Sun 23 Dec 23:50:34 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2od4-1.7-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2od4-1.7-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2od4-1.7-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2od4-1.7-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2od4-1.7-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2od4-1.7-parrot-mrncs ############### 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 23:50:38 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/mrncs/ArpWArp/wArpResults/WorkingDir/2od4-1.7-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2od4-1.7-parrot-mrncs/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-mrncs.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-mrncs.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 1804 atoms. Observations/parameters ratio is 3.11 ------------------------------------------------------ Starting model: R = 0.3350 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2798 (Rfree = 0.000) for 1804 atoms. Found 82 (98 requested) and removed 57 (49 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.81 1.86 NCS extension: 0 residues added, 1829 seeds are put forward Round 1: 162 peptides, 14 chains. Longest chain 31 peptides. Score 0.804 Round 2: 181 peptides, 5 chains. Longest chain 68 peptides. Score 0.933 Round 3: 189 peptides, 5 chains. Longest chain 70 peptides. Score 0.941 Round 4: 190 peptides, 4 chains. Longest chain 94 peptides. Score 0.948 Round 5: 191 peptides, 4 chains. Longest chain 99 peptides. Score 0.949 Taking the results from Round 5 Chains 5, Residues 187, Estimated correctness of the model 99.8 % 4 chains (183 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 36 A and 40 A Built loop between residues 86 A and 89 A 3 chains (192 residues) following loop building 2 chains (188 residues) in sequence following loop building ------------------------------------------------------ 22446 reflections ( 97.68 % complete ) and 1830 restraints for refining 1787 atoms. 272 conditional restraints added. Observations/parameters ratio is 3.14 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2829 (Rfree = 0.000) for 1787 atoms. Found 66 (97 requested) and removed 43 (48 requested) atoms. Cycle 2: After refmac, R = 0.2473 (Rfree = 0.000) for 1807 atoms. Found 67 (96 requested) and removed 12 (49 requested) atoms. Cycle 3: After refmac, R = 0.2304 (Rfree = 0.000) for 1848 atoms. Found 51 (99 requested) and removed 7 (50 requested) atoms. Cycle 4: After refmac, R = 0.2196 (Rfree = 0.000) for 1881 atoms. Found 45 (101 requested) and removed 7 (51 requested) atoms. Cycle 5: After refmac, R = 0.2118 (Rfree = 0.000) for 1912 atoms. Found 34 (102 requested) and removed 10 (52 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.73 1.78 NCS extension: 4 residues added (2 deleted due to clashes), 1941 seeds are put forward Round 1: 191 peptides, 4 chains. Longest chain 98 peptides. Score 0.949 Round 2: 194 peptides, 2 chains. Longest chain 99 peptides. Score 0.963 Round 3: 192 peptides, 5 chains. Longest chain 72 peptides. Score 0.943 Round 4: 193 peptides, 3 chains. Longest chain 94 peptides. Score 0.957 Round 5: 192 peptides, 4 chains. Longest chain 100 peptides. Score 0.950 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 1822 restraints for refining 1851 atoms. 237 conditional restraints added. Observations/parameters ratio is 3.03 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2159 (Rfree = 0.000) for 1851 atoms. Found 65 (98 requested) and removed 28 (50 requested) atoms. Cycle 7: After refmac, R = 0.2016 (Rfree = 0.000) for 1886 atoms. Found 47 (100 requested) and removed 11 (51 requested) atoms. Cycle 8: After refmac, R = 0.1939 (Rfree = 0.000) for 1918 atoms. Found 44 (102 requested) and removed 16 (52 requested) atoms. Cycle 9: After refmac, R = 0.1896 (Rfree = 0.000) for 1943 atoms. Found 35 (103 requested) and removed 12 (52 requested) atoms. Cycle 10: After refmac, R = 0.1854 (Rfree = 0.000) for 1962 atoms. Found 42 (105 requested) and removed 14 (53 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.73 1.78 NCS extension: 4 residues added (0 deleted due to clashes), 1994 seeds are put forward Round 1: 195 peptides, 2 chains. Longest chain 100 peptides. Score 0.964 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: 194 peptides, 3 chains. Longest chain 100 peptides. Score 0.957 Round 5: 192 peptides, 4 chains. Longest chain 81 peptides. Score 0.950 Taking the results from Round 1 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 1805 restraints for refining 1877 atoms. 212 conditional restraints added. Observations/parameters ratio is 2.99 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2006 (Rfree = 0.000) for 1877 atoms. Found 63 (100 requested) and removed 29 (51 requested) atoms. Cycle 12: After refmac, R = 0.1907 (Rfree = 0.000) for 1910 atoms. Found 48 (102 requested) and removed 17 (52 requested) atoms. Cycle 13: After refmac, R = 0.1822 (Rfree = 0.000) for 1940 atoms. Found 55 (103 requested) and removed 9 (52 requested) atoms. Cycle 14: After refmac, R = 0.1801 (Rfree = 0.000) for 1983 atoms. Found 40 (106 requested) and removed 25 (54 requested) atoms. Cycle 15: After refmac, R = 0.1775 (Rfree = 0.000) for 1997 atoms. Found 52 (104 requested) and removed 25 (54 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.72 1.77 NCS extension: 5 residues added (0 deleted due to clashes), 2030 seeds are put forward Round 1: 194 peptides, 2 chains. Longest chain 99 peptides. Score 0.963 Round 2: 193 peptides, 3 chains. Longest chain 99 peptides. Score 0.957 Round 3: 193 peptides, 3 chains. Longest chain 99 peptides. Score 0.957 Round 4: 193 peptides, 3 chains. Longest chain 99 peptides. Score 0.957 Round 5: 193 peptides, 3 chains. Longest chain 99 peptides. Score 0.957 Taking the results from Round 1 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 1844 restraints for refining 1902 atoms. 259 conditional restraints added. Observations/parameters ratio is 2.95 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1935 (Rfree = 0.000) for 1902 atoms. Found 88 (99 requested) and removed 24 (51 requested) atoms. Cycle 17: After refmac, R = 0.1907 (Rfree = 0.000) for 1965 atoms. Found 42 (103 requested) and removed 29 (53 requested) atoms. Cycle 18: After refmac, R = 0.1818 (Rfree = 0.000) for 1973 atoms. Found 49 (101 requested) and removed 22 (53 requested) atoms. Cycle 19: After refmac, R = 0.1806 (Rfree = 0.000) for 1996 atoms. Found 48 (102 requested) and removed 26 (54 requested) atoms. Cycle 20: After refmac, R = 0.1781 (Rfree = 0.000) for 2014 atoms. Found 48 (100 requested) and removed 29 (54 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.71 1.76 NCS extension: 4 residues added (0 deleted due to clashes), 2037 seeds are put forward Round 1: 192 peptides, 4 chains. Longest chain 81 peptides. Score 0.950 Round 2: 193 peptides, 3 chains. Longest chain 99 peptides. Score 0.957 Round 3: 193 peptides, 3 chains. Longest chain 99 peptides. Score 0.957 Round 4: 191 peptides, 5 chains. Longest chain 70 peptides. Score 0.942 Round 5: 194 peptides, 2 chains. Longest chain 99 peptides. Score 0.963 Taking the results from Round 5 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 1847 restraints for refining 1910 atoms. 262 conditional restraints added. Observations/parameters ratio is 2.94 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1950 (Rfree = 0.000) for 1910 atoms. Found 73 (93 requested) and removed 28 (51 requested) atoms. Cycle 22: After refmac, R = 0.1865 (Rfree = 0.000) for 1952 atoms. Found 48 (95 requested) and removed 23 (53 requested) atoms. Cycle 23: After refmac, R = 0.1823 (Rfree = 0.000) for 1975 atoms. Found 57 (96 requested) and removed 14 (53 requested) atoms. Cycle 24: After refmac, R = 0.1806 (Rfree = 0.000) for 2015 atoms. Found 58 (98 requested) and removed 23 (54 requested) atoms. Cycle 25: After refmac, R = 0.1794 (Rfree = 0.000) for 2047 atoms. Found 56 (100 requested) and removed 42 (55 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.71 1.76 NCS extension: 4 residues added (0 deleted due to clashes), 2065 seeds are put forward Round 1: 193 peptides, 3 chains. Longest chain 99 peptides. Score 0.957 Round 2: 194 peptides, 2 chains. Longest chain 99 peptides. Score 0.963 Round 3: 193 peptides, 3 chains. Longest chain 99 peptides. Score 0.957 Round 4: 193 peptides, 3 chains. Longest chain 99 peptides. Score 0.957 Round 5: 193 peptides, 3 chains. Longest chain 99 peptides. Score 0.957 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 1858 restraints for refining 1924 atoms. 273 conditional restraints added. Observations/parameters ratio is 2.92 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1945 (Rfree = 0.000) for 1924 atoms. Found 89 (92 requested) and removed 26 (52 requested) atoms. Cycle 27: After refmac, R = 0.1907 (Rfree = 0.000) for 1984 atoms. Found 49 (95 requested) and removed 17 (54 requested) atoms. Cycle 28: After refmac, R = 0.1840 (Rfree = 0.000) for 2012 atoms. Found 58 (96 requested) and removed 18 (54 requested) atoms. Cycle 29: After refmac, R = 0.1842 (Rfree = 0.000) for 2050 atoms. Found 29 (98 requested) and removed 33 (55 requested) atoms. Cycle 30: After refmac, R = 0.1773 (Rfree = 0.000) for 2043 atoms. Found 47 (95 requested) and removed 17 (55 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.72 1.77 NCS extension: 4 residues added (0 deleted due to clashes), 2077 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: 193 peptides, 3 chains. Longest chain 99 peptides. Score 0.957 Round 4: 192 peptides, 2 chains. Longest chain 97 peptides. Score 0.962 Round 5: 190 peptides, 4 chains. Longest chain 99 peptides. Score 0.948 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 1897 restraints for refining 1923 atoms. 329 conditional restraints added. Observations/parameters ratio is 2.92 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1967 (Rfree = 0.000) for 1923 atoms. Found 89 (89 requested) and removed 24 (52 requested) atoms. Cycle 32: After refmac, R = 0.1935 (Rfree = 0.000) for 1984 atoms. Found 61 (93 requested) and removed 24 (54 requested) atoms. Cycle 33: After refmac, R = 0.1881 (Rfree = 0.000) for 2020 atoms. Found 57 (95 requested) and removed 23 (55 requested) atoms. Cycle 34: After refmac, R = 0.1864 (Rfree = 0.000) for 2054 atoms. Found 54 (95 requested) and removed 32 (55 requested) atoms. Cycle 35: After refmac, R = 0.1837 (Rfree = 0.000) for 2067 atoms. Found 54 (95 requested) and removed 33 (56 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.71 1.76 NCS extension: 0 residues added, 2088 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: 191 peptides, 3 chains. Longest chain 99 peptides. Score 0.955 Round 4: 192 peptides, 4 chains. Longest chain 99 peptides. Score 0.950 Round 5: 192 peptides, 4 chains. Longest chain 95 peptides. Score 0.950 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 1875 restraints for refining 1938 atoms. 290 conditional restraints added. Observations/parameters ratio is 2.90 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1958 (Rfree = 0.000) for 1938 atoms. Found 86 (86 requested) and removed 23 (52 requested) atoms. Cycle 37: After refmac, R = 0.1937 (Rfree = 0.000) for 1998 atoms. Found 58 (89 requested) and removed 23 (54 requested) atoms. Cycle 38: After refmac, R = 0.1855 (Rfree = 0.000) for 2030 atoms. Found 61 (90 requested) and removed 23 (55 requested) atoms. Cycle 39: After refmac, R = 0.1829 (Rfree = 0.000) for 2066 atoms. Found 46 (92 requested) and removed 31 (56 requested) atoms. Cycle 40: After refmac, R = 0.1804 (Rfree = 0.000) for 2075 atoms. Found 55 (90 requested) and removed 28 (56 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.71 1.76 NCS extension: 4 residues added (0 deleted due to clashes), 2106 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: 191 peptides, 3 chains. Longest chain 99 peptides. Score 0.955 Round 4: 192 peptides, 4 chains. Longest chain 99 peptides. Score 0.950 Round 5: 193 peptides, 3 chains. Longest chain 99 peptides. Score 0.957 Taking the results from Round 5 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 41 B and 44 B 2 chains (192 residues) following loop building 2 chains (192 residues) in sequence following loop building ------------------------------------------------------ 22446 reflections ( 97.68 % complete ) and 1890 restraints for refining 1947 atoms. 305 conditional restraints added. Observations/parameters ratio is 2.88 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1946 (Rfree = 0.000) for 1947 atoms. Found 82 (82 requested) and removed 21 (52 requested) atoms. Cycle 42: After refmac, R = 0.1897 (Rfree = 0.000) for 2005 atoms. Found 60 (85 requested) and removed 25 (54 requested) atoms. Cycle 43: After refmac, R = 0.1849 (Rfree = 0.000) for 2039 atoms. Found 44 (87 requested) and removed 33 (55 requested) atoms. Cycle 44: After refmac, R = 0.1837 (Rfree = 0.000) for 2046 atoms. Found 66 (84 requested) and removed 35 (55 requested) atoms. Cycle 45: After refmac, R = 0.1824 (Rfree = 0.000) for 2070 atoms. Found 63 (84 requested) and removed 41 (56 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.72 1.77 NCS extension: 4 residues added (0 deleted due to clashes), 2096 seeds are put forward Round 1: 193 peptides, 3 chains. Longest chain 99 peptides. Score 0.957 Round 2: 194 peptides, 2 chains. Longest chain 99 peptides. Score 0.963 Round 3: 191 peptides, 3 chains. Longest chain 99 peptides. Score 0.955 Round 4: 192 peptides, 4 chains. Longest chain 92 peptides. Score 0.950 Round 5: 194 peptides, 2 chains. Longest chain 99 peptides. Score 0.963 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 2, Residues 192, Estimated correctness of the model 99.9 % 2 chains (192 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 2 chains (192 residues) following loop building 2 chains (192 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 22446 reflections ( 97.68 % complete ) and 1585 restraints for refining 1554 atoms. Observations/parameters ratio is 3.61 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2487 (Rfree = 0.000) for 1554 atoms. Found 36 (60 requested) and removed 0 (60 requested) atoms. Cycle 47: After refmac, R = 0.2279 (Rfree = 0.000) for 1554 atoms. Found 21 (62 requested) and removed 0 (43 requested) atoms. Cycle 48: After refmac, R = 0.2155 (Rfree = 0.000) for 1554 atoms. Found 8 (63 requested) and removed 1 (43 requested) atoms. Cycle 49: After refmac, R = 0.2090 (Rfree = 0.000) for 1554 atoms. TimeTaking 29.93