Sun 30 Dec 03:45:08 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2eth-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2eth-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2eth-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2eth-3.4-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2eth-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2eth-3.4-parrot-mrncs ############### 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 30 Dec 03:46:41 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/mrncs/ArpWArp/wArpResults/WorkingDir/2eth-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2eth-3.4-parrot-mrncs/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 243 and 0 Target number of residues in the AU: 243 Target solvent content: 0.6505 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-3.4-parrot-mrncs.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-3.4-parrot-mrncs.fasta_lf Building free atoms model in initial map for 2464 target number of atoms Had to go as low as 0.80 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 3.400 Wilson plot Bfac: 78.41 5128 reflections ( 98.18 % complete ) and 0 restraints for refining 2716 atoms. Observations/parameters ratio is 0.47 ------------------------------------------------------ Starting model: R = 0.3314 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3261 (Rfree = 0.000) for 2716 atoms. Found 20 (20 requested) and removed 14 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.49 3.22 Search for helices and strands: 0 residues in 0 chains, 2779 seeds are put forward NCS extension: 0 residues added, 2779 seeds are put forward Round 1: 136 peptides, 24 chains. Longest chain 11 peptides. Score 0.365 Round 2: 167 peptides, 22 chains. Longest chain 15 peptides. Score 0.528 Round 3: 180 peptides, 22 chains. Longest chain 16 peptides. Score 0.573 Round 4: 180 peptides, 21 chains. Longest chain 30 peptides. Score 0.589 Round 5: 176 peptides, 21 chains. Longest chain 28 peptides. Score 0.575 Taking the results from Round 4 Chains 22, Residues 159, Estimated correctness of the model 25.0 % 1 chains (27 residues) have been docked in sequence ------------------------------------------------------ 5128 reflections ( 98.18 % complete ) and 4827 restraints for refining 2240 atoms. 4099 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2869 (Rfree = 0.000) for 2240 atoms. Found 14 (16 requested) and removed 21 (8 requested) atoms. Cycle 2: After refmac, R = 0.2897 (Rfree = 0.000) for 2171 atoms. Found 15 (16 requested) and removed 14 (8 requested) atoms. Cycle 3: After refmac, R = 0.2755 (Rfree = 0.000) for 2150 atoms. Found 11 (16 requested) and removed 10 (8 requested) atoms. Cycle 4: After refmac, R = 0.2623 (Rfree = 0.000) for 2137 atoms. Found 6 (16 requested) and removed 11 (8 requested) atoms. Cycle 5: After refmac, R = 0.2547 (Rfree = 0.000) for 2120 atoms. Found 6 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.45 3.18 Search for helices and strands: 0 residues in 0 chains, 2198 seeds are put forward NCS extension: 33 residues added (6 deleted due to clashes), 2231 seeds are put forward Round 1: 158 peptides, 26 chains. Longest chain 14 peptides. Score 0.423 Round 2: 175 peptides, 27 chains. Longest chain 14 peptides. Score 0.474 Round 3: 177 peptides, 25 chains. Longest chain 17 peptides. Score 0.515 Round 4: 182 peptides, 26 chains. Longest chain 18 peptides. Score 0.517 Round 5: 176 peptides, 23 chains. Longest chain 26 peptides. Score 0.544 Taking the results from Round 5 Chains 23, Residues 153, Estimated correctness of the model 9.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5128 reflections ( 98.18 % complete ) and 5175 restraints for refining 2240 atoms. 4586 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2643 (Rfree = 0.000) for 2240 atoms. Found 16 (16 requested) and removed 13 (8 requested) atoms. Cycle 7: After refmac, R = 0.2563 (Rfree = 0.000) for 2225 atoms. Found 10 (16 requested) and removed 14 (8 requested) atoms. Cycle 8: After refmac, R = 0.2449 (Rfree = 0.000) for 2207 atoms. Found 12 (16 requested) and removed 9 (8 requested) atoms. Cycle 9: After refmac, R = 0.2425 (Rfree = 0.000) for 2195 atoms. Found 10 (16 requested) and removed 10 (8 requested) atoms. Cycle 10: After refmac, R = 0.2322 (Rfree = 0.000) for 2190 atoms. Found 8 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.47 3.20 Search for helices and strands: 0 residues in 0 chains, 2308 seeds are put forward NCS extension: 15 residues added (3 deleted due to clashes), 2323 seeds are put forward Round 1: 157 peptides, 28 chains. Longest chain 13 peptides. Score 0.382 Round 2: 178 peptides, 25 chains. Longest chain 17 peptides. Score 0.519 Round 3: 177 peptides, 22 chains. Longest chain 19 peptides. Score 0.563 Round 4: 182 peptides, 20 chains. Longest chain 19 peptides. Score 0.610 Round 5: 179 peptides, 20 chains. Longest chain 25 peptides. Score 0.600 Taking the results from Round 4 Chains 20, Residues 162, Estimated correctness of the model 31.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5128 reflections ( 98.18 % complete ) and 4859 restraints for refining 2241 atoms. 4231 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2462 (Rfree = 0.000) for 2241 atoms. Found 16 (16 requested) and removed 9 (8 requested) atoms. Cycle 12: After refmac, R = 0.2369 (Rfree = 0.000) for 2239 atoms. Found 13 (16 requested) and removed 11 (8 requested) atoms. Cycle 13: After refmac, R = 0.2199 (Rfree = 0.000) for 2236 atoms. Found 4 (16 requested) and removed 11 (8 requested) atoms. Failed to save intermediate PDB Cycle 14: After refmac, R = 0.2143 (Rfree = 0.000) for 2223 atoms. Found 4 (16 requested) and removed 11 (8 requested) atoms. Cycle 15: After refmac, R = 0.2053 (Rfree = 0.000) for 2213 atoms. Found 9 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.49 3.22 Search for helices and strands: 0 residues in 0 chains, 2286 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 2309 seeds are put forward Round 1: 153 peptides, 27 chains. Longest chain 15 peptides. Score 0.383 Round 2: 169 peptides, 24 chains. Longest chain 20 peptides. Score 0.502 Round 3: 165 peptides, 20 chains. Longest chain 27 peptides. Score 0.553 Round 4: 169 peptides, 23 chains. Longest chain 15 peptides. Score 0.518 Round 5: 155 peptides, 22 chains. Longest chain 26 peptides. Score 0.482 Taking the results from Round 3 Chains 20, Residues 145, Estimated correctness of the model 12.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5128 reflections ( 98.18 % complete ) and 5051 restraints for refining 2241 atoms. 4491 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2272 (Rfree = 0.000) for 2241 atoms. Found 15 (16 requested) and removed 9 (8 requested) atoms. Cycle 17: After refmac, R = 0.2124 (Rfree = 0.000) for 2239 atoms. Found 10 (16 requested) and removed 10 (8 requested) atoms. Cycle 18: After refmac, R = 0.2103 (Rfree = 0.000) for 2234 atoms. Found 8 (16 requested) and removed 11 (8 requested) atoms. Cycle 19: After refmac, R = 0.1987 (Rfree = 0.000) for 2230 atoms. Found 1 (16 requested) and removed 8 (8 requested) atoms. Cycle 20: After refmac, R = 0.1980 (Rfree = 0.000) for 2218 atoms. Found 5 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.47 3.20 Search for helices and strands: 0 residues in 0 chains, 2314 seeds are put forward NCS extension: 46 residues added (0 deleted due to clashes), 2360 seeds are put forward Round 1: 153 peptides, 30 chains. Longest chain 9 peptides. Score 0.327 Round 2: 169 peptides, 25 chains. Longest chain 22 peptides. Score 0.485 Round 3: 170 peptides, 25 chains. Longest chain 23 peptides. Score 0.489 Round 4: 175 peptides, 23 chains. Longest chain 25 peptides. Score 0.540 Round 5: 176 peptides, 25 chains. Longest chain 24 peptides. Score 0.511 Taking the results from Round 4 Chains 23, Residues 152, Estimated correctness of the model 7.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5128 reflections ( 98.18 % complete ) and 5019 restraints for refining 2241 atoms. 4434 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2330 (Rfree = 0.000) for 2241 atoms. Found 14 (16 requested) and removed 9 (8 requested) atoms. Cycle 22: After refmac, R = 0.2317 (Rfree = 0.000) for 2235 atoms. Found 11 (16 requested) and removed 8 (8 requested) atoms. Cycle 23: After refmac, R = 0.2212 (Rfree = 0.000) for 2229 atoms. Found 8 (16 requested) and removed 9 (8 requested) atoms. Cycle 24: After refmac, R = 0.2052 (Rfree = 0.000) for 2221 atoms. Found 5 (16 requested) and removed 9 (8 requested) atoms. Cycle 25: After refmac, R = 0.2534 (Rfree = 0.000) for 2215 atoms. Found 16 (16 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.46 3.19 TimeTaking 2880.32