Mon 24 Dec 07:58:47 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 2prx-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2prx-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2prx-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2prx-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/2prx-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2prx-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 07:58:52 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/2prx-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2prx-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 219 and 0 Target number of residues in the AU: 219 Target solvent content: 0.5968 Checking the provided sequence file Detected sequence length: 160 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 320 Adjusted target solvent content: 0.41 Input MTZ file: 2prx-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: 144 Cell parameters: 38.520 38.520 171.590 90.000 90.000 120.000 Input sequence file: 2prx-3.4-parrot-noncs.fasta_lf Building free atoms model in initial map for 2560 target number of atoms Had to go as low as 0.65 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: 28.816 3.400 Wilson plot Bfac: 51.03 3899 reflections ( 99.57 % complete ) and 0 restraints for refining 2844 atoms. Observations/parameters ratio is 0.34 ------------------------------------------------------ Starting model: R = 0.3141 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3063 (Rfree = 0.000) for 2844 atoms. Found 14 (21 requested) and removed 50 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.24 3.66 Search for helices and strands: 0 residues in 0 chains, 2827 seeds are put forward NCS extension: 0 residues added, 2827 seeds are put forward Round 1: 41 peptides, 9 chains. Longest chain 6 peptides. Score 0.211 Round 2: 68 peptides, 15 chains. Longest chain 7 peptides. Score 0.225 Round 3: 95 peptides, 19 chains. Longest chain 8 peptides. Score 0.292 Round 4: 91 peptides, 16 chains. Longest chain 12 peptides. Score 0.346 Round 5: 86 peptides, 17 chains. Longest chain 11 peptides. Score 0.289 Taking the results from Round 4 Chains 16, Residues 75, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3899 reflections ( 99.57 % complete ) and 5501 restraints for refining 2328 atoms. 5217 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2405 (Rfree = 0.000) for 2328 atoms. Found 16 (17 requested) and removed 19 (8 requested) atoms. Cycle 2: After refmac, R = 0.2084 (Rfree = 0.000) for 2319 atoms. Found 10 (17 requested) and removed 13 (8 requested) atoms. Cycle 3: After refmac, R = 0.1918 (Rfree = 0.000) for 2313 atoms. Found 9 (17 requested) and removed 12 (8 requested) atoms. Cycle 4: After refmac, R = 0.1851 (Rfree = 0.000) for 2307 atoms. Found 6 (17 requested) and removed 10 (8 requested) atoms. Cycle 5: After refmac, R = 0.1830 (Rfree = 0.000) for 2299 atoms. Found 7 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.02 3.41 Search for helices and strands: 0 residues in 0 chains, 2318 seeds are put forward NCS extension: 0 residues added, 2318 seeds are put forward Round 1: 97 peptides, 21 chains. Longest chain 8 peptides. Score 0.252 Round 2: 105 peptides, 21 chains. Longest chain 9 peptides. Score 0.302 Round 3: 105 peptides, 19 chains. Longest chain 10 peptides. Score 0.352 Round 4: 111 peptides, 19 chains. Longest chain 12 peptides. Score 0.387 Round 5: 123 peptides, 22 chains. Longest chain 13 peptides. Score 0.381 Taking the results from Round 4 Chains 19, Residues 92, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 3899 reflections ( 99.57 % complete ) and 4942 restraints for refining 2198 atoms. 4554 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2199 (Rfree = 0.000) for 2198 atoms. Found 16 (16 requested) and removed 16 (8 requested) atoms. Cycle 7: After refmac, R = 0.2001 (Rfree = 0.000) for 2196 atoms. Found 6 (16 requested) and removed 8 (8 requested) atoms. Cycle 8: After refmac, R = 0.1961 (Rfree = 0.000) for 2191 atoms. Found 7 (16 requested) and removed 10 (8 requested) atoms. Cycle 9: After refmac, R = 0.1946 (Rfree = 0.000) for 2188 atoms. Found 7 (16 requested) and removed 8 (8 requested) atoms. Cycle 10: After refmac, R = 0.1891 (Rfree = 0.000) for 2186 atoms. Found 1 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.01 3.40 Search for helices and strands: 0 residues in 0 chains, 2207 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 2220 seeds are put forward Round 1: 104 peptides, 22 chains. Longest chain 8 peptides. Score 0.270 Round 2: 127 peptides, 24 chains. Longest chain 10 peptides. Score 0.356 Round 3: 112 peptides, 21 chains. Longest chain 14 peptides. Score 0.343 Round 4: 119 peptides, 23 chains. Longest chain 9 peptides. Score 0.335 Round 5: 120 peptides, 23 chains. Longest chain 10 peptides. Score 0.340 Taking the results from Round 2 Chains 24, Residues 103, Estimated correctness of the model 0.0 % 3 chains (11 residues) have been docked in sequence ------------------------------------------------------ 3899 reflections ( 99.57 % complete ) and 4973 restraints for refining 2222 atoms. 4556 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2183 (Rfree = 0.000) for 2222 atoms. Found 16 (16 requested) and removed 13 (8 requested) atoms. Cycle 12: After refmac, R = 0.2028 (Rfree = 0.000) for 2222 atoms. Found 5 (16 requested) and removed 9 (8 requested) atoms. Cycle 13: After refmac, R = 0.1990 (Rfree = 0.000) for 2218 atoms. Found 7 (16 requested) and removed 8 (8 requested) atoms. Cycle 14: After refmac, R = 0.1921 (Rfree = 0.000) for 2216 atoms. Found 3 (16 requested) and removed 9 (8 requested) atoms. Cycle 15: After refmac, R = 0.1890 (Rfree = 0.000) for 2209 atoms. Found 2 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.98 3.36 Search for helices and strands: 0 residues in 0 chains, 2229 seeds are put forward NCS extension: 8 residues added (1 deleted due to clashes), 2237 seeds are put forward Round 1: 109 peptides, 24 chains. Longest chain 7 peptides. Score 0.250 Round 2: 115 peptides, 21 chains. Longest chain 15 peptides. Score 0.360 Round 3: 119 peptides, 21 chains. Longest chain 14 peptides. Score 0.383 Round 4: 115 peptides, 18 chains. Longest chain 18 peptides. Score 0.432 Round 5: 117 peptides, 21 chains. Longest chain 11 peptides. Score 0.372 Taking the results from Round 4 Chains 18, Residues 97, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3899 reflections ( 99.57 % complete ) and 5138 restraints for refining 2244 atoms. 4768 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2170 (Rfree = 0.000) for 2244 atoms. Found 11 (16 requested) and removed 11 (8 requested) atoms. Cycle 17: After refmac, R = 0.2039 (Rfree = 0.000) for 2242 atoms. Found 7 (16 requested) and removed 11 (8 requested) atoms. Cycle 18: After refmac, R = 0.2012 (Rfree = 0.000) for 2236 atoms. Found 5 (16 requested) and removed 8 (8 requested) atoms. Cycle 19: After refmac, R = 0.1985 (Rfree = 0.000) for 2232 atoms. Found 3 (16 requested) and removed 8 (8 requested) atoms. Cycle 20: After refmac, R = 0.1975 (Rfree = 0.000) for 2227 atoms. Found 4 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.01 3.40 Search for helices and strands: 0 residues in 0 chains, 2259 seeds are put forward NCS extension: 0 residues added, 2259 seeds are put forward Round 1: 103 peptides, 21 chains. Longest chain 8 peptides. Score 0.290 Round 2: 122 peptides, 23 chains. Longest chain 9 peptides. Score 0.352 Round 3: 116 peptides, 23 chains. Longest chain 11 peptides. Score 0.317 Round 4: 121 peptides, 22 chains. Longest chain 10 peptides. Score 0.370 Round 5: 112 peptides, 19 chains. Longest chain 11 peptides. Score 0.392 Taking the results from Round 5 Chains 19, Residues 93, Estimated correctness of the model 0.0 % 2 chains (10 residues) have been docked in sequence ------------------------------------------------------ 3899 reflections ( 99.57 % complete ) and 5228 restraints for refining 2292 atoms. 4854 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2045 (Rfree = 0.000) for 2292 atoms. Found 16 (17 requested) and removed 11 (8 requested) atoms. Cycle 22: After refmac, R = 0.1907 (Rfree = 0.000) for 2292 atoms. Found 2 (17 requested) and removed 10 (8 requested) atoms. Cycle 23: After refmac, R = 0.1884 (Rfree = 0.000) for 2282 atoms. Found 7 (17 requested) and removed 9 (8 requested) atoms. Cycle 24: After refmac, R = 0.1878 (Rfree = 0.000) for 2280 atoms. Found 6 (17 requested) and removed 8 (8 requested) atoms. Failed to save intermediate PDB Cycle 25: After refmac, R = 0.1866 (Rfree = 0.000) for 2278 atoms. Found 6 (17 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.02 3.41 Search for helices and strands: 0 residues in 0 chains, 2298 seeds are put forward NCS extension: 0 residues added, 2298 seeds are put forward Round 1: 99 peptides, 21 chains. Longest chain 7 peptides. Score 0.265 Round 2: 108 peptides, 19 chains. Longest chain 10 peptides. Score 0.369 Round 3: 111 peptides, 19 chains. Longest chain 11 peptides. Score 0.387 Round 4: 126 peptides, 23 chains. Longest chain 10 peptides. Score 0.374 Round 5: 108 peptides, 17 chains. Longest chain 14 peptides. Score 0.418 Taking the results from Round 5 Chains 17, Residues 91, Estimated correctness of the model 0.0 % 3 chains (13 residues) have been docked in sequence ------------------------------------------------------ 3899 reflections ( 99.57 % complete ) and 5408 restraints for refining 2328 atoms. 5035 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2072 (Rfree = 0.000) for 2328 atoms. Found 16 (17 requested) and removed 11 (8 requested) atoms. Cycle 27: After refmac, R = 0.1995 (Rfree = 0.000) for 2327 atoms. Found 8 (17 requested) and removed 8 (8 requested) atoms. Cycle 28: After refmac, R = 0.1939 (Rfree = 0.000) for 2326 atoms. Found 5 (17 requested) and removed 8 (8 requested) atoms. Cycle 29: After refmac, R = 0.1946 (Rfree = 0.000) for 2322 atoms. Found 4 (17 requested) and removed 8 (8 requested) atoms. Cycle 30: After refmac, R = 0.1934 (Rfree = 0.000) for 2317 atoms. Found 3 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.02 3.41 Search for helices and strands: 0 residues in 0 chains, 2338 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 2357 seeds are put forward Round 1: 90 peptides, 19 chains. Longest chain 10 peptides. Score 0.261 Round 2: 105 peptides, 19 chains. Longest chain 12 peptides. Score 0.352 Round 3: 106 peptides, 18 chains. Longest chain 13 peptides. Score 0.383 Round 4: 106 peptides, 19 chains. Longest chain 11 peptides. Score 0.358 Round 5: 103 peptides, 18 chains. Longest chain 10 peptides. Score 0.366 Taking the results from Round 3 Chains 18, Residues 88, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 3899 reflections ( 99.57 % complete ) and 5455 restraints for refining 2318 atoms. 5099 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2076 (Rfree = 0.000) for 2318 atoms. Found 12 (17 requested) and removed 10 (8 requested) atoms. Cycle 32: After refmac, R = 0.2025 (Rfree = 0.000) for 2319 atoms. Found 10 (17 requested) and removed 9 (8 requested) atoms. Cycle 33: After refmac, R = 0.1971 (Rfree = 0.000) for 2320 atoms. Found 3 (17 requested) and removed 8 (8 requested) atoms. Cycle 34: After refmac, R = 0.1943 (Rfree = 0.000) for 2314 atoms. Found 2 (17 requested) and removed 8 (8 requested) atoms. Cycle 35: After refmac, R = 0.1931 (Rfree = 0.000) for 2308 atoms. Found 3 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.05 3.44 Search for helices and strands: 0 residues in 0 chains, 2322 seeds are put forward NCS extension: 0 residues added, 2322 seeds are put forward Round 1: 75 peptides, 16 chains. Longest chain 7 peptides. Score 0.245 Round 2: 90 peptides, 15 chains. Longest chain 11 peptides. Score 0.366 Round 3: 88 peptides, 13 chains. Longest chain 13 peptides. Score 0.407 Round 4: 87 peptides, 14 chains. Longest chain 9 peptides. Score 0.375 Round 5: 84 peptides, 12 chains. Longest chain 11 peptides. Score 0.410 Taking the results from Round 5 Chains 12, Residues 72, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3899 reflections ( 99.57 % complete ) and 5547 restraints for refining 2326 atoms. 5271 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2096 (Rfree = 0.000) for 2326 atoms. Found 13 (17 requested) and removed 8 (8 requested) atoms. Cycle 37: After refmac, R = 0.1992 (Rfree = 0.000) for 2331 atoms. Found 2 (17 requested) and removed 8 (8 requested) atoms. Cycle 38: After refmac, R = 0.1944 (Rfree = 0.000) for 2323 atoms. Found 6 (17 requested) and removed 8 (8 requested) atoms. Cycle 39: After refmac, R = 0.1895 (Rfree = 0.000) for 2321 atoms. Found 2 (17 requested) and removed 8 (8 requested) atoms. Cycle 40: After refmac, R = 0.1875 (Rfree = 0.000) for 2315 atoms. Found 4 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.03 3.42 Search for helices and strands: 0 residues in 0 chains, 2339 seeds are put forward NCS extension: 3 residues added (0 deleted due to clashes), 2342 seeds are put forward Round 1: 78 peptides, 18 chains. Longest chain 6 peptides. Score 0.209 Round 2: 86 peptides, 16 chains. Longest chain 11 peptides. Score 0.316 Round 3: 81 peptides, 16 chains. Longest chain 8 peptides. Score 0.284 Round 4: 82 peptides, 15 chains. Longest chain 9 peptides. Score 0.318 Round 5: 89 peptides, 19 chains. Longest chain 7 peptides. Score 0.254 Taking the results from Round 4 Chains 15, Residues 67, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3899 reflections ( 99.57 % complete ) and 5602 restraints for refining 2313 atoms. 5349 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1999 (Rfree = 0.000) for 2313 atoms. Found 12 (17 requested) and removed 8 (8 requested) atoms. Cycle 42: After refmac, R = 0.1939 (Rfree = 0.000) for 2316 atoms. Found 6 (17 requested) and removed 8 (8 requested) atoms. Cycle 43: After refmac, R = 0.1922 (Rfree = 0.000) for 2314 atoms. Found 7 (17 requested) and removed 8 (8 requested) atoms. Cycle 44: After refmac, R = 0.1895 (Rfree = 0.000) for 2312 atoms. Found 9 (17 requested) and removed 8 (8 requested) atoms. Cycle 45: After refmac, R = 0.1858 (Rfree = 0.000) for 2313 atoms. Found 2 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.06 3.45 Search for helices and strands: 0 residues in 0 chains, 2345 seeds are put forward NCS extension: 0 residues added, 2345 seeds are put forward Round 1: 74 peptides, 16 chains. Longest chain 6 peptides. Score 0.238 Round 2: 82 peptides, 16 chains. Longest chain 7 peptides. Score 0.291 Round 3: 87 peptides, 18 chains. Longest chain 8 peptides. Score 0.268 Round 4: 91 peptides, 18 chains. Longest chain 8 peptides. Score 0.294 Round 5: 89 peptides, 16 chains. Longest chain 12 peptides. Score 0.334 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 16, Residues 73, 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 2prx-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3899 reflections ( 99.57 % complete ) and 5566 restraints for refining 2312 atoms. 5290 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2049 (Rfree = 0.000) for 2312 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2008 (Rfree = 0.000) for 2303 atoms. Found 0 (17 requested) and removed 6 (8 requested) atoms. Cycle 48: After refmac, R = 0.1988 (Rfree = 0.000) for 2297 atoms. Found 0 (17 requested) and removed 1 (8 requested) atoms. Cycle 49: After refmac, R = 0.1969 (Rfree = 0.000) for 2296 atoms. TimeTaking 27.48