null Mon 24 Dec 00:28:37 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 2o8q-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2o8q-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2o8q-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2o8q-3.6-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/2o8q-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2o8q-3.6-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 ============================================================ Mon 24 Dec 00:28:41 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/2o8q-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2o8q-3.6-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 264 and 0 Target number of residues in the AU: 264 Target solvent content: 0.6405 Checking the provided sequence file Detected sequence length: 134 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 268 Adjusted target solvent content: 0.64 Input MTZ file: 2o8q-3.6-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: 94 Cell parameters: 103.170 103.170 74.680 90.000 90.000 90.000 Input sequence file: 2o8q-3.6-parrot-mrncs.fasta_lf Building free atoms model in initial map for 2144 target number of atoms Had to go as low as 0.85 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: 29.026 3.601 Wilson plot Bfac: 71.81 4947 reflections ( 98.53 % complete ) and 0 restraints for refining 2392 atoms. Observations/parameters ratio is 0.52 ------------------------------------------------------ Starting model: R = 0.3014 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2345 (Rfree = 0.000) for 2392 atoms. Found 15 (15 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.45 2.85 Search for helices and strands: 0 residues in 0 chains, 2417 seeds are put forward NCS extension: 0 residues added, 2417 seeds are put forward Round 1: 171 peptides, 24 chains. Longest chain 18 peptides. Score 0.496 Round 2: 196 peptides, 21 chains. Longest chain 26 peptides. Score 0.623 Round 3: 200 peptides, 18 chains. Longest chain 28 peptides. Score 0.673 Round 4: 187 peptides, 19 chains. Longest chain 32 peptides. Score 0.624 Round 5: 182 peptides, 17 chains. Longest chain 32 peptides. Score 0.637 Taking the results from Round 3 Chains 19, Residues 182, Estimated correctness of the model 40.9 % 4 chains (47 residues) have been docked in sequence ------------------------------------------------------ 4947 reflections ( 98.53 % complete ) and 3536 restraints for refining 1941 atoms. 2628 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2423 (Rfree = 0.000) for 1941 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 2: After refmac, R = 0.2353 (Rfree = 0.000) for 1892 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 3: After refmac, R = 0.2343 (Rfree = 0.000) for 1861 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 4: After refmac, R = 0.2229 (Rfree = 0.000) for 1851 atoms. Found 8 (11 requested) and removed 5 (5 requested) atoms. Cycle 5: After refmac, R = 0.2251 (Rfree = 0.000) for 1841 atoms. Found 10 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.46 2.86 Search for helices and strands: 0 residues in 0 chains, 1898 seeds are put forward NCS extension: 26 residues added (15 deleted due to clashes), 1924 seeds are put forward Round 1: 187 peptides, 21 chains. Longest chain 26 peptides. Score 0.596 Round 2: 195 peptides, 21 chains. Longest chain 31 peptides. Score 0.620 Round 3: 206 peptides, 18 chains. Longest chain 46 peptides. Score 0.688 Round 4: 198 peptides, 16 chains. Longest chain 34 peptides. Score 0.693 Round 5: 199 peptides, 16 chains. Longest chain 39 peptides. Score 0.695 Taking the results from Round 5 Chains 16, Residues 183, Estimated correctness of the model 48.0 % 2 chains (58 residues) have been docked in sequence ------------------------------------------------------ 4947 reflections ( 98.53 % complete ) and 3436 restraints for refining 1944 atoms. 2446 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2555 (Rfree = 0.000) for 1944 atoms. Found 10 (12 requested) and removed 22 (6 requested) atoms. Cycle 7: After refmac, R = 0.2428 (Rfree = 0.000) for 1906 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 8: After refmac, R = 0.2478 (Rfree = 0.000) for 1891 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 9: After refmac, R = 0.2401 (Rfree = 0.000) for 1879 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 10: After refmac, R = 0.2487 (Rfree = 0.000) for 1873 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.43 2.83 Search for helices and strands: 0 residues in 0 chains, 1907 seeds are put forward NCS extension: 36 residues added (2 deleted due to clashes), 1943 seeds are put forward Round 1: 196 peptides, 19 chains. Longest chain 37 peptides. Score 0.649 Round 2: 203 peptides, 19 chains. Longest chain 39 peptides. Score 0.668 Round 3: 207 peptides, 22 chains. Longest chain 31 peptides. Score 0.641 Round 4: 196 peptides, 15 chains. Longest chain 38 peptides. Score 0.700 Round 5: 202 peptides, 18 chains. Longest chain 44 peptides. Score 0.678 Taking the results from Round 4 Chains 19, Residues 181, Estimated correctness of the model 49.5 % 3 chains (38 residues) have been docked in sequence ------------------------------------------------------ 4947 reflections ( 98.53 % complete ) and 3723 restraints for refining 1944 atoms. 2855 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2629 (Rfree = 0.000) for 1944 atoms. Found 11 (12 requested) and removed 20 (6 requested) atoms. Cycle 12: After refmac, R = 0.2374 (Rfree = 0.000) for 1921 atoms. Found 7 (12 requested) and removed 8 (6 requested) atoms. Cycle 13: After refmac, R = 0.2371 (Rfree = 0.000) for 1911 atoms. Found 5 (12 requested) and removed 9 (6 requested) atoms. Cycle 14: After refmac, R = 0.2326 (Rfree = 0.000) for 1900 atoms. Found 8 (12 requested) and removed 9 (6 requested) atoms. Cycle 15: After refmac, R = 0.2268 (Rfree = 0.000) for 1895 atoms. Found 4 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.47 2.86 Search for helices and strands: 0 residues in 0 chains, 1944 seeds are put forward NCS extension: 0 residues added, 1944 seeds are put forward Round 1: 183 peptides, 21 chains. Longest chain 37 peptides. Score 0.583 Round 2: 200 peptides, 17 chains. Longest chain 38 peptides. Score 0.685 Round 3: 200 peptides, 19 chains. Longest chain 42 peptides. Score 0.660 Round 4: 199 peptides, 21 chains. Longest chain 34 peptides. Score 0.631 Round 5: 178 peptides, 16 chains. Longest chain 30 peptides. Score 0.639 Taking the results from Round 2 Chains 21, Residues 183, Estimated correctness of the model 44.8 % 4 chains (58 residues) have been docked in sequence ------------------------------------------------------ 4947 reflections ( 98.53 % complete ) and 3415 restraints for refining 1944 atoms. 2475 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2488 (Rfree = 0.000) for 1944 atoms. Found 12 (12 requested) and removed 16 (6 requested) atoms. Cycle 17: After refmac, R = 0.2317 (Rfree = 0.000) for 1931 atoms. Found 8 (12 requested) and removed 9 (6 requested) atoms. Cycle 18: After refmac, R = 0.2310 (Rfree = 0.000) for 1922 atoms. Found 6 (12 requested) and removed 6 (6 requested) atoms. Cycle 19: After refmac, R = 0.2227 (Rfree = 0.000) for 1920 atoms. Found 2 (12 requested) and removed 7 (6 requested) atoms. Cycle 20: After refmac, R = 0.2260 (Rfree = 0.000) for 1911 atoms. Found 6 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.42 2.82 Search for helices and strands: 0 residues in 0 chains, 1943 seeds are put forward NCS extension: 29 residues added (5 deleted due to clashes), 1972 seeds are put forward Round 1: 163 peptides, 22 chains. Longest chain 19 peptides. Score 0.500 Round 2: 188 peptides, 24 chains. Longest chain 19 peptides. Score 0.555 Round 3: 191 peptides, 24 chains. Longest chain 19 peptides. Score 0.565 Round 4: 190 peptides, 23 chains. Longest chain 19 peptides. Score 0.576 Round 5: 186 peptides, 21 chains. Longest chain 28 peptides. Score 0.592 Taking the results from Round 5 Chains 23, Residues 165, Estimated correctness of the model 11.4 % 1 chains (16 residues) have been docked in sequence ------------------------------------------------------ 4947 reflections ( 98.53 % complete ) and 3872 restraints for refining 1944 atoms. 3183 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2511 (Rfree = 0.000) for 1944 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 22: After refmac, R = 0.2373 (Rfree = 0.000) for 1931 atoms. Found 12 (12 requested) and removed 7 (6 requested) atoms. Cycle 23: After refmac, R = 0.2246 (Rfree = 0.000) for 1924 atoms. Found 9 (12 requested) and removed 10 (6 requested) atoms. Cycle 24: After refmac, R = 0.2199 (Rfree = 0.000) for 1919 atoms. Found 6 (12 requested) and removed 7 (6 requested) atoms. Cycle 25: After refmac, R = 0.2194 (Rfree = 0.000) for 1912 atoms. Found 7 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.44 2.84 Search for helices and strands: 0 residues in 0 chains, 1959 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 1973 seeds are put forward Round 1: 182 peptides, 22 chains. Longest chain 25 peptides. Score 0.565 Round 2: 199 peptides, 22 chains. Longest chain 29 peptides. Score 0.618 Round 3: 191 peptides, 21 chains. Longest chain 25 peptides. Score 0.608 Round 4: 198 peptides, 20 chains. Longest chain 26 peptides. Score 0.642 Round 5: 203 peptides, 22 chains. Longest chain 22 peptides. Score 0.629 Taking the results from Round 4 Chains 22, Residues 178, Estimated correctness of the model 30.3 % 3 chains (37 residues) have been docked in sequence ------------------------------------------------------ 4947 reflections ( 98.53 % complete ) and 3734 restraints for refining 1944 atoms. 2913 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2487 (Rfree = 0.000) for 1944 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 27: After refmac, R = 0.2315 (Rfree = 0.000) for 1933 atoms. Found 4 (12 requested) and removed 16 (6 requested) atoms. Cycle 28: After refmac, R = 0.2321 (Rfree = 0.000) for 1919 atoms. Found 6 (12 requested) and removed 7 (6 requested) atoms. Cycle 29: After refmac, R = 0.2223 (Rfree = 0.000) for 1915 atoms. Found 9 (12 requested) and removed 7 (6 requested) atoms. Cycle 30: After refmac, R = 0.2219 (Rfree = 0.000) for 1912 atoms. Found 7 (12 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.44 2.84 Search for helices and strands: 0 residues in 0 chains, 1972 seeds are put forward NCS extension: 15 residues added (3 deleted due to clashes), 1987 seeds are put forward Round 1: 173 peptides, 25 chains. Longest chain 17 peptides. Score 0.487 Round 2: 178 peptides, 21 chains. Longest chain 20 peptides. Score 0.567 Round 3: 190 peptides, 21 chains. Longest chain 20 peptides. Score 0.605 Round 4: 189 peptides, 21 chains. Longest chain 20 peptides. Score 0.602 Round 5: 185 peptides, 22 chains. Longest chain 21 peptides. Score 0.575 Taking the results from Round 3 Chains 22, Residues 169, Estimated correctness of the model 16.5 % 2 chains (27 residues) have been docked in sequence ------------------------------------------------------ 4947 reflections ( 98.53 % complete ) and 3919 restraints for refining 1944 atoms. 3170 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2459 (Rfree = 0.000) for 1944 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 32: After refmac, R = 0.2291 (Rfree = 0.000) for 1927 atoms. Found 9 (12 requested) and removed 9 (6 requested) atoms. Cycle 33: After refmac, R = 0.2258 (Rfree = 0.000) for 1921 atoms. Found 11 (12 requested) and removed 8 (6 requested) atoms. Cycle 34: After refmac, R = 0.2183 (Rfree = 0.000) for 1918 atoms. Found 9 (12 requested) and removed 7 (6 requested) atoms. Cycle 35: After refmac, R = 0.2158 (Rfree = 0.000) for 1918 atoms. Found 4 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.49 2.88 Search for helices and strands: 0 residues in 0 chains, 1948 seeds are put forward NCS extension: 18 residues added (3 deleted due to clashes), 1966 seeds are put forward Round 1: 158 peptides, 21 chains. Longest chain 20 peptides. Score 0.498 Round 2: 197 peptides, 22 chains. Longest chain 37 peptides. Score 0.612 Round 3: 194 peptides, 24 chains. Longest chain 21 peptides. Score 0.574 Round 4: 200 peptides, 21 chains. Longest chain 24 peptides. Score 0.634 Round 5: 198 peptides, 18 chains. Longest chain 29 peptides. Score 0.668 Taking the results from Round 5 Chains 20, Residues 180, Estimated correctness of the model 39.3 % 1 chains (25 residues) have been docked in sequence ------------------------------------------------------ 4947 reflections ( 98.53 % complete ) and 3844 restraints for refining 1944 atoms. 3023 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2463 (Rfree = 0.000) for 1944 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 37: After refmac, R = 0.2294 (Rfree = 0.000) for 1933 atoms. Found 7 (12 requested) and removed 11 (6 requested) atoms. Cycle 38: After refmac, R = 0.2222 (Rfree = 0.000) for 1925 atoms. Found 7 (12 requested) and removed 7 (6 requested) atoms. Cycle 39: After refmac, R = 0.2166 (Rfree = 0.000) for 1924 atoms. Found 1 (12 requested) and removed 9 (6 requested) atoms. Cycle 40: After refmac, R = 0.2156 (Rfree = 0.000) for 1914 atoms. Found 3 (12 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.45 2.85 Search for helices and strands: 0 residues in 0 chains, 1952 seeds are put forward NCS extension: 35 residues added (1 deleted due to clashes), 1987 seeds are put forward Round 1: 166 peptides, 19 chains. Longest chain 37 peptides. Score 0.558 Round 2: 188 peptides, 20 chains. Longest chain 22 peptides. Score 0.613 Round 3: 191 peptides, 21 chains. Longest chain 22 peptides. Score 0.608 Round 4: 176 peptides, 19 chains. Longest chain 22 peptides. Score 0.590 Round 5: 192 peptides, 21 chains. Longest chain 24 peptides. Score 0.611 Taking the results from Round 2 Chains 20, Residues 168, Estimated correctness of the model 19.6 % 2 chains (32 residues) have been docked in sequence ------------------------------------------------------ 4947 reflections ( 98.53 % complete ) and 3850 restraints for refining 1944 atoms. 3039 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2358 (Rfree = 0.000) for 1944 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 42: After refmac, R = 0.2279 (Rfree = 0.000) for 1935 atoms. Found 10 (12 requested) and removed 13 (6 requested) atoms. Cycle 43: After refmac, R = 0.2135 (Rfree = 0.000) for 1925 atoms. Found 8 (12 requested) and removed 9 (6 requested) atoms. Cycle 44: After refmac, R = 0.2156 (Rfree = 0.000) for 1922 atoms. Found 8 (12 requested) and removed 7 (6 requested) atoms. Cycle 45: After refmac, R = 0.2073 (Rfree = 0.000) for 1917 atoms. Found 5 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.45 2.85 Search for helices and strands: 0 residues in 0 chains, 1951 seeds are put forward NCS extension: 26 residues added (4 deleted due to clashes), 1977 seeds are put forward Round 1: 164 peptides, 23 chains. Longest chain 14 peptides. Score 0.487 Round 2: 174 peptides, 16 chains. Longest chain 24 peptides. Score 0.628 Round 3: 176 peptides, 18 chains. Longest chain 23 peptides. Score 0.605 Round 4: 170 peptides, 17 chains. Longest chain 23 peptides. Score 0.601 Round 5: 171 peptides, 18 chains. Longest chain 17 peptides. Score 0.589 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 18, Residues 158, Estimated correctness of the model 25.2 % 3 chains (40 residues) have been docked in sequence Sequence coverage is 25 % Consider running further cycles of model building using 2o8q-3_warpNtrace.pdb as input Building loops using Loopy2018 18 chains (158 residues) following loop building 3 chains (40 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4947 reflections ( 98.53 % complete ) and 3783 restraints for refining 1944 atoms. 2980 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2475 (Rfree = 0.000) for 1944 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.2433 (Rfree = 0.000) for 1927 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.2372 (Rfree = 0.000) for 1917 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.2382 (Rfree = 0.000) for 1907 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 00:58:02 GMT 2018 Job finished. TimeTaking 29.43 Used memory is bytes: 15282952