Mon 24 Dec 07:38:25 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 1vkh-4.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vkh-4.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vkh-4.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkh-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/1vkh-4.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkh-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 07:38:30 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/1vkh-4.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkh-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 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-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: 41.965 85.956 70.476 90.000 97.713 90.000 Input sequence file: 1vkh-4.0-parrot-noncs.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 4854 atoms. Observations/parameters ratio is 0.22 ------------------------------------------------------ Starting model: R = 0.3431 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3359 (Rfree = 0.000) for 4854 atoms. Found 23 (23 requested) and removed 72 (11 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.46 3.91 Search for helices and strands: 0 residues in 0 chains, 4906 seeds are put forward NCS extension: 0 residues added, 4906 seeds are put forward Round 1: 146 peptides, 30 chains. Longest chain 8 peptides. Score 0.270 Round 2: 182 peptides, 33 chains. Longest chain 13 peptides. Score 0.352 Round 3: 198 peptides, 34 chains. Longest chain 11 peptides. Score 0.391 Round 4: 214 peptides, 34 chains. Longest chain 14 peptides. Score 0.441 Round 5: 240 peptides, 41 chains. Longest chain 15 peptides. Score 0.428 Taking the results from Round 4 Chains 34, Residues 180, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4226 reflections ( 99.04 % complete ) and 9709 restraints for refining 3943 atoms. 9023 conditional restraints added. Observations/parameters ratio is 0.27 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2900 (Rfree = 0.000) for 3943 atoms. Found 18 (18 requested) and removed 35 (9 requested) atoms. Cycle 2: After refmac, R = 0.2599 (Rfree = 0.000) for 3875 atoms. Found 18 (18 requested) and removed 31 (9 requested) atoms. Cycle 3: After refmac, R = 0.1822 (Rfree = 0.000) for 3825 atoms. Found 7 (18 requested) and removed 18 (9 requested) atoms. Cycle 4: After refmac, R = 0.2193 (Rfree = 0.000) for 3788 atoms. Found 18 (18 requested) and removed 23 (9 requested) atoms. Cycle 5: After refmac, R = 0.1702 (Rfree = 0.000) for 3763 atoms. Found 7 (17 requested) and removed 17 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.47 3.92 Search for helices and strands: 0 residues in 0 chains, 3907 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 3921 seeds are put forward Round 1: 185 peptides, 38 chains. Longest chain 8 peptides. Score 0.290 Round 2: 196 peptides, 35 chains. Longest chain 14 peptides. Score 0.371 Round 3: 216 peptides, 37 chains. Longest chain 13 peptides. Score 0.407 Round 4: 203 peptides, 32 chains. Longest chain 14 peptides. Score 0.435 Round 5: 221 peptides, 36 chains. Longest chain 13 peptides. Score 0.436 Taking the results from Round 5 Chains 36, Residues 185, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4226 reflections ( 99.04 % complete ) and 9118 restraints for refining 3797 atoms. 8414 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2400 (Rfree = 0.000) for 3797 atoms. Found 18 (18 requested) and removed 45 (9 requested) atoms. Cycle 7: After refmac, R = 0.2322 (Rfree = 0.000) for 3753 atoms. Found 17 (17 requested) and removed 45 (8 requested) atoms. Cycle 8: After refmac, R = 0.2267 (Rfree = 0.000) for 3707 atoms. Found 17 (17 requested) and removed 27 (8 requested) atoms. Cycle 9: After refmac, R = 0.1853 (Rfree = 0.000) for 3688 atoms. Found 8 (17 requested) and removed 29 (8 requested) atoms. Cycle 10: After refmac, R = 0.1462 (Rfree = 0.000) for 3660 atoms. Found 5 (17 requested) and removed 17 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.50 3.95 Search for helices and strands: 0 residues in 0 chains, 3791 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 3805 seeds are put forward Round 1: 204 peptides, 39 chains. Longest chain 11 peptides. Score 0.340 Round 2: 212 peptides, 33 chains. Longest chain 13 peptides. Score 0.449 Round 3: 215 peptides, 36 chains. Longest chain 13 peptides. Score 0.418 Round 4: 210 peptides, 31 chains. Longest chain 14 peptides. Score 0.469 Round 5: 225 peptides, 33 chains. Longest chain 18 peptides. Score 0.487 Taking the results from Round 5 Chains 33, Residues 192, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4226 reflections ( 99.04 % complete ) and 8882 restraints for refining 3807 atoms. 8147 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2081 (Rfree = 0.000) for 3807 atoms. Found 18 (18 requested) and removed 39 (9 requested) atoms. Cycle 12: After refmac, R = 0.2320 (Rfree = 0.000) for 3766 atoms. Found 17 (17 requested) and removed 38 (8 requested) atoms. Cycle 13: After refmac, R = 0.1805 (Rfree = 0.000) for 3727 atoms. Found 17 (17 requested) and removed 27 (8 requested) atoms. Cycle 14: After refmac, R = 0.1373 (Rfree = 0.000) for 3702 atoms. Found 9 (17 requested) and removed 15 (8 requested) atoms. Cycle 15: After refmac, R = 0.1440 (Rfree = 0.000) for 3688 atoms. Found 3 (17 requested) and removed 17 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.50 3.95 Search for helices and strands: 0 residues in 0 chains, 3800 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 3813 seeds are put forward Round 1: 166 peptides, 33 chains. Longest chain 9 peptides. Score 0.297 Round 2: 191 peptides, 30 chains. Longest chain 14 peptides. Score 0.424 Round 3: 197 peptides, 34 chains. Longest chain 14 peptides. Score 0.388 Round 4: 207 peptides, 31 chains. Longest chain 15 peptides. Score 0.460 Round 5: 211 peptides, 33 chains. Longest chain 15 peptides. Score 0.446 Taking the results from Round 4 Chains 31, Residues 176, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4226 reflections ( 99.04 % complete ) and 9034 restraints for refining 3792 atoms. 8361 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1906 (Rfree = 0.000) for 3792 atoms. Found 18 (18 requested) and removed 46 (9 requested) atoms. Cycle 17: After refmac, R = 0.2142 (Rfree = 0.000) for 3754 atoms. Found 17 (17 requested) and removed 28 (8 requested) atoms. Cycle 18: After refmac, R = 0.1987 (Rfree = 0.000) for 3733 atoms. Found 17 (17 requested) and removed 22 (8 requested) atoms. Cycle 19: After refmac, R = 0.1445 (Rfree = 0.000) for 3719 atoms. Found 12 (17 requested) and removed 10 (8 requested) atoms. Cycle 20: After refmac, R = 0.1403 (Rfree = 0.000) for 3712 atoms. Found 12 (17 requested) and removed 17 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.53 3.98 Search for helices and strands: 0 residues in 0 chains, 3828 seeds are put forward NCS extension: 24 residues added (3 deleted due to clashes), 3852 seeds are put forward Round 1: 189 peptides, 37 chains. Longest chain 11 peptides. Score 0.318 Round 2: 215 peptides, 38 chains. Longest chain 10 peptides. Score 0.390 Round 3: 221 peptides, 34 chains. Longest chain 13 peptides. Score 0.462 Round 4: 202 peptides, 34 chains. Longest chain 13 peptides. Score 0.404 Round 5: 211 peptides, 34 chains. Longest chain 14 peptides. Score 0.432 Taking the results from Round 3 Chains 34, Residues 187, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4226 reflections ( 99.04 % complete ) and 8852 restraints for refining 3800 atoms. 8138 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2170 (Rfree = 0.000) for 3800 atoms. Found 18 (18 requested) and removed 35 (9 requested) atoms. Cycle 22: After refmac, R = 0.2033 (Rfree = 0.000) for 3771 atoms. Found 17 (17 requested) and removed 34 (8 requested) atoms. Cycle 23: After refmac, R = 0.1629 (Rfree = 0.000) for 3743 atoms. Found 11 (17 requested) and removed 16 (8 requested) atoms. Cycle 24: After refmac, R = 0.2019 (Rfree = 0.000) for 3730 atoms. Found 7 (17 requested) and removed 21 (8 requested) atoms. Cycle 25: After refmac, R = 0.1297 (Rfree = 0.000) for 3711 atoms. Found 6 (17 requested) and removed 17 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.54 4.00 Search for helices and strands: 0 residues in 0 chains, 3822 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 3838 seeds are put forward Round 1: 173 peptides, 33 chains. Longest chain 10 peptides. Score 0.322 Round 2: 212 peptides, 39 chains. Longest chain 13 peptides. Score 0.367 Round 3: 218 peptides, 38 chains. Longest chain 13 peptides. Score 0.400 Round 4: 214 peptides, 34 chains. Longest chain 14 peptides. Score 0.441 Round 5: 223 peptides, 34 chains. Longest chain 12 peptides. Score 0.468 Taking the results from Round 5 Chains 34, Residues 189, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4226 reflections ( 99.04 % complete ) and 9277 restraints for refining 3942 atoms. 8555 conditional restraints added. Observations/parameters ratio is 0.27 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2129 (Rfree = 0.000) for 3942 atoms. Found 18 (18 requested) and removed 42 (9 requested) atoms. Cycle 27: After refmac, R = 0.2068 (Rfree = 0.000) for 3903 atoms. Found 18 (18 requested) and removed 34 (9 requested) atoms. Cycle 28: After refmac, R = 0.1949 (Rfree = 0.000) for 3874 atoms. Found 18 (18 requested) and removed 25 (9 requested) atoms. Cycle 29: After refmac, R = 0.1387 (Rfree = 0.000) for 3859 atoms. Found 11 (18 requested) and removed 18 (9 requested) atoms. Cycle 30: After refmac, R = 0.1235 (Rfree = 0.000) for 3846 atoms. Found 4 (18 requested) and removed 15 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.51 3.96 Search for helices and strands: 0 residues in 0 chains, 3971 seeds are put forward NCS extension: 9 residues added (0 deleted due to clashes), 3980 seeds are put forward Round 1: 177 peptides, 37 chains. Longest chain 11 peptides. Score 0.276 Round 2: 192 peptides, 34 chains. Longest chain 15 peptides. Score 0.372 Round 3: 188 peptides, 32 chains. Longest chain 12 peptides. Score 0.387 Round 4: 185 peptides, 31 chains. Longest chain 12 peptides. Score 0.391 Round 5: 182 peptides, 30 chains. Longest chain 12 peptides. Score 0.396 Taking the results from Round 5 Chains 30, Residues 152, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4226 reflections ( 99.04 % complete ) and 9825 restraints for refining 3944 atoms. 9247 conditional restraints added. Observations/parameters ratio is 0.27 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2126 (Rfree = 0.000) for 3944 atoms. Found 18 (18 requested) and removed 32 (9 requested) atoms. Cycle 32: After refmac, R = 0.2243 (Rfree = 0.000) for 3909 atoms. Found 18 (18 requested) and removed 29 (9 requested) atoms. Cycle 33: After refmac, R = 0.1581 (Rfree = 0.000) for 3886 atoms. Found 9 (18 requested) and removed 16 (9 requested) atoms. Cycle 34: After refmac, R = 0.1367 (Rfree = 0.000) for 3874 atoms. Found 8 (18 requested) and removed 13 (9 requested) atoms. Cycle 35: After refmac, R = 0.1303 (Rfree = 0.000) for 3864 atoms. Found 6 (18 requested) and removed 18 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.55 4.01 Search for helices and strands: 0 residues in 0 chains, 3957 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 3970 seeds are put forward Round 1: 145 peptides, 30 chains. Longest chain 10 peptides. Score 0.266 Round 2: 170 peptides, 32 chains. Longest chain 10 peptides. Score 0.326 Round 3: 183 peptides, 34 chains. Longest chain 11 peptides. Score 0.341 Round 4: 187 peptides, 32 chains. Longest chain 11 peptides. Score 0.384 Round 5: 176 peptides, 31 chains. Longest chain 10 peptides. Score 0.361 Taking the results from Round 4 Chains 32, Residues 155, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4226 reflections ( 99.04 % complete ) and 9527 restraints for refining 3903 atoms. 8939 conditional restraints added. Observations/parameters ratio is 0.27 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2140 (Rfree = 0.000) for 3903 atoms. Found 18 (18 requested) and removed 44 (9 requested) atoms. Cycle 37: After refmac, R = 0.2180 (Rfree = 0.000) for 3860 atoms. Found 18 (18 requested) and removed 34 (9 requested) atoms. Cycle 38: After refmac, R = 0.2230 (Rfree = 0.000) for 3835 atoms. Found 11 (18 requested) and removed 20 (9 requested) atoms. Cycle 39: After refmac, R = 0.1657 (Rfree = 0.000) for 3815 atoms. Found 18 (18 requested) and removed 21 (9 requested) atoms. Cycle 40: After refmac, R = 0.1356 (Rfree = 0.000) for 3809 atoms. Found 2 (18 requested) and removed 18 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.48 3.93 Search for helices and strands: 0 residues in 0 chains, 3907 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 3920 seeds are put forward Round 1: 114 peptides, 26 chains. Longest chain 7 peptides. Score 0.210 Round 2: 128 peptides, 24 chains. Longest chain 9 peptides. Score 0.299 Round 3: 137 peptides, 24 chains. Longest chain 9 peptides. Score 0.332 Round 4: 129 peptides, 22 chains. Longest chain 9 peptides. Score 0.335 Round 5: 135 peptides, 24 chains. Longest chain 9 peptides. Score 0.325 Taking the results from Round 4 Chains 22, Residues 107, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4226 reflections ( 99.04 % complete ) and 9512 restraints for refining 3830 atoms. 9106 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1982 (Rfree = 0.000) for 3830 atoms. Found 18 (18 requested) and removed 25 (9 requested) atoms. Cycle 42: After refmac, R = 0.1448 (Rfree = 0.000) for 3817 atoms. Found 5 (18 requested) and removed 20 (9 requested) atoms. Cycle 43: After refmac, R = 0.1318 (Rfree = 0.000) for 3798 atoms. Found 2 (18 requested) and removed 15 (9 requested) atoms. Cycle 44: After refmac, R = 0.1293 (Rfree = 0.000) for 3783 atoms. Found 4 (17 requested) and removed 11 (8 requested) atoms. Cycle 45: After refmac, R = 0.1262 (Rfree = 0.000) for 3774 atoms. Found 5 (17 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.50 3.95 Search for helices and strands: 0 residues in 0 chains, 3857 seeds are put forward NCS extension: 0 residues added, 3857 seeds are put forward Round 1: 137 peptides, 30 chains. Longest chain 8 peptides. Score 0.236 Round 2: 149 peptides, 27 chains. Longest chain 11 peptides. Score 0.328 Round 3: 158 peptides, 30 chains. Longest chain 9 peptides. Score 0.314 Round 4: 152 peptides, 28 chains. Longest chain 10 peptides. Score 0.323 Round 5: 156 peptides, 30 chains. Longest chain 7 peptides. Score 0.307 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 27, Residues 122, 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 9404 restraints for refining 3847 atoms. 8943 conditional restraints added. Observations/parameters ratio is 0.27 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2095 (Rfree = 0.000) for 3847 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.1594 (Rfree = 0.000) for 3833 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.1410 (Rfree = 0.000) for 3824 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.1486 (Rfree = 0.000) for 3813 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Writing output files ... TimeTaking 41.15