Mon 24 Dec 07:36:25 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 2o1q-4.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2o1q-4.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2o1q-4.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2o1q-4.0-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/2o1q-4.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2o1q-4.0-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 07:36:30 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/2o1q-4.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2o1q-4.0-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 166 and 0 Target number of residues in the AU: 166 Target solvent content: 0.6485 Checking the provided sequence file Detected sequence length: 145 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 290 Adjusted target solvent content: 0.39 Input MTZ file: 2o1q-4.0-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: 92 Cell parameters: 61.883 61.883 133.475 90.000 90.000 90.000 Input sequence file: 2o1q-4.0-parrot-noncs.fasta_lf Building free atoms model in initial map for 2320 target number of atoms Had to go as low as 0.70 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: 56.142 4.002 Wilson plot Bfac: 76.90 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 2457 reflections ( 99.59 % complete ) and 0 restraints for refining 2589 atoms. Observations/parameters ratio is 0.24 ------------------------------------------------------ Starting model: R = 0.3654 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3233 (Rfree = 0.000) for 2589 atoms. Found 12 (12 requested) and removed 41 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.56 4.13 Search for helices and strands: 0 residues in 0 chains, 2580 seeds are put forward NCS extension: 0 residues added, 2580 seeds are put forward Round 1: 61 peptides, 14 chains. Longest chain 7 peptides. Score 0.208 Round 2: 89 peptides, 20 chains. Longest chain 8 peptides. Score 0.234 Round 3: 92 peptides, 20 chains. Longest chain 8 peptides. Score 0.255 Round 4: 101 peptides, 20 chains. Longest chain 13 peptides. Score 0.318 Round 5: 101 peptides, 19 chains. Longest chain 13 peptides. Score 0.346 Taking the results from Round 5 Chains 19, Residues 82, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 2457 reflections ( 99.59 % complete ) and 4996 restraints for refining 2094 atoms. 4664 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2739 (Rfree = 0.000) for 2094 atoms. Found 8 (9 requested) and removed 11 (4 requested) atoms. Cycle 2: After refmac, R = 0.2666 (Rfree = 0.000) for 2062 atoms. Found 9 (9 requested) and removed 14 (4 requested) atoms. Cycle 3: After refmac, R = 0.2548 (Rfree = 0.000) for 2040 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 4: After refmac, R = 0.2403 (Rfree = 0.000) for 2025 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 5: After refmac, R = 0.1860 (Rfree = 0.000) for 2015 atoms. Found 5 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.63 4.21 Search for helices and strands: 0 residues in 0 chains, 2056 seeds are put forward NCS extension: 0 residues added, 2056 seeds are put forward Round 1: 73 peptides, 17 chains. Longest chain 6 peptides. Score 0.206 Round 2: 95 peptides, 19 chains. Longest chain 9 peptides. Score 0.306 Round 3: 94 peptides, 16 chains. Longest chain 12 peptides. Score 0.384 Round 4: 94 peptides, 17 chains. Longest chain 9 peptides. Score 0.356 Round 5: 101 peptides, 20 chains. Longest chain 8 peptides. Score 0.318 Taking the results from Round 3 Chains 16, Residues 78, Estimated correctness of the model 0.0 % 4 chains (17 residues) have been docked in sequence ------------------------------------------------------ 2457 reflections ( 99.59 % complete ) and 4288 restraints for refining 1874 atoms. 3940 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2417 (Rfree = 0.000) for 1874 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 7: After refmac, R = 0.2563 (Rfree = 0.000) for 1860 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 8: After refmac, R = 0.2621 (Rfree = 0.000) for 1851 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 9: After refmac, R = 0.2719 (Rfree = 0.000) for 1843 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 10: After refmac, R = 0.2708 (Rfree = 0.000) for 1831 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.58 4.16 Search for helices and strands: 0 residues in 0 chains, 1885 seeds are put forward NCS extension: 0 residues added, 1885 seeds are put forward Round 1: 81 peptides, 16 chains. Longest chain 8 peptides. Score 0.296 Round 2: 97 peptides, 17 chains. Longest chain 10 peptides. Score 0.376 Round 3: 94 peptides, 18 chains. Longest chain 9 peptides. Score 0.328 Round 4: 102 peptides, 16 chains. Longest chain 10 peptides. Score 0.435 Round 5: 95 peptides, 17 chains. Longest chain 8 peptides. Score 0.363 Taking the results from Round 4 Chains 16, Residues 86, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 2457 reflections ( 99.59 % complete ) and 3755 restraints for refining 1736 atoms. 3410 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2551 (Rfree = 0.000) for 1736 atoms. Found 8 (8 requested) and removed 16 (4 requested) atoms. Cycle 12: After refmac, R = 0.2415 (Rfree = 0.000) for 1714 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 13: After refmac, R = 0.2275 (Rfree = 0.000) for 1700 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 14: After refmac, R = 0.2260 (Rfree = 0.000) for 1689 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. Cycle 15: After refmac, R = 0.1755 (Rfree = 0.000) for 1682 atoms. Found 3 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.55 4.12 Search for helices and strands: 0 residues in 0 chains, 1718 seeds are put forward NCS extension: 0 residues added, 1718 seeds are put forward Round 1: 88 peptides, 20 chains. Longest chain 6 peptides. Score 0.227 Round 2: 96 peptides, 19 chains. Longest chain 8 peptides. Score 0.312 Round 3: 100 peptides, 19 chains. Longest chain 8 peptides. Score 0.339 Round 4: 108 peptides, 19 chains. Longest chain 9 peptides. Score 0.391 Round 5: 116 peptides, 20 chains. Longest chain 9 peptides. Score 0.414 Taking the results from Round 5 Chains 20, Residues 96, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 2457 reflections ( 99.59 % complete ) and 3805 restraints for refining 1781 atoms. 3427 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2483 (Rfree = 0.000) for 1781 atoms. Found 8 (8 requested) and removed 18 (4 requested) atoms. Cycle 17: After refmac, R = 0.1907 (Rfree = 0.000) for 1749 atoms. Found 3 (8 requested) and removed 8 (4 requested) atoms. Cycle 18: After refmac, R = 0.2253 (Rfree = 0.000) for 1737 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. Cycle 19: After refmac, R = 0.2234 (Rfree = 0.000) for 1735 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 20: After refmac, R = 0.2230 (Rfree = 0.000) for 1729 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.58 4.16 Search for helices and strands: 0 residues in 0 chains, 1775 seeds are put forward NCS extension: 0 residues added, 1775 seeds are put forward Round 1: 69 peptides, 16 chains. Longest chain 6 peptides. Score 0.207 Round 2: 85 peptides, 16 chains. Longest chain 8 peptides. Score 0.324 Round 3: 97 peptides, 17 chains. Longest chain 14 peptides. Score 0.376 Round 4: 103 peptides, 19 chains. Longest chain 9 peptides. Score 0.359 Round 5: 94 peptides, 16 chains. Longest chain 14 peptides. Score 0.384 Taking the results from Round 5 Chains 17, Residues 78, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 2457 reflections ( 99.59 % complete ) and 3823 restraints for refining 1764 atoms. 3501 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2448 (Rfree = 0.000) for 1764 atoms. Found 8 (8 requested) and removed 17 (4 requested) atoms. Cycle 22: After refmac, R = 0.2396 (Rfree = 0.000) for 1745 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 23: After refmac, R = 0.2248 (Rfree = 0.000) for 1738 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. Cycle 24: After refmac, R = 0.1645 (Rfree = 0.000) for 1728 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 25: After refmac, R = 0.1528 (Rfree = 0.000) for 1727 atoms. Found 7 (8 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.57 4.14 Search for helices and strands: 0 residues in 0 chains, 1762 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 1777 seeds are put forward Round 1: 81 peptides, 19 chains. Longest chain 5 peptides. Score 0.205 Round 2: 88 peptides, 18 chains. Longest chain 8 peptides. Score 0.286 Round 3: 92 peptides, 19 chains. Longest chain 8 peptides. Score 0.285 Round 4: 96 peptides, 19 chains. Longest chain 9 peptides. Score 0.312 Round 5: 95 peptides, 17 chains. Longest chain 9 peptides. Score 0.363 Taking the results from Round 5 Chains 17, Residues 78, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2457 reflections ( 99.59 % complete ) and 4157 restraints for refining 1826 atoms. 3862 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2170 (Rfree = 0.000) for 1826 atoms. Found 6 (8 requested) and removed 23 (4 requested) atoms. Cycle 27: After refmac, R = 0.2235 (Rfree = 0.000) for 1803 atoms. Found 8 (8 requested) and removed 16 (4 requested) atoms. Cycle 28: After refmac, R = 0.2043 (Rfree = 0.000) for 1787 atoms. Found 8 (8 requested) and removed 14 (4 requested) atoms. Cycle 29: After refmac, R = 0.2063 (Rfree = 0.000) for 1775 atoms. Found 8 (8 requested) and removed 15 (4 requested) atoms. Cycle 30: After refmac, R = 0.2230 (Rfree = 0.000) for 1765 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.46 4.02 Search for helices and strands: 0 residues in 0 chains, 1818 seeds are put forward NCS extension: 0 residues added, 1818 seeds are put forward Round 1: 74 peptides, 18 chains. Longest chain 5 peptides. Score 0.182 Round 2: 86 peptides, 17 chains. Longest chain 8 peptides. Score 0.302 Round 3: 92 peptides, 18 chains. Longest chain 9 peptides. Score 0.314 Round 4: 96 peptides, 18 chains. Longest chain 9 peptides. Score 0.341 Round 5: 107 peptides, 20 chains. Longest chain 10 peptides. Score 0.357 Taking the results from Round 5 Chains 20, Residues 87, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 2457 reflections ( 99.59 % complete ) and 4025 restraints for refining 1840 atoms. 3673 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1957 (Rfree = 0.000) for 1840 atoms. Found 6 (8 requested) and removed 24 (4 requested) atoms. Cycle 32: After refmac, R = 0.2292 (Rfree = 0.000) for 1815 atoms. Found 8 (8 requested) and removed 20 (4 requested) atoms. Cycle 33: After refmac, R = 0.1899 (Rfree = 0.000) for 1798 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 34: After refmac, R = 0.2122 (Rfree = 0.000) for 1789 atoms. Found 8 (8 requested) and removed 14 (4 requested) atoms. Cycle 35: After refmac, R = 0.1920 (Rfree = 0.000) for 1779 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.47 4.03 Search for helices and strands: 0 residues in 0 chains, 1824 seeds are put forward NCS extension: 0 residues added, 1824 seeds are put forward Round 1: 71 peptides, 17 chains. Longest chain 5 peptides. Score 0.191 Round 2: 86 peptides, 18 chains. Longest chain 8 peptides. Score 0.272 Round 3: 92 peptides, 19 chains. Longest chain 8 peptides. Score 0.285 Round 4: 91 peptides, 18 chains. Longest chain 9 peptides. Score 0.307 Round 5: 82 peptides, 15 chains. Longest chain 11 peptides. Score 0.333 Taking the results from Round 5 Chains 15, Residues 67, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 2457 reflections ( 99.59 % complete ) and 4058 restraints for refining 1797 atoms. 3796 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2362 (Rfree = 0.000) for 1797 atoms. Found 8 (8 requested) and removed 15 (4 requested) atoms. Cycle 37: After refmac, R = 0.2195 (Rfree = 0.000) for 1780 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. Cycle 38: After refmac, R = 0.2239 (Rfree = 0.000) for 1771 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. Cycle 39: After refmac, R = 0.2013 (Rfree = 0.000) for 1762 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. Cycle 40: After refmac, R = 0.2230 (Rfree = 0.000) for 1761 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.48 4.04 Search for helices and strands: 0 residues in 0 chains, 1800 seeds are put forward NCS extension: 4 residues added (0 deleted due to clashes), 1804 seeds are put forward Round 1: 62 peptides, 15 chains. Longest chain 5 peptides. Score 0.183 Round 2: 77 peptides, 16 chains. Longest chain 8 peptides. Score 0.267 Round 3: 83 peptides, 17 chains. Longest chain 9 peptides. Score 0.280 Round 4: 85 peptides, 16 chains. Longest chain 9 peptides. Score 0.324 Round 5: 75 peptides, 16 chains. Longest chain 7 peptides. Score 0.253 Taking the results from Round 4 Chains 16, Residues 69, Estimated correctness of the model 0.0 % 2 chains (10 residues) have been docked in sequence ------------------------------------------------------ 2457 reflections ( 99.59 % complete ) and 3915 restraints for refining 1766 atoms. 3629 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2235 (Rfree = 0.000) for 1766 atoms. Found 8 (8 requested) and removed 26 (4 requested) atoms. Cycle 42: After refmac, R = 0.2023 (Rfree = 0.000) for 1742 atoms. Found 7 (8 requested) and removed 13 (4 requested) atoms. Cycle 43: After refmac, R = 0.1806 (Rfree = 0.000) for 1731 atoms. Found 7 (8 requested) and removed 9 (4 requested) atoms. Cycle 44: After refmac, R = 0.1761 (Rfree = 0.000) for 1728 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 45: After refmac, R = 0.1802 (Rfree = 0.000) for 1729 atoms. Found 6 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.39 3.93 Search for helices and strands: 0 residues in 0 chains, 1745 seeds are put forward NCS extension: 0 residues added, 1745 seeds are put forward Round 1: 74 peptides, 16 chains. Longest chain 7 peptides. Score 0.245 Round 2: 80 peptides, 16 chains. Longest chain 8 peptides. Score 0.289 Round 3: 76 peptides, 14 chains. Longest chain 10 peptides. Score 0.322 Round 4: 71 peptides, 14 chains. Longest chain 8 peptides. Score 0.285 Round 5: 80 peptides, 16 chains. Longest chain 8 peptides. Score 0.289 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 14, Residues 62, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2o1q-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2457 reflections ( 99.59 % complete ) and 3948 restraints for refining 1785 atoms. 3714 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2198 (Rfree = 0.000) for 1785 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.2243 (Rfree = 0.000) for 1774 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.2381 (Rfree = 0.000) for 1763 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.2254 (Rfree = 0.000) for 1755 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Writing output files ... TimeTaking 26.57