null Sun 23 Dec 22:22:56 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 2od4-1.7-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2od4-1.7-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2od4-1.7-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2od4-1.7-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/2od4-1.7-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2od4-1.7-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 22:23:05 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/2od4-1.7-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2od4-1.7-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 213 and 0 Target number of residues in the AU: 213 Target solvent content: 0.4564 Checking the provided sequence file Detected sequence length: 101 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 202 Adjusted target solvent content: 0.48 Input MTZ file: 2od4-1.7-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: 4 Cell parameters: 31.890 77.790 43.810 90.000 102.660 90.000 Input sequence file: 2od4-1.7-parrot-hancs.fasta_lf Building free atoms model in initial map for 1616 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 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: 28.889 1.700 Wilson plot Bfac: 15.50 22446 reflections ( 97.68 % complete ) and 0 restraints for refining 1805 atoms. Observations/parameters ratio is 3.11 ------------------------------------------------------ Starting model: R = 0.3399 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2914 (Rfree = 0.000) for 1805 atoms. Found 55 (98 requested) and removed 56 (49 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.89 1.94 NCS extension: 0 residues added, 1804 seeds are put forward Round 1: 146 peptides, 15 chains. Longest chain 46 peptides. Score 0.733 Round 2: 165 peptides, 13 chains. Longest chain 34 peptides. Score 0.825 Round 3: 185 peptides, 4 chains. Longest chain 96 peptides. Score 0.944 Round 4: 188 peptides, 3 chains. Longest chain 97 peptides. Score 0.953 Round 5: 189 peptides, 3 chains. Longest chain 98 peptides. Score 0.954 Taking the results from Round 5 Chains 4, Residues 186, Estimated correctness of the model 99.9 % 2 chains (171 residues) have been docked in sequence Building loops using Loopy2018 4 chains (186 residues) following loop building 2 chains (171 residues) in sequence following loop building ------------------------------------------------------ 22446 reflections ( 97.68 % complete ) and 1932 restraints for refining 1745 atoms. 470 conditional restraints added. Observations/parameters ratio is 3.22 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2979 (Rfree = 0.000) for 1745 atoms. Found 90 (94 requested) and removed 47 (47 requested) atoms. Cycle 2: After refmac, R = 0.2704 (Rfree = 0.000) for 1786 atoms. Found 63 (95 requested) and removed 25 (48 requested) atoms. Cycle 3: After refmac, R = 0.2574 (Rfree = 0.000) for 1808 atoms. Found 54 (97 requested) and removed 12 (49 requested) atoms. Cycle 4: After refmac, R = 0.2451 (Rfree = 0.000) for 1844 atoms. Found 41 (98 requested) and removed 6 (50 requested) atoms. Cycle 5: After refmac, R = 0.2344 (Rfree = 0.000) for 1860 atoms. Found 45 (100 requested) and removed 8 (51 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.75 1.80 NCS extension: 5 residues added (12 deleted due to clashes), 1903 seeds are put forward Round 1: 189 peptides, 3 chains. Longest chain 97 peptides. Score 0.954 Round 2: 191 peptides, 4 chains. Longest chain 99 peptides. Score 0.949 Round 3: 194 peptides, 2 chains. Longest chain 100 peptides. Score 0.963 Round 4: 190 peptides, 5 chains. Longest chain 72 peptides. Score 0.942 Round 5: 191 peptides, 5 chains. Longest chain 75 peptides. Score 0.942 Taking the results from Round 3 Chains 2, Residues 192, Estimated correctness of the model 99.9 % 2 chains (192 residues) have been docked in sequence Building loops using Loopy2018 2 chains (192 residues) following loop building 2 chains (192 residues) in sequence following loop building ------------------------------------------------------ 22446 reflections ( 97.68 % complete ) and 1800 restraints for refining 1814 atoms. 215 conditional restraints added. Observations/parameters ratio is 3.09 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2289 (Rfree = 0.000) for 1814 atoms. Found 62 (96 requested) and removed 33 (49 requested) atoms. Cycle 7: After refmac, R = 0.2156 (Rfree = 0.000) for 1840 atoms. Found 39 (96 requested) and removed 9 (50 requested) atoms. Cycle 8: After refmac, R = 0.2054 (Rfree = 0.000) for 1870 atoms. Found 37 (97 requested) and removed 8 (50 requested) atoms. Cycle 9: After refmac, R = 0.1989 (Rfree = 0.000) for 1897 atoms. Found 25 (99 requested) and removed 13 (51 requested) atoms. Cycle 10: After refmac, R = 0.1937 (Rfree = 0.000) for 1904 atoms. Found 36 (97 requested) and removed 7 (51 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.73 1.78 NCS extension: 6 residues added (0 deleted due to clashes), 1939 seeds are put forward Round 1: 193 peptides, 3 chains. Longest chain 99 peptides. Score 0.957 Round 2: 193 peptides, 3 chains. Longest chain 99 peptides. Score 0.957 Round 3: 192 peptides, 4 chains. Longest chain 99 peptides. Score 0.950 Round 4: 194 peptides, 3 chains. Longest chain 100 peptides. Score 0.957 Round 5: 195 peptides, 2 chains. Longest chain 100 peptides. Score 0.964 Taking the results from Round 5 Chains 2, Residues 193, Estimated correctness of the model 99.9 % 2 chains (193 residues) have been docked in sequence Building loops using Loopy2018 2 chains (193 residues) following loop building 2 chains (193 residues) in sequence following loop building ------------------------------------------------------ 22446 reflections ( 97.68 % complete ) and 1837 restraints for refining 1861 atoms. 244 conditional restraints added. Observations/parameters ratio is 3.02 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2090 (Rfree = 0.000) for 1861 atoms. Found 69 (95 requested) and removed 34 (50 requested) atoms. Cycle 12: After refmac, R = 0.2005 (Rfree = 0.000) for 1893 atoms. Found 44 (97 requested) and removed 8 (51 requested) atoms. Cycle 13: After refmac, R = 0.1936 (Rfree = 0.000) for 1922 atoms. Found 29 (99 requested) and removed 19 (52 requested) atoms. Cycle 14: After refmac, R = 0.1891 (Rfree = 0.000) for 1930 atoms. Found 43 (97 requested) and removed 12 (52 requested) atoms. Cycle 15: After refmac, R = 0.1869 (Rfree = 0.000) for 1959 atoms. Found 32 (98 requested) and removed 18 (53 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.73 1.78 NCS extension: 5 residues added (0 deleted due to clashes), 1978 seeds are put forward Round 1: 194 peptides, 3 chains. Longest chain 100 peptides. Score 0.957 Round 2: 194 peptides, 3 chains. Longest chain 100 peptides. Score 0.957 Round 3: 194 peptides, 3 chains. Longest chain 100 peptides. Score 0.957 Round 4: 193 peptides, 4 chains. Longest chain 100 peptides. Score 0.951 Round 5: 195 peptides, 2 chains. Longest chain 100 peptides. Score 0.964 Taking the results from Round 5 Chains 2, Residues 193, Estimated correctness of the model 99.9 % 2 chains (193 residues) have been docked in sequence Building loops using Loopy2018 2 chains (193 residues) following loop building 2 chains (193 residues) in sequence following loop building ------------------------------------------------------ 22446 reflections ( 97.68 % complete ) and 1841 restraints for refining 1885 atoms. 248 conditional restraints added. Observations/parameters ratio is 2.98 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2028 (Rfree = 0.000) for 1885 atoms. Found 71 (92 requested) and removed 31 (51 requested) atoms. Cycle 17: After refmac, R = 0.1935 (Rfree = 0.000) for 1923 atoms. Found 42 (94 requested) and removed 18 (52 requested) atoms. Cycle 18: After refmac, R = 0.1883 (Rfree = 0.000) for 1944 atoms. Found 44 (94 requested) and removed 15 (52 requested) atoms. Cycle 19: After refmac, R = 0.1863 (Rfree = 0.000) for 1967 atoms. Found 49 (96 requested) and removed 25 (53 requested) atoms. Cycle 20: After refmac, R = 0.1819 (Rfree = 0.000) for 1990 atoms. Found 43 (95 requested) and removed 26 (54 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.72 1.77 NCS extension: 5 residues added (0 deleted due to clashes), 2012 seeds are put forward Round 1: 193 peptides, 3 chains. Longest chain 99 peptides. Score 0.957 Round 2: 193 peptides, 3 chains. Longest chain 99 peptides. Score 0.957 Round 3: 192 peptides, 3 chains. Longest chain 99 peptides. Score 0.956 Round 4: 190 peptides, 6 chains. Longest chain 99 peptides. Score 0.935 Round 5: 189 peptides, 5 chains. Longest chain 71 peptides. Score 0.941 Taking the results from Round 2 Chains 3, Residues 190, Estimated correctness of the model 99.9 % 3 chains (190 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 86 B and 89 B 2 chains (192 residues) following loop building 2 chains (192 residues) in sequence following loop building ------------------------------------------------------ 22446 reflections ( 97.68 % complete ) and 1842 restraints for refining 1900 atoms. 257 conditional restraints added. Observations/parameters ratio is 2.95 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1957 (Rfree = 0.000) for 1900 atoms. Found 89 (89 requested) and removed 22 (51 requested) atoms. Cycle 22: After refmac, R = 0.1876 (Rfree = 0.000) for 1964 atoms. Found 64 (92 requested) and removed 17 (53 requested) atoms. Cycle 23: After refmac, R = 0.1828 (Rfree = 0.000) for 2007 atoms. Found 43 (94 requested) and removed 30 (54 requested) atoms. Cycle 24: After refmac, R = 0.1812 (Rfree = 0.000) for 2014 atoms. Found 46 (92 requested) and removed 20 (54 requested) atoms. Cycle 25: After refmac, R = 0.1789 (Rfree = 0.000) for 2039 atoms. Found 42 (93 requested) and removed 23 (55 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.72 1.77 NCS extension: 4 residues added (0 deleted due to clashes), 2062 seeds are put forward Round 1: 193 peptides, 3 chains. Longest chain 99 peptides. Score 0.957 Round 2: 192 peptides, 2 chains. Longest chain 97 peptides. Score 0.962 Round 3: 192 peptides, 4 chains. Longest chain 99 peptides. Score 0.950 Round 4: 192 peptides, 2 chains. Longest chain 97 peptides. Score 0.962 Round 5: 193 peptides, 3 chains. Longest chain 99 peptides. Score 0.957 Taking the results from Round 4 Chains 2, Residues 190, Estimated correctness of the model 99.9 % 2 chains (190 residues) have been docked in sequence Building loops using Loopy2018 2 chains (190 residues) following loop building 2 chains (190 residues) in sequence following loop building ------------------------------------------------------ 22446 reflections ( 97.68 % complete ) and 1895 restraints for refining 1921 atoms. 327 conditional restraints added. Observations/parameters ratio is 2.92 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1931 (Rfree = 0.000) for 1921 atoms. Found 85 (85 requested) and removed 22 (52 requested) atoms. Cycle 27: After refmac, R = 0.1892 (Rfree = 0.000) for 1977 atoms. Found 60 (89 requested) and removed 20 (54 requested) atoms. Cycle 28: After refmac, R = 0.1838 (Rfree = 0.000) for 2014 atoms. Found 53 (89 requested) and removed 28 (54 requested) atoms. Cycle 29: After refmac, R = 0.1812 (Rfree = 0.000) for 2037 atoms. Found 51 (89 requested) and removed 18 (55 requested) atoms. Cycle 30: After refmac, R = 0.1788 (Rfree = 0.000) for 2067 atoms. Found 47 (90 requested) and removed 32 (56 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.71 1.76 NCS extension: 0 residues added, 2082 seeds are put forward Round 1: 194 peptides, 3 chains. Longest chain 100 peptides. Score 0.957 Round 2: 195 peptides, 2 chains. Longest chain 100 peptides. Score 0.964 Round 3: 193 peptides, 4 chains. Longest chain 93 peptides. Score 0.951 Round 4: 194 peptides, 3 chains. Longest chain 100 peptides. Score 0.957 Round 5: 194 peptides, 3 chains. Longest chain 100 peptides. Score 0.957 Taking the results from Round 2 Chains 2, Residues 193, Estimated correctness of the model 99.9 % 2 chains (193 residues) have been docked in sequence Building loops using Loopy2018 2 chains (193 residues) following loop building 2 chains (193 residues) in sequence following loop building ------------------------------------------------------ 22446 reflections ( 97.68 % complete ) and 1887 restraints for refining 1956 atoms. 294 conditional restraints added. Observations/parameters ratio is 2.87 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1926 (Rfree = 0.000) for 1956 atoms. Found 83 (83 requested) and removed 27 (53 requested) atoms. Cycle 32: After refmac, R = 0.1867 (Rfree = 0.000) for 2006 atoms. Found 53 (85 requested) and removed 16 (54 requested) atoms. Cycle 33: After refmac, R = 0.1839 (Rfree = 0.000) for 2040 atoms. Found 40 (87 requested) and removed 23 (55 requested) atoms. Cycle 34: After refmac, R = 0.1803 (Rfree = 0.000) for 2048 atoms. Found 46 (84 requested) and removed 19 (55 requested) atoms. Cycle 35: After refmac, R = 0.1795 (Rfree = 0.000) for 2071 atoms. Found 42 (85 requested) and removed 28 (56 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.72 1.77 NCS extension: 5 residues added (0 deleted due to clashes), 2090 seeds are put forward Round 1: 192 peptides, 3 chains. Longest chain 99 peptides. Score 0.956 Round 2: 194 peptides, 2 chains. Longest chain 99 peptides. Score 0.963 Round 3: 192 peptides, 4 chains. Longest chain 99 peptides. Score 0.950 Round 4: 194 peptides, 3 chains. Longest chain 95 peptides. Score 0.957 Round 5: 190 peptides, 6 chains. Longest chain 92 peptides. Score 0.935 Taking the results from Round 2 Chains 2, Residues 192, Estimated correctness of the model 99.9 % 2 chains (192 residues) have been docked in sequence Building loops using Loopy2018 2 chains (192 residues) following loop building 2 chains (192 residues) in sequence following loop building ------------------------------------------------------ 22446 reflections ( 97.68 % complete ) and 1883 restraints for refining 1952 atoms. 298 conditional restraints added. Observations/parameters ratio is 2.87 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1913 (Rfree = 0.000) for 1952 atoms. Found 78 (78 requested) and removed 24 (53 requested) atoms. Cycle 37: After refmac, R = 0.1842 (Rfree = 0.000) for 1999 atoms. Found 70 (81 requested) and removed 17 (54 requested) atoms. Cycle 38: After refmac, R = 0.1792 (Rfree = 0.000) for 2050 atoms. Found 50 (82 requested) and removed 28 (55 requested) atoms. Cycle 39: After refmac, R = 0.1782 (Rfree = 0.000) for 2066 atoms. Found 50 (81 requested) and removed 23 (56 requested) atoms. Cycle 40: After refmac, R = 0.1780 (Rfree = 0.000) for 2090 atoms. Found 49 (81 requested) and removed 27 (56 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.72 1.77 NCS extension: 4 residues added (0 deleted due to clashes), 2116 seeds are put forward Round 1: 193 peptides, 3 chains. Longest chain 99 peptides. Score 0.957 Round 2: 195 peptides, 2 chains. Longest chain 100 peptides. Score 0.964 Round 3: 194 peptides, 3 chains. Longest chain 100 peptides. Score 0.957 Round 4: 195 peptides, 2 chains. Longest chain 100 peptides. Score 0.964 Round 5: 190 peptides, 4 chains. Longest chain 90 peptides. Score 0.948 Taking the results from Round 4 Chains 2, Residues 193, Estimated correctness of the model 99.9 % 2 chains (193 residues) have been docked in sequence Building loops using Loopy2018 2 chains (193 residues) following loop building 2 chains (193 residues) in sequence following loop building ------------------------------------------------------ 22446 reflections ( 97.68 % complete ) and 1896 restraints for refining 1967 atoms. 303 conditional restraints added. Observations/parameters ratio is 2.85 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1928 (Rfree = 0.000) for 1967 atoms. Found 75 (75 requested) and removed 22 (53 requested) atoms. Cycle 42: After refmac, R = 0.1861 (Rfree = 0.000) for 2016 atoms. Found 56 (76 requested) and removed 17 (54 requested) atoms. Cycle 43: After refmac, R = 0.1814 (Rfree = 0.000) for 2052 atoms. Found 55 (78 requested) and removed 18 (55 requested) atoms. Cycle 44: After refmac, R = 0.1790 (Rfree = 0.000) for 2084 atoms. Found 46 (79 requested) and removed 24 (56 requested) atoms. Cycle 45: After refmac, R = 0.1770 (Rfree = 0.000) for 2101 atoms. Found 50 (78 requested) and removed 18 (57 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.72 1.77 NCS extension: 5 residues added (0 deleted due to clashes), 2138 seeds are put forward Round 1: 194 peptides, 3 chains. Longest chain 100 peptides. Score 0.957 Round 2: 192 peptides, 2 chains. Longest chain 97 peptides. Score 0.962 Round 3: 195 peptides, 2 chains. Longest chain 100 peptides. Score 0.964 Round 4: 192 peptides, 4 chains. Longest chain 100 peptides. Score 0.950 Round 5: 189 peptides, 3 chains. Longest chain 97 peptides. Score 0.954 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 2, Residues 193, Estimated correctness of the model 99.9 % 2 chains (193 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 2 chains (193 residues) following loop building 2 chains (193 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 22446 reflections ( 97.68 % complete ) and 1593 restraints for refining 1562 atoms. Observations/parameters ratio is 3.59 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2478 (Rfree = 0.000) for 1562 atoms. Found 36 (58 requested) and removed 0 (58 requested) atoms. Cycle 47: After refmac, R = 0.2257 (Rfree = 0.000) for 1562 atoms. Found 20 (58 requested) and removed 0 (43 requested) atoms. Cycle 48: After refmac, R = 0.2127 (Rfree = 0.000) for 1562 atoms. Found 14 (60 requested) and removed 1 (44 requested) atoms. Cycle 49: After refmac, R = 0.2062 (Rfree = 0.000) for 1562 atoms. Found 13 (60 requested) and removed 1 (44 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:08:39 GMT 2018 Job finished. TimeTaking 45.72 Used memory is bytes: 22286848