Mon 24 Dec 07:27:19 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-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2eth-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2eth-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2eth-3.4-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-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2eth-3.4-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 07:27:23 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/noncs/ArpWArp/wArpResults/WorkingDir/2eth-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2eth-3.4-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 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-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-3.4-parrot-noncs.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 2732 atoms. Observations/parameters ratio is 0.47 ------------------------------------------------------ Starting model: R = 0.3353 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3261 (Rfree = 0.000) for 2732 atoms. Found 20 (20 requested) and removed 17 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.44 3.17 Search for helices and strands: 0 residues in 0 chains, 2787 seeds are put forward NCS extension: 0 residues added, 2787 seeds are put forward Round 1: 130 peptides, 21 chains. Longest chain 11 peptides. Score 0.397 Round 2: 146 peptides, 23 chains. Longest chain 13 peptides. Score 0.428 Round 3: 161 peptides, 21 chains. Longest chain 16 peptides. Score 0.522 Round 4: 163 peptides, 18 chains. Longest chain 21 peptides. Score 0.578 Round 5: 180 peptides, 21 chains. Longest chain 18 peptides. Score 0.589 Taking the results from Round 5 Chains 21, Residues 159, Estimated correctness of the model 25.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5128 reflections ( 98.18 % complete ) and 4785 restraints for refining 2139 atoms. 4170 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2722 (Rfree = 0.000) for 2139 atoms. Found 16 (16 requested) and removed 16 (8 requested) atoms. Cycle 2: After refmac, R = 0.2713 (Rfree = 0.000) for 2104 atoms. Found 16 (16 requested) and removed 15 (8 requested) atoms. Cycle 3: After refmac, R = 0.2554 (Rfree = 0.000) for 2092 atoms. Found 15 (15 requested) and removed 9 (7 requested) atoms. Cycle 4: After refmac, R = 0.2428 (Rfree = 0.000) for 2092 atoms. Found 6 (15 requested) and removed 9 (7 requested) atoms. Cycle 5: After refmac, R = 0.2552 (Rfree = 0.000) for 2083 atoms. Found 6 (15 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.48 3.21 Search for helices and strands: 0 residues in 0 chains, 2199 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 2221 seeds are put forward Round 1: 167 peptides, 24 chains. Longest chain 21 peptides. Score 0.494 Round 2: 183 peptides, 24 chains. Longest chain 19 peptides. Score 0.552 Round 3: 191 peptides, 24 chains. Longest chain 17 peptides. Score 0.580 Round 4: 190 peptides, 23 chains. Longest chain 15 peptides. Score 0.591 Round 5: 197 peptides, 20 chains. Longest chain 19 peptides. Score 0.655 Taking the results from Round 5 Chains 20, Residues 177, Estimated correctness of the model 45.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5128 reflections ( 98.18 % complete ) and 4776 restraints for refining 2173 atoms. 4088 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2768 (Rfree = 0.000) for 2173 atoms. Found 16 (16 requested) and removed 14 (8 requested) atoms. Cycle 7: After refmac, R = 0.2667 (Rfree = 0.000) for 2161 atoms. Found 12 (16 requested) and removed 11 (8 requested) atoms. Cycle 8: After refmac, R = 0.3070 (Rfree = 0.000) for 2156 atoms. Found 16 (16 requested) and removed 17 (8 requested) atoms. Cycle 9: After refmac, R = 0.2408 (Rfree = 0.000) for 2151 atoms. Found 11 (16 requested) and removed 13 (8 requested) atoms. Cycle 10: After refmac, R = 0.2379 (Rfree = 0.000) for 2138 atoms. Found 9 (16 requested) and removed 38 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.53 3.26 Search for helices and strands: 0 residues in 0 chains, 2193 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 2214 seeds are put forward Round 1: 150 peptides, 22 chains. Longest chain 13 peptides. Score 0.462 Round 2: 172 peptides, 25 chains. Longest chain 14 peptides. Score 0.496 Round 3: 179 peptides, 24 chains. Longest chain 17 peptides. Score 0.538 Round 4: 176 peptides, 27 chains. Longest chain 12 peptides. Score 0.478 Round 5: 171 peptides, 23 chains. Longest chain 15 peptides. Score 0.526 Taking the results from Round 3 Chains 24, Residues 155, Estimated correctness of the model 7.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5128 reflections ( 98.18 % complete ) and 4750 restraints for refining 2133 atoms. 4154 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2558 (Rfree = 0.000) for 2133 atoms. Found 12 (16 requested) and removed 16 (8 requested) atoms. Cycle 12: After refmac, R = 0.2510 (Rfree = 0.000) for 2121 atoms. Found 13 (16 requested) and removed 11 (8 requested) atoms. Cycle 13: After refmac, R = 0.2443 (Rfree = 0.000) for 2122 atoms. Found 10 (16 requested) and removed 11 (8 requested) atoms. Cycle 14: After refmac, R = 0.2438 (Rfree = 0.000) for 2112 atoms. Found 6 (15 requested) and removed 18 (7 requested) atoms. Cycle 15: After refmac, R = 0.2374 (Rfree = 0.000) for 2097 atoms. Found 10 (15 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.52 3.25 Search for helices and strands: 0 residues in 0 chains, 2188 seeds are put forward NCS extension: 14 residues added (5 deleted due to clashes), 2202 seeds are put forward Round 1: 146 peptides, 24 chains. Longest chain 16 peptides. Score 0.409 Round 2: 168 peptides, 22 chains. Longest chain 25 peptides. Score 0.531 Round 3: 159 peptides, 22 chains. Longest chain 25 peptides. Score 0.498 Round 4: 161 peptides, 22 chains. Longest chain 15 peptides. Score 0.505 Round 5: 171 peptides, 22 chains. Longest chain 36 peptides. Score 0.542 Taking the results from Round 5 Chains 22, Residues 149, Estimated correctness of the model 8.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5128 reflections ( 98.18 % complete ) and 4887 restraints for refining 2194 atoms. 4313 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2576 (Rfree = 0.000) for 2194 atoms. Found 15 (16 requested) and removed 15 (8 requested) atoms. Cycle 17: After refmac, R = 0.2458 (Rfree = 0.000) for 2185 atoms. Found 11 (16 requested) and removed 12 (8 requested) atoms. Cycle 18: After refmac, R = 0.2431 (Rfree = 0.000) for 2180 atoms. Found 10 (16 requested) and removed 9 (8 requested) atoms. Cycle 19: After refmac, R = 0.2362 (Rfree = 0.000) for 2173 atoms. Found 5 (16 requested) and removed 11 (8 requested) atoms. Cycle 20: After refmac, R = 0.2363 (Rfree = 0.000) for 2161 atoms. Found 9 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.52 3.25 Search for helices and strands: 0 residues in 0 chains, 2273 seeds are put forward NCS extension: 78 residues added (7 deleted due to clashes), 2351 seeds are put forward Round 1: 137 peptides, 23 chains. Longest chain 14 peptides. Score 0.389 Round 2: 162 peptides, 21 chains. Longest chain 17 peptides. Score 0.526 Round 3: 147 peptides, 16 chains. Longest chain 21 peptides. Score 0.555 Round 4: 161 peptides, 19 chains. Longest chain 31 peptides. Score 0.555 Round 5: 144 peptides, 19 chains. Longest chain 23 peptides. Score 0.492 Taking the results from Round 4 Chains 19, Residues 142, Estimated correctness of the model 13.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5128 reflections ( 98.18 % complete ) and 4936 restraints for refining 2201 atoms. 4387 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2381 (Rfree = 0.000) for 2201 atoms. Found 8 (16 requested) and removed 11 (8 requested) atoms. Cycle 22: After refmac, R = 0.2394 (Rfree = 0.000) for 2189 atoms. Found 3 (16 requested) and removed 12 (8 requested) atoms. Cycle 23: After refmac, R = 0.2994 (Rfree = 0.000) for 2171 atoms. Found 16 (16 requested) and removed 18 (8 requested) atoms. Cycle 24: After refmac, R = 0.2905 (Rfree = 0.000) for 2155 atoms. Found 16 (16 requested) and removed 16 (8 requested) atoms. Cycle 25: After refmac, R = 0.2180 (Rfree = 0.000) for 2145 atoms. Found 9 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.46 3.19 Search for helices and strands: 0 residues in 0 chains, 2265 seeds are put forward NCS extension: 36 residues added (9 deleted due to clashes), 2301 seeds are put forward Round 1: 133 peptides, 24 chains. Longest chain 12 peptides. Score 0.352 Round 2: 149 peptides, 23 chains. Longest chain 13 peptides. Score 0.440 Round 3: 155 peptides, 21 chains. Longest chain 13 peptides. Score 0.500 Round 4: 165 peptides, 23 chains. Longest chain 13 peptides. Score 0.503 Round 5: 159 peptides, 24 chains. Longest chain 13 peptides. Score 0.463 Taking the results from Round 4 Chains 23, Residues 142, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5128 reflections ( 98.18 % complete ) and 4914 restraints for refining 2219 atoms. 4369 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2325 (Rfree = 0.000) for 2219 atoms. Found 9 (16 requested) and removed 15 (8 requested) atoms. Cycle 27: After refmac, R = 0.2278 (Rfree = 0.000) for 2208 atoms. Found 7 (16 requested) and removed 9 (8 requested) atoms. Cycle 28: After refmac, R = 0.2213 (Rfree = 0.000) for 2205 atoms. Found 6 (16 requested) and removed 10 (8 requested) atoms. Cycle 29: After refmac, R = 0.2054 (Rfree = 0.000) for 2196 atoms. Found 1 (16 requested) and removed 9 (8 requested) atoms. Cycle 30: After refmac, R = 0.2499 (Rfree = 0.000) for 2181 atoms. Found 15 (16 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.49 3.22 Search for helices and strands: 0 residues in 0 chains, 2285 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 2299 seeds are put forward Round 1: 130 peptides, 22 chains. Longest chain 14 peptides. Score 0.377 Round 2: 134 peptides, 18 chains. Longest chain 23 peptides. Score 0.471 Round 3: 142 peptides, 19 chains. Longest chain 17 peptides. Score 0.484 Round 4: 141 peptides, 19 chains. Longest chain 19 peptides. Score 0.480 Round 5: 142 peptides, 20 chains. Longest chain 26 peptides. Score 0.466 Taking the results from Round 3 Chains 20, Residues 123, Estimated correctness of the model 0.0 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 5128 reflections ( 98.18 % complete ) and 4884 restraints for refining 2241 atoms. 4349 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2795 (Rfree = 0.000) for 2241 atoms. Found 16 (16 requested) and removed 14 (8 requested) atoms. Cycle 32: After refmac, R = 0.2542 (Rfree = 0.000) for 2236 atoms. Found 16 (16 requested) and removed 14 (8 requested) atoms. Cycle 33: After refmac, R = 0.2142 (Rfree = 0.000) for 2230 atoms. Found 11 (16 requested) and removed 11 (8 requested) atoms. Cycle 34: After refmac, R = 0.1985 (Rfree = 0.000) for 2223 atoms. Found 4 (16 requested) and removed 11 (8 requested) atoms. Cycle 35: After refmac, R = 0.2121 (Rfree = 0.000) for 2215 atoms. Found 9 (16 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.48 3.21 Search for helices and strands: 0 residues in 0 chains, 2282 seeds are put forward NCS extension: 15 residues added (3 deleted due to clashes), 2297 seeds are put forward Round 1: 107 peptides, 19 chains. Longest chain 15 peptides. Score 0.332 Round 2: 126 peptides, 21 chains. Longest chain 14 peptides. Score 0.379 Round 3: 132 peptides, 20 chains. Longest chain 16 peptides. Score 0.425 Round 4: 123 peptides, 17 chains. Longest chain 17 peptides. Score 0.444 Round 5: 134 peptides, 19 chains. Longest chain 16 peptides. Score 0.452 Taking the results from Round 5 Chains 19, Residues 115, Estimated correctness of the model 0.0 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 5128 reflections ( 98.18 % complete ) and 4984 restraints for refining 2241 atoms. 4480 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2195 (Rfree = 0.000) for 2241 atoms. Found 16 (16 requested) and removed 11 (8 requested) atoms. Cycle 37: After refmac, R = 0.2151 (Rfree = 0.000) for 2241 atoms. Found 6 (16 requested) and removed 10 (8 requested) atoms. Cycle 38: After refmac, R = 0.2073 (Rfree = 0.000) for 2232 atoms. Found 6 (16 requested) and removed 8 (8 requested) atoms. Cycle 39: After refmac, R = 0.2129 (Rfree = 0.000) for 2229 atoms. Found 3 (16 requested) and removed 8 (8 requested) atoms. Cycle 40: After refmac, R = 0.2049 (Rfree = 0.000) for 2223 atoms. Found 4 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.52 3.25 Search for helices and strands: 0 residues in 0 chains, 2296 seeds are put forward NCS extension: 0 residues added, 2296 seeds are put forward Round 1: 116 peptides, 23 chains. Longest chain 8 peptides. Score 0.292 Round 2: 108 peptides, 19 chains. Longest chain 11 peptides. Score 0.337 Round 3: 114 peptides, 18 chains. Longest chain 13 peptides. Score 0.385 Round 4: 119 peptides, 18 chains. Longest chain 18 peptides. Score 0.407 Round 5: 124 peptides, 19 chains. Longest chain 23 peptides. Score 0.410 Taking the results from Round 5 Chains 19, Residues 105, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5128 reflections ( 98.18 % complete ) and 5263 restraints for refining 2241 atoms. 4862 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2218 (Rfree = 0.000) for 2241 atoms. Found 10 (16 requested) and removed 8 (8 requested) atoms. Cycle 42: After refmac, R = 0.2138 (Rfree = 0.000) for 2237 atoms. Found 3 (16 requested) and removed 8 (8 requested) atoms. Cycle 43: After refmac, R = 0.2097 (Rfree = 0.000) for 2231 atoms. Found 8 (16 requested) and removed 8 (8 requested) atoms. Cycle 44: After refmac, R = 0.2013 (Rfree = 0.000) for 2229 atoms. Found 4 (16 requested) and removed 9 (8 requested) atoms. Cycle 45: After refmac, R = 0.1962 (Rfree = 0.000) for 2221 atoms. Found 8 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.55 3.28 Search for helices and strands: 0 residues in 0 chains, 2308 seeds are put forward NCS extension: 54 residues added (2 deleted due to clashes), 2362 seeds are put forward Round 1: 111 peptides, 21 chains. Longest chain 11 peptides. Score 0.309 Round 2: 109 peptides, 20 chains. Longest chain 13 peptides. Score 0.320 Round 3: 122 peptides, 18 chains. Longest chain 18 peptides. Score 0.420 Round 4: 112 peptides, 16 chains. Longest chain 15 peptides. Score 0.417 Round 5: 127 peptides, 19 chains. Longest chain 18 peptides. Score 0.423 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 19, Residues 108, 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. 5128 reflections ( 98.18 % complete ) and 5161 restraints for refining 2241 atoms. 4748 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2162 (Rfree = 0.000) for 2241 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2162 (Rfree = 0.000) for 2230 atoms. Found 0 (16 requested) and removed 4 (8 requested) atoms. Cycle 48: After refmac, R = 0.2157 (Rfree = 0.000) for 2224 atoms. Found 0 (16 requested) and removed 2 (8 requested) atoms. Cycle 49: After refmac, R = 0.2091 (Rfree = 0.000) for 2218 atoms. TimeTaking 30.32