Mon 24 Dec 07:45:05 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 1vkz-4.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vkz-4.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vkz-4.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkz-4.0-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/1vkz-4.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkz-4.0-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 07:45:09 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/1vkz-4.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkz-4.0-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 603 and 0 Target number of residues in the AU: 603 Target solvent content: 0.6147 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-4.0-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: 4 Cell parameters: 63.745 78.443 85.018 90.000 95.062 90.000 Input sequence file: 1vkz-4.0-parrot-noncs.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 4.001 Wilson plot Bfac: 58.96 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 6916 reflections ( 96.32 % complete ) and 0 restraints for refining 7299 atoms. Observations/parameters ratio is 0.24 ------------------------------------------------------ Starting model: R = 0.3033 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3005 (Rfree = 0.000) for 7299 atoms. Found 34 (34 requested) and removed 271 (17 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.35 3.49 Search for helices and strands: 0 residues in 0 chains, 7092 seeds are put forward NCS extension: 0 residues added, 7092 seeds are put forward Round 1: 190 peptides, 42 chains. Longest chain 7 peptides. Score 0.223 Round 2: 295 peptides, 58 chains. Longest chain 10 peptides. Score 0.308 Round 3: 350 peptides, 61 chains. Longest chain 12 peptides. Score 0.392 Round 4: 356 peptides, 60 chains. Longest chain 17 peptides. Score 0.412 Round 5: 355 peptides, 59 chains. Longest chain 11 peptides. Score 0.418 Taking the results from Round 5 Chains 59, Residues 296, Estimated correctness of the model 0.0 % 8 chains (35 residues) have been docked in sequence ------------------------------------------------------ 6916 reflections ( 96.32 % complete ) and 13443 restraints for refining 5806 atoms. 12216 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2773 (Rfree = 0.000) for 5806 atoms. Found 27 (27 requested) and removed 57 (13 requested) atoms. Cycle 2: After refmac, R = 0.2685 (Rfree = 0.000) for 5648 atoms. Found 27 (27 requested) and removed 56 (13 requested) atoms. Cycle 3: After refmac, R = 0.2334 (Rfree = 0.000) for 5534 atoms. Found 26 (26 requested) and removed 40 (13 requested) atoms. Cycle 4: After refmac, R = 0.2031 (Rfree = 0.000) for 5477 atoms. Found 17 (26 requested) and removed 35 (13 requested) atoms. Cycle 5: After refmac, R = 0.1914 (Rfree = 0.000) for 5432 atoms. Found 18 (25 requested) and removed 23 (12 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.47 3.61 Search for helices and strands: 0 residues in 0 chains, 5565 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 5577 seeds are put forward Round 1: 324 peptides, 64 chains. Longest chain 19 peptides. Score 0.316 Round 2: 394 peptides, 67 chains. Longest chain 12 peptides. Score 0.426 Round 3: 395 peptides, 58 chains. Longest chain 21 peptides. Score 0.496 Round 4: 416 peptides, 60 chains. Longest chain 18 peptides. Score 0.517 Round 5: 460 peptides, 66 chains. Longest chain 19 peptides. Score 0.544 Taking the results from Round 5 Chains 66, Residues 394, Estimated correctness of the model 0.0 % 9 chains (69 residues) have been docked in sequence ------------------------------------------------------ 6916 reflections ( 96.32 % complete ) and 11374 restraints for refining 5496 atoms. 9630 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2293 (Rfree = 0.000) for 5496 atoms. Found 26 (26 requested) and removed 111 (13 requested) atoms. Cycle 7: After refmac, R = 0.2108 (Rfree = 0.000) for 5319 atoms. Found 19 (25 requested) and removed 46 (12 requested) atoms. Cycle 8: After refmac, R = 0.1977 (Rfree = 0.000) for 5256 atoms. Found 17 (25 requested) and removed 41 (12 requested) atoms. Cycle 9: After refmac, R = 0.1923 (Rfree = 0.000) for 5205 atoms. Found 17 (24 requested) and removed 28 (12 requested) atoms. Cycle 10: After refmac, R = 0.1858 (Rfree = 0.000) for 5179 atoms. Found 17 (24 requested) and removed 32 (12 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.39 3.53 Search for helices and strands: 0 residues in 0 chains, 5360 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 5375 seeds are put forward Round 1: 357 peptides, 60 chains. Longest chain 12 peptides. Score 0.414 Round 2: 392 peptides, 62 chains. Longest chain 16 peptides. Score 0.461 Round 3: 400 peptides, 56 chains. Longest chain 20 peptides. Score 0.519 Round 4: 401 peptides, 53 chains. Longest chain 18 peptides. Score 0.543 Round 5: 412 peptides, 60 chains. Longest chain 19 peptides. Score 0.510 Taking the results from Round 4 Chains 59, Residues 348, Estimated correctness of the model 0.0 % 9 chains (73 residues) have been docked in sequence ------------------------------------------------------ 6916 reflections ( 96.32 % complete ) and 11780 restraints for refining 5583 atoms. 10196 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2231 (Rfree = 0.000) for 5583 atoms. Found 22 (26 requested) and removed 152 (13 requested) atoms. Cycle 12: After refmac, R = 0.2006 (Rfree = 0.000) for 5367 atoms. Found 25 (25 requested) and removed 56 (12 requested) atoms. Cycle 13: After refmac, R = 0.1939 (Rfree = 0.000) for 5303 atoms. Found 19 (25 requested) and removed 42 (12 requested) atoms. Cycle 14: After refmac, R = 0.1880 (Rfree = 0.000) for 5251 atoms. Found 15 (25 requested) and removed 27 (12 requested) atoms. Cycle 15: After refmac, R = 0.1740 (Rfree = 0.000) for 5224 atoms. Found 10 (24 requested) and removed 27 (12 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.38 3.52 Search for helices and strands: 0 residues in 0 chains, 5342 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 5356 seeds are put forward Round 1: 358 peptides, 65 chains. Longest chain 19 peptides. Score 0.375 Round 2: 415 peptides, 65 chains. Longest chain 18 peptides. Score 0.478 Round 3: 438 peptides, 65 chains. Longest chain 20 peptides. Score 0.517 Round 4: 423 peptides, 61 chains. Longest chain 17 peptides. Score 0.521 Round 5: 429 peptides, 66 chains. Longest chain 18 peptides. Score 0.495 Taking the results from Round 4 Chains 61, Residues 362, Estimated correctness of the model 0.0 % 4 chains (18 residues) have been docked in sequence ------------------------------------------------------ 6916 reflections ( 96.32 % complete ) and 12174 restraints for refining 5566 atoms. 10744 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2342 (Rfree = 0.000) for 5566 atoms. Found 26 (26 requested) and removed 66 (13 requested) atoms. Cycle 17: After refmac, R = 0.2134 (Rfree = 0.000) for 5429 atoms. Found 26 (26 requested) and removed 54 (13 requested) atoms. Cycle 18: After refmac, R = 0.1952 (Rfree = 0.000) for 5363 atoms. Found 19 (25 requested) and removed 42 (12 requested) atoms. Cycle 19: After refmac, R = 0.1555 (Rfree = 0.000) for 5305 atoms. Found 12 (25 requested) and removed 18 (12 requested) atoms. Cycle 20: After refmac, R = 0.1434 (Rfree = 0.000) for 5288 atoms. Found 5 (25 requested) and removed 18 (12 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.45 3.59 Search for helices and strands: 0 residues in 0 chains, 5422 seeds are put forward NCS extension: 20 residues added (3 deleted due to clashes), 5442 seeds are put forward Round 1: 323 peptides, 61 chains. Longest chain 13 peptides. Score 0.339 Round 2: 371 peptides, 55 chains. Longest chain 20 peptides. Score 0.478 Round 3: 380 peptides, 60 chains. Longest chain 17 peptides. Score 0.455 Round 4: 395 peptides, 58 chains. Longest chain 26 peptides. Score 0.496 Round 5: 374 peptides, 53 chains. Longest chain 23 peptides. Score 0.499 Taking the results from Round 5 Chains 54, Residues 321, Estimated correctness of the model 0.0 % 8 chains (61 residues) have been docked in sequence ------------------------------------------------------ 6916 reflections ( 96.32 % complete ) and 12203 restraints for refining 5672 atoms. 10755 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2670 (Rfree = 0.000) for 5672 atoms. Found 26 (26 requested) and removed 92 (13 requested) atoms. Cycle 22: After refmac, R = 0.2573 (Rfree = 0.000) for 5501 atoms. Found 26 (26 requested) and removed 56 (13 requested) atoms. Cycle 23: After refmac, R = 0.1924 (Rfree = 0.000) for 5417 atoms. Found 15 (25 requested) and removed 25 (12 requested) atoms. Cycle 24: After refmac, R = 0.2212 (Rfree = 0.000) for 5367 atoms. Found 25 (25 requested) and removed 29 (12 requested) atoms. Cycle 25: After refmac, R = 0.2219 (Rfree = 0.000) for 5337 atoms. Found 25 (25 requested) and removed 31 (12 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.35 3.49 Search for helices and strands: 0 residues in 0 chains, 5466 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 5483 seeds are put forward Round 1: 298 peptides, 64 chains. Longest chain 10 peptides. Score 0.261 Round 2: 365 peptides, 63 chains. Longest chain 17 peptides. Score 0.404 Round 3: 350 peptides, 58 chains. Longest chain 24 peptides. Score 0.417 Round 4: 366 peptides, 61 chains. Longest chain 17 peptides. Score 0.422 Round 5: 358 peptides, 56 chains. Longest chain 18 peptides. Score 0.447 Taking the results from Round 5 Chains 56, Residues 302, Estimated correctness of the model 0.0 % 3 chains (13 residues) have been docked in sequence ------------------------------------------------------ 6916 reflections ( 96.32 % complete ) and 12200 restraints for refining 5446 atoms. 11010 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2502 (Rfree = 0.000) for 5446 atoms. Found 25 (25 requested) and removed 89 (12 requested) atoms. Cycle 27: After refmac, R = 0.2368 (Rfree = 0.000) for 5322 atoms. Found 25 (25 requested) and removed 36 (12 requested) atoms. Cycle 28: After refmac, R = 0.2263 (Rfree = 0.000) for 5268 atoms. Found 25 (25 requested) and removed 33 (12 requested) atoms. Cycle 29: After refmac, R = 0.2121 (Rfree = 0.000) for 5238 atoms. Found 24 (24 requested) and removed 26 (12 requested) atoms. Cycle 30: After refmac, R = 0.1694 (Rfree = 0.000) for 5218 atoms. Found 14 (24 requested) and removed 18 (12 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.42 3.56 Search for helices and strands: 0 residues in 0 chains, 5348 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 5370 seeds are put forward Round 1: 310 peptides, 63 chains. Longest chain 14 peptides. Score 0.295 Round 2: 342 peptides, 59 chains. Longest chain 18 peptides. Score 0.393 Round 3: 350 peptides, 56 chains. Longest chain 13 peptides. Score 0.433 Round 4: 347 peptides, 61 chains. Longest chain 15 peptides. Score 0.387 Round 5: 351 peptides, 56 chains. Longest chain 12 peptides. Score 0.435 Taking the results from Round 5 Chains 56, Residues 295, Estimated correctness of the model 0.0 % 3 chains (14 residues) have been docked in sequence ------------------------------------------------------ 6916 reflections ( 96.32 % complete ) and 12036 restraints for refining 5425 atoms. 10864 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2293 (Rfree = 0.000) for 5425 atoms. Found 25 (25 requested) and removed 59 (12 requested) atoms. Cycle 32: After refmac, R = 0.2157 (Rfree = 0.000) for 5346 atoms. Found 25 (25 requested) and removed 42 (12 requested) atoms. Cycle 33: After refmac, R = 0.1637 (Rfree = 0.000) for 5299 atoms. Found 16 (25 requested) and removed 21 (12 requested) atoms. Cycle 34: After refmac, R = 0.1435 (Rfree = 0.000) for 5278 atoms. Found 10 (25 requested) and removed 19 (12 requested) atoms. Cycle 35: After refmac, R = 0.1363 (Rfree = 0.000) for 5266 atoms. Found 6 (25 requested) and removed 16 (12 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.44 3.58 Search for helices and strands: 0 residues in 0 chains, 5379 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 5391 seeds are put forward Round 1: 310 peptides, 64 chains. Longest chain 9 peptides. Score 0.286 Round 2: 348 peptides, 57 chains. Longest chain 19 peptides. Score 0.421 Round 3: 336 peptides, 56 chains. Longest chain 11 peptides. Score 0.407 Round 4: 345 peptides, 55 chains. Longest chain 14 peptides. Score 0.432 Round 5: 344 peptides, 55 chains. Longest chain 14 peptides. Score 0.430 Taking the results from Round 4 Chains 55, Residues 290, Estimated correctness of the model 0.0 % 2 chains (16 residues) have been docked in sequence ------------------------------------------------------ 6916 reflections ( 96.32 % complete ) and 12332 restraints for refining 5532 atoms. 11166 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2045 (Rfree = 0.000) for 5532 atoms. Found 26 (26 requested) and removed 57 (13 requested) atoms. Cycle 37: After refmac, R = 0.2110 (Rfree = 0.000) for 5472 atoms. Found 26 (26 requested) and removed 35 (13 requested) atoms. Cycle 38: After refmac, R = 0.1974 (Rfree = 0.000) for 5439 atoms. Found 25 (25 requested) and removed 31 (12 requested) atoms. Cycle 39: After refmac, R = 0.1835 (Rfree = 0.000) for 5413 atoms. Found 25 (25 requested) and removed 28 (12 requested) atoms. Cycle 40: After refmac, R = 0.1816 (Rfree = 0.000) for 5387 atoms. Found 25 (25 requested) and removed 22 (12 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.39 3.53 Search for helices and strands: 0 residues in 0 chains, 5548 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 5563 seeds are put forward Round 1: 253 peptides, 52 chains. Longest chain 10 peptides. Score 0.272 Round 2: 311 peptides, 57 chains. Longest chain 16 peptides. Score 0.350 Round 3: 322 peptides, 55 chains. Longest chain 15 peptides. Score 0.388 Round 4: 319 peptides, 57 chains. Longest chain 13 peptides. Score 0.365 Round 5: 317 peptides, 56 chains. Longest chain 11 peptides. Score 0.370 Taking the results from Round 3 Chains 57, Residues 267, Estimated correctness of the model 0.0 % 6 chains (41 residues) have been docked in sequence ------------------------------------------------------ 6916 reflections ( 96.32 % complete ) and 11963 restraints for refining 5457 atoms. 10813 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2223 (Rfree = 0.000) for 5457 atoms. Found 25 (25 requested) and removed 41 (12 requested) atoms. Cycle 42: After refmac, R = 0.2112 (Rfree = 0.000) for 5408 atoms. Found 25 (25 requested) and removed 37 (12 requested) atoms. Cycle 43: After refmac, R = 0.1973 (Rfree = 0.000) for 5362 atoms. Found 25 (25 requested) and removed 37 (12 requested) atoms. Cycle 44: After refmac, R = 0.1939 (Rfree = 0.000) for 5335 atoms. Found 25 (25 requested) and removed 34 (12 requested) atoms. Cycle 45: After refmac, R = 0.1850 (Rfree = 0.000) for 5316 atoms. Found 25 (25 requested) and removed 21 (12 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.45 3.59 Search for helices and strands: 0 residues in 0 chains, 5434 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 5450 seeds are put forward Round 1: 231 peptides, 53 chains. Longest chain 8 peptides. Score 0.213 Round 2: 261 peptides, 50 chains. Longest chain 14 peptides. Score 0.308 Round 3: 272 peptides, 49 chains. Longest chain 15 peptides. Score 0.340 Round 4: 275 peptides, 51 chains. Longest chain 9 peptides. Score 0.329 Round 5: 276 peptides, 50 chains. Longest chain 10 peptides. Score 0.340 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 50, Residues 226, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence Sequence coverage is 3 % Consider running further cycles of model building using 1vkz-4_warpNtrace.pdb as input Building loops using Loopy2018 50 chains (226 residues) following loop building 2 chains (9 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6916 reflections ( 96.32 % complete ) and 12555 restraints for refining 5448 atoms. 11675 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2149 (Rfree = 0.000) for 5448 atoms. Found 0 (25 requested) and removed 12 (12 requested) atoms. Cycle 47: After refmac, R = 0.1921 (Rfree = 0.000) for 5402 atoms. Found 0 (25 requested) and removed 12 (12 requested) atoms. Cycle 48: After refmac, R = 0.1500 (Rfree = 0.000) for 5377 atoms. Found 0 (25 requested) and removed 12 (12 requested) atoms. Cycle 49: After refmac, R = 0.1517 (Rfree = 0.000) for 5356 atoms. TimeTaking 49.7