null Mon 24 Dec 07:38:00 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 1vll-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vll-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vll-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vll-3.4-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/1vll-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vll-3.4-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 07:38:05 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/1vll-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vll-3.4-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 426 and 0 Target number of residues in the AU: 426 Target solvent content: 0.6761 Checking the provided sequence file Detected sequence length: 334 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 668 Adjusted target solvent content: 0.49 Input MTZ file: 1vll-3.4-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: 19 Cell parameters: 57.294 93.405 133.015 90.000 90.000 90.000 Input sequence file: 1vll-3.4-parrot-noncs.fasta_lf Building free atoms model in initial map for 5344 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: 76.441 3.400 Wilson plot Bfac: 97.07 10325 reflections ( 99.97 % complete ) and 0 restraints for refining 5936 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Starting model: R = 0.3632 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2862 (Rfree = 0.000) for 5936 atoms. Found 20 (44 requested) and removed 46 (22 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.70 3.75 Search for helices and strands: 0 residues in 0 chains, 6034 seeds are put forward NCS extension: 0 residues added, 6034 seeds are put forward Round 1: 285 peptides, 53 chains. Longest chain 12 peptides. Score 0.354 Round 2: 337 peptides, 52 chains. Longest chain 19 peptides. Score 0.478 Round 3: 365 peptides, 49 chains. Longest chain 20 peptides. Score 0.557 Round 4: 384 peptides, 48 chains. Longest chain 19 peptides. Score 0.598 Round 5: 394 peptides, 50 chains. Longest chain 17 peptides. Score 0.600 Taking the results from Round 5 Chains 51, Residues 344, Estimated correctness of the model 28.7 % 6 chains (55 residues) have been docked in sequence ------------------------------------------------------ 10325 reflections ( 99.97 % complete ) and 10600 restraints for refining 4854 atoms. 9095 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2826 (Rfree = 0.000) for 4854 atoms. Found 12 (36 requested) and removed 41 (18 requested) atoms. Cycle 2: After refmac, R = 0.2645 (Rfree = 0.000) for 4764 atoms. Found 9 (36 requested) and removed 31 (18 requested) atoms. Cycle 3: After refmac, R = 0.2621 (Rfree = 0.000) for 4722 atoms. Found 15 (35 requested) and removed 22 (17 requested) atoms. Cycle 4: After refmac, R = 0.2567 (Rfree = 0.000) for 4704 atoms. Found 5 (35 requested) and removed 32 (17 requested) atoms. Cycle 5: After refmac, R = 0.2518 (Rfree = 0.000) for 4666 atoms. Found 9 (35 requested) and removed 21 (17 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.67 3.72 Search for helices and strands: 0 residues in 0 chains, 4866 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 4885 seeds are put forward Round 1: 335 peptides, 60 chains. Longest chain 13 peptides. Score 0.400 Round 2: 345 peptides, 45 chains. Longest chain 27 peptides. Score 0.554 Round 3: 357 peptides, 46 chains. Longest chain 23 peptides. Score 0.567 Round 4: 356 peptides, 47 chains. Longest chain 18 peptides. Score 0.557 Round 5: 351 peptides, 45 chains. Longest chain 20 peptides. Score 0.565 Taking the results from Round 3 Chains 46, Residues 311, Estimated correctness of the model 17.5 % 2 chains (11 residues) have been docked in sequence ------------------------------------------------------ 10325 reflections ( 99.97 % complete ) and 11310 restraints for refining 4859 atoms. 10077 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2564 (Rfree = 0.000) for 4859 atoms. Found 21 (36 requested) and removed 51 (18 requested) atoms. Cycle 7: After refmac, R = 0.2785 (Rfree = 0.000) for 4801 atoms. Found 25 (36 requested) and removed 50 (18 requested) atoms. Cycle 8: After refmac, R = 0.2401 (Rfree = 0.000) for 4763 atoms. Found 8 (36 requested) and removed 23 (18 requested) atoms. Cycle 9: After refmac, R = 0.2292 (Rfree = 0.000) for 4745 atoms. Found 4 (35 requested) and removed 18 (17 requested) atoms. Cycle 10: After refmac, R = 0.2247 (Rfree = 0.000) for 4728 atoms. Found 3 (35 requested) and removed 18 (17 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.69 3.74 Search for helices and strands: 0 residues in 0 chains, 4907 seeds are put forward NCS extension: 28 residues added (4 deleted due to clashes), 4935 seeds are put forward Round 1: 298 peptides, 53 chains. Longest chain 15 peptides. Score 0.384 Round 2: 314 peptides, 46 chains. Longest chain 20 peptides. Score 0.485 Round 3: 319 peptides, 47 chains. Longest chain 30 peptides. Score 0.486 Round 4: 341 peptides, 46 chains. Longest chain 23 peptides. Score 0.538 Round 5: 321 peptides, 43 chains. Longest chain 19 peptides. Score 0.525 Taking the results from Round 4 Chains 47, Residues 295, Estimated correctness of the model 7.2 % 4 chains (26 residues) have been docked in sequence ------------------------------------------------------ 10325 reflections ( 99.97 % complete ) and 11111 restraints for refining 4859 atoms. 9899 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2449 (Rfree = 0.000) for 4859 atoms. Found 24 (36 requested) and removed 32 (18 requested) atoms. Cycle 12: After refmac, R = 0.2444 (Rfree = 0.000) for 4823 atoms. Found 16 (36 requested) and removed 27 (18 requested) atoms. Cycle 13: After refmac, R = 0.2473 (Rfree = 0.000) for 4800 atoms. Found 21 (36 requested) and removed 27 (18 requested) atoms. Cycle 14: After refmac, R = 0.2321 (Rfree = 0.000) for 4765 atoms. Found 11 (36 requested) and removed 28 (18 requested) atoms. Cycle 15: After refmac, R = 0.2177 (Rfree = 0.000) for 4738 atoms. Found 3 (35 requested) and removed 25 (17 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.66 3.71 Search for helices and strands: 0 residues in 0 chains, 4891 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 4917 seeds are put forward Round 1: 293 peptides, 51 chains. Longest chain 14 peptides. Score 0.392 Round 2: 314 peptides, 46 chains. Longest chain 17 peptides. Score 0.485 Round 3: 324 peptides, 42 chains. Longest chain 19 peptides. Score 0.540 Round 4: 329 peptides, 46 chains. Longest chain 18 peptides. Score 0.515 Round 5: 320 peptides, 46 chains. Longest chain 16 peptides. Score 0.497 Taking the results from Round 3 Chains 44, Residues 282, Estimated correctness of the model 7.9 % 5 chains (52 residues) have been docked in sequence ------------------------------------------------------ 10325 reflections ( 99.97 % complete ) and 10826 restraints for refining 4859 atoms. 9568 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2413 (Rfree = 0.000) for 4859 atoms. Found 8 (36 requested) and removed 44 (18 requested) atoms. Cycle 17: After refmac, R = 0.2452 (Rfree = 0.000) for 4807 atoms. Found 10 (36 requested) and removed 29 (18 requested) atoms. Cycle 18: After refmac, R = 0.2456 (Rfree = 0.000) for 4783 atoms. Found 11 (36 requested) and removed 30 (18 requested) atoms. Cycle 19: After refmac, R = 0.2468 (Rfree = 0.000) for 4757 atoms. Found 16 (35 requested) and removed 26 (17 requested) atoms. Cycle 20: After refmac, R = 0.2367 (Rfree = 0.000) for 4740 atoms. Found 7 (35 requested) and removed 22 (17 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.68 3.73 Search for helices and strands: 0 residues in 0 chains, 4872 seeds are put forward NCS extension: 11 residues added (2 deleted due to clashes), 4883 seeds are put forward Round 1: 279 peptides, 49 chains. Longest chain 13 peptides. Score 0.380 Round 2: 293 peptides, 41 chains. Longest chain 16 peptides. Score 0.487 Round 3: 305 peptides, 46 chains. Longest chain 15 peptides. Score 0.466 Round 4: 300 peptides, 41 chains. Longest chain 18 peptides. Score 0.502 Round 5: 288 peptides, 42 chains. Longest chain 19 peptides. Score 0.468 Taking the results from Round 4 Chains 41, Residues 259, Estimated correctness of the model 0.0 % 2 chains (24 residues) have been docked in sequence ------------------------------------------------------ 10325 reflections ( 99.97 % complete ) and 11275 restraints for refining 4858 atoms. 10195 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2419 (Rfree = 0.000) for 4858 atoms. Found 6 (36 requested) and removed 30 (18 requested) atoms. Cycle 22: After refmac, R = 0.2389 (Rfree = 0.000) for 4820 atoms. Found 15 (36 requested) and removed 25 (18 requested) atoms. Cycle 23: After refmac, R = 0.2300 (Rfree = 0.000) for 4805 atoms. Found 7 (36 requested) and removed 27 (18 requested) atoms. Cycle 24: After refmac, R = 0.2240 (Rfree = 0.000) for 4780 atoms. Found 13 (36 requested) and removed 24 (18 requested) atoms. Cycle 25: After refmac, R = 0.2054 (Rfree = 0.000) for 4768 atoms. Found 3 (36 requested) and removed 19 (18 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.65 3.70 Search for helices and strands: 0 residues in 0 chains, 4901 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 4920 seeds are put forward Round 1: 246 peptides, 44 chains. Longest chain 11 peptides. Score 0.353 Round 2: 269 peptides, 41 chains. Longest chain 11 peptides. Score 0.436 Round 3: 282 peptides, 41 chains. Longest chain 15 peptides. Score 0.464 Round 4: 269 peptides, 39 chains. Longest chain 12 peptides. Score 0.456 Round 5: 284 peptides, 41 chains. Longest chain 15 peptides. Score 0.469 Taking the results from Round 5 Chains 41, Residues 243, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10325 reflections ( 99.97 % complete ) and 11546 restraints for refining 4859 atoms. 10615 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2371 (Rfree = 0.000) for 4859 atoms. Found 7 (36 requested) and removed 43 (18 requested) atoms. Cycle 27: After refmac, R = 0.2374 (Rfree = 0.000) for 4811 atoms. Found 16 (36 requested) and removed 32 (18 requested) atoms. Cycle 28: After refmac, R = 0.2316 (Rfree = 0.000) for 4787 atoms. Found 11 (36 requested) and removed 24 (18 requested) atoms. Cycle 29: After refmac, R = 0.2304 (Rfree = 0.000) for 4766 atoms. Found 7 (36 requested) and removed 25 (18 requested) atoms. Cycle 30: After refmac, R = 0.2221 (Rfree = 0.000) for 4746 atoms. Found 8 (35 requested) and removed 20 (17 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.66 3.71 Search for helices and strands: 0 residues in 0 chains, 4893 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 4910 seeds are put forward Round 1: 265 peptides, 51 chains. Longest chain 11 peptides. Score 0.327 Round 2: 280 peptides, 44 chains. Longest chain 12 peptides. Score 0.431 Round 3: 294 peptides, 45 chains. Longest chain 14 peptides. Score 0.452 Round 4: 275 peptides, 43 chains. Longest chain 14 peptides. Score 0.430 Round 5: 291 peptides, 42 chains. Longest chain 13 peptides. Score 0.474 Taking the results from Round 5 Chains 42, Residues 249, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 10325 reflections ( 99.97 % complete ) and 11337 restraints for refining 4859 atoms. 10351 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2316 (Rfree = 0.000) for 4859 atoms. Found 12 (36 requested) and removed 26 (18 requested) atoms. Cycle 32: After refmac, R = 0.2260 (Rfree = 0.000) for 4834 atoms. Found 3 (36 requested) and removed 25 (18 requested) atoms. Cycle 33: After refmac, R = 0.2238 (Rfree = 0.000) for 4796 atoms. Found 5 (36 requested) and removed 20 (18 requested) atoms. Cycle 34: After refmac, R = 0.2305 (Rfree = 0.000) for 4774 atoms. Found 6 (36 requested) and removed 24 (18 requested) atoms. Cycle 35: After refmac, R = 0.2231 (Rfree = 0.000) for 4748 atoms. Found 4 (35 requested) and removed 23 (17 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.65 3.70 Search for helices and strands: 0 residues in 0 chains, 4890 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 4903 seeds are put forward Round 1: 234 peptides, 48 chains. Longest chain 10 peptides. Score 0.281 Round 2: 270 peptides, 44 chains. Longest chain 12 peptides. Score 0.409 Round 3: 269 peptides, 44 chains. Longest chain 14 peptides. Score 0.407 Round 4: 288 peptides, 41 chains. Longest chain 19 peptides. Score 0.477 Round 5: 278 peptides, 41 chains. Longest chain 14 peptides. Score 0.456 Taking the results from Round 4 Chains 42, Residues 247, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 10325 reflections ( 99.97 % complete ) and 11359 restraints for refining 4859 atoms. 10366 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2293 (Rfree = 0.000) for 4859 atoms. Found 12 (36 requested) and removed 24 (18 requested) atoms. Cycle 37: After refmac, R = 0.2314 (Rfree = 0.000) for 4827 atoms. Found 18 (36 requested) and removed 28 (18 requested) atoms. Cycle 38: After refmac, R = 0.2297 (Rfree = 0.000) for 4811 atoms. Found 17 (36 requested) and removed 26 (18 requested) atoms. Cycle 39: After refmac, R = 0.2055 (Rfree = 0.000) for 4798 atoms. Found 5 (36 requested) and removed 20 (18 requested) atoms. Cycle 40: After refmac, R = 0.2032 (Rfree = 0.000) for 4780 atoms. Found 4 (36 requested) and removed 19 (18 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.70 3.75 Search for helices and strands: 0 residues in 0 chains, 4912 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 4927 seeds are put forward Round 1: 239 peptides, 47 chains. Longest chain 10 peptides. Score 0.304 Round 2: 260 peptides, 46 chains. Longest chain 11 peptides. Score 0.366 Round 3: 266 peptides, 42 chains. Longest chain 12 peptides. Score 0.420 Round 4: 278 peptides, 46 chains. Longest chain 11 peptides. Score 0.407 Round 5: 292 peptides, 44 chains. Longest chain 17 peptides. Score 0.457 Taking the results from Round 5 Chains 44, Residues 248, Estimated correctness of the model 0.0 % 6 chains (36 residues) have been docked in sequence ------------------------------------------------------ 10325 reflections ( 99.97 % complete ) and 10959 restraints for refining 4859 atoms. 9893 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2323 (Rfree = 0.000) for 4859 atoms. Found 10 (36 requested) and removed 25 (18 requested) atoms. Cycle 42: After refmac, R = 0.2282 (Rfree = 0.000) for 4835 atoms. Found 13 (36 requested) and removed 19 (18 requested) atoms. Cycle 43: After refmac, R = 0.2329 (Rfree = 0.000) for 4823 atoms. Found 13 (36 requested) and removed 26 (18 requested) atoms. Cycle 44: After refmac, R = 0.2272 (Rfree = 0.000) for 4806 atoms. Found 11 (36 requested) and removed 21 (18 requested) atoms. Cycle 45: After refmac, R = 0.2044 (Rfree = 0.000) for 4792 atoms. Found 3 (36 requested) and removed 23 (18 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.65 3.70 Search for helices and strands: 0 residues in 0 chains, 4927 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 4953 seeds are put forward Round 1: 197 peptides, 42 chains. Longest chain 7 peptides. Score 0.249 Round 2: 229 peptides, 40 chains. Longest chain 14 peptides. Score 0.354 Round 3: 218 peptides, 37 chains. Longest chain 11 peptides. Score 0.359 Round 4: 236 peptides, 38 chains. Longest chain 13 peptides. Score 0.392 Round 5: 220 peptides, 37 chains. Longest chain 11 peptides. Score 0.364 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 38, Residues 198, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence Sequence coverage is 7 % Consider running further cycles of model building using 1vll-3_warpNtrace.pdb as input Building loops using Loopy2018 38 chains (198 residues) following loop building 2 chains (15 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 10325 reflections ( 99.97 % complete ) and 11355 restraints for refining 4859 atoms. 10540 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2345 (Rfree = 0.000) for 4859 atoms. Found 0 (36 requested) and removed 18 (18 requested) atoms. Cycle 47: After refmac, R = 0.2391 (Rfree = 0.000) for 4831 atoms. Found 0 (36 requested) and removed 18 (18 requested) atoms. Cycle 48: After refmac, R = 0.2417 (Rfree = 0.000) for 4805 atoms. Found 0 (36 requested) and removed 18 (18 requested) atoms. Cycle 49: After refmac, R = 0.2262 (Rfree = 0.000) for 4779 atoms. Found 0 (36 requested) and removed 18 (18 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:30:25 GMT 2018 Job finished. TimeTaking 52.41 Used memory is bytes: 17029608