null Sun 23 Dec 22:22:52 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 2nuj-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2nuj-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2nuj-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2nuj-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/2nuj-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2nuj-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 22:23:02 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/2nuj-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2nuj-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 306 and 0 Target number of residues in the AU: 306 Target solvent content: 0.6441 Checking the provided sequence file Detected sequence length: 163 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 326 Adjusted target solvent content: 0.62 Input MTZ file: 2nuj-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: 91 Cell parameters: 78.401 78.401 151.418 90.000 90.000 90.000 Input sequence file: 2nuj-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 2608 target number of atoms Had to go as low as 0.90 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: 78.401 4.001 Wilson plot Bfac: 74.31 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 4253 reflections ( 97.23 % complete ) and 0 restraints for refining 2902 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Starting model: R = 0.3747 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3294 (Rfree = 0.000) for 2902 atoms. Found 8 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.63 3.08 Search for helices and strands: 0 residues in 0 chains, 2926 seeds are put forward NCS extension: 0 residues added, 2926 seeds are put forward Round 1: 112 peptides, 24 chains. Longest chain 6 peptides. Score 0.240 Round 2: 136 peptides, 25 chains. Longest chain 12 peptides. Score 0.321 Round 3: 143 peptides, 27 chains. Longest chain 9 peptides. Score 0.314 Round 4: 150 peptides, 29 chains. Longest chain 9 peptides. Score 0.308 Round 5: 171 peptides, 30 chains. Longest chain 13 peptides. Score 0.371 Taking the results from Round 5 Chains 31, Residues 141, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4253 reflections ( 97.23 % complete ) and 5194 restraints for refining 2353 atoms. 4621 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3360 (Rfree = 0.000) for 2353 atoms. Found 9 (11 requested) and removed 7 (5 requested) atoms. Cycle 2: After refmac, R = 0.3265 (Rfree = 0.000) for 2353 atoms. Found 1 (11 requested) and removed 5 (5 requested) atoms. Cycle 3: After refmac, R = 0.3040 (Rfree = 0.000) for 2347 atoms. Found 3 (11 requested) and removed 6 (5 requested) atoms. Cycle 4: After refmac, R = 0.2940 (Rfree = 0.000) for 2337 atoms. Found 7 (11 requested) and removed 5 (5 requested) atoms. Cycle 5: After refmac, R = 0.2869 (Rfree = 0.000) for 2330 atoms. Found 2 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.61 3.07 Search for helices and strands: 0 residues in 0 chains, 2358 seeds are put forward NCS extension: 0 residues added, 2358 seeds are put forward Round 1: 149 peptides, 28 chains. Longest chain 10 peptides. Score 0.321 Round 2: 184 peptides, 32 chains. Longest chain 10 peptides. Score 0.386 Round 3: 191 peptides, 32 chains. Longest chain 15 peptides. Score 0.410 Round 4: 180 peptides, 33 chains. Longest chain 11 peptides. Score 0.356 Round 5: 190 peptides, 32 chains. Longest chain 18 peptides. Score 0.407 Taking the results from Round 3 Chains 32, Residues 159, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 4253 reflections ( 97.23 % complete ) and 5312 restraints for refining 2355 atoms. 4694 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2975 (Rfree = 0.000) for 2355 atoms. Found 8 (11 requested) and removed 5 (5 requested) atoms. Cycle 7: After refmac, R = 0.2855 (Rfree = 0.000) for 2356 atoms. Found 2 (11 requested) and removed 6 (5 requested) atoms. Cycle 8: After refmac, R = 0.2805 (Rfree = 0.000) for 2351 atoms. Found 1 (11 requested) and removed 7 (5 requested) atoms. Cycle 9: After refmac, R = 0.2787 (Rfree = 0.000) for 2343 atoms. Found 1 (11 requested) and removed 5 (5 requested) atoms. Cycle 10: After refmac, R = 0.2759 (Rfree = 0.000) for 2338 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.72 3.16 Search for helices and strands: 0 residues in 0 chains, 2378 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 2396 seeds are put forward Round 1: 150 peptides, 30 chains. Longest chain 11 peptides. Score 0.292 Round 2: 172 peptides, 29 chains. Longest chain 12 peptides. Score 0.390 Round 3: 180 peptides, 27 chains. Longest chain 13 peptides. Score 0.447 Round 4: 174 peptides, 25 chains. Longest chain 16 peptides. Score 0.457 Round 5: 172 peptides, 27 chains. Longest chain 13 peptides. Score 0.420 Taking the results from Round 4 Chains 25, Residues 149, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4253 reflections ( 97.23 % complete ) and 5395 restraints for refining 2354 atoms. 4824 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3059 (Rfree = 0.000) for 2354 atoms. Found 10 (11 requested) and removed 5 (5 requested) atoms. Cycle 12: After refmac, R = 0.2909 (Rfree = 0.000) for 2358 atoms. Found 1 (11 requested) and removed 5 (5 requested) atoms. Cycle 13: After refmac, R = 0.2876 (Rfree = 0.000) for 2354 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 14: After refmac, R = 0.2852 (Rfree = 0.000) for 2347 atoms. Found 1 (11 requested) and removed 6 (5 requested) atoms. Cycle 15: After refmac, R = 0.2822 (Rfree = 0.000) for 2341 atoms. Found 2 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.67 3.12 Search for helices and strands: 0 residues in 0 chains, 2366 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 2382 seeds are put forward Round 1: 154 peptides, 31 chains. Longest chain 9 peptides. Score 0.291 Round 2: 161 peptides, 27 chains. Longest chain 12 peptides. Score 0.382 Round 3: 162 peptides, 28 chains. Longest chain 16 peptides. Score 0.369 Round 4: 177 peptides, 27 chains. Longest chain 15 peptides. Score 0.437 Round 5: 175 peptides, 29 chains. Longest chain 20 peptides. Score 0.400 Taking the results from Round 4 Chains 27, Residues 150, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4253 reflections ( 97.23 % complete ) and 5427 restraints for refining 2355 atoms. 4854 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3128 (Rfree = 0.000) for 2355 atoms. Found 10 (11 requested) and removed 5 (5 requested) atoms. Cycle 17: After refmac, R = 0.2980 (Rfree = 0.000) for 2359 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 18: After refmac, R = 0.2899 (Rfree = 0.000) for 2351 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 19: After refmac, R = 0.2845 (Rfree = 0.000) for 2346 atoms. Found 2 (11 requested) and removed 5 (5 requested) atoms. Cycle 20: After refmac, R = 0.2806 (Rfree = 0.000) for 2340 atoms. Found 1 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.59 3.05 Search for helices and strands: 0 residues in 0 chains, 2373 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 2397 seeds are put forward Round 1: 163 peptides, 33 chains. Longest chain 10 peptides. Score 0.293 Round 2: 156 peptides, 24 chains. Longest chain 11 peptides. Score 0.411 Round 3: 176 peptides, 26 chains. Longest chain 16 peptides. Score 0.449 Round 4: 160 peptides, 26 chains. Longest chain 16 peptides. Score 0.394 Round 5: 172 peptides, 30 chains. Longest chain 13 peptides. Score 0.374 Taking the results from Round 3 Chains 26, Residues 150, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4253 reflections ( 97.23 % complete ) and 5328 restraints for refining 2355 atoms. 4723 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3082 (Rfree = 0.000) for 2355 atoms. Found 10 (11 requested) and removed 7 (5 requested) atoms. Cycle 22: After refmac, R = 0.2946 (Rfree = 0.000) for 2355 atoms. Found 5 (11 requested) and removed 6 (5 requested) atoms. Cycle 23: After refmac, R = 0.2865 (Rfree = 0.000) for 2353 atoms. Found 4 (11 requested) and removed 5 (5 requested) atoms. Cycle 24: After refmac, R = 0.2785 (Rfree = 0.000) for 2351 atoms. Found 1 (11 requested) and removed 5 (5 requested) atoms. Cycle 25: After refmac, R = 0.2723 (Rfree = 0.000) for 2345 atoms. Found 2 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.67 3.12 Search for helices and strands: 0 residues in 0 chains, 2367 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 2385 seeds are put forward Round 1: 144 peptides, 29 chains. Longest chain 8 peptides. Score 0.285 Round 2: 157 peptides, 26 chains. Longest chain 11 peptides. Score 0.383 Round 3: 158 peptides, 29 chains. Longest chain 10 peptides. Score 0.339 Round 4: 155 peptides, 23 chains. Longest chain 11 peptides. Score 0.423 Round 5: 169 peptides, 25 chains. Longest chain 14 peptides. Score 0.440 Taking the results from Round 5 Chains 25, Residues 144, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 4253 reflections ( 97.23 % complete ) and 5310 restraints for refining 2353 atoms. 4707 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3026 (Rfree = 0.000) for 2353 atoms. Found 5 (11 requested) and removed 10 (5 requested) atoms. Cycle 27: After refmac, R = 0.2844 (Rfree = 0.000) for 2342 atoms. Found 3 (11 requested) and removed 5 (5 requested) atoms. Cycle 28: After refmac, R = 0.2757 (Rfree = 0.000) for 2339 atoms. Found 1 (11 requested) and removed 5 (5 requested) atoms. Cycle 29: After refmac, R = 0.2717 (Rfree = 0.000) for 2333 atoms. Found 1 (11 requested) and removed 5 (5 requested) atoms. Cycle 30: After refmac, R = 0.2726 (Rfree = 0.000) for 2329 atoms. Found 3 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.65 3.10 Search for helices and strands: 0 residues in 0 chains, 2365 seeds are put forward NCS extension: 0 residues added, 2365 seeds are put forward Round 1: 136 peptides, 27 chains. Longest chain 8 peptides. Score 0.287 Round 2: 158 peptides, 27 chains. Longest chain 10 peptides. Score 0.371 Round 3: 151 peptides, 25 chains. Longest chain 11 peptides. Score 0.377 Round 4: 157 peptides, 27 chains. Longest chain 11 peptides. Score 0.367 Round 5: 152 peptides, 26 chains. Longest chain 11 peptides. Score 0.365 Taking the results from Round 3 Chains 25, Residues 126, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4253 reflections ( 97.23 % complete ) and 5581 restraints for refining 2355 atoms. 5102 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2945 (Rfree = 0.000) for 2355 atoms. Found 11 (11 requested) and removed 5 (5 requested) atoms. Cycle 32: After refmac, R = 0.2836 (Rfree = 0.000) for 2360 atoms. Found 2 (11 requested) and removed 5 (5 requested) atoms. Cycle 33: After refmac, R = 0.3059 (Rfree = 0.000) for 2355 atoms. Found 9 (11 requested) and removed 5 (5 requested) atoms. Cycle 34: After refmac, R = 0.2914 (Rfree = 0.000) for 2350 atoms. Found 4 (11 requested) and removed 5 (5 requested) atoms. Cycle 35: After refmac, R = 0.2815 (Rfree = 0.000) for 2348 atoms. Found 1 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.66 3.11 Search for helices and strands: 0 residues in 0 chains, 2387 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 2400 seeds are put forward Round 1: 135 peptides, 29 chains. Longest chain 8 peptides. Score 0.248 Round 2: 139 peptides, 26 chains. Longest chain 8 peptides. Score 0.316 Round 3: 137 peptides, 24 chains. Longest chain 11 peptides. Score 0.341 Round 4: 153 peptides, 24 chains. Longest chain 12 peptides. Score 0.400 Round 5: 137 peptides, 24 chains. Longest chain 10 peptides. Score 0.341 Taking the results from Round 4 Chains 24, Residues 129, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4253 reflections ( 97.23 % complete ) and 5500 restraints for refining 2354 atoms. 5008 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3079 (Rfree = 0.000) for 2354 atoms. Found 10 (11 requested) and removed 8 (5 requested) atoms. Cycle 37: After refmac, R = 0.2938 (Rfree = 0.000) for 2354 atoms. Found 3 (11 requested) and removed 6 (5 requested) atoms. Cycle 38: After refmac, R = 0.2867 (Rfree = 0.000) for 2348 atoms. Found 3 (11 requested) and removed 5 (5 requested) atoms. Cycle 39: After refmac, R = 0.2849 (Rfree = 0.000) for 2344 atoms. Found 4 (11 requested) and removed 5 (5 requested) atoms. Cycle 40: After refmac, R = 0.2824 (Rfree = 0.000) for 2342 atoms. Found 2 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.63 3.08 Search for helices and strands: 0 residues in 0 chains, 2369 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 2386 seeds are put forward Round 1: 129 peptides, 29 chains. Longest chain 8 peptides. Score 0.223 Round 2: 142 peptides, 26 chains. Longest chain 10 peptides. Score 0.327 Round 3: 139 peptides, 23 chains. Longest chain 10 peptides. Score 0.365 Round 4: 128 peptides, 23 chains. Longest chain 13 peptides. Score 0.323 Round 5: 139 peptides, 24 chains. Longest chain 11 peptides. Score 0.349 Taking the results from Round 3 Chains 23, Residues 116, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4253 reflections ( 97.23 % complete ) and 5584 restraints for refining 2354 atoms. 5106 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2907 (Rfree = 0.000) for 2354 atoms. Found 3 (11 requested) and removed 5 (5 requested) atoms. Cycle 42: After refmac, R = 0.2818 (Rfree = 0.000) for 2350 atoms. Found 1 (11 requested) and removed 5 (5 requested) atoms. Cycle 43: After refmac, R = 0.2775 (Rfree = 0.000) for 2342 atoms. Found 1 (11 requested) and removed 5 (5 requested) atoms. Cycle 44: After refmac, R = 0.2809 (Rfree = 0.000) for 2334 atoms. Found 2 (11 requested) and removed 5 (5 requested) atoms. Cycle 45: After refmac, R = 0.2776 (Rfree = 0.000) for 2330 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.69 3.13 Search for helices and strands: 0 residues in 0 chains, 2349 seeds are put forward NCS extension: 0 residues added, 2349 seeds are put forward Round 1: 113 peptides, 25 chains. Longest chain 6 peptides. Score 0.226 Round 2: 151 peptides, 27 chains. Longest chain 11 peptides. Score 0.345 Round 3: 148 peptides, 26 chains. Longest chain 12 peptides. Score 0.350 Round 4: 147 peptides, 27 chains. Longest chain 9 peptides. Score 0.330 Round 5: 148 peptides, 27 chains. Longest chain 14 peptides. Score 0.333 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 26, 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 2nuj-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4253 reflections ( 97.23 % complete ) and 5690 restraints for refining 2355 atoms. 5228 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3098 (Rfree = 0.000) for 2355 atoms. Found 0 (11 requested) and removed 1 (5 requested) atoms. Cycle 47: After refmac, R = 0.3019 (Rfree = 0.000) for 2354 atoms. Found 0 (11 requested) and removed 3 (5 requested) atoms. Cycle 48: After refmac, R = 0.2976 (Rfree = 0.000) for 2351 atoms. Found 0 (11 requested) and removed 2 (5 requested) atoms. Cycle 49: After refmac, R = 0.2946 (Rfree = 0.000) for 2349 atoms. Found 0 (11 requested) and removed 0 (5 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:08:46 GMT 2018 Job finished. TimeTaking 45.9 Used memory is bytes: 12690040