Sun 23 Dec 23:46:44 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 1vll-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vll-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vll-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vll-3.6-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/1vll-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vll-3.6-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 ============================================================ Sun 23 Dec 23:46:48 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/1vll-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vll-3.6-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 416 and 0 Target number of residues in the AU: 416 Target solvent content: 0.6837 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-3.6-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: 19 Cell parameters: 57.294 93.405 133.015 90.000 90.000 90.000 Input sequence file: 1vll-3.6-parrot-mrncs.fasta_lf Building free atoms model in initial map for 5344 target number of atoms Had to go as low as 0.75 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 3.600 Wilson plot Bfac: 104.31 8728 reflections ( 99.97 % complete ) and 0 restraints for refining 5920 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Starting model: R = 0.3682 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3317 (Rfree = 0.000) for 5920 atoms. Found 37 (37 requested) and removed 34 (18 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.84 3.89 Search for helices and strands: 0 residues in 0 chains, 6047 seeds are put forward NCS extension: 0 residues added, 6047 seeds are put forward Round 1: 249 peptides, 44 chains. Longest chain 15 peptides. Score 0.360 Round 2: 312 peptides, 47 chains. Longest chain 15 peptides. Score 0.472 Round 3: 362 peptides, 51 chains. Longest chain 29 peptides. Score 0.535 Round 4: 342 peptides, 44 chains. Longest chain 18 peptides. Score 0.556 Round 5: 367 peptides, 48 chains. Longest chain 17 peptides. Score 0.569 Taking the results from Round 5 Chains 49, Residues 319, Estimated correctness of the model 2.2 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 8728 reflections ( 99.97 % complete ) and 11297 restraints for refining 4842 atoms. 10022 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2658 (Rfree = 0.000) for 4842 atoms. Found 12 (31 requested) and removed 36 (15 requested) atoms. Cycle 2: After refmac, R = 0.2442 (Rfree = 0.000) for 4731 atoms. Found 9 (30 requested) and removed 28 (15 requested) atoms. Cycle 3: After refmac, R = 0.2402 (Rfree = 0.000) for 4661 atoms. Found 12 (30 requested) and removed 32 (15 requested) atoms. Cycle 4: After refmac, R = 0.2311 (Rfree = 0.000) for 4614 atoms. Found 12 (29 requested) and removed 24 (14 requested) atoms. Cycle 5: After refmac, R = 0.2242 (Rfree = 0.000) for 4583 atoms. Found 8 (29 requested) and removed 28 (14 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.79 3.84 Search for helices and strands: 0 residues in 0 chains, 4778 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 4799 seeds are put forward Round 1: 300 peptides, 56 chains. Longest chain 16 peptides. Score 0.359 Round 2: 306 peptides, 50 chains. Longest chain 16 peptides. Score 0.431 Round 3: 341 peptides, 51 chains. Longest chain 18 peptides. Score 0.495 Round 4: 350 peptides, 48 chains. Longest chain 15 peptides. Score 0.538 Round 5: 342 peptides, 48 chains. Longest chain 17 peptides. Score 0.523 Taking the results from Round 4 Chains 48, Residues 302, Estimated correctness of the model 0.0 % 3 chains (13 residues) have been docked in sequence ------------------------------------------------------ 8728 reflections ( 99.97 % complete ) and 10710 restraints for refining 4692 atoms. 9512 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2368 (Rfree = 0.000) for 4692 atoms. Found 11 (30 requested) and removed 41 (15 requested) atoms. Cycle 7: After refmac, R = 0.2253 (Rfree = 0.000) for 4627 atoms. Found 9 (29 requested) and removed 30 (14 requested) atoms. Cycle 8: After refmac, R = 0.2212 (Rfree = 0.000) for 4593 atoms. Found 5 (29 requested) and removed 29 (14 requested) atoms. Cycle 9: After refmac, R = 0.2163 (Rfree = 0.000) for 4561 atoms. Found 5 (29 requested) and removed 34 (14 requested) atoms. Cycle 10: After refmac, R = 0.2058 (Rfree = 0.000) for 4524 atoms. Found 5 (29 requested) and removed 21 (14 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.77 3.82 Search for helices and strands: 0 residues in 0 chains, 4714 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 4734 seeds are put forward Round 1: 277 peptides, 52 chains. Longest chain 14 peptides. Score 0.345 Round 2: 322 peptides, 48 chains. Longest chain 16 peptides. Score 0.483 Round 3: 317 peptides, 45 chains. Longest chain 16 peptides. Score 0.500 Round 4: 319 peptides, 46 chains. Longest chain 18 peptides. Score 0.495 Round 5: 342 peptides, 46 chains. Longest chain 18 peptides. Score 0.540 Taking the results from Round 5 Chains 46, Residues 296, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 8728 reflections ( 99.97 % complete ) and 11115 restraints for refining 4844 atoms. 9960 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2235 (Rfree = 0.000) for 4844 atoms. Found 5 (31 requested) and removed 59 (15 requested) atoms. Cycle 12: After refmac, R = 0.2076 (Rfree = 0.000) for 4768 atoms. Found 7 (30 requested) and removed 33 (15 requested) atoms. Cycle 13: After refmac, R = 0.2011 (Rfree = 0.000) for 4727 atoms. Found 3 (30 requested) and removed 43 (15 requested) atoms. Cycle 14: After refmac, R = 0.1735 (Rfree = 0.000) for 4680 atoms. Found 4 (30 requested) and removed 18 (15 requested) atoms. Cycle 15: After refmac, R = 0.1652 (Rfree = 0.000) for 4663 atoms. Found 1 (29 requested) and removed 18 (14 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.78 3.83 Search for helices and strands: 0 residues in 0 chains, 4859 seeds are put forward NCS extension: 24 residues added (2 deleted due to clashes), 4883 seeds are put forward Round 1: 281 peptides, 56 chains. Longest chain 9 peptides. Score 0.314 Round 2: 318 peptides, 47 chains. Longest chain 23 peptides. Score 0.484 Round 3: 316 peptides, 47 chains. Longest chain 17 peptides. Score 0.480 Round 4: 333 peptides, 45 chains. Longest chain 26 peptides. Score 0.531 Round 5: 332 peptides, 44 chains. Longest chain 26 peptides. Score 0.538 Taking the results from Round 5 Chains 47, Residues 288, Estimated correctness of the model 0.0 % 3 chains (30 residues) have been docked in sequence ------------------------------------------------------ 8728 reflections ( 99.97 % complete ) and 10872 restraints for refining 4844 atoms. 9653 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2259 (Rfree = 0.000) for 4844 atoms. Found 10 (31 requested) and removed 35 (15 requested) atoms. Cycle 17: After refmac, R = 0.2315 (Rfree = 0.000) for 4789 atoms. Found 11 (30 requested) and removed 30 (15 requested) atoms. Cycle 18: After refmac, R = 0.2233 (Rfree = 0.000) for 4754 atoms. Found 8 (30 requested) and removed 31 (15 requested) atoms. Cycle 19: After refmac, R = 0.1982 (Rfree = 0.000) for 4720 atoms. Found 1 (30 requested) and removed 24 (15 requested) atoms. Failed to save intermediate PDB Cycle 20: After refmac, R = 0.1936 (Rfree = 0.000) for 4690 atoms. Found 0 (30 requested) and removed 18 (15 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.77 3.82 Search for helices and strands: 0 residues in 0 chains, 4818 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 4830 seeds are put forward Round 1: 278 peptides, 47 chains. Longest chain 16 peptides. Score 0.398 Round 2: 315 peptides, 44 chains. Longest chain 25 peptides. Score 0.505 Round 3: 326 peptides, 48 chains. Longest chain 25 peptides. Score 0.491 Round 4: 324 peptides, 41 chains. Longest chain 25 peptides. Score 0.548 Round 5: 319 peptides, 45 chains. Longest chain 22 peptides. Score 0.504 Taking the results from Round 4 Chains 44, Residues 283, Estimated correctness of the model 0.0 % 4 chains (48 residues) have been docked in sequence ------------------------------------------------------ 8728 reflections ( 99.97 % complete ) and 10847 restraints for refining 4844 atoms. 9593 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2261 (Rfree = 0.000) for 4844 atoms. Found 20 (31 requested) and removed 28 (15 requested) atoms. Cycle 22: After refmac, R = 0.2193 (Rfree = 0.000) for 4815 atoms. Found 6 (31 requested) and removed 20 (15 requested) atoms. Cycle 23: After refmac, R = 0.2122 (Rfree = 0.000) for 4794 atoms. Found 7 (30 requested) and removed 26 (15 requested) atoms. Cycle 24: After refmac, R = 0.2026 (Rfree = 0.000) for 4764 atoms. Found 12 (30 requested) and removed 25 (15 requested) atoms. Cycle 25: After refmac, R = 0.1929 (Rfree = 0.000) for 4748 atoms. Found 8 (30 requested) and removed 22 (15 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.74 3.79 Search for helices and strands: 0 residues in 0 chains, 4902 seeds are put forward NCS extension: 41 residues added (2 deleted due to clashes), 4943 seeds are put forward Round 1: 266 peptides, 52 chains. Longest chain 10 peptides. Score 0.319 Round 2: 311 peptides, 49 chains. Longest chain 15 peptides. Score 0.451 Round 3: 305 peptides, 47 chains. Longest chain 18 peptides. Score 0.457 Round 4: 310 peptides, 43 chains. Longest chain 26 peptides. Score 0.504 Round 5: 326 peptides, 49 chains. Longest chain 22 peptides. Score 0.482 Taking the results from Round 4 Chains 43, Residues 267, Estimated correctness of the model 0.0 % 2 chains (31 residues) have been docked in sequence ------------------------------------------------------ 8728 reflections ( 99.97 % complete ) and 11130 restraints for refining 4844 atoms. 9993 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2135 (Rfree = 0.000) for 4844 atoms. Found 21 (31 requested) and removed 33 (15 requested) atoms. Cycle 27: After refmac, R = 0.1983 (Rfree = 0.000) for 4816 atoms. Found 2 (31 requested) and removed 21 (15 requested) atoms. Cycle 28: After refmac, R = 0.1929 (Rfree = 0.000) for 4792 atoms. Found 2 (30 requested) and removed 22 (15 requested) atoms. Cycle 29: After refmac, R = 0.1853 (Rfree = 0.000) for 4766 atoms. Found 4 (30 requested) and removed 20 (15 requested) atoms. Cycle 30: After refmac, R = 0.1745 (Rfree = 0.000) for 4744 atoms. Found 0 (30 requested) and removed 17 (15 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.79 3.84 Search for helices and strands: 0 residues in 0 chains, 4885 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 4910 seeds are put forward Round 1: 249 peptides, 49 chains. Longest chain 9 peptides. Score 0.308 Round 2: 300 peptides, 47 chains. Longest chain 15 peptides. Score 0.446 Round 3: 305 peptides, 50 chains. Longest chain 16 peptides. Score 0.429 Round 4: 315 peptides, 47 chains. Longest chain 15 peptides. Score 0.478 Round 5: 316 peptides, 44 chains. Longest chain 21 peptides. Score 0.507 Taking the results from Round 5 Chains 44, Residues 272, Estimated correctness of the model 0.0 % 2 chains (23 residues) have been docked in sequence ------------------------------------------------------ 8728 reflections ( 99.97 % complete ) and 11133 restraints for refining 4844 atoms. 10007 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1972 (Rfree = 0.000) for 4844 atoms. Found 4 (31 requested) and removed 32 (15 requested) atoms. Cycle 32: After refmac, R = 0.1847 (Rfree = 0.000) for 4806 atoms. Found 2 (30 requested) and removed 21 (15 requested) atoms. Cycle 33: After refmac, R = 0.1845 (Rfree = 0.000) for 4780 atoms. Found 5 (30 requested) and removed 20 (15 requested) atoms. Cycle 34: After refmac, R = 0.1867 (Rfree = 0.000) for 4760 atoms. Found 4 (30 requested) and removed 18 (15 requested) atoms. Cycle 35: After refmac, R = 0.1861 (Rfree = 0.000) for 4744 atoms. Found 4 (30 requested) and removed 19 (15 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.75 3.80 Search for helices and strands: 0 residues in 0 chains, 4884 seeds are put forward NCS extension: 29 residues added (2 deleted due to clashes), 4913 seeds are put forward Round 1: 255 peptides, 47 chains. Longest chain 12 peptides. Score 0.344 Round 2: 288 peptides, 41 chains. Longest chain 24 peptides. Score 0.477 Round 3: 268 peptides, 42 chains. Longest chain 14 peptides. Score 0.424 Round 4: 282 peptides, 44 chains. Longest chain 19 peptides. Score 0.436 Round 5: 285 peptides, 40 chains. Longest chain 22 peptides. Score 0.480 Taking the results from Round 5 Chains 44, Residues 245, Estimated correctness of the model 0.0 % 3 chains (23 residues) have been docked in sequence ------------------------------------------------------ 8728 reflections ( 99.97 % complete ) and 11281 restraints for refining 4843 atoms. 10293 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2071 (Rfree = 0.000) for 4843 atoms. Found 8 (31 requested) and removed 25 (15 requested) atoms. Cycle 37: After refmac, R = 0.1952 (Rfree = 0.000) for 4812 atoms. Found 8 (30 requested) and removed 20 (15 requested) atoms. Cycle 38: After refmac, R = 0.1778 (Rfree = 0.000) for 4797 atoms. Found 2 (30 requested) and removed 16 (15 requested) atoms. Cycle 39: After refmac, R = 0.1803 (Rfree = 0.000) for 4783 atoms. Found 2 (30 requested) and removed 16 (15 requested) atoms. Cycle 40: After refmac, R = 0.1752 (Rfree = 0.000) for 4767 atoms. Found 3 (30 requested) and removed 15 (15 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.78 3.83 Search for helices and strands: 0 residues in 0 chains, 4925 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 4937 seeds are put forward Round 1: 229 peptides, 46 chains. Longest chain 19 peptides. Score 0.290 Round 2: 233 peptides, 39 chains. Longest chain 13 peptides. Score 0.374 Round 3: 243 peptides, 39 chains. Longest chain 23 peptides. Score 0.398 Round 4: 241 peptides, 40 chains. Longest chain 14 peptides. Score 0.383 Round 5: 254 peptides, 40 chains. Longest chain 13 peptides. Score 0.413 Taking the results from Round 5 Chains 40, Residues 214, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8728 reflections ( 99.97 % complete ) and 11767 restraints for refining 4844 atoms. 10951 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2092 (Rfree = 0.000) for 4844 atoms. Found 6 (31 requested) and removed 16 (15 requested) atoms. Cycle 42: After refmac, R = 0.1992 (Rfree = 0.000) for 4827 atoms. Found 9 (31 requested) and removed 20 (15 requested) atoms. Cycle 43: After refmac, R = 0.2041 (Rfree = 0.000) for 4813 atoms. Found 12 (30 requested) and removed 20 (15 requested) atoms. Cycle 44: After refmac, R = 0.2036 (Rfree = 0.000) for 4803 atoms. Found 21 (30 requested) and removed 18 (15 requested) atoms. Cycle 45: After refmac, R = 0.1972 (Rfree = 0.000) for 4803 atoms. Found 8 (30 requested) and removed 23 (15 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.77 3.82 Search for helices and strands: 0 residues in 0 chains, 4956 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 4969 seeds are put forward Round 1: 179 peptides, 37 chains. Longest chain 8 peptides. Score 0.258 Round 2: 224 peptides, 39 chains. Longest chain 11 peptides. Score 0.352 Round 3: 233 peptides, 39 chains. Longest chain 12 peptides. Score 0.374 Round 4: 237 peptides, 40 chains. Longest chain 17 peptides. Score 0.373 Round 5: 224 peptides, 39 chains. Longest chain 20 peptides. Score 0.352 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 39, Residues 194, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence Sequence coverage is 3 % Consider running further cycles of model building using 1vll-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8728 reflections ( 99.97 % complete ) and 11770 restraints for refining 4844 atoms. 11010 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2108 (Rfree = 0.000) for 4844 atoms. Found 0 (31 requested) and removed 15 (15 requested) atoms. Cycle 47: After refmac, R = 0.2308 (Rfree = 0.000) for 4815 atoms. Found 0 (30 requested) and removed 15 (15 requested) atoms. Cycle 48: After refmac, R = 0.1944 (Rfree = 0.000) for 4782 atoms. Found 0 (30 requested) and removed 15 (15 requested) atoms. Cycle 49: After refmac, R = 0.2040 (Rfree = 0.000) for 4754 atoms. TimeTaking 45.45