (15 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.27 3.40 Search for helices and strands: 0 residues in 0 chains, 5952 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 5973 seeds are put forward Round 1: 396 peptides, 69 chains. Longest chain 17 peptides. Score 0.414 Round 2: 404 peptides, 62 chains. Longest chain 17 peptides. Score 0.482 Round 3: 427 peptides, 61 chains. Longest chain 25 peptides. Score 0.527 Round 4: 422 peptides, 58 chains. Longest chain 20 peptides. Score 0.540 Round 5: 418 peptides, 60 chains. Longest chain 22 peptides. Score 0.520 Taking the results from Round 4 Chains 58, Residues 364, Estimated correctness of the model 0.0 % 4 chains (27 residues) have been docked in sequence ------------------------------------------------------ 8080 reflections ( 96.28 % complete ) and 13494 restraints for refining 5963 atoms. 12003 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2043 (Rfree = 0.000) for 5963 atoms. Found 30 (32 requested) and removed 42 (16 requested) atoms. Cycle 17: After refmac, R = 0.2083 (Rfree = 0.000) for 5884 atoms. Found 32 (32 requested) and removed 22 (16 requested) atoms. Cycle 18: After refmac, R = 0.2170 (Rfree = 0.000) for 5844 atoms. Found 32 (32 requested) and removed 33 (16 requested) atoms. Cycle 19: After refmac, R = 0.2196 (Rfree = 0.000) for 5790 atoms. Found 32 (32 requested) and removed 35 (16 requested) atoms. Cycle 20: After refmac, R = 0.2130 (Rfree = 0.000) for 5747 atoms. Found 31 (31 requested) and removed 24 (15 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.22 3.35 Search for helices and strands: 0 residues in 0 chains, 5885 seeds are put forward NCS extension: 37 residues added (1 deleted due to clashes), 5922 seeds are put forward Round 1: 317 peptides, 64 chains. Longest chain 12 peptides. Score 0.301 Round 2: 368 peptides, 62 chains. Longest chain 14 peptides. Score 0.418 Round 3: 392 peptides, 63 chains. Longest chain 16 peptides. Score 0.454 Round 4: 409 peptides, 59 chains. Longest chain 15 peptides. Score 0.512 Round 5: 415 peptides, 62 chains. Longest chain 16 peptides. Score 0.501 Taking the results from Round 4 Chains 63, Residues 350, Estimated correctness of the model 0.0 % 7 chains (60 residues) have been docked in sequence ------------------------------------------------------ 8080 reflections ( 96.28 % complete ) and 12681 restraints for refining 5850 atoms. 11112 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2202 (Rfree = 0.000) for 5850 atoms. Found 32 (32 requested) and removed 53 (16 requested) atoms. Cycle 22: After refmac, R = 0.2065 (Rfree = 0.000) for 5772 atoms. Found 32 (32 requested) and removed 44 (16 requested) atoms. Cycle 23: After refmac, R = 0.1833 (Rfree = 0.000) for 5734 atoms. Found 17 (31 requested) and removed 25 (15 requested) atoms. Cycle 24: After refmac, R = 0.1683 (Rfree = 0.000) for 5705 atoms. Found 7 (31 requested) and removed 28 (15 requested) atoms. Cycle 25: After refmac, R = 0.1655 (Rfree = 0.000) for 5669 atoms. Found 2 (31 requested) and removed 21 (15 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.24 3.37 Search for helices and strands: 0 residues in 0 chains, 5810 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 5829 seeds are put forward Round 1: 326 peptides, 63 chains. Longest chain 10 peptides. Score 0.328 Round 2: 397 peptides, 66 chains. Longest chain 16 peptides. Score 0.439 Round 3: 408 peptides, 65 chains. Longest chain 12 peptides. Score 0.466 Round 4: 389 peptides, 64 chains. Longest chain 12 peptides. Score 0.441 Round 5: 395 peptides, 64 chains. Longest chain 16 peptides. Score 0.451 Taking the results from Round 3 Chains 66, Residues 343, Estimated correctness of the model 0.0 % 6 chains (33 residues) have been docked in sequence ------------------------------------------------------ 8080 reflections ( 96.28 % complete ) and 13165 restraints for refining 5875 atoms. 11776 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2074 (Rfree = 0.000) for 5875 atoms. Found 32 (32 requested) and removed 49 (16 requested) atoms. Cycle 27: After refmac, R = 0.1908 (Rfree = 0.000) for 5822 atoms. Found 18 (32 requested) and removed 26 (16 requested) atoms. Cycle 28: After refmac, R = 0.1857 (Rfree = 0.000) for 5798 atoms. Found 10 (31 requested) and removed 22 (15 requested) atoms. Cycle 29: After refmac, R = 0.1834 (Rfree = 0.000) for 5782 atoms. Found 12 (31 requested) and removed 22 (15 requested) atoms. Cycle 30: After refmac, R = 0.1830 (Rfree = 0.000) for 5765 atoms. Found 12 (31 requested) and removed 18 (15 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.28 3.41 Search for helices and strands: 0 residues in 0 chains, 5905 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 5918 seeds are put forward Round 1: 302 peptides, 62 chains. Longest chain 10 peptides. Score 0.287 Round 2: 361 peptides, 62 chains. Longest chain 11 peptides. Score 0.405 Round 3: 369 peptides, 61 chains. Longest chain 12 peptides. Score 0.428 Round 4: 347 peptides, 58 chains. Longest chain 13 peptides. Score 0.411 Round 5: 329 peptides, 53 chains. Longest chain 12 peptides. Score 0.418 Taking the results from Round 3 Chains 61, Residues 308, Estimated correctness of the model 0.0 % 9 chains (39 residues) have been docked in sequence ------------------------------------------------------ 8080 reflections ( 96.28 % complete ) and 13206 restraints for refining 5908 atoms. 11927 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1979 (Rfree = 0.000) for 5908 atoms. Found 25 (32 requested) and removed 48 (16 requested) atoms. Cycle 32: After refmac, R = 0.1857 (Rfree = 0.000) for 5855 atoms. Found 19 (32 requested) and removed 30 (16 requested) atoms. Cycle 33: After refmac, R = 0.1750 (Rfree = 0.000) for 5833 atoms. Found 8 (32 requested) and removed 24 (16 requested) atoms. Cycle 34: After refmac, R = 0.1738 (Rfree = 0.000) for 5806 atoms. Found 8 (31 requested) and removed 16 (15 requested) atoms. Cycle 35: After refmac, R = 0.1711 (Rfree = 0.000) for 5792 atoms. Found 5 (31 requested) and removed 15 (15 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.27 3.40 Search for helices and strands: 0 residues in 0 chains, 5917 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 5931 seeds are put forward Round 1: 310 peptides, 63 chains. Longest chain 12 peptides. Score 0.295 Round 2: 374 peptides, 68 chains. Longest chain 13 peptides. Score 0.381 Round 3: 363 peptides, 64 chains. Longest chain 16 peptides. Score 0.393 Round 4: 384 peptides, 64 chains. Longest chain 14 peptides. Score 0.431 Round 5: 379 peptides, 64 chains. Longest chain 17 peptides. Score 0.422 Taking the results from Round 4 Chains 64, Residues 320, Estimated correctness of the model 0.0 % 6 chains (30 residues) have been docked in sequence ------------------------------------------------------ 8080 reflections ( 96.28 % complete ) and 13622 restraints for refining 5954 atoms. 12322 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2105 (Rfree = 0.000) for 5954 atoms. Found 32 (32 requested) and removed 41 (16 requested) atoms. Cycle 37: After refmac, R = 0.1933 (Rfree = 0.000) for 5922 atoms. Found 13 (32 requested) and removed 24 (16 requested) atoms. Cycle 38: After refmac, R = 0.1868 (Rfree = 0.000) for 5900 atoms. Found 14 (32 requested) and removed 22 (16 requested) atoms. Cycle 39: After refmac, R = 0.1811 (Rfree = 0.000) for 5888 atoms. Found 6 (32 requested) and removed 20 (16 requested) atoms. Cycle 40: After refmac, R = 0.1815 (Rfree = 0.000) for 5866 atoms. Found 10 (32 requested) and removed 19 (16 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.31 3.45 Search for helices and strands: 0 residues in 0 chains, 6005 seeds are put forward NCS extension: 19 residues added (3 deleted due to clashes), 6024 seeds are put forward Round 1: 298 peptides, 62 chains. Longest chain 12 peptides. Score 0.279 Round 2: 358 peptides, 61 chains. Longest chain 14 peptides. Score 0.407 Round 3: 349 peptides, 57 chains. Longest chain 16 peptides. Score 0.423 Round 4: 348 peptides, 65 chains. Longest chain 12 peptides. Score 0.355 Round 5: 355 peptides, 58 chains. Longest chain 14 peptides. Score 0.426 Taking the results from Round 5 Chains 59, Residues 297, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 8080 reflections ( 96.28 % complete ) and 13843 restraints for refining 5963 atoms. 12675 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2032 (Rfree = 0.000) for 5963 atoms. Found 30 (32 requested) and removed 36 (16 requested) atoms. Cycle 42: After refmac, R = 0.1882 (Rfree = 0.000) for 5934 atoms. Found 13 (32 requested) and removed 22 (16 requested) atoms. Cycle 43: After refmac, R = 0.1804 (Rfree = 0.000) for 5912 atoms. Found 6 (32 requested) and removed 18 (16 requested) atoms. Cycle 44: After refmac, R = 0.1752 (Rfree = 0.000) for 5895 atoms. Found 11 (32 requested) and removed 17 (16 requested) atoms. Cycle 45: After refmac, R = 0.1722 (Rfree = 0.000) for 5884 atoms. Found 10 (32 requested) and removed 17 (16 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.26 3.39 Search for helices and strands: 0 residues in 0 chains, 6007 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 6023 seeds are put forward Round 1: 286 peptides, 57 chains. Longest chain 11 peptides. Score 0.298 Round 2: 307 peptides, 50 chains. Longest chain 15 peptides. Score 0.401 Round 3: 307 peptides, 52 chains. Longest chain 12 peptides. Score 0.384 Round 4: 298 peptides, 47 chains. Longest chain 15 peptides. Score 0.410 Round 5: 297 peptides, 48 chains. Longest chain 11 peptides. Score 0.399 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 49, Residues 251, Estimated correctness of the model 0.0 % 7 chains (36 residues) have been docked in sequence Sequence coverage is 14 % Consider running further cycles of model building using 1vkz-3_warpNtrace.pdb as input Building loops using Loopy2018 49 chains (251 residues) following loop building 7 chains (36 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8080 reflections ( 96.28 % complete ) and 13812 restraints for refining 5963 atoms. 12740 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2001 (Rfree = 0.000) for 5963 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 47: After refmac, R = 0.1919 (Rfree = 0.000) for 5936 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 48: After refmac, R = 0.1883 (Rfree = 0.000) for 5918 atoms. Found 0 (32 requested) and removed 15 (16 requested) atoms. Cycle 49: After refmac, R = 0.1843 (Rfree = 0.000) for 5900 atoms. Found 0 (32 requested) and removed 8 (16 requested) atoms. Writing output files ... TimeTaking 68.97