Mon 24 Dec 07:55:56 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-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2o8q-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2o8q-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2o8q-3.6-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-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2o8q-3.6-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 07:56:00 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-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2o8q-3.6-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 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-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-3.6-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 3.601 Wilson plot Bfac: 71.81 4947 reflections ( 98.53 % complete ) and 0 restraints for refining 2371 atoms. Observations/parameters ratio is 0.52 ------------------------------------------------------ Starting model: R = 0.3185 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2930 (Rfree = 0.000) for 2371 atoms. Found 15 (15 requested) and removed 13 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.48 2.87 Search for helices and strands: 0 residues in 0 chains, 2396 seeds are put forward NCS extension: 0 residues added, 2396 seeds are put forward Round 1: 155 peptides, 24 chains. Longest chain 22 peptides. Score 0.436 Round 2: 181 peptides, 16 chains. Longest chain 36 peptides. Score 0.648 Round 3: 184 peptides, 18 chains. Longest chain 36 peptides. Score 0.629 Round 4: 184 peptides, 16 chains. Longest chain 42 peptides. Score 0.656 Round 5: 199 peptides, 16 chains. Longest chain 51 peptides. Score 0.695 Taking the results from Round 5 Chains 18, Residues 183, Estimated correctness of the model 48.0 % 1 chains (20 residues) have been docked in sequence ------------------------------------------------------ 4947 reflections ( 98.53 % complete ) and 3793 restraints for refining 1942 atoms. 3008 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2755 (Rfree = 0.000) for 1942 atoms. Found 12 (12 requested) and removed 17 (6 requested) atoms. Cycle 2: After refmac, R = 0.2546 (Rfree = 0.000) for 1901 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 3: After refmac, R = 0.2496 (Rfree = 0.000) for 1880 atoms. Found 11 (12 requested) and removed 10 (6 requested) atoms. Cycle 4: After refmac, R = 0.2462 (Rfree = 0.000) for 1875 atoms. Found 10 (12 requested) and removed 9 (6 requested) atoms. Cycle 5: After refmac, R = 0.2397 (Rfree = 0.000) for 1861 atoms. Found 11 (12 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.44 2.84 Search for helices and strands: 0 residues in 0 chains, 1915 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 1930 seeds are put forward Round 1: 180 peptides, 17 chains. Longest chain 44 peptides. Score 0.631 Round 2: 182 peptides, 20 chains. Longest chain 25 peptides. Score 0.594 Round 3: 179 peptides, 19 chains. Longest chain 27 peptides. Score 0.600 Round 4: 185 peptides, 20 chains. Longest chain 26 peptides. Score 0.604 Round 5: 185 peptides, 21 chains. Longest chain 23 peptides. Score 0.589 Taking the results from Round 1 Chains 19, Residues 163, Estimated correctness of the model 26.3 % 3 chains (37 residues) have been docked in sequence ------------------------------------------------------ 4947 reflections ( 98.53 % complete ) and 3936 restraints for refining 1944 atoms. 3165 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2555 (Rfree = 0.000) for 1944 atoms. Found 12 (12 requested) and removed 16 (6 requested) atoms. Cycle 7: After refmac, R = 0.2381 (Rfree = 0.000) for 1925 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 8: After refmac, R = 0.2313 (Rfree = 0.000) for 1918 atoms. Found 8 (12 requested) and removed 8 (6 requested) atoms. Cycle 9: After refmac, R = 0.2191 (Rfree = 0.000) for 1914 atoms. Found 6 (12 requested) and removed 9 (6 requested) atoms. Cycle 10: After refmac, R = 0.2227 (Rfree = 0.000) for 1905 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.49 2.88 Search for helices and strands: 0 residues in 0 chains, 1964 seeds are put forward NCS extension: 54 residues added (5 deleted due to clashes), 2018 seeds are put forward Round 1: 167 peptides, 18 chains. Longest chain 33 peptides. Score 0.577 Round 2: 181 peptides, 20 chains. Longest chain 27 peptides. Score 0.591 Round 3: 181 peptides, 19 chains. Longest chain 35 peptides. Score 0.606 Round 4: 189 peptides, 20 chains. Longest chain 36 peptides. Score 0.616 Round 5: 186 peptides, 19 chains. Longest chain 37 peptides. Score 0.621 Taking the results from Round 5 Chains 21, Residues 167, Estimated correctness of the model 22.6 % 3 chains (29 residues) have been docked in sequence ------------------------------------------------------ 4947 reflections ( 98.53 % complete ) and 3928 restraints for refining 1944 atoms. 3155 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2530 (Rfree = 0.000) for 1944 atoms. Found 9 (12 requested) and removed 16 (6 requested) atoms. Cycle 12: After refmac, R = 0.2429 (Rfree = 0.000) for 1925 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 13: After refmac, R = 0.2335 (Rfree = 0.000) for 1921 atoms. Found 10 (12 requested) and removed 10 (6 requested) atoms. Cycle 14: After refmac, R = 0.2247 (Rfree = 0.000) for 1914 atoms. Found 6 (12 requested) and removed 11 (6 requested) atoms. Cycle 15: After refmac, R = 0.2166 (Rfree = 0.000) for 1905 atoms. Found 6 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.45 2.85 Search for helices and strands: 0 residues in 0 chains, 1917 seeds are put forward NCS extension: 0 residues added, 1917 seeds are put forward Round 1: 170 peptides, 20 chains. Longest chain 29 peptides. Score 0.556 Round 2: 183 peptides, 18 chains. Longest chain 40 peptides. Score 0.626 Round 3: 181 peptides, 19 chains. Longest chain 28 peptides. Score 0.606 Round 4: 169 peptides, 18 chains. Longest chain 21 peptides. Score 0.583 Round 5: 186 peptides, 20 chains. Longest chain 36 peptides. Score 0.607 Taking the results from Round 2 Chains 20, Residues 165, Estimated correctness of the model 24.5 % 1 chains (16 residues) have been docked in sequence ------------------------------------------------------ 4947 reflections ( 98.53 % complete ) and 3987 restraints for refining 1944 atoms. 3268 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2476 (Rfree = 0.000) for 1944 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. Cycle 17: After refmac, R = 0.2373 (Rfree = 0.000) for 1936 atoms. Found 6 (12 requested) and removed 10 (6 requested) atoms. Cycle 18: After refmac, R = 0.2290 (Rfree = 0.000) for 1926 atoms. Found 7 (12 requested) and removed 10 (6 requested) atoms. Cycle 19: After refmac, R = 0.2183 (Rfree = 0.000) for 1922 atoms. Found 3 (12 requested) and removed 8 (6 requested) atoms. Cycle 20: After refmac, R = 0.2171 (Rfree = 0.000) for 1913 atoms. Found 3 (12 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.43 2.83 Search for helices and strands: 0 residues in 0 chains, 1956 seeds are put forward NCS extension: 18 residues added (9 deleted due to clashes), 1974 seeds are put forward Round 1: 155 peptides, 23 chains. Longest chain 16 peptides. Score 0.453 Round 2: 176 peptides, 20 chains. Longest chain 35 peptides. Score 0.576 Round 3: 182 peptides, 23 chains. Longest chain 19 peptides. Score 0.550 Round 4: 182 peptides, 23 chains. Longest chain 23 peptides. Score 0.550 Round 5: 184 peptides, 21 chains. Longest chain 22 peptides. Score 0.586 Taking the results from Round 5 Chains 21, Residues 163, Estimated correctness of the model 9.0 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 4947 reflections ( 98.53 % complete ) and 4080 restraints for refining 1944 atoms. 3419 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2645 (Rfree = 0.000) for 1944 atoms. Found 12 (12 requested) and removed 17 (6 requested) atoms. Cycle 22: After refmac, R = 0.2398 (Rfree = 0.000) for 1925 atoms. Found 10 (12 requested) and removed 9 (6 requested) atoms. Cycle 23: After refmac, R = 0.2410 (Rfree = 0.000) for 1913 atoms. Found 7 (12 requested) and removed 8 (6 requested) atoms. Cycle 24: After refmac, R = 0.2299 (Rfree = 0.000) for 1903 atoms. Found 7 (12 requested) and removed 9 (6 requested) atoms. Cycle 25: After refmac, R = 0.2177 (Rfree = 0.000) for 1888 atoms. Found 8 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.40 2.81 Search for helices and strands: 0 residues in 0 chains, 1942 seeds are put forward NCS extension: 25 residues added (6 deleted due to clashes), 1967 seeds are put forward Round 1: 180 peptides, 27 chains. Longest chain 17 peptides. Score 0.480 Round 2: 187 peptides, 26 chains. Longest chain 23 peptides. Score 0.521 Round 3: 185 peptides, 23 chains. Longest chain 28 peptides. Score 0.560 Round 4: 186 peptides, 24 chains. Longest chain 29 peptides. Score 0.548 Round 5: 191 peptides, 22 chains. Longest chain 30 peptides. Score 0.594 Taking the results from Round 5 Chains 22, Residues 169, Estimated correctness of the model 12.2 % 2 chains (10 residues) have been docked in sequence ------------------------------------------------------ 4947 reflections ( 98.53 % complete ) and 4175 restraints for refining 1944 atoms. 3499 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2676 (Rfree = 0.000) for 1944 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 27: After refmac, R = 0.2590 (Rfree = 0.000) for 1927 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 28: After refmac, R = 0.2499 (Rfree = 0.000) for 1917 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 29: After refmac, R = 0.2354 (Rfree = 0.000) for 1912 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 30: After refmac, R = 0.2432 (Rfree = 0.000) for 1909 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.39 2.80 Search for helices and strands: 0 residues in 0 chains, 1979 seeds are put forward NCS extension: 58 residues added (2 deleted due to clashes), 2037 seeds are put forward Round 1: 152 peptides, 19 chains. Longest chain 25 peptides. Score 0.509 Round 2: 170 peptides, 20 chains. Longest chain 26 peptides. Score 0.556 Round 3: 193 peptides, 25 chains. Longest chain 20 peptides. Score 0.556 Round 4: 173 peptides, 20 chains. Longest chain 24 peptides. Score 0.566 Round 5: 157 peptides, 16 chains. Longest chain 26 peptides. Score 0.575 Taking the results from Round 5 Chains 16, Residues 141, Estimated correctness of the model 4.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4947 reflections ( 98.53 % complete ) and 4287 restraints for refining 1944 atoms. 3739 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2591 (Rfree = 0.000) for 1944 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 32: After refmac, R = 0.2465 (Rfree = 0.000) for 1929 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 33: After refmac, R = 0.2432 (Rfree = 0.000) for 1927 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 34: After refmac, R = 0.2292 (Rfree = 0.000) for 1921 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 35: After refmac, R = 0.2263 (Rfree = 0.000) for 1917 atoms. Found 10 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.45 2.85 Search for helices and strands: 0 residues in 0 chains, 1969 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 1994 seeds are put forward Round 1: 152 peptides, 22 chains. Longest chain 18 peptides. Score 0.459 Round 2: 165 peptides, 21 chains. Longest chain 27 peptides. Score 0.523 Round 3: 175 peptides, 23 chains. Longest chain 24 peptides. Score 0.526 Round 4: 181 peptides, 20 chains. Longest chain 30 peptides. Score 0.591 Round 5: 183 peptides, 23 chains. Longest chain 19 peptides. Score 0.553 Taking the results from Round 4 Chains 20, Residues 161, Estimated correctness of the model 11.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4947 reflections ( 98.53 % complete ) and 4089 restraints for refining 1943 atoms. 3448 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2591 (Rfree = 0.000) for 1943 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 37: After refmac, R = 0.2310 (Rfree = 0.000) for 1926 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 38: After refmac, R = 0.2206 (Rfree = 0.000) for 1927 atoms. Found 7 (12 requested) and removed 11 (6 requested) atoms. Cycle 39: After refmac, R = 0.2153 (Rfree = 0.000) for 1922 atoms. Found 4 (12 requested) and removed 7 (6 requested) atoms. Cycle 40: After refmac, R = 0.2134 (Rfree = 0.000) for 1915 atoms. Found 5 (12 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.48 2.87 Search for helices and strands: 0 residues in 0 chains, 1963 seeds are put forward NCS extension: 26 residues added (6 deleted due to clashes), 1989 seeds are put forward Round 1: 150 peptides, 24 chains. Longest chain 14 peptides. Score 0.416 Round 2: 175 peptides, 21 chains. Longest chain 25 peptides. Score 0.557 Round 3: 175 peptides, 21 chains. Longest chain 18 peptides. Score 0.557 Round 4: 173 peptides, 23 chains. Longest chain 20 peptides. Score 0.519 Round 5: 178 peptides, 22 chains. Longest chain 18 peptides. Score 0.552 Taking the results from Round 3 Chains 21, Residues 154, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 4947 reflections ( 98.53 % complete ) and 4241 restraints for refining 1943 atoms. 3630 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2432 (Rfree = 0.000) for 1943 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 42: After refmac, R = 0.2266 (Rfree = 0.000) for 1935 atoms. Found 5 (12 requested) and removed 9 (6 requested) atoms. Cycle 43: After refmac, R = 0.2225 (Rfree = 0.000) for 1926 atoms. Found 6 (12 requested) and removed 7 (6 requested) atoms. Cycle 44: After refmac, R = 0.2151 (Rfree = 0.000) for 1925 atoms. Found 3 (12 requested) and removed 9 (6 requested) atoms. Cycle 45: After refmac, R = 0.2098 (Rfree = 0.000) for 1916 atoms. Found 3 (12 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.45 2.85 Search for helices and strands: 0 residues in 0 chains, 1940 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 1959 seeds are put forward Round 1: 170 peptides, 24 chains. Longest chain 22 peptides. Score 0.492 Round 2: 174 peptides, 25 chains. Longest chain 18 peptides. Score 0.491 Round 3: 182 peptides, 18 chains. Longest chain 24 peptides. Score 0.623 Round 4: 189 peptides, 19 chains. Longest chain 24 peptides. Score 0.629 Round 5: 181 peptides, 22 chains. Longest chain 21 peptides. Score 0.562 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 20, Residues 170, Estimated correctness of the model 25.6 % 1 chains (11 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 2o8q-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4947 reflections ( 98.53 % complete ) and 4081 restraints for refining 1943 atoms. 3388 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2404 (Rfree = 0.000) for 1943 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.2240 (Rfree = 0.000) for 1928 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.2196 (Rfree = 0.000) for 1920 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.2164 (Rfree = 0.000) for 1909 atoms. TimeTaking 32.32