Sun 23 Dec 23:44:18 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-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2eth-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2eth-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2eth-3.2-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-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2eth-3.2-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 23 Dec 23:44:23 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-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2eth-3.2-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 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-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-3.2-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 3.200 Wilson plot Bfac: 75.64 6145 reflections ( 98.19 % complete ) and 0 restraints for refining 2712 atoms. Observations/parameters ratio is 0.57 ------------------------------------------------------ Starting model: R = 0.3341 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3063 (Rfree = 0.000) for 2712 atoms. Found 23 (24 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.35 3.09 Search for helices and strands: 0 residues in 0 chains, 2765 seeds are put forward NCS extension: 0 residues added, 2765 seeds are put forward Round 1: 145 peptides, 25 chains. Longest chain 12 peptides. Score 0.386 Round 2: 174 peptides, 24 chains. Longest chain 14 peptides. Score 0.520 Round 3: 174 peptides, 24 chains. Longest chain 20 peptides. Score 0.520 Round 4: 176 peptides, 19 chains. Longest chain 22 peptides. Score 0.606 Round 5: 190 peptides, 21 chains. Longest chain 26 peptides. Score 0.620 Taking the results from Round 5 Chains 22, Residues 169, Estimated correctness of the model 46.3 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 6145 reflections ( 98.19 % complete ) and 4882 restraints for refining 2220 atoms. 4162 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2933 (Rfree = 0.000) for 2220 atoms. Found 13 (19 requested) and removed 17 (9 requested) atoms. Cycle 2: After refmac, R = 0.2786 (Rfree = 0.000) for 2194 atoms. Found 10 (19 requested) and removed 15 (9 requested) atoms. Cycle 3: After refmac, R = 0.2733 (Rfree = 0.000) for 2170 atoms. Found 9 (19 requested) and removed 13 (9 requested) atoms. Cycle 4: After refmac, R = 0.3017 (Rfree = 0.000) for 2155 atoms. Found 19 (19 requested) and removed 19 (9 requested) atoms. Cycle 5: After refmac, R = 0.2615 (Rfree = 0.000) for 2146 atoms. Found 6 (19 requested) and removed 16 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.36 3.10 Search for helices and strands: 0 residues in 0 chains, 2268 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 2290 seeds are put forward Round 1: 164 peptides, 22 chains. Longest chain 22 peptides. Score 0.517 Round 2: 192 peptides, 23 chains. Longest chain 23 peptides. Score 0.598 Round 3: 190 peptides, 21 chains. Longest chain 20 peptides. Score 0.620 Round 4: 199 peptides, 23 chains. Longest chain 17 peptides. Score 0.620 Round 5: 190 peptides, 22 chains. Longest chain 18 peptides. Score 0.606 Taking the results from Round 4 Chains 23, Residues 176, Estimated correctness of the model 46.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6145 reflections ( 98.19 % complete ) and 4721 restraints for refining 2165 atoms. 4040 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2558 (Rfree = 0.000) for 2165 atoms. Found 9 (19 requested) and removed 17 (9 requested) atoms. Cycle 7: After refmac, R = 0.2424 (Rfree = 0.000) for 2145 atoms. Found 7 (19 requested) and removed 15 (9 requested) atoms. Cycle 8: After refmac, R = 0.2806 (Rfree = 0.000) for 2127 atoms. Found 19 (19 requested) and removed 15 (9 requested) atoms. Cycle 9: After refmac, R = 0.2979 (Rfree = 0.000) for 2120 atoms. Found 19 (19 requested) and removed 16 (9 requested) atoms. Cycle 10: After refmac, R = 0.2804 (Rfree = 0.000) for 2112 atoms. Found 19 (19 requested) and removed 14 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.39 3.13 Search for helices and strands: 0 residues in 0 chains, 2225 seeds are put forward NCS extension: 18 residues added (3 deleted due to clashes), 2243 seeds are put forward Round 1: 173 peptides, 26 chains. Longest chain 15 peptides. Score 0.483 Round 2: 187 peptides, 24 chains. Longest chain 16 peptides. Score 0.566 Round 3: 183 peptides, 23 chains. Longest chain 16 peptides. Score 0.568 Round 4: 183 peptides, 23 chains. Longest chain 24 peptides. Score 0.568 Round 5: 191 peptides, 22 chains. Longest chain 24 peptides. Score 0.609 Taking the results from Round 5 Chains 22, Residues 169, Estimated correctness of the model 43.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6145 reflections ( 98.19 % complete ) and 4754 restraints for refining 2204 atoms. 4100 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2653 (Rfree = 0.000) for 2204 atoms. Found 19 (19 requested) and removed 27 (9 requested) atoms. Cycle 12: After refmac, R = 0.2413 (Rfree = 0.000) for 2184 atoms. Found 10 (19 requested) and removed 12 (9 requested) atoms. Cycle 13: After refmac, R = 0.2421 (Rfree = 0.000) for 2171 atoms. Found 12 (19 requested) and removed 11 (9 requested) atoms. Cycle 14: After refmac, R = 0.2224 (Rfree = 0.000) for 2164 atoms. Found 14 (19 requested) and removed 11 (9 requested) atoms. Cycle 15: After refmac, R = 0.2525 (Rfree = 0.000) for 2159 atoms. Found 19 (19 requested) and removed 13 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.35 3.09 Search for helices and strands: 0 residues in 0 chains, 2272 seeds are put forward NCS extension: 28 residues added (1 deleted due to clashes), 2300 seeds are put forward Round 1: 165 peptides, 24 chains. Longest chain 18 peptides. Score 0.486 Round 2: 190 peptides, 23 chains. Longest chain 23 peptides. Score 0.591 Round 3: 186 peptides, 20 chains. Longest chain 23 peptides. Score 0.622 Round 4: 189 peptides, 22 chains. Longest chain 23 peptides. Score 0.603 Round 5: 189 peptides, 23 chains. Longest chain 17 peptides. Score 0.588 Taking the results from Round 3 Chains 21, Residues 166, Estimated correctness of the model 46.9 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 6145 reflections ( 98.19 % complete ) and 4771 restraints for refining 2250 atoms. 4086 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2402 (Rfree = 0.000) for 2250 atoms. Found 11 (20 requested) and removed 17 (10 requested) atoms. Cycle 17: After refmac, R = 0.2234 (Rfree = 0.000) for 2235 atoms. Found 10 (20 requested) and removed 15 (10 requested) atoms. Cycle 18: After refmac, R = 0.2187 (Rfree = 0.000) for 2228 atoms. Found 3 (20 requested) and removed 11 (10 requested) atoms. Cycle 19: After refmac, R = 0.2131 (Rfree = 0.000) for 2217 atoms. Found 4 (19 requested) and removed 9 (9 requested) atoms. Failed to save intermediate PDB Cycle 20: After refmac, R = 0.2122 (Rfree = 0.000) for 2209 atoms. Found 1 (19 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.37 3.11 Search for helices and strands: 0 residues in 0 chains, 2277 seeds are put forward NCS extension: 36 residues added (2 deleted due to clashes), 2313 seeds are put forward Round 1: 166 peptides, 23 chains. Longest chain 24 peptides. Score 0.507 Round 2: 178 peptides, 23 chains. Longest chain 18 peptides. Score 0.551 Round 3: 175 peptides, 24 chains. Longest chain 12 peptides. Score 0.524 Round 4: 191 peptides, 25 chains. Longest chain 21 peptides. Score 0.565 Round 5: 175 peptides, 22 chains. Longest chain 19 peptides. Score 0.556 Taking the results from Round 4 Chains 25, Residues 166, Estimated correctness of the model 31.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6145 reflections ( 98.19 % complete ) and 4964 restraints for refining 2250 atoms. 4325 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2376 (Rfree = 0.000) for 2250 atoms. Found 3 (20 requested) and removed 12 (10 requested) atoms. Cycle 22: After refmac, R = 0.2383 (Rfree = 0.000) for 2235 atoms. Found 9 (20 requested) and removed 10 (10 requested) atoms. Cycle 23: After refmac, R = 0.2114 (Rfree = 0.000) for 2227 atoms. Found 6 (20 requested) and removed 11 (10 requested) atoms. Cycle 24: After refmac, R = 0.1982 (Rfree = 0.000) for 2215 atoms. Found 2 (19 requested) and removed 9 (9 requested) atoms. Cycle 25: After refmac, R = 0.1899 (Rfree = 0.000) for 2208 atoms. Found 2 (19 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.36 3.10 Search for helices and strands: 0 residues in 0 chains, 2287 seeds are put forward NCS extension: 31 residues added (3 deleted due to clashes), 2318 seeds are put forward Round 1: 171 peptides, 26 chains. Longest chain 15 peptides. Score 0.475 Round 2: 185 peptides, 24 chains. Longest chain 15 peptides. Score 0.559 Round 3: 185 peptides, 26 chains. Longest chain 17 peptides. Score 0.528 Round 4: 181 peptides, 25 chains. Longest chain 26 peptides. Score 0.530 Round 5: 188 peptides, 27 chains. Longest chain 14 peptides. Score 0.523 Taking the results from Round 2 Chains 24, Residues 161, Estimated correctness of the model 29.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6145 reflections ( 98.19 % complete ) and 5000 restraints for refining 2250 atoms. 4380 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2543 (Rfree = 0.000) for 2250 atoms. Found 20 (20 requested) and removed 12 (10 requested) atoms. Cycle 27: After refmac, R = 0.2709 (Rfree = 0.000) for 2246 atoms. Found 20 (20 requested) and removed 14 (10 requested) atoms. Cycle 28: After refmac, R = 0.2584 (Rfree = 0.000) for 2244 atoms. Found 20 (20 requested) and removed 13 (10 requested) atoms. Cycle 29: After refmac, R = 0.2035 (Rfree = 0.000) for 2245 atoms. Found 9 (20 requested) and removed 11 (10 requested) atoms. Cycle 30: After refmac, R = 0.1869 (Rfree = 0.000) for 2237 atoms. Found 11 (20 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.35 3.09 Search for helices and strands: 0 residues in 0 chains, 2348 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 2361 seeds are put forward Round 1: 160 peptides, 28 chains. Longest chain 14 peptides. Score 0.395 Round 2: 169 peptides, 25 chains. Longest chain 14 peptides. Score 0.485 Round 3: 172 peptides, 22 chains. Longest chain 23 peptides. Score 0.546 Round 4: 176 peptides, 27 chains. Longest chain 18 peptides. Score 0.478 Round 5: 167 peptides, 24 chains. Longest chain 12 peptides. Score 0.494 Taking the results from Round 3 Chains 22, Residues 150, Estimated correctness of the model 25.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6145 reflections ( 98.19 % complete ) and 4949 restraints for refining 2250 atoms. 4371 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2111 (Rfree = 0.000) for 2250 atoms. Found 14 (20 requested) and removed 12 (10 requested) atoms. Cycle 32: After refmac, R = 0.2194 (Rfree = 0.000) for 2246 atoms. Found 14 (20 requested) and removed 10 (10 requested) atoms. Cycle 33: After refmac, R = 0.2078 (Rfree = 0.000) for 2243 atoms. Found 11 (20 requested) and removed 10 (10 requested) atoms. Cycle 34: After refmac, R = 0.1906 (Rfree = 0.000) for 2238 atoms. Found 7 (20 requested) and removed 11 (10 requested) atoms. Cycle 35: After refmac, R = 0.1882 (Rfree = 0.000) for 2231 atoms. Found 6 (20 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.37 3.11 Search for helices and strands: 0 residues in 0 chains, 2312 seeds are put forward NCS extension: 12 residues added (3 deleted due to clashes), 2324 seeds are put forward Round 1: 157 peptides, 25 chains. Longest chain 17 peptides. Score 0.437 Round 2: 175 peptides, 27 chains. Longest chain 14 peptides. Score 0.474 Round 3: 175 peptides, 26 chains. Longest chain 14 peptides. Score 0.491 Round 4: 172 peptides, 23 chains. Longest chain 21 peptides. Score 0.529 Round 5: 165 peptides, 23 chains. Longest chain 17 peptides. Score 0.503 Taking the results from Round 4 Chains 25, Residues 149, Estimated correctness of the model 20.5 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 6145 reflections ( 98.19 % complete ) and 4678 restraints for refining 2250 atoms. 4044 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2620 (Rfree = 0.000) for 2250 atoms. Found 19 (20 requested) and removed 12 (10 requested) atoms. Cycle 37: After refmac, R = 0.2202 (Rfree = 0.000) for 2246 atoms. Found 13 (20 requested) and removed 11 (10 requested) atoms. Cycle 38: After refmac, R = 0.1991 (Rfree = 0.000) for 2238 atoms. Found 13 (20 requested) and removed 11 (10 requested) atoms. Cycle 39: After refmac, R = 0.1915 (Rfree = 0.000) for 2237 atoms. Found 5 (20 requested) and removed 10 (10 requested) atoms. Cycle 40: After refmac, R = 0.1955 (Rfree = 0.000) for 2231 atoms. Found 7 (20 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.35 3.09 Search for helices and strands: 0 residues in 0 chains, 2330 seeds are put forward NCS extension: 28 residues added (2 deleted due to clashes), 2358 seeds are put forward Round 1: 146 peptides, 27 chains. Longest chain 10 peptides. Score 0.353 Round 2: 172 peptides, 28 chains. Longest chain 11 peptides. Score 0.445 Round 3: 173 peptides, 25 chains. Longest chain 20 peptides. Score 0.500 Round 4: 177 peptides, 27 chains. Longest chain 20 peptides. Score 0.482 Round 5: 168 peptides, 26 chains. Longest chain 15 peptides. Score 0.464 Taking the results from Round 3 Chains 25, Residues 148, Estimated correctness of the model 11.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6145 reflections ( 98.19 % complete ) and 4894 restraints for refining 2250 atoms. 4327 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2731 (Rfree = 0.000) for 2250 atoms. Found 20 (20 requested) and removed 21 (10 requested) atoms. Cycle 42: After refmac, R = 0.2714 (Rfree = 0.000) for 2240 atoms. Found 20 (20 requested) and removed 16 (10 requested) atoms. Cycle 43: After refmac, R = 0.2218 (Rfree = 0.000) for 2235 atoms. Found 10 (20 requested) and removed 12 (10 requested) atoms. Cycle 44: After refmac, R = 0.2104 (Rfree = 0.000) for 2228 atoms. Found 11 (20 requested) and removed 10 (10 requested) atoms. Cycle 45: After refmac, R = 0.1942 (Rfree = 0.000) for 2226 atoms. Found 8 (19 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.36 3.10 Search for helices and strands: 0 residues in 0 chains, 2308 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 2332 seeds are put forward Round 1: 137 peptides, 25 chains. Longest chain 16 peptides. Score 0.351 Round 2: 151 peptides, 26 chains. Longest chain 12 peptides. Score 0.393 Round 3: 164 peptides, 26 chains. Longest chain 14 peptides. Score 0.448 Round 4: 160 peptides, 25 chains. Longest chain 14 peptides. Score 0.449 Round 5: 154 peptides, 24 chains. Longest chain 14 peptides. Score 0.443 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 25, Residues 135, 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 2eth-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6145 reflections ( 98.19 % complete ) and 4971 restraints for refining 2249 atoms. 4456 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2190 (Rfree = 0.000) for 2249 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 47: After refmac, R = 0.2068 (Rfree = 0.000) for 2235 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 48: After refmac, R = 0.2708 (Rfree = 0.000) for 2223 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.2079 (Rfree = 0.000) for 2213 atoms. TimeTaking 32.87