null Mon 24 Dec 07:31:26 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 2eth-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2eth-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2eth-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2eth-3.2-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/2eth-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2eth-3.2-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 07:31:30 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/2eth-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2eth-3.2-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 246 and 0 Target number of residues in the AU: 246 Target solvent content: 0.6462 Checking the provided sequence file Detected sequence length: 154 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 308 Adjusted target solvent content: 0.56 Input MTZ file: 2eth-3.2-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: 5 Cell parameters: 98.852 58.439 80.432 90.000 125.913 90.000 Input sequence file: 2eth-3.2-parrot-noncs.fasta_lf Building free atoms model in initial map for 2464 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: 65.143 3.200 Wilson plot Bfac: 75.64 6145 reflections ( 98.19 % complete ) and 0 restraints for refining 2742 atoms. Observations/parameters ratio is 0.56 ------------------------------------------------------ Starting model: R = 0.3392 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3048 (Rfree = 0.000) for 2742 atoms. Found 20 (24 requested) and removed 16 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.41 3.15 Search for helices and strands: 0 residues in 0 chains, 2809 seeds are put forward NCS extension: 0 residues added, 2809 seeds are put forward Round 1: 140 peptides, 26 chains. Longest chain 10 peptides. Score 0.345 Round 2: 166 peptides, 23 chains. Longest chain 16 peptides. Score 0.507 Round 3: 185 peptides, 22 chains. Longest chain 22 peptides. Score 0.590 Round 4: 191 peptides, 25 chains. Longest chain 26 peptides. Score 0.565 Round 5: 199 peptides, 19 chains. Longest chain 28 peptides. Score 0.674 Taking the results from Round 5 Chains 19, Residues 180, Estimated correctness of the model 59.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6145 reflections ( 98.19 % complete ) and 4639 restraints for refining 2126 atoms. 3938 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2895 (Rfree = 0.000) for 2126 atoms. Found 18 (19 requested) and removed 18 (9 requested) atoms. Cycle 2: After refmac, R = 0.2849 (Rfree = 0.000) for 2085 atoms. Found 13 (19 requested) and removed 14 (9 requested) atoms. Cycle 3: After refmac, R = 0.3009 (Rfree = 0.000) for 2066 atoms. Found 16 (18 requested) and removed 17 (9 requested) atoms. Cycle 4: After refmac, R = 0.2917 (Rfree = 0.000) for 2054 atoms. Found 15 (18 requested) and removed 17 (9 requested) atoms. Cycle 5: After refmac, R = 0.2938 (Rfree = 0.000) for 2039 atoms. Found 17 (18 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.34 3.08 Search for helices and strands: 0 residues in 0 chains, 2168 seeds are put forward NCS extension: 37 residues added (1 deleted due to clashes), 2205 seeds are put forward Round 1: 169 peptides, 23 chains. Longest chain 13 peptides. Score 0.518 Round 2: 197 peptides, 25 chains. Longest chain 23 peptides. Score 0.585 Round 3: 184 peptides, 24 chains. Longest chain 17 peptides. Score 0.556 Round 4: 192 peptides, 21 chains. Longest chain 22 peptides. Score 0.626 Round 5: 184 peptides, 21 chains. Longest chain 21 peptides. Score 0.602 Taking the results from Round 4 Chains 21, Residues 171, Estimated correctness of the model 47.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6145 reflections ( 98.19 % complete ) and 4453 restraints for refining 2069 atoms. 3790 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2890 (Rfree = 0.000) for 2069 atoms. Found 18 (18 requested) and removed 23 (9 requested) atoms. Cycle 7: After refmac, R = 0.2877 (Rfree = 0.000) for 2054 atoms. Found 18 (18 requested) and removed 20 (9 requested) atoms. Cycle 8: After refmac, R = 0.2796 (Rfree = 0.000) for 2045 atoms. Found 18 (18 requested) and removed 21 (9 requested) atoms. Cycle 9: After refmac, R = 0.2627 (Rfree = 0.000) for 2038 atoms. Found 18 (18 requested) and removed 15 (9 requested) atoms. Cycle 10: After refmac, R = 0.2654 (Rfree = 0.000) for 2038 atoms. Found 18 (18 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.42 3.16 Search for helices and strands: 0 residues in 0 chains, 2155 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 2177 seeds are put forward Round 1: 159 peptides, 22 chains. Longest chain 22 peptides. Score 0.498 Round 2: 191 peptides, 24 chains. Longest chain 22 peptides. Score 0.580 Round 3: 183 peptides, 22 chains. Longest chain 19 peptides. Score 0.583 Round 4: 180 peptides, 24 chains. Longest chain 16 peptides. Score 0.542 Round 5: 180 peptides, 23 chains. Longest chain 19 peptides. Score 0.558 Taking the results from Round 3 Chains 22, Residues 161, Estimated correctness of the model 36.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6145 reflections ( 98.19 % complete ) and 4609 restraints for refining 2125 atoms. 3987 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2411 (Rfree = 0.000) for 2125 atoms. Found 10 (19 requested) and removed 20 (9 requested) atoms. Cycle 12: After refmac, R = 0.2187 (Rfree = 0.000) for 2108 atoms. Found 7 (18 requested) and removed 13 (9 requested) atoms. Cycle 13: After refmac, R = 0.2037 (Rfree = 0.000) for 2095 atoms. Found 2 (18 requested) and removed 9 (9 requested) atoms. Cycle 14: After refmac, R = 0.2013 (Rfree = 0.000) for 2085 atoms. Found 1 (18 requested) and removed 10 (9 requested) atoms. Cycle 15: After refmac, R = 0.1929 (Rfree = 0.000) for 2075 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.38 3.12 Search for helices and strands: 0 residues in 0 chains, 2176 seeds are put forward NCS extension: 29 residues added (2 deleted due to clashes), 2205 seeds are put forward Round 1: 161 peptides, 24 chains. Longest chain 14 peptides. Score 0.471 Round 2: 182 peptides, 27 chains. Longest chain 14 peptides. Score 0.501 Round 3: 175 peptides, 24 chains. Longest chain 14 peptides. Score 0.524 Round 4: 163 peptides, 22 chains. Longest chain 14 peptides. Score 0.513 Round 5: 166 peptides, 22 chains. Longest chain 15 peptides. Score 0.524 Taking the results from Round 5 Chains 22, Residues 144, Estimated correctness of the model 19.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6145 reflections ( 98.19 % complete ) and 4970 restraints for refining 2226 atoms. 4416 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2423 (Rfree = 0.000) for 2226 atoms. Found 9 (19 requested) and removed 16 (9 requested) atoms. Cycle 17: After refmac, R = 0.2393 (Rfree = 0.000) for 2210 atoms. Found 8 (19 requested) and removed 10 (9 requested) atoms. Cycle 18: After refmac, R = 0.2237 (Rfree = 0.000) for 2201 atoms. Found 5 (19 requested) and removed 10 (9 requested) atoms. Cycle 19: After refmac, R = 0.2319 (Rfree = 0.000) for 2189 atoms. Found 6 (19 requested) and removed 11 (9 requested) atoms. Cycle 20: After refmac, R = 0.2179 (Rfree = 0.000) for 2182 atoms. Found 3 (19 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.39 3.13 Search for helices and strands: 0 residues in 0 chains, 2284 seeds are put forward NCS extension: 23 residues added (3 deleted due to clashes), 2307 seeds are put forward Round 1: 158 peptides, 25 chains. Longest chain 12 peptides. Score 0.441 Round 2: 181 peptides, 26 chains. Longest chain 17 peptides. Score 0.513 Round 3: 167 peptides, 24 chains. Longest chain 17 peptides. Score 0.494 Round 4: 173 peptides, 24 chains. Longest chain 16 peptides. Score 0.517 Round 5: 162 peptides, 26 chains. Longest chain 11 peptides. Score 0.440 Taking the results from Round 4 Chains 24, Residues 149, Estimated correctness of the model 16.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6145 reflections ( 98.19 % complete ) and 5004 restraints for refining 2247 atoms. 4432 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2360 (Rfree = 0.000) for 2247 atoms. Found 20 (20 requested) and removed 15 (10 requested) atoms. Cycle 22: After refmac, R = 0.2458 (Rfree = 0.000) for 2247 atoms. Found 14 (20 requested) and removed 13 (10 requested) atoms. Cycle 23: After refmac, R = 0.2137 (Rfree = 0.000) for 2243 atoms. Found 4 (20 requested) and removed 10 (10 requested) atoms. Cycle 24: After refmac, R = 0.2088 (Rfree = 0.000) for 2230 atoms. Found 7 (20 requested) and removed 13 (10 requested) atoms. Cycle 25: After refmac, R = 0.2052 (Rfree = 0.000) for 2220 atoms. Found 19 (19 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.41 3.15 Search for helices and strands: 0 residues in 0 chains, 2338 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 2356 seeds are put forward Round 1: 158 peptides, 28 chains. Longest chain 12 peptides. Score 0.387 Round 2: 184 peptides, 26 chains. Longest chain 17 peptides. Score 0.524 Round 3: 182 peptides, 24 chains. Longest chain 15 peptides. Score 0.549 Round 4: 179 peptides, 27 chains. Longest chain 15 peptides. Score 0.489 Round 5: 164 peptides, 24 chains. Longest chain 15 peptides. Score 0.482 Taking the results from Round 3 Chains 24, Residues 158, Estimated correctness of the model 26.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6145 reflections ( 98.19 % complete ) and 4923 restraints for refining 2250 atoms. 4315 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2337 (Rfree = 0.000) for 2250 atoms. Found 9 (20 requested) and removed 12 (10 requested) atoms. Cycle 27: After refmac, R = 0.2280 (Rfree = 0.000) for 2243 atoms. Found 15 (20 requested) and removed 13 (10 requested) atoms. Cycle 28: After refmac, R = 0.2269 (Rfree = 0.000) for 2238 atoms. Found 9 (20 requested) and removed 11 (10 requested) atoms. Cycle 29: After refmac, R = 0.2181 (Rfree = 0.000) for 2234 atoms. Found 6 (20 requested) and removed 11 (10 requested) atoms. Cycle 30: After refmac, R = 0.2497 (Rfree = 0.000) for 2227 atoms. Found 19 (19 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.36 3.10 Search for helices and strands: 0 residues in 0 chains, 2339 seeds are put forward NCS extension: 15 residues added (4 deleted due to clashes), 2354 seeds are put forward Round 1: 159 peptides, 28 chains. Longest chain 13 peptides. Score 0.391 Round 2: 149 peptides, 24 chains. Longest chain 13 peptides. Score 0.422 Round 3: 161 peptides, 24 chains. Longest chain 16 peptides. Score 0.471 Round 4: 166 peptides, 24 chains. Longest chain 12 peptides. Score 0.490 Round 5: 181 peptides, 27 chains. Longest chain 13 peptides. Score 0.497 Taking the results from Round 5 Chains 27, Residues 154, Estimated correctness of the model 10.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6145 reflections ( 98.19 % complete ) and 5090 restraints for refining 2250 atoms. 4501 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2445 (Rfree = 0.000) for 2250 atoms. Found 16 (20 requested) and removed 11 (10 requested) atoms. Cycle 32: After refmac, R = 0.2340 (Rfree = 0.000) for 2246 atoms. Found 5 (20 requested) and removed 12 (10 requested) atoms. Cycle 33: After refmac, R = 0.2416 (Rfree = 0.000) for 2233 atoms. Found 18 (20 requested) and removed 13 (10 requested) atoms. Cycle 34: After refmac, R = 0.2361 (Rfree = 0.000) for 2233 atoms. Found 15 (20 requested) and removed 14 (10 requested) atoms. Cycle 35: After refmac, R = 0.2378 (Rfree = 0.000) for 2229 atoms. Found 11 (20 requested) and removed 12 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.36 3.10 Search for helices and strands: 0 residues in 0 chains, 2326 seeds are put forward NCS extension: 11 residues added (3 deleted due to clashes), 2337 seeds are put forward Round 1: 153 peptides, 27 chains. Longest chain 13 peptides. Score 0.383 Round 2: 173 peptides, 27 chains. Longest chain 13 peptides. Score 0.466 Round 3: 166 peptides, 25 chains. Longest chain 12 peptides. Score 0.473 Round 4: 167 peptides, 25 chains. Longest chain 12 peptides. Score 0.477 Round 5: 181 peptides, 28 chains. Longest chain 12 peptides. Score 0.480 Taking the results from Round 5 Chains 28, Residues 153, Estimated correctness of the model 4.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6145 reflections ( 98.19 % complete ) and 4962 restraints for refining 2250 atoms. 4378 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2869 (Rfree = 0.000) for 2250 atoms. Found 20 (20 requested) and removed 12 (10 requested) atoms. Cycle 37: After refmac, R = 0.2626 (Rfree = 0.000) for 2252 atoms. Found 20 (20 requested) and removed 12 (10 requested) atoms. Cycle 38: After refmac, R = 0.2299 (Rfree = 0.000) for 2252 atoms. Found 16 (20 requested) and removed 11 (10 requested) atoms. Cycle 39: After refmac, R = 0.2009 (Rfree = 0.000) for 2252 atoms. Found 15 (20 requested) and removed 11 (10 requested) atoms. Cycle 40: After refmac, R = 0.2002 (Rfree = 0.000) for 2250 atoms. Found 14 (20 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.45 3.18 Search for helices and strands: 0 residues in 0 chains, 2353 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 2368 seeds are put forward Round 1: 148 peptides, 26 chains. Longest chain 13 peptides. Score 0.380 Round 2: 169 peptides, 26 chains. Longest chain 13 peptides. Score 0.468 Round 3: 156 peptides, 23 chains. Longest chain 14 peptides. Score 0.468 Round 4: 148 peptides, 25 chains. Longest chain 14 peptides. Score 0.399 Round 5: 149 peptides, 22 chains. Longest chain 14 peptides. Score 0.458 Taking the results from Round 3 Chains 23, Residues 133, Estimated correctness of the model 0.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6145 reflections ( 98.19 % complete ) and 5067 restraints for refining 2250 atoms. 4558 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2222 (Rfree = 0.000) for 2250 atoms. Found 14 (20 requested) and removed 10 (10 requested) atoms. Cycle 42: After refmac, R = 0.2079 (Rfree = 0.000) for 2253 atoms. Found 12 (20 requested) and removed 10 (10 requested) atoms. Cycle 43: After refmac, R = 0.2565 (Rfree = 0.000) for 2250 atoms. Found 20 (20 requested) and removed 13 (10 requested) atoms. Cycle 44: After refmac, R = 0.1996 (Rfree = 0.000) for 2253 atoms. Found 7 (20 requested) and removed 10 (10 requested) atoms. Cycle 45: After refmac, R = 0.2381 (Rfree = 0.000) for 2249 atoms. Found 20 (20 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.36 3.10 Search for helices and strands: 0 residues in 0 chains, 2348 seeds are put forward NCS extension: 9 residues added (3 deleted due to clashes), 2357 seeds are put forward Round 1: 138 peptides, 26 chains. Longest chain 13 peptides. Score 0.336 Round 2: 150 peptides, 22 chains. Longest chain 15 peptides. Score 0.462 Round 3: 138 peptides, 22 chains. Longest chain 13 peptides. Score 0.413 Round 4: 147 peptides, 21 chains. Longest chain 15 peptides. Score 0.468 Round 5: 140 peptides, 22 chains. Longest chain 13 peptides. Score 0.421 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 21, Residues 126, Estimated correctness of the model 0.7 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2eth-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6145 reflections ( 98.19 % complete ) and 5035 restraints for refining 2250 atoms. 4552 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2549 (Rfree = 0.000) for 2250 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 47: After refmac, R = 0.2963 (Rfree = 0.000) for 2232 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 48: After refmac, R = 0.2280 (Rfree = 0.000) for 2217 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.2062 (Rfree = 0.000) for 2204 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:01:49 GMT 2018 Job finished. TimeTaking 30.38 Used memory is bytes: 12534320