Mon 24 Dec 07:38:56 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 2o8q-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2o8q-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2o8q-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2o8q-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/2o8q-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2o8q-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 07:39:01 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/2o8q-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2o8q-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 274 and 0 Target number of residues in the AU: 274 Target solvent content: 0.6269 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-3.4-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: 94 Cell parameters: 103.170 103.170 74.680 90.000 90.000 90.000 Input sequence file: 2o8q-3.4-parrot-noncs.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 3.400 Wilson plot Bfac: 64.56 5837 reflections ( 98.66 % complete ) and 0 restraints for refining 2374 atoms. Observations/parameters ratio is 0.61 ------------------------------------------------------ Starting model: R = 0.3192 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2751 (Rfree = 0.000) for 2374 atoms. Found 17 (17 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.31 2.73 Search for helices and strands: 0 residues in 0 chains, 2401 seeds are put forward NCS extension: 0 residues added, 2401 seeds are put forward Round 1: 169 peptides, 23 chains. Longest chain 19 peptides. Score 0.505 Round 2: 182 peptides, 21 chains. Longest chain 23 peptides. Score 0.580 Round 3: 192 peptides, 18 chains. Longest chain 25 peptides. Score 0.651 Round 4: 200 peptides, 17 chains. Longest chain 42 peptides. Score 0.685 Round 5: 204 peptides, 16 chains. Longest chain 46 peptides. Score 0.707 Taking the results from Round 5 Chains 16, Residues 188, Estimated correctness of the model 59.7 % 1 chains (45 residues) have been docked in sequence ------------------------------------------------------ 5837 reflections ( 98.66 % complete ) and 3573 restraints for refining 1946 atoms. 2648 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2685 (Rfree = 0.000) for 1946 atoms. Found 14 (14 requested) and removed 14 (7 requested) atoms. Cycle 2: After refmac, R = 0.2586 (Rfree = 0.000) for 1915 atoms. Found 12 (14 requested) and removed 10 (7 requested) atoms. Cycle 3: After refmac, R = 0.2516 (Rfree = 0.000) for 1904 atoms. Found 12 (13 requested) and removed 7 (7 requested) atoms. Cycle 4: After refmac, R = 0.2490 (Rfree = 0.000) for 1893 atoms. Found 10 (13 requested) and removed 10 (7 requested) atoms. Cycle 5: After refmac, R = 0.2378 (Rfree = 0.000) for 1888 atoms. Found 6 (13 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.32 2.74 Search for helices and strands: 0 residues in 0 chains, 1911 seeds are put forward NCS extension: 42 residues added (11 deleted due to clashes), 1953 seeds are put forward Round 1: 189 peptides, 16 chains. Longest chain 35 peptides. Score 0.669 Round 2: 198 peptides, 18 chains. Longest chain 33 peptides. Score 0.668 Round 3: 197 peptides, 14 chains. Longest chain 29 peptides. Score 0.714 Round 4: 195 peptides, 16 chains. Longest chain 40 peptides. Score 0.685 Round 5: 197 peptides, 19 chains. Longest chain 26 peptides. Score 0.652 Taking the results from Round 3 Chains 19, Residues 183, Estimated correctness of the model 61.4 % 4 chains (50 residues) have been docked in sequence Building loops using Loopy2018 19 chains (183 residues) following loop building 4 chains (50 residues) in sequence following loop building ------------------------------------------------------ 5837 reflections ( 98.66 % complete ) and 3570 restraints for refining 1950 atoms. 2662 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2616 (Rfree = 0.000) for 1950 atoms. Found 13 (13 requested) and removed 18 (7 requested) atoms. Cycle 7: After refmac, R = 0.2400 (Rfree = 0.000) for 1933 atoms. Found 6 (12 requested) and removed 11 (7 requested) atoms. Cycle 8: After refmac, R = 0.2281 (Rfree = 0.000) for 1921 atoms. Found 4 (12 requested) and removed 10 (7 requested) atoms. Cycle 9: After refmac, R = 0.2237 (Rfree = 0.000) for 1912 atoms. Found 3 (12 requested) and removed 14 (7 requested) atoms. Cycle 10: After refmac, R = 0.2343 (Rfree = 0.000) for 1896 atoms. Found 6 (11 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.29 2.72 Search for helices and strands: 0 residues in 0 chains, 1923 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 1948 seeds are put forward Round 1: 180 peptides, 18 chains. Longest chain 36 peptides. Score 0.617 Round 2: 196 peptides, 18 chains. Longest chain 30 peptides. Score 0.662 Round 3: 185 peptides, 17 chains. Longest chain 34 peptides. Score 0.645 Round 4: 205 peptides, 14 chains. Longest chain 55 peptides. Score 0.732 Round 5: 192 peptides, 17 chains. Longest chain 29 peptides. Score 0.664 Taking the results from Round 4 Chains 18, Residues 191, Estimated correctness of the model 65.7 % 4 chains (44 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 59 A and 68 A 16 chains (190 residues) following loop building 3 chains (52 residues) in sequence following loop building ------------------------------------------------------ 5837 reflections ( 98.66 % complete ) and 3417 restraints for refining 1950 atoms. 2484 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2679 (Rfree = 0.000) for 1950 atoms. Found 11 (11 requested) and removed 27 (7 requested) atoms. Cycle 12: After refmac, R = 0.2505 (Rfree = 0.000) for 1915 atoms. Found 11 (11 requested) and removed 18 (7 requested) atoms. Cycle 13: After refmac, R = 0.2384 (Rfree = 0.000) for 1894 atoms. Found 11 (11 requested) and removed 10 (7 requested) atoms. Cycle 14: After refmac, R = 0.2306 (Rfree = 0.000) for 1885 atoms. Found 5 (10 requested) and removed 10 (7 requested) atoms. Cycle 15: After refmac, R = 0.2330 (Rfree = 0.000) for 1872 atoms. Found 6 (10 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.25 2.68 Search for helices and strands: 0 residues in 0 chains, 1911 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 1928 seeds are put forward Round 1: 186 peptides, 20 chains. Longest chain 19 peptides. Score 0.607 Round 2: 204 peptides, 18 chains. Longest chain 29 peptides. Score 0.683 Round 3: 197 peptides, 17 chains. Longest chain 32 peptides. Score 0.678 Round 4: 195 peptides, 20 chains. Longest chain 22 peptides. Score 0.633 Round 5: 192 peptides, 20 chains. Longest chain 23 peptides. Score 0.624 Taking the results from Round 2 Chains 20, Residues 186, Estimated correctness of the model 53.4 % 3 chains (63 residues) have been docked in sequence ------------------------------------------------------ 5837 reflections ( 98.66 % complete ) and 3349 restraints for refining 1949 atoms. 2352 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2671 (Rfree = 0.000) for 1949 atoms. Found 10 (10 requested) and removed 19 (7 requested) atoms. Cycle 17: After refmac, R = 0.2491 (Rfree = 0.000) for 1928 atoms. Found 10 (10 requested) and removed 19 (7 requested) atoms. Cycle 18: After refmac, R = 0.2349 (Rfree = 0.000) for 1914 atoms. Found 5 (10 requested) and removed 12 (7 requested) atoms. Cycle 19: After refmac, R = 0.2335 (Rfree = 0.000) for 1901 atoms. Found 10 (10 requested) and removed 11 (7 requested) atoms. Cycle 20: After refmac, R = 0.2324 (Rfree = 0.000) for 1899 atoms. Found 5 (10 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.21 2.65 Search for helices and strands: 0 residues in 0 chains, 1935 seeds are put forward NCS extension: 22 residues added (8 deleted due to clashes), 1957 seeds are put forward Round 1: 174 peptides, 20 chains. Longest chain 21 peptides. Score 0.569 Round 2: 192 peptides, 18 chains. Longest chain 28 peptides. Score 0.651 Round 3: 187 peptides, 16 chains. Longest chain 21 peptides. Score 0.664 Round 4: 185 peptides, 17 chains. Longest chain 36 peptides. Score 0.645 Round 5: 181 peptides, 14 chains. Longest chain 44 peptides. Score 0.674 Taking the results from Round 5 Chains 17, Residues 167, Estimated correctness of the model 50.9 % 3 chains (44 residues) have been docked in sequence ------------------------------------------------------ 5837 reflections ( 98.66 % complete ) and 3699 restraints for refining 1950 atoms. 2849 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2643 (Rfree = 0.000) for 1950 atoms. Found 10 (10 requested) and removed 20 (7 requested) atoms. Cycle 22: After refmac, R = 0.2689 (Rfree = 0.000) for 1933 atoms. Found 10 (10 requested) and removed 15 (7 requested) atoms. Cycle 23: After refmac, R = 0.2633 (Rfree = 0.000) for 1921 atoms. Found 10 (10 requested) and removed 16 (7 requested) atoms. Cycle 24: After refmac, R = 0.2549 (Rfree = 0.000) for 1909 atoms. Found 10 (10 requested) and removed 11 (7 requested) atoms. Cycle 25: After refmac, R = 0.2511 (Rfree = 0.000) for 1906 atoms. Found 10 (10 requested) and removed 13 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.15 2.60 Search for helices and strands: 0 residues in 0 chains, 1939 seeds are put forward NCS extension: 15 residues added (4 deleted due to clashes), 1954 seeds are put forward Round 1: 176 peptides, 21 chains. Longest chain 24 peptides. Score 0.560 Round 2: 177 peptides, 15 chains. Longest chain 29 peptides. Score 0.650 Round 3: 186 peptides, 16 chains. Longest chain 37 peptides. Score 0.661 Round 4: 199 peptides, 19 chains. Longest chain 33 peptides. Score 0.657 Round 5: 190 peptides, 20 chains. Longest chain 27 peptides. Score 0.619 Taking the results from Round 3 Chains 19, Residues 170, Estimated correctness of the model 47.3 % 2 chains (42 residues) have been docked in sequence ------------------------------------------------------ 5837 reflections ( 98.66 % complete ) and 3609 restraints for refining 1949 atoms. 2753 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2576 (Rfree = 0.000) for 1949 atoms. Found 10 (10 requested) and removed 18 (7 requested) atoms. Cycle 27: After refmac, R = 0.2373 (Rfree = 0.000) for 1925 atoms. Found 10 (10 requested) and removed 14 (7 requested) atoms. Cycle 28: After refmac, R = 0.2360 (Rfree = 0.000) for 1916 atoms. Found 10 (10 requested) and removed 10 (7 requested) atoms. Cycle 29: After refmac, R = 0.2333 (Rfree = 0.000) for 1912 atoms. Found 10 (10 requested) and removed 10 (7 requested) atoms. Cycle 30: After refmac, R = 0.2270 (Rfree = 0.000) for 1910 atoms. Found 10 (10 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.20 2.64 Search for helices and strands: 0 residues in 0 chains, 1953 seeds are put forward NCS extension: 11 residues added (5 deleted due to clashes), 1964 seeds are put forward Round 1: 193 peptides, 23 chains. Longest chain 22 peptides. Score 0.586 Round 2: 208 peptides, 18 chains. Longest chain 34 peptides. Score 0.693 Round 3: 208 peptides, 16 chains. Longest chain 39 peptides. Score 0.717 Round 4: 212 peptides, 15 chains. Longest chain 49 peptides. Score 0.737 Round 5: 206 peptides, 14 chains. Longest chain 46 peptides. Score 0.735 Taking the results from Round 4 Chains 20, Residues 197, Estimated correctness of the model 66.9 % 3 chains (38 residues) have been docked in sequence Building loops using Loopy2018 20 chains (197 residues) following loop building 3 chains (38 residues) in sequence following loop building ------------------------------------------------------ 5837 reflections ( 98.66 % complete ) and 3612 restraints for refining 1950 atoms. 2702 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2567 (Rfree = 0.000) for 1950 atoms. Found 10 (10 requested) and removed 19 (7 requested) atoms. Cycle 32: After refmac, R = 0.2344 (Rfree = 0.000) for 1933 atoms. Found 9 (10 requested) and removed 15 (7 requested) atoms. Cycle 33: After refmac, R = 0.2226 (Rfree = 0.000) for 1923 atoms. Found 4 (9 requested) and removed 12 (7 requested) atoms. Cycle 34: After refmac, R = 0.2151 (Rfree = 0.000) for 1914 atoms. Found 2 (9 requested) and removed 8 (7 requested) atoms. Cycle 35: After refmac, R = 0.2093 (Rfree = 0.000) for 1906 atoms. Found 4 (9 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.20 2.64 Search for helices and strands: 0 residues in 0 chains, 1931 seeds are put forward NCS extension: 28 residues added (24 deleted due to clashes), 1959 seeds are put forward Round 1: 179 peptides, 19 chains. Longest chain 25 peptides. Score 0.600 Round 2: 202 peptides, 16 chains. Longest chain 47 peptides. Score 0.702 Round 3: 206 peptides, 17 chains. Longest chain 32 peptides. Score 0.700 Round 4: 199 peptides, 19 chains. Longest chain 45 peptides. Score 0.657 Round 5: 204 peptides, 16 chains. Longest chain 51 peptides. Score 0.707 Taking the results from Round 5 Chains 16, Residues 188, Estimated correctness of the model 59.7 % 1 chains (50 residues) have been docked in sequence ------------------------------------------------------ 5837 reflections ( 98.66 % complete ) and 3507 restraints for refining 1949 atoms. 2552 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2671 (Rfree = 0.000) for 1949 atoms. Found 8 (8 requested) and removed 19 (7 requested) atoms. Cycle 37: After refmac, R = 0.2569 (Rfree = 0.000) for 1930 atoms. Found 8 (8 requested) and removed 15 (7 requested) atoms. Cycle 38: After refmac, R = 0.2417 (Rfree = 0.000) for 1916 atoms. Found 8 (8 requested) and removed 9 (7 requested) atoms. Cycle 39: After refmac, R = 0.2322 (Rfree = 0.000) for 1908 atoms. Found 8 (8 requested) and removed 9 (7 requested) atoms. Cycle 40: After refmac, R = 0.2262 (Rfree = 0.000) for 1906 atoms. Found 7 (7 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.05 2.52 Search for helices and strands: 0 residues in 0 chains, 1919 seeds are put forward NCS extension: 53 residues added (25 deleted due to clashes), 1972 seeds are put forward Round 1: 187 peptides, 21 chains. Longest chain 39 peptides. Score 0.596 Round 2: 197 peptides, 19 chains. Longest chain 25 peptides. Score 0.652 Round 3: 185 peptides, 19 chains. Longest chain 24 peptides. Score 0.618 Round 4: 185 peptides, 18 chains. Longest chain 36 peptides. Score 0.632 Round 5: 192 peptides, 21 chains. Longest chain 26 peptides. Score 0.611 Taking the results from Round 2 Chains 25, Residues 178, Estimated correctness of the model 44.7 % 4 chains (61 residues) have been docked in sequence ------------------------------------------------------ 5837 reflections ( 98.66 % complete ) and 3384 restraints for refining 1950 atoms. 2409 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2719 (Rfree = 0.000) for 1950 atoms. Found 7 (7 requested) and removed 55 (7 requested) atoms. Cycle 42: After refmac, R = 0.2535 (Rfree = 0.000) for 1894 atoms. Found 7 (7 requested) and removed 15 (7 requested) atoms. Cycle 43: After refmac, R = 0.2463 (Rfree = 0.000) for 1882 atoms. Found 7 (7 requested) and removed 14 (7 requested) atoms. Cycle 44: After refmac, R = 0.2419 (Rfree = 0.000) for 1873 atoms. Found 7 (7 requested) and removed 9 (7 requested) atoms. Cycle 45: After refmac, R = 0.2382 (Rfree = 0.000) for 1870 atoms. Found 7 (7 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.13 2.58 Search for helices and strands: 0 residues in 0 chains, 1908 seeds are put forward NCS extension: 17 residues added (12 deleted due to clashes), 1925 seeds are put forward Round 1: 168 peptides, 21 chains. Longest chain 22 peptides. Score 0.533 Round 2: 169 peptides, 19 chains. Longest chain 26 peptides. Score 0.568 Round 3: 171 peptides, 17 chains. Longest chain 29 peptides. Score 0.604 Round 4: 171 peptides, 16 chains. Longest chain 27 peptides. Score 0.619 Round 5: 159 peptides, 15 chains. Longest chain 25 peptides. Score 0.597 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 19, Residues 155, Estimated correctness of the model 34.8 % 3 chains (51 residues) have been docked in sequence Sequence coverage is 32 % Consider running further cycles of model building using 2o8q-3_warpNtrace.pdb as input Building loops using Loopy2018 19 chains (155 residues) following loop building 3 chains (51 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5837 reflections ( 98.66 % complete ) and 3600 restraints for refining 1950 atoms. 2753 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2639 (Rfree = 0.000) for 1950 atoms. Found 0 (7 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.2485 (Rfree = 0.000) for 1936 atoms. Found 0 (7 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.2788 (Rfree = 0.000) for 1915 atoms. Found 0 (7 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.2425 (Rfree = 0.000) for 1904 atoms. TimeTaking 30.23