null Sun 23 Dec 22:22:46 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vkh-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vkh-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vkh-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkh-4.0-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/1vkh-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkh-4.0-parrot-hancs ############### 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 22:22:56 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/hancs/ArpWArp/wArpResults/WorkingDir/1vkh-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkh-4.0-parrot-hancs/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 344 and 0 Target number of residues in the AU: 344 Target solvent content: 0.6305 Checking the provided sequence file Detected sequence length: 273 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 546 Adjusted target solvent content: 0.41 Input MTZ file: 1vkh-4.0-parrot-hancs.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: 41.965 85.956 70.476 90.000 97.713 90.000 Input sequence file: 1vkh-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 4368 target number of atoms Had to go as low as 0.65 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: 19.289 4.000 Wilson plot Bfac: 66.32 4226 reflections ( 99.04 % complete ) and 0 restraints for refining 4827 atoms. Observations/parameters ratio is 0.22 ------------------------------------------------------ Starting model: R = 0.3371 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3431 (Rfree = 0.000) for 4827 atoms. Found 22 (22 requested) and removed 80 (11 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.39 3.83 Search for helices and strands: 0 residues in 0 chains, 4873 seeds are put forward NCS extension: 0 residues added, 4873 seeds are put forward Round 1: 145 peptides, 32 chains. Longest chain 8 peptides. Score 0.234 Round 2: 182 peptides, 35 chains. Longest chain 9 peptides. Score 0.323 Round 3: 191 peptides, 36 chains. Longest chain 10 peptides. Score 0.340 Round 4: 189 peptides, 34 chains. Longest chain 10 peptides. Score 0.362 Round 5: 196 peptides, 34 chains. Longest chain 11 peptides. Score 0.385 Taking the results from Round 5 Chains 34, Residues 162, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4226 reflections ( 99.04 % complete ) and 9797 restraints for refining 3940 atoms. 9183 conditional restraints added. Observations/parameters ratio is 0.27 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2783 (Rfree = 0.000) for 3940 atoms. Found 18 (18 requested) and removed 31 (9 requested) atoms. Cycle 2: After refmac, R = 0.2896 (Rfree = 0.000) for 3874 atoms. Found 18 (18 requested) and removed 27 (9 requested) atoms. Cycle 3: After refmac, R = 0.2766 (Rfree = 0.000) for 3807 atoms. Found 18 (18 requested) and removed 28 (9 requested) atoms. Cycle 4: After refmac, R = 0.1938 (Rfree = 0.000) for 3750 atoms. Found 12 (18 requested) and removed 14 (9 requested) atoms. Cycle 5: After refmac, R = 0.2533 (Rfree = 0.000) for 3729 atoms. Found 17 (17 requested) and removed 28 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.52 3.97 Search for helices and strands: 0 residues in 0 chains, 3873 seeds are put forward NCS extension: 9 residues added (1 deleted due to clashes), 3882 seeds are put forward Round 1: 173 peptides, 37 chains. Longest chain 8 peptides. Score 0.262 Round 2: 194 peptides, 35 chains. Longest chain 12 peptides. Score 0.364 Round 3: 230 peptides, 37 chains. Longest chain 14 peptides. Score 0.450 Round 4: 214 peptides, 35 chains. Longest chain 14 peptides. Score 0.428 Round 5: 233 peptides, 36 chains. Longest chain 14 peptides. Score 0.472 Taking the results from Round 5 Chains 36, Residues 197, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4226 reflections ( 99.04 % complete ) and 8396 restraints for refining 3627 atoms. 7644 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2587 (Rfree = 0.000) for 3627 atoms. Found 17 (17 requested) and removed 34 (8 requested) atoms. Cycle 7: After refmac, R = 0.2510 (Rfree = 0.000) for 3589 atoms. Found 17 (17 requested) and removed 37 (8 requested) atoms. Cycle 8: After refmac, R = 0.2253 (Rfree = 0.000) for 3551 atoms. Found 16 (16 requested) and removed 24 (8 requested) atoms. Cycle 9: After refmac, R = 0.1716 (Rfree = 0.000) for 3524 atoms. Found 10 (16 requested) and removed 20 (8 requested) atoms. Cycle 10: After refmac, R = 0.1527 (Rfree = 0.000) for 3506 atoms. Found 6 (16 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.53 3.98 Search for helices and strands: 0 residues in 0 chains, 3665 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 3687 seeds are put forward Round 1: 209 peptides, 42 chains. Longest chain 9 peptides. Score 0.315 Round 2: 231 peptides, 40 chains. Longest chain 14 peptides. Score 0.414 Round 3: 232 peptides, 38 chains. Longest chain 11 peptides. Score 0.443 Round 4: 244 peptides, 40 chains. Longest chain 14 peptides. Score 0.453 Round 5: 251 peptides, 39 chains. Longest chain 14 peptides. Score 0.486 Taking the results from Round 5 Chains 39, Residues 212, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4226 reflections ( 99.04 % complete ) and 8539 restraints for refining 3726 atoms. 7730 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2456 (Rfree = 0.000) for 3726 atoms. Found 17 (17 requested) and removed 33 (8 requested) atoms. Cycle 12: After refmac, R = 0.2425 (Rfree = 0.000) for 3684 atoms. Found 17 (17 requested) and removed 30 (8 requested) atoms. Cycle 13: After refmac, R = 0.2207 (Rfree = 0.000) for 3650 atoms. Found 17 (17 requested) and removed 21 (8 requested) atoms. Cycle 14: After refmac, R = 0.1673 (Rfree = 0.000) for 3630 atoms. Found 8 (17 requested) and removed 21 (8 requested) atoms. Cycle 15: After refmac, R = 0.1483 (Rfree = 0.000) for 3609 atoms. Found 7 (17 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.55 4.01 Search for helices and strands: 0 residues in 0 chains, 3730 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 3748 seeds are put forward Round 1: 186 peptides, 37 chains. Longest chain 10 peptides. Score 0.308 Round 2: 217 peptides, 40 chains. Longest chain 14 peptides. Score 0.369 Round 3: 228 peptides, 39 chains. Longest chain 15 peptides. Score 0.418 Round 4: 220 peptides, 38 chains. Longest chain 11 peptides. Score 0.406 Round 5: 234 peptides, 42 chains. Longest chain 12 peptides. Score 0.396 Taking the results from Round 3 Chains 39, Residues 189, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4226 reflections ( 99.04 % complete ) and 8624 restraints for refining 3724 atoms. 7907 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2271 (Rfree = 0.000) for 3724 atoms. Found 17 (17 requested) and removed 38 (8 requested) atoms. Cycle 17: After refmac, R = 0.2220 (Rfree = 0.000) for 3685 atoms. Found 17 (17 requested) and removed 35 (8 requested) atoms. Cycle 18: After refmac, R = 0.1983 (Rfree = 0.000) for 3648 atoms. Found 17 (17 requested) and removed 26 (8 requested) atoms. Cycle 19: After refmac, R = 0.1903 (Rfree = 0.000) for 3632 atoms. Found 17 (17 requested) and removed 22 (8 requested) atoms. Cycle 20: After refmac, R = 0.1355 (Rfree = 0.000) for 3612 atoms. Found 8 (17 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.50 3.95 Search for helices and strands: 0 residues in 0 chains, 3726 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 3743 seeds are put forward Round 1: 186 peptides, 37 chains. Longest chain 13 peptides. Score 0.308 Round 2: 194 peptides, 35 chains. Longest chain 10 peptides. Score 0.364 Round 3: 199 peptides, 37 chains. Longest chain 14 peptides. Score 0.352 Round 4: 203 peptides, 36 chains. Longest chain 14 peptides. Score 0.379 Round 5: 209 peptides, 37 chains. Longest chain 14 peptides. Score 0.385 Taking the results from Round 5 Chains 37, Residues 172, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4226 reflections ( 99.04 % complete ) and 8803 restraints for refining 3729 atoms. 8152 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2123 (Rfree = 0.000) for 3729 atoms. Found 17 (17 requested) and removed 28 (8 requested) atoms. Cycle 22: After refmac, R = 0.1992 (Rfree = 0.000) for 3694 atoms. Found 17 (17 requested) and removed 22 (8 requested) atoms. Cycle 23: After refmac, R = 0.1767 (Rfree = 0.000) for 3677 atoms. Found 17 (17 requested) and removed 22 (8 requested) atoms. Cycle 24: After refmac, R = 0.1790 (Rfree = 0.000) for 3661 atoms. Found 17 (17 requested) and removed 19 (8 requested) atoms. Cycle 25: After refmac, R = 0.1476 (Rfree = 0.000) for 3652 atoms. Found 8 (17 requested) and removed 18 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.51 3.96 Search for helices and strands: 0 residues in 0 chains, 3760 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 3777 seeds are put forward Round 1: 189 peptides, 41 chains. Longest chain 8 peptides. Score 0.260 Round 2: 192 peptides, 36 chains. Longest chain 14 peptides. Score 0.343 Round 3: 196 peptides, 36 chains. Longest chain 11 peptides. Score 0.356 Round 4: 212 peptides, 37 chains. Longest chain 14 peptides. Score 0.395 Round 5: 200 peptides, 32 chains. Longest chain 14 peptides. Score 0.425 Taking the results from Round 5 Chains 33, Residues 168, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4226 reflections ( 99.04 % complete ) and 8916 restraints for refining 3793 atoms. 8241 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2375 (Rfree = 0.000) for 3793 atoms. Found 18 (18 requested) and removed 42 (9 requested) atoms. Cycle 27: After refmac, R = 0.1957 (Rfree = 0.000) for 3752 atoms. Found 17 (17 requested) and removed 34 (8 requested) atoms. Cycle 28: After refmac, R = 0.1954 (Rfree = 0.000) for 3725 atoms. Found 17 (17 requested) and removed 33 (8 requested) atoms. Cycle 29: After refmac, R = 0.1721 (Rfree = 0.000) for 3704 atoms. Found 17 (17 requested) and removed 14 (8 requested) atoms. Cycle 30: After refmac, R = 0.1305 (Rfree = 0.000) for 3697 atoms. Found 6 (17 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.49 3.94 Search for helices and strands: 0 residues in 0 chains, 3832 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 3844 seeds are put forward Round 1: 153 peptides, 34 chains. Longest chain 7 peptides. Score 0.233 Round 2: 181 peptides, 36 chains. Longest chain 9 peptides. Score 0.305 Round 3: 193 peptides, 37 chains. Longest chain 10 peptides. Score 0.332 Round 4: 188 peptides, 38 chains. Longest chain 10 peptides. Score 0.300 Round 5: 183 peptides, 36 chains. Longest chain 10 peptides. Score 0.312 Taking the results from Round 3 Chains 37, Residues 156, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4226 reflections ( 99.04 % complete ) and 8898 restraints for refining 3760 atoms. 8311 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1858 (Rfree = 0.000) for 3760 atoms. Found 15 (17 requested) and removed 39 (8 requested) atoms. Cycle 32: After refmac, R = 0.1917 (Rfree = 0.000) for 3727 atoms. Found 17 (17 requested) and removed 21 (8 requested) atoms. Cycle 33: After refmac, R = 0.1900 (Rfree = 0.000) for 3711 atoms. Found 17 (17 requested) and removed 25 (8 requested) atoms. Cycle 34: After refmac, R = 0.1559 (Rfree = 0.000) for 3695 atoms. Found 17 (17 requested) and removed 17 (8 requested) atoms. Cycle 35: After refmac, R = 0.1186 (Rfree = 0.000) for 3687 atoms. Found 5 (17 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.50 3.95 Search for helices and strands: 0 residues in 0 chains, 3806 seeds are put forward NCS extension: 9 residues added (0 deleted due to clashes), 3815 seeds are put forward Round 1: 163 peptides, 35 chains. Longest chain 9 peptides. Score 0.255 Round 2: 184 peptides, 36 chains. Longest chain 11 peptides. Score 0.316 Round 3: 182 peptides, 35 chains. Longest chain 11 peptides. Score 0.323 Round 4: 186 peptides, 36 chains. Longest chain 13 peptides. Score 0.322 Round 5: 185 peptides, 35 chains. Longest chain 9 peptides. Score 0.334 Taking the results from Round 5 Chains 35, Residues 150, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4226 reflections ( 99.04 % complete ) and 9329 restraints for refining 3841 atoms. 8764 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2283 (Rfree = 0.000) for 3841 atoms. Found 18 (18 requested) and removed 37 (9 requested) atoms. Cycle 37: After refmac, R = 0.1989 (Rfree = 0.000) for 3808 atoms. Found 18 (18 requested) and removed 33 (9 requested) atoms. Cycle 38: After refmac, R = 0.1868 (Rfree = 0.000) for 3785 atoms. Found 18 (18 requested) and removed 23 (9 requested) atoms. Cycle 39: After refmac, R = 0.1442 (Rfree = 0.000) for 3769 atoms. Found 12 (17 requested) and removed 12 (8 requested) atoms. Cycle 40: After refmac, R = 0.1236 (Rfree = 0.000) for 3757 atoms. Found 7 (17 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.52 3.97 Search for helices and strands: 0 residues in 0 chains, 3875 seeds are put forward NCS extension: 0 residues added, 3875 seeds are put forward Round 1: 134 peptides, 28 chains. Longest chain 11 peptides. Score 0.256 Round 2: 154 peptides, 31 chains. Longest chain 9 peptides. Score 0.284 Round 3: 163 peptides, 30 chains. Longest chain 8 peptides. Score 0.331 Round 4: 165 peptides, 32 chains. Longest chain 8 peptides. Score 0.308 Round 5: 165 peptides, 31 chains. Longest chain 11 peptides. Score 0.323 Taking the results from Round 3 Chains 30, Residues 133, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4226 reflections ( 99.04 % complete ) and 9355 restraints for refining 3828 atoms. 8853 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2364 (Rfree = 0.000) for 3828 atoms. Found 18 (18 requested) and removed 36 (9 requested) atoms. Cycle 42: After refmac, R = 0.2052 (Rfree = 0.000) for 3804 atoms. Found 18 (18 requested) and removed 27 (9 requested) atoms. Cycle 43: After refmac, R = 0.1449 (Rfree = 0.000) for 3791 atoms. Found 9 (18 requested) and removed 20 (9 requested) atoms. Cycle 44: After refmac, R = 0.1488 (Rfree = 0.000) for 3778 atoms. Found 16 (17 requested) and removed 13 (8 requested) atoms. Cycle 45: After refmac, R = 0.1837 (Rfree = 0.000) for 3781 atoms. Found 17 (17 requested) and removed 26 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.49 3.94 Search for helices and strands: 0 residues in 0 chains, 3870 seeds are put forward NCS extension: 0 residues added, 3870 seeds are put forward Round 1: 129 peptides, 28 chains. Longest chain 10 peptides. Score 0.237 Round 2: 158 peptides, 29 chains. Longest chain 11 peptides. Score 0.329 Round 3: 153 peptides, 30 chains. Longest chain 10 peptides. Score 0.296 Round 4: 160 peptides, 28 chains. Longest chain 12 peptides. Score 0.351 Round 5: 156 peptides, 28 chains. Longest chain 15 peptides. Score 0.337 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 28, Residues 132, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 1vkh-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4226 reflections ( 99.04 % complete ) and 9422 restraints for refining 3885 atoms. 8922 conditional restraints added. Observations/parameters ratio is 0.27 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2336 (Rfree = 0.000) for 3885 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.1972 (Rfree = 0.000) for 3866 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.1944 (Rfree = 0.000) for 3844 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.1382 (Rfree = 0.000) for 3825 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:18:39 GMT 2018 Job finished. TimeTaking 55.88 Used memory is bytes: 20797976