null Mon 24 Dec 07:30:54 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-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2o8q-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2o8q-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2o8q-3.8-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-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2o8q-3.8-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 07:30:59 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-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2o8q-3.8-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 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-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-3.8-parrot-noncs.fasta_lf Building free atoms model in initial map for 2144 target number of atoms Had to go as low as 0.90 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 2359 atoms. Observations/parameters ratio is 0.45 ------------------------------------------------------ Starting model: R = 0.3232 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3102 (Rfree = 0.000) for 2359 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.59 2.96 Search for helices and strands: 0 residues in 0 chains, 2390 seeds are put forward NCS extension: 0 residues added, 2390 seeds are put forward Round 1: 154 peptides, 29 chains. Longest chain 10 peptides. Score 0.343 Round 2: 175 peptides, 22 chains. Longest chain 21 peptides. Score 0.542 Round 3: 202 peptides, 19 chains. Longest chain 19 peptides. Score 0.665 Round 4: 198 peptides, 20 chains. Longest chain 36 peptides. Score 0.642 Round 5: 200 peptides, 18 chains. Longest chain 34 peptides. Score 0.673 Taking the results from Round 5 Chains 21, Residues 182, Estimated correctness of the model 30.0 % 2 chains (25 residues) have been docked in sequence ------------------------------------------------------ 4222 reflections ( 98.37 % complete ) and 3872 restraints for refining 1936 atoms. 3088 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2565 (Rfree = 0.000) for 1936 atoms. Found 7 (10 requested) and removed 18 (5 requested) atoms. Cycle 2: After refmac, R = 0.2524 (Rfree = 0.000) for 1891 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. Cycle 3: After refmac, R = 0.2535 (Rfree = 0.000) for 1859 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. Cycle 4: After refmac, R = 0.2444 (Rfree = 0.000) for 1845 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 5: After refmac, R = 0.2464 (Rfree = 0.000) for 1835 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.61 2.98 Search for helices and strands: 0 residues in 0 chains, 1903 seeds are put forward NCS extension: 19 residues added (5 deleted due to clashes), 1922 seeds are put forward Round 1: 157 peptides, 25 chains. Longest chain 13 peptides. Score 0.426 Round 2: 182 peptides, 22 chains. Longest chain 16 peptides. Score 0.565 Round 3: 185 peptides, 20 chains. Longest chain 19 peptides. Score 0.604 Round 4: 183 peptides, 23 chains. Longest chain 17 peptides. Score 0.553 Round 5: 180 peptides, 21 chains. Longest chain 27 peptides. Score 0.574 Taking the results from Round 3 Chains 20, Residues 165, Estimated correctness of the model 0.7 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4222 reflections ( 98.37 % complete ) and 3960 restraints for refining 1939 atoms. 3302 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2499 (Rfree = 0.000) for 1939 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. Cycle 7: After refmac, R = 0.2415 (Rfree = 0.000) for 1913 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. Cycle 8: After refmac, R = 0.2347 (Rfree = 0.000) for 1907 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 9: After refmac, R = 0.2279 (Rfree = 0.000) for 1892 atoms. Found 10 (10 requested) and removed 15 (5 requested) atoms. Cycle 10: After refmac, R = 0.2222 (Rfree = 0.000) for 1877 atoms. Found 9 (10 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.72 3.07 Search for helices and strands: 0 residues in 0 chains, 1950 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 1967 seeds are put forward Round 1: 163 peptides, 24 chains. Longest chain 18 peptides. Score 0.467 Round 2: 177 peptides, 20 chains. Longest chain 20 peptides. Score 0.579 Round 3: 175 peptides, 20 chains. Longest chain 33 peptides. Score 0.572 Round 4: 173 peptides, 20 chains. Longest chain 29 peptides. Score 0.566 Round 5: 177 peptides, 19 chains. Longest chain 28 peptides. Score 0.593 Taking the results from Round 5 Chains 21, Residues 158, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 4222 reflections ( 98.37 % complete ) and 4050 restraints for refining 1939 atoms. 3407 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2420 (Rfree = 0.000) for 1939 atoms. Found 10 (10 requested) and removed 17 (5 requested) atoms. Cycle 12: After refmac, R = 0.2465 (Rfree = 0.000) for 1917 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 13: After refmac, R = 0.2540 (Rfree = 0.000) for 1907 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. Cycle 14: After refmac, R = 0.2400 (Rfree = 0.000) for 1896 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. Cycle 15: After refmac, R = 0.2429 (Rfree = 0.000) for 1893 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.72 3.07 Search for helices and strands: 0 residues in 0 chains, 1971 seeds are put forward NCS extension: 29 residues added (2 deleted due to clashes), 2000 seeds are put forward Round 1: 150 peptides, 22 chains. Longest chain 18 peptides. Score 0.451 Round 2: 156 peptides, 23 chains. Longest chain 19 peptides. Score 0.457 Round 3: 168 peptides, 25 chains. Longest chain 18 peptides. Score 0.469 Round 4: 170 peptides, 23 chains. Longest chain 27 peptides. Score 0.509 Round 5: 194 peptides, 23 chains. Longest chain 22 peptides. Score 0.589 Taking the results from Round 5 Chains 24, Residues 171, Estimated correctness of the model 0.0 % 3 chains (19 residues) have been docked in sequence ------------------------------------------------------ 4222 reflections ( 98.37 % complete ) and 3918 restraints for refining 1939 atoms. 3207 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2580 (Rfree = 0.000) for 1939 atoms. Found 10 (10 requested) and removed 14 (5 requested) atoms. Cycle 17: After refmac, R = 0.2526 (Rfree = 0.000) for 1901 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 18: After refmac, R = 0.2412 (Rfree = 0.000) for 1887 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. Cycle 19: After refmac, R = 0.2234 (Rfree = 0.000) for 1880 atoms. Found 9 (10 requested) and removed 12 (5 requested) atoms. Cycle 20: After refmac, R = 0.2358 (Rfree = 0.000) for 1863 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.71 3.06 Search for helices and strands: 0 residues in 0 chains, 1903 seeds are put forward NCS extension: 35 residues added (1 deleted due to clashes), 1938 seeds are put forward Round 1: 160 peptides, 25 chains. Longest chain 15 peptides. Score 0.438 Round 2: 166 peptides, 22 chains. Longest chain 21 peptides. Score 0.510 Round 3: 162 peptides, 21 chains. Longest chain 21 peptides. Score 0.512 Round 4: 160 peptides, 20 chains. Longest chain 19 peptides. Score 0.522 Round 5: 170 peptides, 19 chains. Longest chain 22 peptides. Score 0.571 Taking the results from Round 5 Chains 19, Residues 151, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4222 reflections ( 98.37 % complete ) and 4303 restraints for refining 1939 atoms. 3710 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2630 (Rfree = 0.000) for 1939 atoms. Found 10 (10 requested) and removed 13 (5 requested) atoms. Cycle 22: After refmac, R = 0.2601 (Rfree = 0.000) for 1924 atoms. Found 10 (10 requested) and removed 17 (5 requested) atoms. Cycle 23: After refmac, R = 0.2565 (Rfree = 0.000) for 1907 atoms. Found 10 (10 requested) and removed 16 (5 requested) atoms. Cycle 24: After refmac, R = 0.2549 (Rfree = 0.000) for 1898 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. Cycle 25: After refmac, R = 0.2510 (Rfree = 0.000) for 1889 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.57 2.95 Search for helices and strands: 0 residues in 0 chains, 1942 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 1966 seeds are put forward Round 1: 151 peptides, 25 chains. Longest chain 12 peptides. Score 0.402 Round 2: 159 peptides, 21 chains. Longest chain 16 peptides. Score 0.502 Round 3: 156 peptides, 18 chains. Longest chain 21 peptides. Score 0.540 Round 4: 165 peptides, 22 chains. Longest chain 16 peptides. Score 0.507 Round 5: 169 peptides, 22 chains. Longest chain 23 peptides. Score 0.521 Taking the results from Round 3 Chains 18, Residues 138, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4222 reflections ( 98.37 % complete ) and 4335 restraints for refining 1938 atoms. 3801 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2538 (Rfree = 0.000) for 1938 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 27: After refmac, R = 0.2457 (Rfree = 0.000) for 1926 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. Cycle 28: After refmac, R = 0.2366 (Rfree = 0.000) for 1920 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 29: After refmac, R = 0.2415 (Rfree = 0.000) for 1911 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 30: After refmac, R = 0.2285 (Rfree = 0.000) for 1906 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.56 2.94 Search for helices and strands: 0 residues in 0 chains, 1974 seeds are put forward NCS extension: 39 residues added (2 deleted due to clashes), 2013 seeds are put forward Round 1: 151 peptides, 28 chains. Longest chain 11 peptides. Score 0.348 Round 2: 173 peptides, 26 chains. Longest chain 22 peptides. Score 0.471 Round 3: 159 peptides, 22 chains. Longest chain 24 peptides. Score 0.485 Round 4: 177 peptides, 23 chains. Longest chain 24 peptides. Score 0.533 Round 5: 171 peptides, 24 chains. Longest chain 20 peptides. Score 0.496 Taking the results from Round 4 Chains 23, Residues 154, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4222 reflections ( 98.37 % complete ) and 4300 restraints for refining 1938 atoms. 3707 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2611 (Rfree = 0.000) for 1938 atoms. Found 10 (10 requested) and removed 14 (5 requested) atoms. Cycle 32: After refmac, R = 0.2535 (Rfree = 0.000) for 1919 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 33: After refmac, R = 0.2208 (Rfree = 0.000) for 1911 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. Cycle 34: After refmac, R = 0.2127 (Rfree = 0.000) for 1910 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 35: After refmac, R = 0.2107 (Rfree = 0.000) for 1907 atoms. Found 5 (10 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.58 2.96 Search for helices and strands: 0 residues in 0 chains, 1969 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 1988 seeds are put forward Round 1: 172 peptides, 30 chains. Longest chain 21 peptides. Score 0.400 Round 2: 189 peptides, 23 chains. Longest chain 30 peptides. Score 0.573 Round 3: 166 peptides, 24 chains. Longest chain 16 peptides. Score 0.478 Round 4: 171 peptides, 20 chains. Longest chain 20 peptides. Score 0.559 Round 5: 188 peptides, 21 chains. Longest chain 44 peptides. Score 0.599 Taking the results from Round 5 Chains 21, Residues 167, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4222 reflections ( 98.37 % complete ) and 4146 restraints for refining 1939 atoms. 3469 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2557 (Rfree = 0.000) for 1939 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 37: After refmac, R = 0.2507 (Rfree = 0.000) for 1932 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. Cycle 38: After refmac, R = 0.2436 (Rfree = 0.000) for 1922 atoms. Found 9 (10 requested) and removed 10 (5 requested) atoms. Cycle 39: After refmac, R = 0.2408 (Rfree = 0.000) for 1917 atoms. Found 8 (10 requested) and removed 9 (5 requested) atoms. Cycle 40: After refmac, R = 0.2358 (Rfree = 0.000) for 1911 atoms. Found 7 (10 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.68 3.04 Search for helices and strands: 0 residues in 0 chains, 1962 seeds are put forward NCS extension: 27 residues added (14 deleted due to clashes), 1989 seeds are put forward Round 1: 130 peptides, 21 chains. Longest chain 11 peptides. Score 0.388 Round 2: 148 peptides, 21 chains. Longest chain 15 peptides. Score 0.461 Round 3: 163 peptides, 19 chains. Longest chain 23 peptides. Score 0.548 Round 4: 170 peptides, 22 chains. Longest chain 19 peptides. Score 0.525 Round 5: 166 peptides, 20 chains. Longest chain 15 peptides. Score 0.542 Taking the results from Round 3 Chains 22, Residues 144, Estimated correctness of the model 0.0 % 4 chains (29 residues) have been docked in sequence ------------------------------------------------------ 4222 reflections ( 98.37 % complete ) and 4155 restraints for refining 1939 atoms. 3522 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2529 (Rfree = 0.000) for 1939 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. Cycle 42: After refmac, R = 0.2429 (Rfree = 0.000) for 1921 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. Cycle 43: After refmac, R = 0.2385 (Rfree = 0.000) for 1919 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 44: After refmac, R = 0.2360 (Rfree = 0.000) for 1914 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. Cycle 45: After refmac, R = 0.2352 (Rfree = 0.000) for 1906 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.66 3.02 Search for helices and strands: 0 residues in 0 chains, 1959 seeds are put forward NCS extension: 24 residues added (3 deleted due to clashes), 1983 seeds are put forward Round 1: 133 peptides, 27 chains. Longest chain 8 peptides. Score 0.288 Round 2: 149 peptides, 23 chains. Longest chain 20 peptides. Score 0.430 Round 3: 165 peptides, 23 chains. Longest chain 21 peptides. Score 0.491 Round 4: 149 peptides, 20 chains. Longest chain 21 peptides. Score 0.482 Round 5: 148 peptides, 18 chains. Longest chain 22 peptides. Score 0.512 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 18, Residues 130, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence Sequence coverage is 4 % Consider running further cycles of model building using 2o8q-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4222 reflections ( 98.37 % complete ) and 4411 restraints for refining 1939 atoms. 3893 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2605 (Rfree = 0.000) for 1939 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.2522 (Rfree = 0.000) for 1924 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.2472 (Rfree = 0.000) for 1912 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.2468 (Rfree = 0.000) for 1901 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:01:00 GMT 2018 Job finished. TimeTaking 30.1 Used memory is bytes: 20455000