Sun 23 Dec 22:22:40 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1zko-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1zko-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1zko-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zko-3.6-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/1zko-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zko-3.6-parrot-hancs ############### 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 ============================================================ Sun 23 Dec 22:22:49 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/hancs/ArpWArp/wArpResults/WorkingDir/1zko-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zko-3.6-parrot-hancs/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 173 and 0 Target number of residues in the AU: 173 Target solvent content: 0.6164 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-3.6-parrot-hancs.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-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 2176 target number of atoms Had to go as low as 0.60 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 3.600 Wilson plot Bfac: 59.59 2852 reflections ( 92.51 % complete ) and 0 restraints for refining 2422 atoms. Observations/parameters ratio is 0.29 ------------------------------------------------------ Starting model: R = 0.3551 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3789 (Rfree = 0.000) for 2422 atoms. Found 15 (15 requested) and removed 32 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.29 3.77 Search for helices and strands: 0 residues in 0 chains, 2423 seeds are put forward NCS extension: 0 residues added, 2423 seeds are put forward Round 1: 46 peptides, 11 chains. Longest chain 5 peptides. Score 0.186 Round 2: 64 peptides, 14 chains. Longest chain 7 peptides. Score 0.234 Round 3: 70 peptides, 14 chains. Longest chain 8 peptides. Score 0.282 Round 4: 81 peptides, 15 chains. Longest chain 11 peptides. Score 0.332 Round 5: 66 peptides, 12 chains. Longest chain 11 peptides. Score 0.317 Taking the results from Round 4 Chains 15, Residues 66, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2852 reflections ( 92.51 % complete ) and 4808 restraints for refining 1971 atoms. 4559 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3267 (Rfree = 0.000) for 1971 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. Cycle 2: After refmac, R = 0.3034 (Rfree = 0.000) for 1939 atoms. Found 12 (12 requested) and removed 17 (6 requested) atoms. Cycle 3: After refmac, R = 0.3027 (Rfree = 0.000) for 1912 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 4: After refmac, R = 0.3305 (Rfree = 0.000) for 1900 atoms. Found 12 (12 requested) and removed 18 (6 requested) atoms. Cycle 5: After refmac, R = 0.2832 (Rfree = 0.000) for 1878 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.47 3.97 Search for helices and strands: 0 residues in 0 chains, 1906 seeds are put forward NCS extension: 3 residues added (0 deleted due to clashes), 1909 seeds are put forward Round 1: 69 peptides, 16 chains. Longest chain 6 peptides. Score 0.208 Round 2: 91 peptides, 18 chains. Longest chain 7 peptides. Score 0.312 Round 3: 90 peptides, 17 chains. Longest chain 8 peptides. Score 0.335 Round 4: 97 peptides, 18 chains. Longest chain 8 peptides. Score 0.354 Round 5: 93 peptides, 17 chains. Longest chain 9 peptides. Score 0.356 Taking the results from Round 5 Chains 17, Residues 76, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2852 reflections ( 92.51 % complete ) and 4090 restraints for refining 1763 atoms. 3803 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2988 (Rfree = 0.000) for 1763 atoms. Found 11 (11 requested) and removed 18 (5 requested) atoms. Cycle 7: After refmac, R = 0.2387 (Rfree = 0.000) for 1743 atoms. Found 8 (11 requested) and removed 9 (5 requested) atoms. Cycle 8: After refmac, R = 0.2714 (Rfree = 0.000) for 1731 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 9: After refmac, R = 0.2478 (Rfree = 0.000) for 1723 atoms. Found 11 (11 requested) and removed 7 (5 requested) atoms. Cycle 10: After refmac, R = 0.2722 (Rfree = 0.000) for 1720 atoms. Found 11 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.24 3.71 Search for helices and strands: 0 residues in 0 chains, 1771 seeds are put forward NCS extension: 0 residues added, 1771 seeds are put forward Round 1: 103 peptides, 22 chains. Longest chain 9 peptides. Score 0.279 Round 2: 114 peptides, 23 chains. Longest chain 11 peptides. Score 0.326 Round 3: 103 peptides, 19 chains. Longest chain 11 peptides. Score 0.366 Round 4: 99 peptides, 21 chains. Longest chain 7 peptides. Score 0.280 Round 5: 112 peptides, 19 chains. Longest chain 11 peptides. Score 0.425 Taking the results from Round 5 Chains 19, Residues 93, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2852 reflections ( 92.51 % complete ) and 4016 restraints for refining 1790 atoms. 3663 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2423 (Rfree = 0.000) for 1790 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. Cycle 12: After refmac, R = 0.2339 (Rfree = 0.000) for 1779 atoms. Found 10 (11 requested) and removed 7 (5 requested) atoms. Cycle 13: After refmac, R = 0.2173 (Rfree = 0.000) for 1778 atoms. Found 7 (11 requested) and removed 8 (5 requested) atoms. Cycle 14: After refmac, R = 0.2229 (Rfree = 0.000) for 1774 atoms. Found 10 (11 requested) and removed 9 (5 requested) atoms. Cycle 15: After refmac, R = 0.1919 (Rfree = 0.000) for 1769 atoms. Found 7 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.37 3.86 Search for helices and strands: 0 residues in 0 chains, 1810 seeds are put forward NCS extension: 0 residues added, 1810 seeds are put forward Round 1: 87 peptides, 19 chains. Longest chain 7 peptides. Score 0.252 Round 2: 103 peptides, 20 chains. Longest chain 8 peptides. Score 0.337 Round 3: 104 peptides, 20 chains. Longest chain 9 peptides. Score 0.344 Round 4: 105 peptides, 19 chains. Longest chain 12 peptides. Score 0.379 Round 5: 101 peptides, 18 chains. Longest chain 10 peptides. Score 0.381 Taking the results from Round 5 Chains 18, Residues 83, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2852 reflections ( 92.51 % complete ) and 4172 restraints for refining 1834 atoms. 3858 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2564 (Rfree = 0.000) for 1834 atoms. Found 11 (11 requested) and removed 15 (5 requested) atoms. Cycle 17: After refmac, R = 0.2462 (Rfree = 0.000) for 1823 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. Cycle 18: After refmac, R = 0.2043 (Rfree = 0.000) for 1818 atoms. Found 6 (11 requested) and removed 6 (5 requested) atoms. Cycle 19: After refmac, R = 0.2006 (Rfree = 0.000) for 1811 atoms. Found 7 (11 requested) and removed 5 (5 requested) atoms. Cycle 20: After refmac, R = 0.1856 (Rfree = 0.000) for 1809 atoms. Found 6 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.38 3.87 Search for helices and strands: 0 residues in 0 chains, 1846 seeds are put forward NCS extension: 0 residues added, 1846 seeds are put forward Round 1: 96 peptides, 20 chains. Longest chain 9 peptides. Score 0.288 Round 2: 109 peptides, 18 chains. Longest chain 19 peptides. Score 0.433 Round 3: 113 peptides, 19 chains. Longest chain 12 peptides. Score 0.431 Round 4: 107 peptides, 17 chains. Longest chain 11 peptides. Score 0.448 Round 5: 104 peptides, 17 chains. Longest chain 12 peptides. Score 0.429 Taking the results from Round 4 Chains 17, Residues 90, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2852 reflections ( 92.51 % complete ) and 4336 restraints for refining 1878 atoms. 3993 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2592 (Rfree = 0.000) for 1878 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 22: After refmac, R = 0.2315 (Rfree = 0.000) for 1869 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 23: After refmac, R = 0.2023 (Rfree = 0.000) for 1856 atoms. Found 8 (11 requested) and removed 7 (5 requested) atoms. Cycle 24: After refmac, R = 0.2047 (Rfree = 0.000) for 1844 atoms. Found 11 (11 requested) and removed 7 (5 requested) atoms. Cycle 25: After refmac, R = 0.2870 (Rfree = 0.000) for 1843 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.25 3.72 Search for helices and strands: 0 residues in 0 chains, 1875 seeds are put forward NCS extension: 0 residues added, 1875 seeds are put forward Round 1: 66 peptides, 15 chains. Longest chain 6 peptides. Score 0.217 Round 2: 85 peptides, 17 chains. Longest chain 9 peptides. Score 0.299 Round 3: 95 peptides, 18 chains. Longest chain 10 peptides. Score 0.340 Round 4: 94 peptides, 15 chains. Longest chain 11 peptides. Score 0.421 Round 5: 92 peptides, 16 chains. Longest chain 11 peptides. Score 0.379 Taking the results from Round 4 Chains 15, Residues 79, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2852 reflections ( 92.51 % complete ) and 4151 restraints for refining 1814 atoms. 3850 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2365 (Rfree = 0.000) for 1814 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 27: After refmac, R = 0.2259 (Rfree = 0.000) for 1802 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 28: After refmac, R = 0.2118 (Rfree = 0.000) for 1800 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. Cycle 29: After refmac, R = 0.2065 (Rfree = 0.000) for 1800 atoms. Found 7 (11 requested) and removed 9 (5 requested) atoms. Cycle 30: After refmac, R = 0.1838 (Rfree = 0.000) for 1795 atoms. Found 5 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.34 3.82 Search for helices and strands: 0 residues in 0 chains, 1812 seeds are put forward NCS extension: 0 residues added, 1812 seeds are put forward Round 1: 72 peptides, 15 chains. Longest chain 9 peptides. Score 0.265 Round 2: 95 peptides, 18 chains. Longest chain 10 peptides. Score 0.340 Round 3: 98 peptides, 17 chains. Longest chain 11 peptides. Score 0.390 Round 4: 98 peptides, 16 chains. Longest chain 12 peptides. Score 0.418 Round 5: 100 peptides, 18 chains. Longest chain 10 peptides. Score 0.375 Taking the results from Round 4 Chains 16, Residues 82, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2852 reflections ( 92.51 % complete ) and 4262 restraints for refining 1820 atoms. 3950 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2368 (Rfree = 0.000) for 1820 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 32: After refmac, R = 0.1958 (Rfree = 0.000) for 1814 atoms. Found 8 (11 requested) and removed 6 (5 requested) atoms. Cycle 33: After refmac, R = 0.1868 (Rfree = 0.000) for 1812 atoms. Found 9 (11 requested) and removed 5 (5 requested) atoms. Cycle 34: After refmac, R = 0.1767 (Rfree = 0.000) for 1815 atoms. Found 3 (11 requested) and removed 5 (5 requested) atoms. Cycle 35: After refmac, R = 0.1788 (Rfree = 0.000) for 1813 atoms. Found 6 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.31 3.79 Search for helices and strands: 0 residues in 0 chains, 1843 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 1856 seeds are put forward Round 1: 77 peptides, 16 chains. Longest chain 9 peptides. Score 0.271 Round 2: 82 peptides, 14 chains. Longest chain 9 peptides. Score 0.370 Round 3: 89 peptides, 16 chains. Longest chain 9 peptides. Score 0.358 Round 4: 95 peptides, 17 chains. Longest chain 10 peptides. Score 0.370 Round 5: 95 peptides, 16 chains. Longest chain 11 peptides. Score 0.399 Taking the results from Round 5 Chains 16, Residues 79, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2852 reflections ( 92.51 % complete ) and 4246 restraints for refining 1850 atoms. 3946 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2381 (Rfree = 0.000) for 1850 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 37: After refmac, R = 0.1921 (Rfree = 0.000) for 1845 atoms. Found 10 (11 requested) and removed 7 (5 requested) atoms. Cycle 38: After refmac, R = 0.1859 (Rfree = 0.000) for 1847 atoms. Found 6 (11 requested) and removed 5 (5 requested) atoms. Cycle 39: After refmac, R = 0.1828 (Rfree = 0.000) for 1845 atoms. Found 5 (11 requested) and removed 6 (5 requested) atoms. Cycle 40: After refmac, R = 0.1787 (Rfree = 0.000) for 1843 atoms. Found 3 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.35 3.83 Search for helices and strands: 0 residues in 0 chains, 1871 seeds are put forward NCS extension: 0 residues added, 1871 seeds are put forward Round 1: 91 peptides, 19 chains. Longest chain 8 peptides. Score 0.282 Round 2: 94 peptides, 18 chains. Longest chain 9 peptides. Score 0.333 Round 3: 98 peptides, 17 chains. Longest chain 11 peptides. Score 0.390 Round 4: 90 peptides, 17 chains. Longest chain 9 peptides. Score 0.335 Round 5: 94 peptides, 17 chains. Longest chain 12 peptides. Score 0.363 Taking the results from Round 3 Chains 17, Residues 81, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2852 reflections ( 92.51 % complete ) and 4313 restraints for refining 1865 atoms. 4006 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2400 (Rfree = 0.000) for 1865 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. Cycle 42: After refmac, R = 0.2288 (Rfree = 0.000) for 1861 atoms. Found 11 (11 requested) and removed 7 (5 requested) atoms. Cycle 43: After refmac, R = 0.2205 (Rfree = 0.000) for 1863 atoms. Found 6 (11 requested) and removed 7 (5 requested) atoms. Cycle 44: After refmac, R = 0.2080 (Rfree = 0.000) for 1862 atoms. Found 2 (11 requested) and removed 6 (5 requested) atoms. Cycle 45: After refmac, R = 0.2001 (Rfree = 0.000) for 1856 atoms. Found 1 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.35 3.83 Search for helices and strands: 0 residues in 0 chains, 1873 seeds are put forward NCS extension: 0 residues added, 1873 seeds are put forward Round 1: 78 peptides, 18 chains. Longest chain 7 peptides. Score 0.215 Round 2: 83 peptides, 15 chains. Longest chain 11 peptides. Score 0.346 Round 3: 83 peptides, 13 chains. Longest chain 13 peptides. Score 0.407 Round 4: 86 peptides, 15 chains. Longest chain 11 peptides. Score 0.367 Round 5: 88 peptides, 16 chains. Longest chain 8 peptides. Score 0.351 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 13, Residues 70, 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 1zko-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2852 reflections ( 92.51 % complete ) and 4489 restraints for refining 1880 atoms. 4222 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2144 (Rfree = 0.000) for 1880 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.2070 (Rfree = 0.000) for 1869 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.1914 (Rfree = 0.000) for 1862 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.2201 (Rfree = 0.000) for 1856 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Writing output files ... TimeTaking 29.42