null Mon 24 Dec 07:40:38 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 1zko-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1zko-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1zko-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1zko-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/1zko-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1zko-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 07:40:43 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/1zko-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1zko-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 172 and 0 Target number of residues in the AU: 172 Target solvent content: 0.6187 Checking the provided sequence file Detected sequence length: 136 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 272 Adjusted target solvent content: 0.40 Input MTZ file: 1zko-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: 19 Cell parameters: 54.005 65.321 69.197 90.000 90.000 90.000 Input sequence file: 1zko-3.8-parrot-noncs.fasta_lf Building free atoms model in initial map for 2176 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: 47.500 3.801 Wilson plot Bfac: 60.61 2442 reflections ( 92.68 % complete ) and 0 restraints for refining 2419 atoms. Observations/parameters ratio is 0.25 ------------------------------------------------------ Starting model: R = 0.3627 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3465 (Rfree = 0.000) for 2419 atoms. Found 12 (13 requested) and removed 39 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.28 3.75 Search for helices and strands: 0 residues in 0 chains, 2404 seeds are put forward NCS extension: 0 residues added, 2404 seeds are put forward Round 1: 47 peptides, 10 chains. Longest chain 7 peptides. Score 0.233 Round 2: 64 peptides, 13 chains. Longest chain 7 peptides. Score 0.268 Round 3: 70 peptides, 13 chains. Longest chain 8 peptides. Score 0.314 Round 4: 65 peptides, 11 chains. Longest chain 8 peptides. Score 0.342 Round 5: 71 peptides, 13 chains. Longest chain 10 peptides. Score 0.322 Taking the results from Round 4 Chains 11, Residues 54, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2442 reflections ( 92.68 % complete ) and 4787 restraints for refining 1968 atoms. 4582 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2923 (Rfree = 0.000) for 1968 atoms. Found 10 (10 requested) and removed 24 (5 requested) atoms. Cycle 2: After refmac, R = 0.2798 (Rfree = 0.000) for 1938 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 3: After refmac, R = 0.2186 (Rfree = 0.000) for 1929 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 4: After refmac, R = 0.2586 (Rfree = 0.000) for 1923 atoms. Found 10 (10 requested) and removed 16 (5 requested) atoms. Cycle 5: After refmac, R = 0.2537 (Rfree = 0.000) for 1908 atoms. Found 10 (10 requested) and removed 28 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.41 3.90 Search for helices and strands: 0 residues in 0 chains, 1906 seeds are put forward NCS extension: 0 residues added, 1906 seeds are put forward Round 1: 76 peptides, 16 chains. Longest chain 7 peptides. Score 0.263 Round 2: 98 peptides, 18 chains. Longest chain 11 peptides. Score 0.361 Round 3: 92 peptides, 16 chains. Longest chain 11 peptides. Score 0.379 Round 4: 95 peptides, 17 chains. Longest chain 13 peptides. Score 0.370 Round 5: 94 peptides, 17 chains. Longest chain 10 peptides. Score 0.363 Taking the results from Round 3 Chains 16, Residues 76, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2442 reflections ( 92.68 % complete ) and 3914 restraints for refining 1745 atoms. 3626 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2430 (Rfree = 0.000) for 1745 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 7: After refmac, R = 0.2387 (Rfree = 0.000) for 1730 atoms. Found 9 (9 requested) and removed 14 (4 requested) atoms. Cycle 8: After refmac, R = 0.1946 (Rfree = 0.000) for 1715 atoms. Found 4 (9 requested) and removed 10 (4 requested) atoms. Cycle 9: After refmac, R = 0.2097 (Rfree = 0.000) for 1702 atoms. Found 9 (9 requested) and removed 5 (4 requested) atoms. Cycle 10: After refmac, R = 0.1944 (Rfree = 0.000) for 1703 atoms. Found 2 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.36 3.85 Search for helices and strands: 0 residues in 0 chains, 1731 seeds are put forward NCS extension: 0 residues added, 1731 seeds are put forward Round 1: 85 peptides, 16 chains. Longest chain 11 peptides. Score 0.330 Round 2: 91 peptides, 16 chains. Longest chain 12 peptides. Score 0.372 Round 3: 90 peptides, 14 chains. Longest chain 15 peptides. Score 0.424 Round 4: 91 peptides, 13 chains. Longest chain 12 peptides. Score 0.459 Round 5: 92 peptides, 14 chains. Longest chain 14 peptides. Score 0.437 Taking the results from Round 4 Chains 13, Residues 78, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2442 reflections ( 92.68 % complete ) and 3901 restraints for refining 1773 atoms. 3602 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2800 (Rfree = 0.000) for 1773 atoms. Found 9 (9 requested) and removed 17 (4 requested) atoms. Cycle 12: After refmac, R = 0.2526 (Rfree = 0.000) for 1757 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 13: After refmac, R = 0.2751 (Rfree = 0.000) for 1746 atoms. Found 9 (9 requested) and removed 14 (4 requested) atoms. Cycle 14: After refmac, R = 0.2489 (Rfree = 0.000) for 1730 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 15: After refmac, R = 0.2838 (Rfree = 0.000) for 1721 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.34 3.82 Search for helices and strands: 0 residues in 0 chains, 1751 seeds are put forward NCS extension: 0 residues added, 1751 seeds are put forward Round 1: 88 peptides, 18 chains. Longest chain 8 peptides. Score 0.290 Round 2: 94 peptides, 19 chains. Longest chain 8 peptides. Score 0.303 Round 3: 95 peptides, 16 chains. Longest chain 11 peptides. Score 0.399 Round 4: 98 peptides, 17 chains. Longest chain 10 peptides. Score 0.390 Round 5: 103 peptides, 19 chains. Longest chain 10 peptides. Score 0.366 Taking the results from Round 3 Chains 16, Residues 79, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2442 reflections ( 92.68 % complete ) and 3746 restraints for refining 1731 atoms. 3446 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2532 (Rfree = 0.000) for 1731 atoms. Found 9 (9 requested) and removed 16 (4 requested) atoms. Cycle 17: After refmac, R = 0.2229 (Rfree = 0.000) for 1718 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 18: After refmac, R = 0.2241 (Rfree = 0.000) for 1712 atoms. Found 4 (9 requested) and removed 6 (4 requested) atoms. Cycle 19: After refmac, R = 0.2241 (Rfree = 0.000) for 1710 atoms. Found 2 (9 requested) and removed 5 (4 requested) atoms. Cycle 20: After refmac, R = 0.2235 (Rfree = 0.000) for 1707 atoms. Found 1 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.50 4.01 Search for helices and strands: 0 residues in 0 chains, 1732 seeds are put forward NCS extension: 0 residues added, 1732 seeds are put forward Round 1: 86 peptides, 18 chains. Longest chain 7 peptides. Score 0.276 Round 2: 99 peptides, 19 chains. Longest chain 9 peptides. Score 0.339 Round 3: 109 peptides, 18 chains. Longest chain 11 peptides. Score 0.433 Round 4: 99 peptides, 18 chains. Longest chain 14 peptides. Score 0.368 Round 5: 91 peptides, 15 chains. Longest chain 10 peptides. Score 0.401 Taking the results from Round 3 Chains 19, Residues 91, Estimated correctness of the model 0.0 % 2 chains (14 residues) have been docked in sequence ------------------------------------------------------ 2442 reflections ( 92.68 % complete ) and 3880 restraints for refining 1828 atoms. 3473 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2490 (Rfree = 0.000) for 1828 atoms. Found 10 (10 requested) and removed 17 (5 requested) atoms. Cycle 22: After refmac, R = 0.2301 (Rfree = 0.000) for 1812 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. Cycle 23: After refmac, R = 0.2302 (Rfree = 0.000) for 1807 atoms. Found 6 (9 requested) and removed 7 (4 requested) atoms. Cycle 24: After refmac, R = 0.2326 (Rfree = 0.000) for 1805 atoms. Found 2 (9 requested) and removed 4 (4 requested) atoms. Cycle 25: After refmac, R = 0.2315 (Rfree = 0.000) for 1801 atoms. Found 2 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.47 3.97 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: 97 peptides, 19 chains. Longest chain 8 peptides. Score 0.325 Round 2: 107 peptides, 20 chains. Longest chain 10 peptides. Score 0.364 Round 3: 110 peptides, 19 chains. Longest chain 9 peptides. Score 0.412 Round 4: 108 peptides, 18 chains. Longest chain 11 peptides. Score 0.427 Round 5: 105 peptides, 18 chains. Longest chain 10 peptides. Score 0.408 Taking the results from Round 4 Chains 18, Residues 90, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2442 reflections ( 92.68 % complete ) and 4294 restraints for refining 1870 atoms. 3952 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2811 (Rfree = 0.000) for 1870 atoms. Found 10 (10 requested) and removed 18 (5 requested) atoms. Cycle 27: After refmac, R = 0.2950 (Rfree = 0.000) for 1844 atoms. Found 10 (10 requested) and removed 17 (5 requested) atoms. Cycle 28: After refmac, R = 0.2088 (Rfree = 0.000) for 1817 atoms. Found 10 (10 requested) and removed 13 (5 requested) atoms. Cycle 29: After refmac, R = 0.1784 (Rfree = 0.000) for 1804 atoms. Found 6 (9 requested) and removed 6 (4 requested) atoms. Cycle 30: After refmac, R = 0.1638 (Rfree = 0.000) for 1795 atoms. Found 5 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.42 3.91 Search for helices and strands: 0 residues in 0 chains, 1830 seeds are put forward NCS extension: 0 residues added, 1830 seeds are put forward Round 1: 75 peptides, 15 chains. Longest chain 8 peptides. Score 0.288 Round 2: 92 peptides, 17 chains. Longest chain 8 peptides. Score 0.349 Round 3: 103 peptides, 16 chains. Longest chain 12 peptides. Score 0.450 Round 4: 96 peptides, 16 chains. Longest chain 13 peptides. Score 0.405 Round 5: 94 peptides, 15 chains. Longest chain 15 peptides. Score 0.421 Taking the results from Round 3 Chains 16, Residues 87, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2442 reflections ( 92.68 % complete ) and 3963 restraints for refining 1779 atoms. 3631 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2440 (Rfree = 0.000) for 1779 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 32: After refmac, R = 0.2419 (Rfree = 0.000) for 1769 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. Cycle 33: After refmac, R = 0.1860 (Rfree = 0.000) for 1752 atoms. Found 8 (9 requested) and removed 9 (4 requested) atoms. Cycle 34: After refmac, R = 0.1866 (Rfree = 0.000) for 1744 atoms. Found 9 (9 requested) and removed 5 (4 requested) atoms. Cycle 35: After refmac, R = 0.2149 (Rfree = 0.000) for 1747 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.37 3.86 Search for helices and strands: 0 residues in 0 chains, 1788 seeds are put forward NCS extension: 0 residues added, 1788 seeds are put forward Round 1: 77 peptides, 17 chains. Longest chain 6 peptides. Score 0.239 Round 2: 95 peptides, 17 chains. Longest chain 9 peptides. Score 0.370 Round 3: 96 peptides, 18 chains. Longest chain 8 peptides. Score 0.347 Round 4: 86 peptides, 14 chains. Longest chain 10 peptides. Score 0.397 Round 5: 98 peptides, 17 chains. Longest chain 11 peptides. Score 0.390 Taking the results from Round 4 Chains 14, Residues 72, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 2442 reflections ( 92.68 % complete ) and 3903 restraints for refining 1779 atoms. 3600 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2780 (Rfree = 0.000) for 1779 atoms. Found 9 (9 requested) and removed 21 (4 requested) atoms. Cycle 37: After refmac, R = 0.3255 (Rfree = 0.000) for 1754 atoms. Found 9 (9 requested) and removed 18 (4 requested) atoms. Cycle 38: After refmac, R = 0.2604 (Rfree = 0.000) for 1734 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. Cycle 39: After refmac, R = 0.1913 (Rfree = 0.000) for 1725 atoms. Found 8 (9 requested) and removed 6 (4 requested) atoms. Cycle 40: After refmac, R = 0.1809 (Rfree = 0.000) for 1715 atoms. Found 9 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.34 3.82 Search for helices and strands: 0 residues in 0 chains, 1742 seeds are put forward NCS extension: 0 residues added, 1742 seeds are put forward Round 1: 58 peptides, 13 chains. Longest chain 6 peptides. Score 0.219 Round 2: 73 peptides, 15 chains. Longest chain 8 peptides. Score 0.272 Round 3: 76 peptides, 15 chains. Longest chain 8 peptides. Score 0.295 Round 4: 73 peptides, 13 chains. Longest chain 10 peptides. Score 0.337 Round 5: 80 peptides, 15 chains. Longest chain 10 peptides. Score 0.325 Taking the results from Round 4 Chains 13, Residues 60, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2442 reflections ( 92.68 % complete ) and 3951 restraints for refining 1733 atoms. 3724 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2446 (Rfree = 0.000) for 1733 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. Cycle 42: After refmac, R = 0.2110 (Rfree = 0.000) for 1730 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. Cycle 43: After refmac, R = 0.1604 (Rfree = 0.000) for 1731 atoms. Found 4 (9 requested) and removed 6 (4 requested) atoms. Cycle 44: After refmac, R = 0.1619 (Rfree = 0.000) for 1728 atoms. Found 3 (9 requested) and removed 5 (4 requested) atoms. Cycle 45: After refmac, R = 0.1492 (Rfree = 0.000) for 1723 atoms. Found 2 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.35 3.83 Search for helices and strands: 0 residues in 0 chains, 1742 seeds are put forward NCS extension: 0 residues added, 1742 seeds are put forward Round 1: 70 peptides, 16 chains. Longest chain 6 peptides. Score 0.216 Round 2: 76 peptides, 16 chains. Longest chain 7 peptides. Score 0.263 Round 3: 74 peptides, 14 chains. Longest chain 7 peptides. Score 0.312 Round 4: 75 peptides, 14 chains. Longest chain 10 peptides. Score 0.320 Round 5: 73 peptides, 14 chains. Longest chain 9 peptides. Score 0.305 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 14, Residues 61, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence Sequence coverage is 9 % Consider running further cycles of model building using 1zko-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2442 reflections ( 92.68 % complete ) and 3941 restraints for refining 1763 atoms. 3685 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2033 (Rfree = 0.000) for 1763 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.2582 (Rfree = 0.000) for 1746 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.2249 (Rfree = 0.000) for 1731 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.2337 (Rfree = 0.000) for 1715 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:06:35 GMT 2018 Job finished. TimeTaking 25.95 Used memory is bytes: 567416