null Sun 23 Dec 22:22:49 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 2o62-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2o62-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2o62-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o62-3.8-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/2o62-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o62-3.8-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 22:22:59 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/2o62-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o62-3.8-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 397 and 0 Target number of residues in the AU: 397 Target solvent content: 0.6318 Checking the provided sequence file Detected sequence length: 270 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 540 Adjusted target solvent content: 0.50 Input MTZ file: 2o62-3.8-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: 19 Cell parameters: 61.210 71.880 132.610 90.000 90.000 90.000 Input sequence file: 2o62-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 4320 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: 66.305 3.800 Wilson plot Bfac: 67.27 6019 reflections ( 97.97 % complete ) and 0 restraints for refining 4801 atoms. Observations/parameters ratio is 0.31 ------------------------------------------------------ Starting model: R = 0.3779 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3542 (Rfree = 0.000) for 4801 atoms. Found 26 (26 requested) and removed 102 (13 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.66 3.66 Search for helices and strands: 0 residues in 0 chains, 4750 seeds are put forward NCS extension: 0 residues added, 4750 seeds are put forward Round 1: 127 peptides, 28 chains. Longest chain 7 peptides. Score 0.223 Round 2: 164 peptides, 35 chains. Longest chain 8 peptides. Score 0.250 Round 3: 174 peptides, 36 chains. Longest chain 8 peptides. Score 0.269 Round 4: 171 peptides, 30 chains. Longest chain 11 peptides. Score 0.340 Round 5: 192 peptides, 37 chains. Longest chain 10 peptides. Score 0.312 Taking the results from Round 4 Chains 30, Residues 141, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6019 reflections ( 97.97 % complete ) and 9559 restraints for refining 3905 atoms. 9025 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3071 (Rfree = 0.000) for 3905 atoms. Found 16 (21 requested) and removed 32 (10 requested) atoms. Cycle 2: After refmac, R = 0.2961 (Rfree = 0.000) for 3849 atoms. Found 21 (21 requested) and removed 25 (10 requested) atoms. Cycle 3: After refmac, R = 0.2844 (Rfree = 0.000) for 3823 atoms. Found 19 (21 requested) and removed 27 (10 requested) atoms. Cycle 4: After refmac, R = 0.2313 (Rfree = 0.000) for 3790 atoms. Found 7 (20 requested) and removed 25 (10 requested) atoms. Cycle 5: After refmac, R = 0.2349 (Rfree = 0.000) for 3753 atoms. Found 9 (20 requested) and removed 18 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.46 3.46 Search for helices and strands: 0 residues in 0 chains, 3780 seeds are put forward NCS extension: 0 residues added, 3780 seeds are put forward Round 1: 175 peptides, 38 chains. Longest chain 10 peptides. Score 0.245 Round 2: 221 peptides, 42 chains. Longest chain 10 peptides. Score 0.335 Round 3: 233 peptides, 42 chains. Longest chain 11 peptides. Score 0.370 Round 4: 225 peptides, 43 chains. Longest chain 12 peptides. Score 0.334 Round 5: 222 peptides, 39 chains. Longest chain 11 peptides. Score 0.375 Taking the results from Round 5 Chains 39, Residues 183, Estimated correctness of the model 0.0 % 4 chains (16 residues) have been docked in sequence ------------------------------------------------------ 6019 reflections ( 97.97 % complete ) and 8955 restraints for refining 3782 atoms. 8229 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2603 (Rfree = 0.000) for 3782 atoms. Found 20 (20 requested) and removed 38 (10 requested) atoms. Cycle 7: After refmac, R = 0.2679 (Rfree = 0.000) for 3716 atoms. Found 20 (20 requested) and removed 34 (10 requested) atoms. Cycle 8: After refmac, R = 0.2537 (Rfree = 0.000) for 3680 atoms. Found 20 (20 requested) and removed 25 (10 requested) atoms. Cycle 9: After refmac, R = 0.2430 (Rfree = 0.000) for 3651 atoms. Found 20 (20 requested) and removed 18 (10 requested) atoms. Cycle 10: After refmac, R = 0.2422 (Rfree = 0.000) for 3641 atoms. Found 18 (20 requested) and removed 22 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.43 3.43 Search for helices and strands: 0 residues in 0 chains, 3703 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 3717 seeds are put forward Round 1: 200 peptides, 45 chains. Longest chain 7 peptides. Score 0.232 Round 2: 230 peptides, 44 chains. Longest chain 11 peptides. Score 0.337 Round 3: 229 peptides, 42 chains. Longest chain 11 peptides. Score 0.358 Round 4: 216 peptides, 37 chains. Longest chain 11 peptides. Score 0.383 Round 5: 236 peptides, 40 chains. Longest chain 14 peptides. Score 0.402 Taking the results from Round 5 Chains 40, Residues 196, Estimated correctness of the model 0.0 % 4 chains (23 residues) have been docked in sequence ------------------------------------------------------ 6019 reflections ( 97.97 % complete ) and 8942 restraints for refining 3884 atoms. 8131 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2619 (Rfree = 0.000) for 3884 atoms. Found 21 (21 requested) and removed 60 (10 requested) atoms. Cycle 12: After refmac, R = 0.2441 (Rfree = 0.000) for 3811 atoms. Found 21 (21 requested) and removed 31 (10 requested) atoms. Cycle 13: After refmac, R = 0.1940 (Rfree = 0.000) for 3783 atoms. Found 10 (20 requested) and removed 21 (10 requested) atoms. Cycle 14: After refmac, R = 0.1816 (Rfree = 0.000) for 3764 atoms. Found 8 (20 requested) and removed 22 (10 requested) atoms. Cycle 15: After refmac, R = 0.1758 (Rfree = 0.000) for 3742 atoms. Found 5 (20 requested) and removed 24 (10 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.50 3.50 Search for helices and strands: 0 residues in 0 chains, 3788 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 3811 seeds are put forward Round 1: 189 peptides, 39 chains. Longest chain 9 peptides. Score 0.276 Round 2: 230 peptides, 43 chains. Longest chain 12 peptides. Score 0.349 Round 3: 221 peptides, 39 chains. Longest chain 13 peptides. Score 0.372 Round 4: 230 peptides, 39 chains. Longest chain 15 peptides. Score 0.398 Round 5: 224 peptides, 36 chains. Longest chain 13 peptides. Score 0.417 Taking the results from Round 5 Chains 36, Residues 188, Estimated correctness of the model 0.0 % 2 chains (10 residues) have been docked in sequence ------------------------------------------------------ 6019 reflections ( 97.97 % complete ) and 8879 restraints for refining 3907 atoms. 8141 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2567 (Rfree = 0.000) for 3907 atoms. Found 21 (21 requested) and removed 50 (10 requested) atoms. Cycle 17: After refmac, R = 0.2362 (Rfree = 0.000) for 3840 atoms. Found 21 (21 requested) and removed 28 (10 requested) atoms. Cycle 18: After refmac, R = 0.2228 (Rfree = 0.000) for 3806 atoms. Found 21 (21 requested) and removed 22 (10 requested) atoms. Cycle 19: After refmac, R = 0.2278 (Rfree = 0.000) for 3788 atoms. Found 20 (20 requested) and removed 19 (10 requested) atoms. Cycle 20: After refmac, R = 0.2152 (Rfree = 0.000) for 3776 atoms. Found 20 (20 requested) and removed 19 (10 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.37 3.37 Search for helices and strands: 0 residues in 0 chains, 3832 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 3848 seeds are put forward Round 1: 201 peptides, 43 chains. Longest chain 9 peptides. Score 0.262 Round 2: 216 peptides, 42 chains. Longest chain 9 peptides. Score 0.320 Round 3: 223 peptides, 42 chains. Longest chain 11 peptides. Score 0.341 Round 4: 228 peptides, 40 chains. Longest chain 12 peptides. Score 0.380 Round 5: 224 peptides, 38 chains. Longest chain 11 peptides. Score 0.393 Taking the results from Round 5 Chains 38, Residues 186, Estimated correctness of the model 0.0 % 4 chains (16 residues) have been docked in sequence ------------------------------------------------------ 6019 reflections ( 97.97 % complete ) and 8808 restraints for refining 3863 atoms. 8068 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2360 (Rfree = 0.000) for 3863 atoms. Found 21 (21 requested) and removed 33 (10 requested) atoms. Cycle 22: After refmac, R = 0.2227 (Rfree = 0.000) for 3828 atoms. Found 21 (21 requested) and removed 26 (10 requested) atoms. Cycle 23: After refmac, R = 0.1846 (Rfree = 0.000) for 3813 atoms. Found 6 (21 requested) and removed 16 (10 requested) atoms. Cycle 24: After refmac, R = 0.1752 (Rfree = 0.000) for 3798 atoms. Found 10 (20 requested) and removed 11 (10 requested) atoms. Cycle 25: After refmac, R = 0.1719 (Rfree = 0.000) for 3790 atoms. Found 4 (20 requested) and removed 13 (10 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.38 3.38 Search for helices and strands: 0 residues in 0 chains, 3848 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 3860 seeds are put forward Round 1: 216 peptides, 47 chains. Longest chain 9 peptides. Score 0.257 Round 2: 239 peptides, 48 chains. Longest chain 11 peptides. Score 0.314 Round 3: 241 peptides, 48 chains. Longest chain 10 peptides. Score 0.320 Round 4: 253 peptides, 44 chains. Longest chain 11 peptides. Score 0.402 Round 5: 248 peptides, 44 chains. Longest chain 11 peptides. Score 0.388 Taking the results from Round 4 Chains 44, Residues 209, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 6019 reflections ( 97.97 % complete ) and 8946 restraints for refining 3907 atoms. 8141 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2477 (Rfree = 0.000) for 3907 atoms. Found 21 (21 requested) and removed 30 (10 requested) atoms. Cycle 27: After refmac, R = 0.2558 (Rfree = 0.000) for 3873 atoms. Found 21 (21 requested) and removed 27 (10 requested) atoms. Cycle 28: After refmac, R = 0.2398 (Rfree = 0.000) for 3845 atoms. Found 21 (21 requested) and removed 16 (10 requested) atoms. Cycle 29: After refmac, R = 0.2375 (Rfree = 0.000) for 3830 atoms. Found 21 (21 requested) and removed 16 (10 requested) atoms. Cycle 30: After refmac, R = 0.1915 (Rfree = 0.000) for 3822 atoms. Found 19 (21 requested) and removed 14 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.44 3.44 Search for helices and strands: 0 residues in 0 chains, 3889 seeds are put forward NCS extension: 11 residues added (3 deleted due to clashes), 3900 seeds are put forward Round 1: 185 peptides, 42 chains. Longest chain 7 peptides. Score 0.224 Round 2: 215 peptides, 41 chains. Longest chain 9 peptides. Score 0.330 Round 3: 210 peptides, 37 chains. Longest chain 9 peptides. Score 0.366 Round 4: 208 peptides, 37 chains. Longest chain 9 peptides. Score 0.360 Round 5: 206 peptides, 39 chains. Longest chain 9 peptides. Score 0.329 Taking the results from Round 3 Chains 37, Residues 173, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 6019 reflections ( 97.97 % complete ) and 677 restraints for refining 3859 atoms. 0 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2516 (Rfree = 0.000) for 3859 atoms. Found 21 (21 requested) and removed 37 (10 requested) atoms. Cycle 32: After refmac, R = 0.2394 (Rfree = 0.000) for 3823 atoms. Found 21 (21 requested) and removed 16 (10 requested) atoms. Cycle 33: After refmac, R = 0.2400 (Rfree = 0.000) for 3811 atoms. Found 21 (21 requested) and removed 21 (10 requested) atoms. Cycle 34: After refmac, R = 0.1867 (Rfree = 0.000) for 3800 atoms. Found 6 (20 requested) and removed 19 (10 requested) atoms. Cycle 35: After refmac, R = 0.1786 (Rfree = 0.000) for 3779 atoms. Found 15 (20 requested) and removed 12 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.46 3.46 Search for helices and strands: 0 residues in 0 chains, 3807 seeds are put forward NCS extension: 0 residues added, 3807 seeds are put forward Round 1: 136 peptides, 30 chains. Longest chain 7 peptides. Score 0.226 Round 2: 178 peptides, 34 chains. Longest chain 10 peptides. Score 0.308 Round 3: 201 peptides, 38 chains. Longest chain 11 peptides. Score 0.326 Round 4: 191 peptides, 34 chains. Longest chain 12 peptides. Score 0.348 Round 5: 197 peptides, 33 chains. Longest chain 12 peptides. Score 0.378 Taking the results from Round 5 Chains 33, Residues 164, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 6019 reflections ( 97.97 % complete ) and 9061 restraints for refining 3889 atoms. 8417 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2630 (Rfree = 0.000) for 3889 atoms. Found 21 (21 requested) and removed 49 (10 requested) atoms. Cycle 37: After refmac, R = 0.2656 (Rfree = 0.000) for 3850 atoms. Found 21 (21 requested) and removed 37 (10 requested) atoms. Cycle 38: After refmac, R = 0.2275 (Rfree = 0.000) for 3815 atoms. Found 21 (21 requested) and removed 20 (10 requested) atoms. Cycle 39: After refmac, R = 0.2134 (Rfree = 0.000) for 3801 atoms. Found 20 (20 requested) and removed 17 (10 requested) atoms. Cycle 40: After refmac, R = 0.2365 (Rfree = 0.000) for 3799 atoms. Found 20 (20 requested) and removed 21 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.45 3.45 Search for helices and strands: 0 residues in 0 chains, 3845 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 3860 seeds are put forward Round 1: 163 peptides, 38 chains. Longest chain 7 peptides. Score 0.205 Round 2: 189 peptides, 41 chains. Longest chain 8 peptides. Score 0.250 Round 3: 197 peptides, 40 chains. Longest chain 10 peptides. Score 0.288 Round 4: 215 peptides, 41 chains. Longest chain 12 peptides. Score 0.330 Round 5: 209 peptides, 37 chains. Longest chain 16 peptides. Score 0.363 Taking the results from Round 5 Chains 37, Residues 172, Estimated correctness of the model 0.0 % 4 chains (17 residues) have been docked in sequence ------------------------------------------------------ 6019 reflections ( 97.97 % complete ) and 8876 restraints for refining 3907 atoms. 8188 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2597 (Rfree = 0.000) for 3907 atoms. Found 21 (21 requested) and removed 30 (10 requested) atoms. Cycle 42: After refmac, R = 0.2485 (Rfree = 0.000) for 3878 atoms. Found 21 (21 requested) and removed 30 (10 requested) atoms. Cycle 43: After refmac, R = 0.2430 (Rfree = 0.000) for 3855 atoms. Found 21 (21 requested) and removed 25 (10 requested) atoms. Cycle 44: After refmac, R = 0.2487 (Rfree = 0.000) for 3842 atoms. Found 21 (21 requested) and removed 19 (10 requested) atoms. Cycle 45: After refmac, R = 0.2393 (Rfree = 0.000) for 3829 atoms. Found 21 (21 requested) and removed 20 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.51 3.51 Search for helices and strands: 0 residues in 0 chains, 3865 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 3887 seeds are put forward Round 1: 155 peptides, 34 chains. Longest chain 8 peptides. Score 0.234 Round 2: 167 peptides, 33 chains. Longest chain 11 peptides. Score 0.287 Round 3: 157 peptides, 30 chains. Longest chain 10 peptides. Score 0.296 Round 4: 161 peptides, 30 chains. Longest chain 13 peptides. Score 0.309 Round 5: 162 peptides, 31 chains. Longest chain 11 peptides. Score 0.298 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 30, Residues 131, Estimated correctness of the model 0.0 % 3 chains (11 residues) have been docked in sequence Sequence coverage is 8 % Consider running further cycles of model building using 2o62-3_warpNtrace.pdb as input Building loops using Loopy2018 30 chains (131 residues) following loop building 3 chains (11 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6019 reflections ( 97.97 % complete ) and 8751 restraints for refining 3788 atoms. 8231 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2408 (Rfree = 0.000) for 3788 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 47: After refmac, R = 0.2457 (Rfree = 0.000) for 3765 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 48: After refmac, R = 0.1852 (Rfree = 0.000) for 3743 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 49: After refmac, R = 0.1653 (Rfree = 0.000) for 3725 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:20:31 GMT 2018 Job finished. TimeTaking 57.7 Used memory is bytes: 10460960