Mon 24 Dec 00:51:46 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-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2o8q-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2o8q-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2o8q-3.8-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-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2o8q-3.8-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 00:51:50 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-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2o8q-3.8-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 256 and 0 Target number of residues in the AU: 256 Target solvent content: 0.6514 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-3.8-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-3.8-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 3.801 Wilson plot Bfac: 78.53 4222 reflections ( 98.37 % complete ) and 0 restraints for refining 2364 atoms. Observations/parameters ratio is 0.45 ------------------------------------------------------ Starting model: R = 0.3110 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3036 (Rfree = 0.000) for 2364 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.58 2.96 Search for helices and strands: 0 residues in 0 chains, 2379 seeds are put forward NCS extension: 0 residues added, 2379 seeds are put forward Round 1: 153 peptides, 25 chains. Longest chain 13 peptides. Score 0.410 Round 2: 188 peptides, 24 chains. Longest chain 19 peptides. Score 0.555 Round 3: 195 peptides, 24 chains. Longest chain 21 peptides. Score 0.577 Round 4: 192 peptides, 19 chains. Longest chain 44 peptides. Score 0.638 Round 5: 195 peptides, 19 chains. Longest chain 33 peptides. Score 0.646 Taking the results from Round 5 Chains 21, Residues 176, Estimated correctness of the model 19.1 % 3 chains (43 residues) have been docked in sequence ------------------------------------------------------ 4222 reflections ( 98.37 % complete ) and 3753 restraints for refining 1937 atoms. 2905 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2649 (Rfree = 0.000) for 1937 atoms. Found 10 (10 requested) and removed 19 (5 requested) atoms. Cycle 2: After refmac, R = 0.2580 (Rfree = 0.000) for 1888 atoms. Found 10 (10 requested) and removed 18 (5 requested) atoms. Cycle 3: After refmac, R = 0.2667 (Rfree = 0.000) for 1861 atoms. Found 10 (10 requested) and removed 18 (5 requested) atoms. Cycle 4: After refmac, R = 0.2551 (Rfree = 0.000) for 1837 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. Cycle 5: After refmac, R = 0.2498 (Rfree = 0.000) for 1824 atoms. Found 10 (10 requested) and removed 15 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.72 3.07 Search for helices and strands: 0 residues in 0 chains, 1853 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 1876 seeds are put forward Round 1: 170 peptides, 21 chains. Longest chain 25 peptides. Score 0.540 Round 2: 171 peptides, 18 chains. Longest chain 41 peptides. Score 0.589 Round 3: 192 peptides, 25 chains. Longest chain 20 peptides. Score 0.553 Round 4: 193 peptides, 20 chains. Longest chain 32 peptides. Score 0.627 Round 5: 180 peptides, 19 chains. Longest chain 26 peptides. Score 0.603 Taking the results from Round 4 Chains 22, Residues 173, Estimated correctness of the model 11.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 4222 reflections ( 98.37 % complete ) and 4069 restraints for refining 1938 atoms. 3352 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2515 (Rfree = 0.000) for 1938 atoms. Found 10 (10 requested) and removed 14 (5 requested) atoms. Cycle 7: After refmac, R = 0.2495 (Rfree = 0.000) for 1912 atoms. Found 10 (10 requested) and removed 15 (5 requested) atoms. Cycle 8: After refmac, R = 0.2262 (Rfree = 0.000) for 1896 atoms. Found 6 (10 requested) and removed 13 (5 requested) atoms. Cycle 9: After refmac, R = 0.2417 (Rfree = 0.000) for 1883 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 10: After refmac, R = 0.2475 (Rfree = 0.000) for 1871 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.58 2.96 Search for helices and strands: 0 residues in 0 chains, 1930 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 1954 seeds are put forward Round 1: 175 peptides, 25 chains. Longest chain 22 peptides. Score 0.494 Round 2: 185 peptides, 21 chains. Longest chain 27 peptides. Score 0.589 Round 3: 191 peptides, 16 chains. Longest chain 37 peptides. Score 0.675 Round 4: 195 peptides, 19 chains. Longest chain 30 peptides. Score 0.646 Round 5: 207 peptides, 16 chains. Longest chain 51 peptides. Score 0.714 Taking the results from Round 5 Chains 16, Residues 191, Estimated correctness of the model 45.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4222 reflections ( 98.37 % complete ) and 4059 restraints for refining 1939 atoms. 3311 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2713 (Rfree = 0.000) for 1939 atoms. Found 10 (10 requested) and removed 13 (5 requested) atoms. Cycle 12: After refmac, R = 0.2665 (Rfree = 0.000) for 1927 atoms. Found 10 (10 requested) and removed 16 (5 requested) atoms. Cycle 13: After refmac, R = 0.2553 (Rfree = 0.000) for 1916 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 14: After refmac, R = 0.2532 (Rfree = 0.000) for 1907 atoms. Found 9 (9 requested) and removed 14 (5 requested) atoms. Cycle 15: After refmac, R = 0.2472 (Rfree = 0.000) for 1894 atoms. Found 9 (9 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.60 2.97 Search for helices and strands: 0 residues in 0 chains, 1962 seeds are put forward NCS extension: 43 residues added (17 deleted due to clashes), 2005 seeds are put forward Round 1: 177 peptides, 26 chains. Longest chain 14 peptides. Score 0.486 Round 2: 189 peptides, 17 chains. Longest chain 30 peptides. Score 0.656 Round 3: 190 peptides, 21 chains. Longest chain 20 peptides. Score 0.605 Round 4: 192 peptides, 18 chains. Longest chain 25 peptides. Score 0.651 Round 5: 189 peptides, 18 chains. Longest chain 22 peptides. Score 0.643 Taking the results from Round 2 Chains 21, Residues 172, Estimated correctness of the model 23.2 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 4222 reflections ( 98.37 % complete ) and 3955 restraints for refining 1938 atoms. 3219 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2648 (Rfree = 0.000) for 1938 atoms. Found 9 (9 requested) and removed 16 (5 requested) atoms. Cycle 17: After refmac, R = 0.2584 (Rfree = 0.000) for 1908 atoms. Found 9 (9 requested) and removed 12 (5 requested) atoms. Cycle 18: After refmac, R = 0.2536 (Rfree = 0.000) for 1895 atoms. Found 9 (9 requested) and removed 14 (5 requested) atoms. Cycle 19: After refmac, R = 0.2460 (Rfree = 0.000) for 1880 atoms. Found 9 (9 requested) and removed 6 (5 requested) atoms. Cycle 20: After refmac, R = 0.2513 (Rfree = 0.000) for 1870 atoms. Found 9 (9 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.51 2.90 Search for helices and strands: 0 residues in 0 chains, 1923 seeds are put forward NCS extension: 27 residues added (0 deleted due to clashes), 1950 seeds are put forward Round 1: 160 peptides, 24 chains. Longest chain 13 peptides. Score 0.455 Round 2: 180 peptides, 22 chains. Longest chain 21 peptides. Score 0.559 Round 3: 183 peptides, 19 chains. Longest chain 28 peptides. Score 0.612 Round 4: 184 peptides, 16 chains. Longest chain 27 peptides. Score 0.656 Round 5: 173 peptides, 18 chains. Longest chain 22 peptides. Score 0.596 Taking the results from Round 4 Chains 17, Residues 168, Estimated correctness of the model 23.2 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 4222 reflections ( 98.37 % complete ) and 4033 restraints for refining 1938 atoms. 3338 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2570 (Rfree = 0.000) for 1938 atoms. Found 9 (9 requested) and removed 16 (5 requested) atoms. Cycle 22: After refmac, R = 0.2485 (Rfree = 0.000) for 1915 atoms. Found 9 (9 requested) and removed 10 (5 requested) atoms. Cycle 23: After refmac, R = 0.2434 (Rfree = 0.000) for 1905 atoms. Found 9 (9 requested) and removed 13 (5 requested) atoms. Cycle 24: After refmac, R = 0.2395 (Rfree = 0.000) for 1892 atoms. Found 9 (9 requested) and removed 10 (5 requested) atoms. Cycle 25: After refmac, R = 0.2354 (Rfree = 0.000) for 1882 atoms. Found 9 (9 requested) and removed 11 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.56 2.94 Search for helices and strands: 0 residues in 0 chains, 1931 seeds are put forward NCS extension: 30 residues added (3 deleted due to clashes), 1961 seeds are put forward Round 1: 159 peptides, 23 chains. Longest chain 16 peptides. Score 0.468 Round 2: 173 peptides, 19 chains. Longest chain 25 peptides. Score 0.581 Round 3: 171 peptides, 19 chains. Longest chain 20 peptides. Score 0.574 Round 4: 173 peptides, 17 chains. Longest chain 36 peptides. Score 0.610 Round 5: 172 peptides, 16 chains. Longest chain 36 peptides. Score 0.622 Taking the results from Round 5 Chains 16, Residues 156, Estimated correctness of the model 8.8 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 4222 reflections ( 98.37 % complete ) and 4215 restraints for refining 1938 atoms. 3591 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2482 (Rfree = 0.000) for 1938 atoms. Found 9 (9 requested) and removed 10 (5 requested) atoms. Cycle 27: After refmac, R = 0.2476 (Rfree = 0.000) for 1926 atoms. Found 9 (9 requested) and removed 7 (5 requested) atoms. Cycle 28: After refmac, R = 0.2479 (Rfree = 0.000) for 1915 atoms. Found 9 (9 requested) and removed 7 (5 requested) atoms. Cycle 29: After refmac, R = 0.2402 (Rfree = 0.000) for 1906 atoms. Found 9 (9 requested) and removed 7 (5 requested) atoms. Cycle 30: After refmac, R = 0.2318 (Rfree = 0.000) for 1901 atoms. Found 9 (9 requested) and removed 13 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.58 2.96 Search for helices and strands: 0 residues in 0 chains, 1952 seeds are put forward NCS extension: 22 residues added (15 deleted due to clashes), 1974 seeds are put forward Round 1: 135 peptides, 21 chains. Longest chain 16 peptides. Score 0.409 Round 2: 158 peptides, 19 chains. Longest chain 19 peptides. Score 0.531 Round 3: 158 peptides, 17 chains. Longest chain 24 peptides. Score 0.563 Round 4: 165 peptides, 18 chains. Longest chain 32 peptides. Score 0.570 Round 5: 177 peptides, 17 chains. Longest chain 48 peptides. Score 0.622 Taking the results from Round 5 Chains 19, Residues 160, Estimated correctness of the model 8.8 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 4222 reflections ( 98.37 % complete ) and 4044 restraints for refining 1938 atoms. 3377 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2403 (Rfree = 0.000) for 1938 atoms. Found 9 (9 requested) and removed 15 (5 requested) atoms. Cycle 32: After refmac, R = 0.2246 (Rfree = 0.000) for 1921 atoms. Found 9 (9 requested) and removed 12 (5 requested) atoms. Cycle 33: After refmac, R = 0.2191 (Rfree = 0.000) for 1916 atoms. Found 9 (9 requested) and removed 9 (5 requested) atoms. Cycle 34: After refmac, R = 0.2174 (Rfree = 0.000) for 1913 atoms. Found 9 (9 requested) and removed 6 (5 requested) atoms. Cycle 35: After refmac, R = 0.2222 (Rfree = 0.000) for 1916 atoms. Found 9 (9 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.60 2.97 Search for helices and strands: 0 residues in 0 chains, 1970 seeds are put forward NCS extension: 59 residues added (17 deleted due to clashes), 2029 seeds are put forward Round 1: 153 peptides, 20 chains. Longest chain 17 peptides. Score 0.496 Round 2: 174 peptides, 18 chains. Longest chain 25 peptides. Score 0.599 Round 3: 168 peptides, 17 chains. Longest chain 28 peptides. Score 0.595 Round 4: 173 peptides, 19 chains. Longest chain 34 peptides. Score 0.581 Round 5: 171 peptides, 17 chains. Longest chain 48 peptides. Score 0.604 Taking the results from Round 5 Chains 19, Residues 154, Estimated correctness of the model 0.7 % 3 chains (65 residues) have been docked in sequence ------------------------------------------------------ 4222 reflections ( 98.37 % complete ) and 3648 restraints for refining 1939 atoms. 2798 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2544 (Rfree = 0.000) for 1939 atoms. Found 9 (9 requested) and removed 17 (5 requested) atoms. Cycle 37: After refmac, R = 0.2320 (Rfree = 0.000) for 1911 atoms. Found 9 (9 requested) and removed 10 (5 requested) atoms. Cycle 38: After refmac, R = 0.2294 (Rfree = 0.000) for 1900 atoms. Found 9 (9 requested) and removed 9 (5 requested) atoms. Cycle 39: After refmac, R = 0.2287 (Rfree = 0.000) for 1894 atoms. Found 9 (9 requested) and removed 8 (5 requested) atoms. Cycle 40: After refmac, R = 0.2260 (Rfree = 0.000) for 1890 atoms. Found 9 (9 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.63 3.00 Search for helices and strands: 0 residues in 0 chains, 1926 seeds are put forward NCS extension: 70 residues added (9 deleted due to clashes), 1996 seeds are put forward Round 1: 141 peptides, 22 chains. Longest chain 16 peptides. Score 0.415 Round 2: 166 peptides, 19 chains. Longest chain 26 peptides. Score 0.558 Round 3: 164 peptides, 19 chains. Longest chain 23 peptides. Score 0.551 Round 4: 164 peptides, 17 chains. Longest chain 17 peptides. Score 0.582 Round 5: 170 peptides, 18 chains. Longest chain 28 peptides. Score 0.586 Taking the results from Round 5 Chains 21, Residues 152, Estimated correctness of the model 0.0 % 2 chains (21 residues) have been docked in sequence ------------------------------------------------------ 4222 reflections ( 98.37 % complete ) and 4076 restraints for refining 1939 atoms. 3425 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2564 (Rfree = 0.000) for 1939 atoms. Found 9 (9 requested) and removed 19 (5 requested) atoms. Cycle 42: After refmac, R = 0.2344 (Rfree = 0.000) for 1919 atoms. Found 9 (9 requested) and removed 8 (5 requested) atoms. Cycle 43: After refmac, R = 0.2338 (Rfree = 0.000) for 1917 atoms. Found 9 (9 requested) and removed 18 (5 requested) atoms. Cycle 44: After refmac, R = 0.2287 (Rfree = 0.000) for 1902 atoms. Found 9 (9 requested) and removed 11 (5 requested) atoms. Cycle 45: After refmac, R = 0.2312 (Rfree = 0.000) for 1898 atoms. Found 9 (9 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.61 2.98 Search for helices and strands: 0 residues in 0 chains, 1943 seeds are put forward NCS extension: 0 residues added, 1943 seeds are put forward Round 1: 135 peptides, 19 chains. Longest chain 17 peptides. Score 0.445 Round 2: 156 peptides, 21 chains. Longest chain 16 peptides. Score 0.491 Round 3: 150 peptides, 20 chains. Longest chain 16 peptides. Score 0.485 Round 4: 166 peptides, 23 chains. Longest chain 20 peptides. Score 0.494 Round 5: 152 peptides, 21 chains. Longest chain 19 peptides. Score 0.476 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 24, Residues 143, Estimated correctness of the model 0.0 % 2 chains (19 residues) have been docked in sequence Sequence coverage is 13 % Consider running further cycles of model building using 2o8q-3_warpNtrace.pdb as input Building loops using Loopy2018 24 chains (143 residues) following loop building 2 chains (19 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4222 reflections ( 98.37 % complete ) and 4117 restraints for refining 1939 atoms. 3487 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2466 (Rfree = 0.000) for 1939 atoms. Found 0 (9 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.2499 (Rfree = 0.000) for 1924 atoms. Found 0 (9 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.2346 (Rfree = 0.000) for 1911 atoms. Found 0 (9 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.2270 (Rfree = 0.000) for 1903 atoms. TimeTaking 30.47