null Sun 23 Dec 22:23:02 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 2ghs-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ghs-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ghs-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ghs-3.4-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/2ghs-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ghs-3.4-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 22:23:12 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/2ghs-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ghs-3.4-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 201 and 0 Target number of residues in the AU: 201 Target solvent content: 0.6190 Checking the provided sequence file Detected sequence length: 326 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 326 Adjusted target solvent content: 0.38 Input MTZ file: 2ghs-3.4-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: 46.258 75.703 81.538 90.000 90.000 90.000 Input sequence file: 2ghs-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 2608 target number of atoms Had to go as low as 0.55 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 Loops will be built when appropriate and at the last cycle Resolution range: 55.478 3.400 Wilson plot Bfac: 60.57 4219 reflections ( 99.36 % complete ) and 0 restraints for refining 2882 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Starting model: R = 0.3278 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2190 (Rfree = 0.000) for 2882 atoms. Found 13 (21 requested) and removed 30 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.18 3.74 Search for helices and strands: 0 residues in 0 chains, 2922 seeds are put forward Round 1: 125 peptides, 26 chains. Longest chain 10 peptides. Score 0.299 Round 2: 164 peptides, 24 chains. Longest chain 14 peptides. Score 0.550 Round 3: 174 peptides, 25 chains. Longest chain 19 peptides. Score 0.574 Round 4: 184 peptides, 26 chains. Longest chain 14 peptides. Score 0.598 Round 5: 187 peptides, 22 chains. Longest chain 22 peptides. Score 0.676 Taking the results from Round 5 Chains 23, Residues 165, Estimated correctness of the model 51.5 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ 4219 reflections ( 99.36 % complete ) and 5289 restraints for refining 2370 atoms. 4595 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2703 (Rfree = 0.000) for 2370 atoms. Found 17 (17 requested) and removed 28 (8 requested) atoms. Cycle 2: After refmac, R = 0.2554 (Rfree = 0.000) for 2331 atoms. Found 7 (17 requested) and removed 10 (8 requested) atoms. Cycle 3: After refmac, R = 0.2468 (Rfree = 0.000) for 2313 atoms. Found 5 (17 requested) and removed 9 (8 requested) atoms. Cycle 4: After refmac, R = 0.2388 (Rfree = 0.000) for 2302 atoms. Found 4 (17 requested) and removed 9 (8 requested) atoms. Cycle 5: After refmac, R = 0.2343 (Rfree = 0.000) for 2287 atoms. Found 5 (17 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.22 3.79 Search for helices and strands: 0 residues in 0 chains, 2343 seeds are put forward Round 1: 143 peptides, 24 chains. Longest chain 14 peptides. Score 0.448 Round 2: 182 peptides, 25 chains. Longest chain 14 peptides. Score 0.608 Round 3: 187 peptides, 23 chains. Longest chain 20 peptides. Score 0.660 Round 4: 197 peptides, 24 chains. Longest chain 24 peptides. Score 0.679 Round 5: 189 peptides, 23 chains. Longest chain 20 peptides. Score 0.667 Taking the results from Round 4 Chains 29, Residues 173, Estimated correctness of the model 52.3 % 6 chains (48 residues) have been docked in sequence ------------------------------------------------------ 4219 reflections ( 99.36 % complete ) and 4952 restraints for refining 2327 atoms. 4150 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2703 (Rfree = 0.000) for 2327 atoms. Found 17 (17 requested) and removed 47 (8 requested) atoms. Cycle 7: After refmac, R = 0.2495 (Rfree = 0.000) for 2286 atoms. Found 7 (17 requested) and removed 21 (8 requested) atoms. Cycle 8: After refmac, R = 0.2428 (Rfree = 0.000) for 2261 atoms. Found 6 (17 requested) and removed 18 (8 requested) atoms. Cycle 9: After refmac, R = 0.2399 (Rfree = 0.000) for 2245 atoms. Found 2 (16 requested) and removed 13 (8 requested) atoms. Cycle 10: After refmac, R = 0.2336 (Rfree = 0.000) for 2230 atoms. Found 4 (16 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.22 3.79 Search for helices and strands: 0 residues in 0 chains, 2290 seeds are put forward Round 1: 161 peptides, 25 chains. Longest chain 12 peptides. Score 0.516 Round 2: 190 peptides, 27 chains. Longest chain 19 peptides. Score 0.604 Round 3: 177 peptides, 26 chains. Longest chain 13 peptides. Score 0.569 Round 4: 175 peptides, 21 chains. Longest chain 18 peptides. Score 0.649 Round 5: 188 peptides, 25 chains. Longest chain 19 peptides. Score 0.631 Taking the results from Round 4 Chains 23, Residues 154, Estimated correctness of the model 43.8 % 4 chains (32 residues) have been docked in sequence ------------------------------------------------------ 4219 reflections ( 99.36 % complete ) and 5179 restraints for refining 2297 atoms. 4508 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2603 (Rfree = 0.000) for 2297 atoms. Found 13 (17 requested) and removed 20 (8 requested) atoms. Cycle 12: After refmac, R = 0.2375 (Rfree = 0.000) for 2283 atoms. Found 2 (17 requested) and removed 9 (8 requested) atoms. Cycle 13: After refmac, R = 0.2334 (Rfree = 0.000) for 2271 atoms. Found 5 (17 requested) and removed 14 (8 requested) atoms. Cycle 14: After refmac, R = 0.2151 (Rfree = 0.000) for 2258 atoms. Found 3 (17 requested) and removed 11 (8 requested) atoms. Cycle 15: After refmac, R = 0.2191 (Rfree = 0.000) for 2249 atoms. Found 6 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.21 3.78 Search for helices and strands: 0 residues in 0 chains, 2299 seeds are put forward Round 1: 158 peptides, 26 chains. Longest chain 13 peptides. Score 0.480 Round 2: 172 peptides, 24 chains. Longest chain 17 peptides. Score 0.585 Round 3: 185 peptides, 28 chains. Longest chain 13 peptides. Score 0.566 Round 4: 178 peptides, 22 chains. Longest chain 16 peptides. Score 0.644 Round 5: 185 peptides, 25 chains. Longest chain 17 peptides. Score 0.619 Taking the results from Round 4 Chains 26, Residues 156, Estimated correctness of the model 42.4 % 3 chains (30 residues) have been docked in sequence ------------------------------------------------------ 4219 reflections ( 99.36 % complete ) and 5220 restraints for refining 2370 atoms. 4512 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2440 (Rfree = 0.000) for 2370 atoms. Found 13 (17 requested) and removed 36 (8 requested) atoms. Cycle 17: After refmac, R = 0.2270 (Rfree = 0.000) for 2336 atoms. Found 5 (17 requested) and removed 12 (8 requested) atoms. Cycle 18: After refmac, R = 0.2209 (Rfree = 0.000) for 2324 atoms. Found 4 (17 requested) and removed 13 (8 requested) atoms. Cycle 19: After refmac, R = 0.2152 (Rfree = 0.000) for 2313 atoms. Found 5 (17 requested) and removed 8 (8 requested) atoms. Cycle 20: After refmac, R = 0.2116 (Rfree = 0.000) for 2308 atoms. Found 4 (17 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.23 3.80 Search for helices and strands: 0 residues in 0 chains, 2346 seeds are put forward Round 1: 143 peptides, 27 chains. Longest chain 11 peptides. Score 0.379 Round 2: 164 peptides, 28 chains. Longest chain 14 peptides. Score 0.468 Round 3: 178 peptides, 28 chains. Longest chain 16 peptides. Score 0.535 Round 4: 176 peptides, 26 chains. Longest chain 16 peptides. Score 0.564 Round 5: 183 peptides, 25 chains. Longest chain 16 peptides. Score 0.612 Taking the results from Round 5 Chains 25, Residues 158, Estimated correctness of the model 32.5 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4219 reflections ( 99.36 % complete ) and 5468 restraints for refining 2370 atoms. 4832 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2480 (Rfree = 0.000) for 2370 atoms. Found 16 (17 requested) and removed 15 (8 requested) atoms. Cycle 22: After refmac, R = 0.2271 (Rfree = 0.000) for 2362 atoms. Found 6 (17 requested) and removed 12 (8 requested) atoms. Cycle 23: After refmac, R = 0.2193 (Rfree = 0.000) for 2351 atoms. Found 4 (17 requested) and removed 9 (8 requested) atoms. Cycle 24: After refmac, R = 0.2120 (Rfree = 0.000) for 2343 atoms. Found 6 (17 requested) and removed 10 (8 requested) atoms. Cycle 25: After refmac, R = 0.2064 (Rfree = 0.000) for 2331 atoms. Found 3 (17 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.21 3.78 Search for helices and strands: 0 residues in 0 chains, 2374 seeds are put forward Round 1: 132 peptides, 26 chains. Longest chain 13 peptides. Score 0.340 Round 2: 156 peptides, 23 chains. Longest chain 16 peptides. Score 0.533 Round 3: 162 peptides, 26 chains. Longest chain 16 peptides. Score 0.500 Round 4: 171 peptides, 27 chains. Longest chain 13 peptides. Score 0.522 Round 5: 151 peptides, 26 chains. Longest chain 12 peptides. Score 0.445 Taking the results from Round 2 Chains 23, Residues 133, Estimated correctness of the model 5.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4219 reflections ( 99.36 % complete ) and 5660 restraints for refining 2367 atoms. 5151 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2187 (Rfree = 0.000) for 2367 atoms. Found 13 (17 requested) and removed 9 (8 requested) atoms. Cycle 27: After refmac, R = 0.2002 (Rfree = 0.000) for 2364 atoms. Found 4 (17 requested) and removed 8 (8 requested) atoms. Cycle 28: After refmac, R = 0.1981 (Rfree = 0.000) for 2360 atoms. Found 5 (17 requested) and removed 9 (8 requested) atoms. Cycle 29: After refmac, R = 0.1965 (Rfree = 0.000) for 2354 atoms. Found 4 (17 requested) and removed 9 (8 requested) atoms. Cycle 30: After refmac, R = 0.1940 (Rfree = 0.000) for 2345 atoms. Found 3 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.21 3.78 Search for helices and strands: 0 residues in 0 chains, 2408 seeds are put forward Round 1: 123 peptides, 23 chains. Longest chain 12 peptides. Score 0.361 Round 2: 129 peptides, 21 chains. Longest chain 16 peptides. Score 0.442 Round 3: 137 peptides, 23 chains. Longest chain 14 peptides. Score 0.439 Round 4: 149 peptides, 23 chains. Longest chain 16 peptides. Score 0.500 Round 5: 153 peptides, 22 chains. Longest chain 16 peptides. Score 0.540 Taking the results from Round 5 Chains 23, Residues 131, Estimated correctness of the model 7.9 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 4219 reflections ( 99.36 % complete ) and 5528 restraints for refining 2371 atoms. 4981 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2320 (Rfree = 0.000) for 2371 atoms. Found 12 (17 requested) and removed 14 (8 requested) atoms. Cycle 32: After refmac, R = 0.2089 (Rfree = 0.000) for 2364 atoms. Found 6 (17 requested) and removed 8 (8 requested) atoms. Cycle 33: After refmac, R = 0.1938 (Rfree = 0.000) for 2361 atoms. Found 3 (17 requested) and removed 10 (8 requested) atoms. Cycle 34: After refmac, R = 0.1984 (Rfree = 0.000) for 2352 atoms. Found 4 (17 requested) and removed 10 (8 requested) atoms. Cycle 35: After refmac, R = 0.1909 (Rfree = 0.000) for 2342 atoms. Found 3 (17 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.22 3.79 Search for helices and strands: 0 residues in 0 chains, 2401 seeds are put forward Round 1: 135 peptides, 24 chains. Longest chain 14 peptides. Score 0.405 Round 2: 140 peptides, 23 chains. Longest chain 13 peptides. Score 0.454 Round 3: 158 peptides, 24 chains. Longest chain 13 peptides. Score 0.522 Round 4: 157 peptides, 22 chains. Longest chain 15 peptides. Score 0.558 Round 5: 143 peptides, 21 chains. Longest chain 15 peptides. Score 0.513 Taking the results from Round 4 Chains 23, Residues 135, Estimated correctness of the model 14.4 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4219 reflections ( 99.36 % complete ) and 5559 restraints for refining 2371 atoms. 5010 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2213 (Rfree = 0.000) for 2371 atoms. Found 11 (17 requested) and removed 13 (8 requested) atoms. Cycle 37: After refmac, R = 0.2052 (Rfree = 0.000) for 2362 atoms. Found 5 (17 requested) and removed 8 (8 requested) atoms. Cycle 38: After refmac, R = 0.1991 (Rfree = 0.000) for 2355 atoms. Found 7 (17 requested) and removed 9 (8 requested) atoms. Cycle 39: After refmac, R = 0.1927 (Rfree = 0.000) for 2352 atoms. Found 4 (17 requested) and removed 11 (8 requested) atoms. Cycle 40: After refmac, R = 0.1870 (Rfree = 0.000) for 2341 atoms. Found 3 (17 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.22 3.79 Search for helices and strands: 0 residues in 0 chains, 2382 seeds are put forward Round 1: 115 peptides, 22 chains. Longest chain 9 peptides. Score 0.339 Round 2: 153 peptides, 24 chains. Longest chain 16 peptides. Score 0.498 Round 3: 157 peptides, 24 chains. Longest chain 16 peptides. Score 0.517 Round 4: 155 peptides, 24 chains. Longest chain 14 peptides. Score 0.508 Round 5: 156 peptides, 21 chains. Longest chain 16 peptides. Score 0.573 Taking the results from Round 5 Chains 21, Residues 135, Estimated correctness of the model 19.6 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 4219 reflections ( 99.36 % complete ) and 5490 restraints for refining 2371 atoms. 4942 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2072 (Rfree = 0.000) for 2371 atoms. Found 11 (17 requested) and removed 8 (8 requested) atoms. Cycle 42: After refmac, R = 0.1869 (Rfree = 0.000) for 2369 atoms. Found 8 (17 requested) and removed 8 (8 requested) atoms. Cycle 43: After refmac, R = 0.1809 (Rfree = 0.000) for 2366 atoms. Found 4 (17 requested) and removed 8 (8 requested) atoms. Cycle 44: After refmac, R = 0.1786 (Rfree = 0.000) for 2356 atoms. Found 8 (17 requested) and removed 9 (8 requested) atoms. Cycle 45: After refmac, R = 0.1800 (Rfree = 0.000) for 2354 atoms. Found 4 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.20 3.77 Search for helices and strands: 0 residues in 0 chains, 2399 seeds are put forward Round 1: 101 peptides, 21 chains. Longest chain 8 peptides. Score 0.279 Round 2: 120 peptides, 22 chains. Longest chain 14 peptides. Score 0.368 Round 3: 130 peptides, 18 chains. Longest chain 16 peptides. Score 0.515 Round 4: 119 peptides, 20 chains. Longest chain 14 peptides. Score 0.411 Round 5: 118 peptides, 20 chains. Longest chain 15 peptides. Score 0.406 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 19, Residues 112, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence Sequence coverage is 10 % Consider running further cycles of model building using 2ghs-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4219 reflections ( 99.36 % complete ) and 5604 restraints for refining 2371 atoms. 5146 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1965 (Rfree = 0.000) for 2371 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.1854 (Rfree = 0.000) for 2359 atoms. Found 0 (17 requested) and removed 7 (8 requested) atoms. Cycle 48: After refmac, R = 0.1868 (Rfree = 0.000) for 2351 atoms. Found 0 (17 requested) and removed 1 (8 requested) atoms. Cycle 49: After refmac, R = 0.1812 (Rfree = 0.000) for 2348 atoms. Found 0 (17 requested) and removed 0 (8 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:09:02 GMT 2018 Job finished. TimeTaking 46.01 Used memory is bytes: 19144024