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 2eth-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2eth-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2eth-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2eth-3.2-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/2eth-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2eth-3.2-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/2eth-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2eth-3.2-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 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-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: 5 Cell parameters: 98.852 58.439 80.432 90.000 125.913 90.000 Input sequence file: 2eth-3.2-parrot-hancs.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 2713 atoms. Observations/parameters ratio is 0.57 ------------------------------------------------------ Starting model: R = 0.3346 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2940 (Rfree = 0.000) for 2713 atoms. Found 17 (24 requested) and removed 25 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.36 3.10 Search for helices and strands: 0 residues in 0 chains, 2767 seeds are put forward NCS extension: 0 residues added, 2767 seeds are put forward Round 1: 123 peptides, 22 chains. Longest chain 11 peptides. Score 0.346 Round 2: 144 peptides, 25 chains. Longest chain 12 peptides. Score 0.382 Round 3: 153 peptides, 25 chains. Longest chain 15 peptides. Score 0.420 Round 4: 168 peptides, 21 chains. Longest chain 19 peptides. Score 0.547 Round 5: 176 peptides, 23 chains. Longest chain 19 peptides. Score 0.544 Taking the results from Round 4 Chains 21, Residues 147, Estimated correctness of the model 26.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6145 reflections ( 98.19 % complete ) and 4966 restraints for refining 2214 atoms. 4399 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2773 (Rfree = 0.000) for 2214 atoms. Found 10 (19 requested) and removed 17 (9 requested) atoms. Cycle 2: After refmac, R = 0.2659 (Rfree = 0.000) for 2181 atoms. Found 11 (19 requested) and removed 12 (9 requested) atoms. Cycle 3: After refmac, R = 0.2542 (Rfree = 0.000) for 2171 atoms. Found 6 (19 requested) and removed 10 (9 requested) atoms. Cycle 4: After refmac, R = 0.2495 (Rfree = 0.000) for 2162 atoms. Found 5 (19 requested) and removed 9 (9 requested) atoms. Cycle 5: After refmac, R = 0.2445 (Rfree = 0.000) for 2153 atoms. Found 1 (19 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.34 3.08 Search for helices and strands: 0 residues in 0 chains, 2246 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 2265 seeds are put forward Round 1: 160 peptides, 25 chains. Longest chain 14 peptides. Score 0.449 Round 2: 173 peptides, 23 chains. Longest chain 16 peptides. Score 0.533 Round 3: 176 peptides, 21 chains. Longest chain 18 peptides. Score 0.575 Round 4: 186 peptides, 20 chains. Longest chain 25 peptides. Score 0.622 Round 5: 186 peptides, 23 chains. Longest chain 19 peptides. Score 0.578 Taking the results from Round 4 Chains 21, Residues 166, Estimated correctness of the model 46.9 % 1 chains (21 residues) have been docked in sequence ------------------------------------------------------ 6145 reflections ( 98.19 % complete ) and 4618 restraints for refining 2187 atoms. 3878 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2721 (Rfree = 0.000) for 2187 atoms. Found 19 (19 requested) and removed 18 (9 requested) atoms. Cycle 7: After refmac, R = 0.2469 (Rfree = 0.000) for 2166 atoms. Found 12 (19 requested) and removed 38 (9 requested) atoms. Cycle 8: After refmac, R = 0.2424 (Rfree = 0.000) for 2125 atoms. Found 9 (19 requested) and removed 14 (9 requested) atoms. Cycle 9: After refmac, R = 0.2375 (Rfree = 0.000) for 2117 atoms. Found 3 (19 requested) and removed 12 (9 requested) atoms. Cycle 10: After refmac, R = 0.2347 (Rfree = 0.000) for 2104 atoms. Found 1 (18 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.36 3.10 Search for helices and strands: 0 residues in 0 chains, 2179 seeds are put forward NCS extension: 28 residues added (1 deleted due to clashes), 2207 seeds are put forward Round 1: 169 peptides, 27 chains. Longest chain 11 peptides. Score 0.450 Round 2: 180 peptides, 23 chains. Longest chain 18 peptides. Score 0.558 Round 3: 174 peptides, 22 chains. Longest chain 23 peptides. Score 0.553 Round 4: 178 peptides, 22 chains. Longest chain 17 peptides. Score 0.566 Round 5: 166 peptides, 20 chains. Longest chain 20 peptides. Score 0.557 Taking the results from Round 4 Chains 22, Residues 156, Estimated correctness of the model 31.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6145 reflections ( 98.19 % complete ) and 4791 restraints for refining 2150 atoms. 4189 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2617 (Rfree = 0.000) for 2150 atoms. Found 12 (19 requested) and removed 10 (9 requested) atoms. Cycle 12: After refmac, R = 0.2452 (Rfree = 0.000) for 2141 atoms. Found 7 (19 requested) and removed 10 (9 requested) atoms. Cycle 13: After refmac, R = 0.2403 (Rfree = 0.000) for 2131 atoms. Found 3 (19 requested) and removed 9 (9 requested) atoms. Cycle 14: After refmac, R = 0.2391 (Rfree = 0.000) for 2124 atoms. Found 3 (19 requested) and removed 9 (9 requested) atoms. Cycle 15: After refmac, R = 0.2345 (Rfree = 0.000) for 2117 atoms. Found 2 (18 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.39 3.13 Search for helices and strands: 0 residues in 0 chains, 2199 seeds are put forward NCS extension: 4 residues added (0 deleted due to clashes), 2203 seeds are put forward Round 1: 168 peptides, 24 chains. Longest chain 20 peptides. Score 0.498 Round 2: 197 peptides, 20 chains. Longest chain 28 peptides. Score 0.655 Round 3: 183 peptides, 20 chains. Longest chain 24 peptides. Score 0.613 Round 4: 194 peptides, 22 chains. Longest chain 21 peptides. Score 0.618 Round 5: 180 peptides, 24 chains. Longest chain 18 peptides. Score 0.542 Taking the results from Round 2 Chains 21, Residues 177, Estimated correctness of the model 55.0 % 2 chains (44 residues) have been docked in sequence ------------------------------------------------------ 6145 reflections ( 98.19 % complete ) and 4223 restraints for refining 2207 atoms. 3345 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2901 (Rfree = 0.000) for 2207 atoms. Found 12 (19 requested) and removed 23 (9 requested) atoms. Cycle 17: After refmac, R = 0.2653 (Rfree = 0.000) for 2169 atoms. Found 10 (19 requested) and removed 14 (9 requested) atoms. Cycle 18: After refmac, R = 0.2547 (Rfree = 0.000) for 2156 atoms. Found 5 (19 requested) and removed 12 (9 requested) atoms. Cycle 19: After refmac, R = 0.2245 (Rfree = 0.000) for 2146 atoms. Found 3 (19 requested) and removed 9 (9 requested) atoms. Cycle 20: After refmac, R = 0.2224 (Rfree = 0.000) for 2134 atoms. Found 2 (19 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.32 3.06 Search for helices and strands: 0 residues in 0 chains, 2222 seeds are put forward NCS extension: 30 residues added (5 deleted due to clashes), 2252 seeds are put forward Round 1: 167 peptides, 22 chains. Longest chain 20 peptides. Score 0.528 Round 2: 185 peptides, 22 chains. Longest chain 26 peptides. Score 0.590 Round 3: 184 peptides, 21 chains. Longest chain 20 peptides. Score 0.602 Round 4: 177 peptides, 21 chains. Longest chain 28 peptides. Score 0.579 Round 5: 173 peptides, 24 chains. Longest chain 18 peptides. Score 0.517 Taking the results from Round 3 Chains 21, Residues 163, Estimated correctness of the model 41.6 % 2 chains (28 residues) have been docked in sequence ------------------------------------------------------ 6145 reflections ( 98.19 % complete ) and 4559 restraints for refining 2212 atoms. 3801 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2631 (Rfree = 0.000) for 2212 atoms. Found 12 (19 requested) and removed 22 (9 requested) atoms. Cycle 22: After refmac, R = 0.2756 (Rfree = 0.000) for 2189 atoms. Found 18 (19 requested) and removed 16 (9 requested) atoms. Cycle 23: After refmac, R = 0.2765 (Rfree = 0.000) for 2183 atoms. Found 19 (19 requested) and removed 16 (9 requested) atoms. Cycle 24: After refmac, R = 0.2255 (Rfree = 0.000) for 2175 atoms. Found 5 (19 requested) and removed 14 (9 requested) atoms. Cycle 25: After refmac, R = 0.2255 (Rfree = 0.000) for 2162 atoms. Found 5 (19 requested) and removed 13 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.38 3.12 Search for helices and strands: 0 residues in 0 chains, 2249 seeds are put forward NCS extension: 28 residues added (0 deleted due to clashes), 2277 seeds are put forward Round 1: 155 peptides, 20 chains. Longest chain 17 peptides. Score 0.517 Round 2: 173 peptides, 20 chains. Longest chain 19 peptides. Score 0.581 Round 3: 171 peptides, 19 chains. Longest chain 20 peptides. Score 0.589 Round 4: 182 peptides, 25 chains. Longest chain 18 peptides. Score 0.533 Round 5: 185 peptides, 25 chains. Longest chain 16 peptides. Score 0.544 Taking the results from Round 3 Chains 19, Residues 152, Estimated correctness of the model 38.1 % 1 chains (19 residues) have been docked in sequence ------------------------------------------------------ 6145 reflections ( 98.19 % complete ) and 4663 restraints for refining 2210 atoms. 3994 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2738 (Rfree = 0.000) for 2210 atoms. Found 19 (19 requested) and removed 14 (9 requested) atoms. Cycle 27: After refmac, R = 0.2831 (Rfree = 0.000) for 2206 atoms. Found 19 (19 requested) and removed 18 (9 requested) atoms. Cycle 28: After refmac, R = 0.2742 (Rfree = 0.000) for 2195 atoms. Found 19 (19 requested) and removed 16 (9 requested) atoms. Cycle 29: After refmac, R = 0.2307 (Rfree = 0.000) for 2188 atoms. Found 10 (19 requested) and removed 12 (9 requested) atoms. Cycle 30: After refmac, R = 0.2260 (Rfree = 0.000) for 2179 atoms. Found 7 (19 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.36 3.10 Search for helices and strands: 0 residues in 0 chains, 2271 seeds are put forward NCS extension: 22 residues added (3 deleted due to clashes), 2293 seeds are put forward Round 1: 150 peptides, 22 chains. Longest chain 13 peptides. Score 0.462 Round 2: 184 peptides, 20 chains. Longest chain 21 peptides. Score 0.616 Round 3: 183 peptides, 24 chains. Longest chain 16 peptides. Score 0.552 Round 4: 185 peptides, 23 chains. Longest chain 17 peptides. Score 0.575 Round 5: 172 peptides, 25 chains. Longest chain 17 peptides. Score 0.496 Taking the results from Round 2 Chains 20, Residues 164, Estimated correctness of the model 45.3 % 1 chains (20 residues) have been docked in sequence ------------------------------------------------------ 6145 reflections ( 98.19 % complete ) and 4443 restraints for refining 2179 atoms. 3722 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2617 (Rfree = 0.000) for 2179 atoms. Found 19 (19 requested) and removed 14 (9 requested) atoms. Cycle 32: After refmac, R = 0.2719 (Rfree = 0.000) for 2178 atoms. Found 19 (19 requested) and removed 17 (9 requested) atoms. Cycle 33: After refmac, R = 0.2719 (Rfree = 0.000) for 2174 atoms. Found 18 (19 requested) and removed 12 (9 requested) atoms. Cycle 34: After refmac, R = 0.2628 (Rfree = 0.000) for 2171 atoms. Found 17 (19 requested) and removed 14 (9 requested) atoms. Cycle 35: After refmac, R = 0.2208 (Rfree = 0.000) for 2170 atoms. Found 5 (19 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.37 3.11 Search for helices and strands: 0 residues in 0 chains, 2269 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 2283 seeds are put forward Round 1: 129 peptides, 19 chains. Longest chain 13 peptides. Score 0.431 Round 2: 164 peptides, 24 chains. Longest chain 18 peptides. Score 0.482 Round 3: 162 peptides, 24 chains. Longest chain 12 peptides. Score 0.475 Round 4: 174 peptides, 24 chains. Longest chain 18 peptides. Score 0.520 Round 5: 176 peptides, 22 chains. Longest chain 21 peptides. Score 0.560 Taking the results from Round 5 Chains 22, Residues 154, Estimated correctness of the model 29.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6145 reflections ( 98.19 % complete ) and 4868 restraints for refining 2250 atoms. 4274 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2322 (Rfree = 0.000) for 2250 atoms. Found 8 (20 requested) and removed 12 (10 requested) atoms. Cycle 37: After refmac, R = 0.2198 (Rfree = 0.000) for 2245 atoms. Found 3 (20 requested) and removed 11 (10 requested) atoms. Cycle 38: After refmac, R = 0.2136 (Rfree = 0.000) for 2233 atoms. Found 4 (20 requested) and removed 10 (10 requested) atoms. Cycle 39: After refmac, R = 0.2166 (Rfree = 0.000) for 2227 atoms. Found 4 (19 requested) and removed 9 (9 requested) atoms. Cycle 40: After refmac, R = 0.2146 (Rfree = 0.000) for 2219 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.37 3.11 Search for helices and strands: 0 residues in 0 chains, 2284 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 2309 seeds are put forward Round 1: 145 peptides, 23 chains. Longest chain 12 peptides. Score 0.424 Round 2: 172 peptides, 22 chains. Longest chain 19 peptides. Score 0.546 Round 3: 159 peptides, 19 chains. Longest chain 18 peptides. Score 0.548 Round 4: 154 peptides, 21 chains. Longest chain 12 peptides. Score 0.496 Round 5: 149 peptides, 19 chains. Longest chain 14 peptides. Score 0.511 Taking the results from Round 3 Chains 19, Residues 140, Estimated correctness of the model 26.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6145 reflections ( 98.19 % complete ) and 5055 restraints for refining 2249 atoms. 4514 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2282 (Rfree = 0.000) for 2249 atoms. Found 7 (20 requested) and removed 11 (10 requested) atoms. Cycle 42: After refmac, R = 0.2184 (Rfree = 0.000) for 2241 atoms. Found 2 (20 requested) and removed 10 (10 requested) atoms. Cycle 43: After refmac, R = 0.2143 (Rfree = 0.000) for 2232 atoms. Found 3 (20 requested) and removed 10 (10 requested) atoms. Cycle 44: After refmac, R = 0.2118 (Rfree = 0.000) for 2223 atoms. Found 1 (19 requested) and removed 9 (9 requested) atoms. Cycle 45: After refmac, R = 0.2091 (Rfree = 0.000) for 2214 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.39 3.13 Search for helices and strands: 0 residues in 0 chains, 2267 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 2281 seeds are put forward Round 1: 144 peptides, 22 chains. Longest chain 13 peptides. Score 0.438 Round 2: 153 peptides, 23 chains. Longest chain 13 peptides. Score 0.456 Round 3: 154 peptides, 22 chains. Longest chain 13 peptides. Score 0.478 Round 4: 164 peptides, 22 chains. Longest chain 22 peptides. Score 0.517 Round 5: 163 peptides, 23 chains. Longest chain 22 peptides. Score 0.496 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 22, Residues 142, Estimated correctness of the model 16.8 % 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 5070 restraints for refining 2250 atoms. 4524 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2327 (Rfree = 0.000) for 2250 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 47: After refmac, R = 0.2289 (Rfree = 0.000) for 2237 atoms. Found 0 (20 requested) and removed 6 (10 requested) atoms. Cycle 48: After refmac, R = 0.2216 (Rfree = 0.000) for 2231 atoms. Found 0 (20 requested) and removed 7 (10 requested) atoms. Cycle 49: After refmac, R = 0.2225 (Rfree = 0.000) for 2222 atoms. Found 0 (19 requested) and removed 6 (9 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:10:20 GMT 2018 Job finished. TimeTaking 47.51 Used memory is bytes: 3007280