Sun 23 Dec 22:23:13 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 2ou6-1.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ou6-1.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ou6-1.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ou6-1.8-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/2ou6-1.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ou6-1.8-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 22:23:22 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/2ou6-1.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ou6-1.8-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 238 and 0 Target number of residues in the AU: 238 Target solvent content: 0.4699 Checking the provided sequence file Detected sequence length: 190 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 190 Adjusted target solvent content: 0.58 Input MTZ file: 2ou6-1.8-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: 179 Cell parameters: 57.933 57.933 250.773 90.000 90.000 120.000 Input sequence file: 2ou6-1.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 1520 target number of atoms Had to go as low as 0.45 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 1 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 Loops will be built when appropriate and at the last cycle Resolution range: 50.171 1.797 Wilson plot Bfac: 17.59 22103 reflections ( 91.05 % complete ) and 0 restraints for refining 1674 atoms. Observations/parameters ratio is 3.30 ------------------------------------------------------ Starting model: R = 0.3384 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2902 (Rfree = 0.000) for 1674 atoms. Found 77 (77 requested) and removed 30 (38 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.79 1.61 Round 1: 170 peptides, 8 chains. Longest chain 43 peptides. Score 0.862 Round 2: 177 peptides, 4 chains. Longest chain 101 peptides. Score 0.912 Round 3: 180 peptides, 3 chains. Longest chain 126 peptides. Score 0.924 Round 4: 180 peptides, 3 chains. Longest chain 113 peptides. Score 0.924 Round 5: 181 peptides, 2 chains. Longest chain 128 peptides. Score 0.933 Taking the results from Round 5 Chains 2, Residues 179, Estimated correctness of the model 99.6 % 2 chains (179 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 130 A and 133 A 1 chains (181 residues) following loop building 1 chains (181 residues) in sequence following loop building ------------------------------------------------------ 22103 reflections ( 91.05 % complete ) and 1692 restraints for refining 1697 atoms. 230 conditional restraints added. Observations/parameters ratio is 3.26 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2787 (Rfree = 0.000) for 1697 atoms. Found 78 (78 requested) and removed 34 (39 requested) atoms. Cycle 2: After refmac, R = 0.2392 (Rfree = 0.000) for 1737 atoms. Found 80 (80 requested) and removed 20 (40 requested) atoms. Cycle 3: After refmac, R = 0.2210 (Rfree = 0.000) for 1791 atoms. Found 78 (83 requested) and removed 25 (41 requested) atoms. Cycle 4: After refmac, R = 0.2079 (Rfree = 0.000) for 1837 atoms. Found 55 (85 requested) and removed 28 (42 requested) atoms. Cycle 5: After refmac, R = 0.1992 (Rfree = 0.000) for 1855 atoms. Found 55 (84 requested) and removed 23 (43 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.74 1.56 Round 1: 181 peptides, 3 chains. Longest chain 171 peptides. Score 0.925 Round 2: 181 peptides, 2 chains. Longest chain 126 peptides. Score 0.933 Round 3: 182 peptides, 2 chains. Longest chain 126 peptides. Score 0.934 Round 4: 182 peptides, 1 chains. Longest chain 182 peptides. Score 0.942 Round 5: 181 peptides, 2 chains. Longest chain 126 peptides. Score 0.933 Taking the results from Round 4 Chains 1, Residues 181, Estimated correctness of the model 99.7 % 1 chains (181 residues) have been docked in sequence ------------------------------------------------------ 22103 reflections ( 91.05 % complete ) and 1701 restraints for refining 1770 atoms. 239 conditional restraints added. Observations/parameters ratio is 3.12 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1956 (Rfree = 0.000) for 1770 atoms. Found 80 (80 requested) and removed 12 (41 requested) atoms. Cycle 7: After refmac, R = 0.1878 (Rfree = 0.000) for 1833 atoms. Found 55 (83 requested) and removed 19 (42 requested) atoms. Cycle 8: After refmac, R = 0.1818 (Rfree = 0.000) for 1866 atoms. Found 54 (84 requested) and removed 29 (43 requested) atoms. Cycle 9: After refmac, R = 0.1796 (Rfree = 0.000) for 1888 atoms. Found 45 (84 requested) and removed 31 (43 requested) atoms. Cycle 10: After refmac, R = 0.1747 (Rfree = 0.000) for 1899 atoms. Found 47 (83 requested) and removed 33 (44 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.74 1.56 Round 1: 181 peptides, 2 chains. Longest chain 126 peptides. Score 0.933 Round 2: 181 peptides, 2 chains. Longest chain 130 peptides. Score 0.933 Round 3: 180 peptides, 2 chains. Longest chain 132 peptides. Score 0.932 Round 4: 180 peptides, 2 chains. Longest chain 126 peptides. Score 0.932 Round 5: 181 peptides, 1 chains. Longest chain 181 peptides. Score 0.941 Taking the results from Round 5 Chains 1, Residues 180, Estimated correctness of the model 99.7 % 1 chains (180 residues) have been docked in sequence ------------------------------------------------------ 22103 reflections ( 91.05 % complete ) and 1724 restraints for refining 1804 atoms. 270 conditional restraints added. Observations/parameters ratio is 3.06 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1829 (Rfree = 0.000) for 1804 atoms. Found 76 (76 requested) and removed 12 (41 requested) atoms. Cycle 12: After refmac, R = 0.1803 (Rfree = 0.000) for 1861 atoms. Found 50 (79 requested) and removed 34 (43 requested) atoms. Cycle 13: After refmac, R = 0.1737 (Rfree = 0.000) for 1875 atoms. Found 57 (78 requested) and removed 22 (43 requested) atoms. Cycle 14: After refmac, R = 0.1734 (Rfree = 0.000) for 1907 atoms. Found 45 (79 requested) and removed 41 (44 requested) atoms. Cycle 15: After refmac, R = 0.1708 (Rfree = 0.000) for 1910 atoms. Found 52 (77 requested) and removed 33 (44 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.74 1.56 Round 1: 181 peptides, 1 chains. Longest chain 181 peptides. Score 0.941 Round 2: 180 peptides, 2 chains. Longest chain 126 peptides. Score 0.932 Round 3: 181 peptides, 1 chains. Longest chain 181 peptides. Score 0.941 Round 4: 181 peptides, 1 chains. Longest chain 181 peptides. Score 0.941 Round 5: 180 peptides, 2 chains. Longest chain 126 peptides. Score 0.932 Taking the results from Round 4 Chains 1, Residues 180, Estimated correctness of the model 99.7 % 1 chains (180 residues) have been docked in sequence ------------------------------------------------------ 22103 reflections ( 91.05 % complete ) and 1768 restraints for refining 1814 atoms. 314 conditional restraints added. Observations/parameters ratio is 3.05 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1837 (Rfree = 0.000) for 1814 atoms. Found 72 (72 requested) and removed 17 (42 requested) atoms. Cycle 17: After refmac, R = 0.1805 (Rfree = 0.000) for 1866 atoms. Found 51 (74 requested) and removed 37 (43 requested) atoms. Cycle 18: After refmac, R = 0.1756 (Rfree = 0.000) for 1874 atoms. Found 54 (73 requested) and removed 27 (43 requested) atoms. Cycle 19: After refmac, R = 0.1743 (Rfree = 0.000) for 1901 atoms. Found 48 (74 requested) and removed 34 (44 requested) atoms. Cycle 20: After refmac, R = 0.1709 (Rfree = 0.000) for 1914 atoms. Found 50 (72 requested) and removed 37 (44 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.74 1.56 Round 1: 181 peptides, 1 chains. Longest chain 181 peptides. Score 0.941 Round 2: 180 peptides, 2 chains. Longest chain 126 peptides. Score 0.932 Round 3: 181 peptides, 1 chains. Longest chain 181 peptides. Score 0.941 Round 4: 181 peptides, 1 chains. Longest chain 181 peptides. Score 0.941 Round 5: 179 peptides, 3 chains. Longest chain 98 peptides. Score 0.923 Taking the results from Round 4 Chains 1, Residues 180, Estimated correctness of the model 99.7 % 1 chains (180 residues) have been docked in sequence ------------------------------------------------------ 22103 reflections ( 91.05 % complete ) and 1743 restraints for refining 1808 atoms. 289 conditional restraints added. Observations/parameters ratio is 3.06 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1808 (Rfree = 0.000) for 1808 atoms. Found 67 (67 requested) and removed 17 (42 requested) atoms. Cycle 22: After refmac, R = 0.1752 (Rfree = 0.000) for 1855 atoms. Found 68 (69 requested) and removed 25 (43 requested) atoms. Cycle 23: After refmac, R = 0.1727 (Rfree = 0.000) for 1897 atoms. Found 47 (70 requested) and removed 43 (43 requested) atoms. Cycle 24: After refmac, R = 0.1709 (Rfree = 0.000) for 1898 atoms. Found 64 (69 requested) and removed 33 (44 requested) atoms. Cycle 25: After refmac, R = 0.1710 (Rfree = 0.000) for 1928 atoms. Found 63 (68 requested) and removed 41 (44 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.73 1.55 Round 1: 181 peptides, 1 chains. Longest chain 181 peptides. Score 0.941 Round 2: 180 peptides, 2 chains. Longest chain 126 peptides. Score 0.932 Round 3: 181 peptides, 1 chains. Longest chain 181 peptides. Score 0.941 Round 4: 181 peptides, 1 chains. Longest chain 181 peptides. Score 0.941 Round 5: 179 peptides, 3 chains. Longest chain 86 peptides. Score 0.923 Taking the results from Round 4 Chains 1, Residues 180, Estimated correctness of the model 99.7 % 1 chains (180 residues) have been docked in sequence ------------------------------------------------------ 22103 reflections ( 91.05 % complete ) and 1742 restraints for refining 1821 atoms. 288 conditional restraints added. Observations/parameters ratio is 3.03 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1823 (Rfree = 0.000) for 1821 atoms. Found 62 (62 requested) and removed 17 (42 requested) atoms. Cycle 27: After refmac, R = 0.1766 (Rfree = 0.000) for 1866 atoms. Found 55 (64 requested) and removed 30 (43 requested) atoms. Cycle 28: After refmac, R = 0.1722 (Rfree = 0.000) for 1889 atoms. Found 61 (63 requested) and removed 32 (43 requested) atoms. Cycle 29: After refmac, R = 0.1718 (Rfree = 0.000) for 1918 atoms. Found 51 (62 requested) and removed 46 (44 requested) atoms. Cycle 30: After refmac, R = 0.1695 (Rfree = 0.000) for 1920 atoms. Found 61 (61 requested) and removed 45 (44 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.73 1.55 Round 1: 181 peptides, 1 chains. Longest chain 181 peptides. Score 0.941 Round 2: 180 peptides, 2 chains. Longest chain 126 peptides. Score 0.932 Round 3: 181 peptides, 1 chains. Longest chain 181 peptides. Score 0.941 Round 4: 181 peptides, 1 chains. Longest chain 181 peptides. Score 0.941 Round 5: 180 peptides, 2 chains. Longest chain 126 peptides. Score 0.932 Taking the results from Round 4 Chains 1, Residues 180, Estimated correctness of the model 99.7 % 1 chains (180 residues) have been docked in sequence ------------------------------------------------------ 22103 reflections ( 91.05 % complete ) and 1735 restraints for refining 1813 atoms. 281 conditional restraints added. Observations/parameters ratio is 3.05 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1794 (Rfree = 0.000) for 1813 atoms. Found 55 (55 requested) and removed 11 (42 requested) atoms. Cycle 32: After refmac, R = 0.1724 (Rfree = 0.000) for 1854 atoms. Found 57 (57 requested) and removed 20 (43 requested) atoms. Cycle 33: After refmac, R = 0.1699 (Rfree = 0.000) for 1889 atoms. Found 56 (57 requested) and removed 36 (43 requested) atoms. Cycle 34: After refmac, R = 0.1708 (Rfree = 0.000) for 1907 atoms. Found 56 (56 requested) and removed 42 (44 requested) atoms. Cycle 35: After refmac, R = 0.1681 (Rfree = 0.000) for 1921 atoms. Found 55 (55 requested) and removed 41 (44 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.73 1.55 Round 1: 181 peptides, 1 chains. Longest chain 181 peptides. Score 0.941 Round 2: 180 peptides, 2 chains. Longest chain 126 peptides. Score 0.932 Round 3: 180 peptides, 2 chains. Longest chain 128 peptides. Score 0.932 Round 4: 181 peptides, 1 chains. Longest chain 181 peptides. Score 0.941 Round 5: 180 peptides, 2 chains. Longest chain 126 peptides. Score 0.932 Taking the results from Round 4 Chains 1, Residues 180, Estimated correctness of the model 99.7 % 1 chains (180 residues) have been docked in sequence ------------------------------------------------------ 22103 reflections ( 91.05 % complete ) and 1719 restraints for refining 1817 atoms. 265 conditional restraints added. Observations/parameters ratio is 3.04 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1819 (Rfree = 0.000) for 1817 atoms. Found 50 (50 requested) and removed 18 (42 requested) atoms. Cycle 37: After refmac, R = 0.1748 (Rfree = 0.000) for 1847 atoms. Found 51 (51 requested) and removed 12 (42 requested) atoms. Cycle 38: After refmac, R = 0.1714 (Rfree = 0.000) for 1884 atoms. Found 44 (52 requested) and removed 37 (43 requested) atoms. Cycle 39: After refmac, R = 0.1682 (Rfree = 0.000) for 1889 atoms. Found 50 (50 requested) and removed 36 (43 requested) atoms. Cycle 40: After refmac, R = 0.1689 (Rfree = 0.000) for 1903 atoms. Found 49 (49 requested) and removed 40 (44 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.74 1.56 Round 1: 181 peptides, 1 chains. Longest chain 181 peptides. Score 0.941 Round 2: 180 peptides, 2 chains. Longest chain 126 peptides. Score 0.932 Round 3: 180 peptides, 2 chains. Longest chain 128 peptides. Score 0.932 Round 4: 181 peptides, 1 chains. Longest chain 181 peptides. Score 0.941 Round 5: 178 peptides, 2 chains. Longest chain 124 peptides. Score 0.930 Taking the results from Round 4 Chains 1, Residues 180, Estimated correctness of the model 99.7 % 1 chains (180 residues) have been docked in sequence ------------------------------------------------------ 22103 reflections ( 91.05 % complete ) and 1727 restraints for refining 1804 atoms. 273 conditional restraints added. Observations/parameters ratio is 3.06 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1847 (Rfree = 0.000) for 1804 atoms. Found 45 (45 requested) and removed 14 (41 requested) atoms. Cycle 42: After refmac, R = 0.1762 (Rfree = 0.000) for 1832 atoms. Found 46 (46 requested) and removed 15 (42 requested) atoms. Cycle 43: After refmac, R = 0.1702 (Rfree = 0.000) for 1863 atoms. Found 46 (46 requested) and removed 24 (43 requested) atoms. Cycle 44: After refmac, R = 0.1692 (Rfree = 0.000) for 1883 atoms. Found 45 (45 requested) and removed 29 (43 requested) atoms. Cycle 45: After refmac, R = 0.1671 (Rfree = 0.000) for 1897 atoms. Found 44 (44 requested) and removed 33 (44 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.74 1.56 Round 1: 181 peptides, 1 chains. Longest chain 181 peptides. Score 0.941 Round 2: 180 peptides, 2 chains. Longest chain 126 peptides. Score 0.932 Round 3: 180 peptides, 2 chains. Longest chain 128 peptides. Score 0.932 Round 4: 181 peptides, 1 chains. Longest chain 181 peptides. Score 0.941 Round 5: 180 peptides, 2 chains. Longest chain 126 peptides. Score 0.932 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 1, Residues 180, Estimated correctness of the model 99.7 % 1 chains (180 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 22103 reflections ( 91.05 % complete ) and 1454 restraints for refining 1415 atoms. Observations/parameters ratio is 3.91 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2718 (Rfree = 0.000) for 1415 atoms. Found 32 (32 requested) and removed 0 (32 requested) atoms. Cycle 47: After refmac, R = 0.2547 (Rfree = 0.000) for 1415 atoms. Found 33 (33 requested) and removed 0 (33 requested) atoms. Cycle 48: After refmac, R = 0.2402 (Rfree = 0.000) for 1415 atoms. Found 34 (34 requested) and removed 0 (34 requested) atoms. Cycle 49: After refmac, R = 0.2261 (Rfree = 0.000) for 1415 atoms. TimeTaking 47.38