Mon 24 Dec 07:29:54 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 2od4-1.7-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2od4-1.7-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2od4-1.7-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2od4-1.7-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/2od4-1.7-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2od4-1.7-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 07:29:59 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/2od4-1.7-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2od4-1.7-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 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-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: 4 Cell parameters: 31.890 77.790 43.810 90.000 102.660 90.000 Input sequence file: 2od4-1.7-parrot-noncs.fasta_lf Building free atoms model in initial map for 1616 target number of atoms Had to go as low as 0.40 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 1783 atoms. Observations/parameters ratio is 3.15 ------------------------------------------------------ Starting model: R = 0.3354 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2875 (Rfree = 0.000) for 1783 atoms. Found 74 (97 requested) and removed 49 (48 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.82 1.87 NCS extension: 0 residues added, 1808 seeds are put forward Round 1: 137 peptides, 17 chains. Longest chain 17 peptides. Score 0.654 Round 2: 168 peptides, 13 chains. Longest chain 54 peptides. Score 0.833 Round 3: 175 peptides, 11 chains. Longest chain 49 peptides. Score 0.871 Round 4: 183 peptides, 8 chains. Longest chain 51 peptides. Score 0.911 Round 5: 186 peptides, 5 chains. Longest chain 70 peptides. Score 0.938 Taking the results from Round 5 Chains 6, Residues 181, Estimated correctness of the model 99.7 % 3 chains (161 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 52 A and 58 A 4 chains (185 residues) following loop building 2 chains (166 residues) in sequence following loop building ------------------------------------------------------ 22446 reflections ( 97.68 % complete ) and 1951 restraints for refining 1745 atoms. 518 conditional restraints added. Observations/parameters ratio is 3.22 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3004 (Rfree = 0.000) for 1745 atoms. Found 70 (94 requested) and removed 49 (47 requested) atoms. Cycle 2: After refmac, R = 0.2668 (Rfree = 0.000) for 1762 atoms. Found 59 (94 requested) and removed 24 (48 requested) atoms. Cycle 3: After refmac, R = 0.2470 (Rfree = 0.000) for 1790 atoms. Found 58 (95 requested) and removed 15 (48 requested) atoms. Cycle 4: After refmac, R = 0.2359 (Rfree = 0.000) for 1818 atoms. Found 51 (97 requested) and removed 13 (49 requested) atoms. Cycle 5: After refmac, R = 0.2260 (Rfree = 0.000) for 1850 atoms. Found 42 (99 requested) and removed 11 (50 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.74 1.79 NCS extension: 91 residues added (12 deleted due to clashes), 1972 seeds are put forward Round 1: 191 peptides, 3 chains. Longest chain 98 peptides. Score 0.955 Round 2: 192 peptides, 2 chains. Longest chain 98 peptides. Score 0.962 Round 3: 191 peptides, 3 chains. Longest chain 98 peptides. Score 0.955 Round 4: 188 peptides, 5 chains. Longest chain 98 peptides. Score 0.940 Round 5: 192 peptides, 3 chains. Longest chain 98 peptides. Score 0.956 Taking the results from Round 2 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 1839 restraints for refining 1819 atoms. 274 conditional restraints added. Observations/parameters ratio is 3.08 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2242 (Rfree = 0.000) for 1819 atoms. Found 66 (97 requested) and removed 40 (49 requested) atoms. Cycle 7: After refmac, R = 0.2118 (Rfree = 0.000) for 1844 atoms. Found 57 (96 requested) and removed 10 (50 requested) atoms. Cycle 8: After refmac, R = 0.2044 (Rfree = 0.000) for 1889 atoms. Found 56 (98 requested) and removed 18 (51 requested) atoms. Cycle 9: After refmac, R = 0.1974 (Rfree = 0.000) for 1924 atoms. Found 42 (100 requested) and removed 19 (52 requested) atoms. Cycle 10: After refmac, R = 0.1942 (Rfree = 0.000) for 1945 atoms. Found 40 (101 requested) and removed 21 (52 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.73 1.78 NCS extension: 4 residues added (0 deleted due to clashes), 1968 seeds are put forward Round 1: 194 peptides, 2 chains. Longest chain 99 peptides. Score 0.963 Round 2: 191 peptides, 3 chains. Longest chain 97 peptides. Score 0.955 Round 3: 193 peptides, 3 chains. Longest chain 99 peptides. Score 0.957 Round 4: 194 peptides, 2 chains. Longest chain 99 peptides. Score 0.963 Round 5: 190 peptides, 4 chains. Longest chain 97 peptides. Score 0.948 Taking the results from Round 4 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 1838 restraints for refining 1878 atoms. 253 conditional restraints added. Observations/parameters ratio is 2.99 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2026 (Rfree = 0.000) for 1878 atoms. Found 74 (96 requested) and removed 23 (51 requested) atoms. Cycle 12: After refmac, R = 0.1937 (Rfree = 0.000) for 1925 atoms. Found 36 (99 requested) and removed 26 (52 requested) atoms. Cycle 13: After refmac, R = 0.1858 (Rfree = 0.000) for 1934 atoms. Found 48 (97 requested) and removed 11 (52 requested) atoms. Cycle 14: After refmac, R = 0.1828 (Rfree = 0.000) for 1968 atoms. Found 35 (98 requested) and removed 16 (53 requested) atoms. Cycle 15: After refmac, R = 0.1789 (Rfree = 0.000) for 1983 atoms. Found 31 (99 requested) and removed 12 (54 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.73 1.78 NCS extension: 4 residues added (0 deleted due to clashes), 2006 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: 194 peptides, 2 chains. Longest chain 99 peptides. Score 0.963 Round 5: 192 peptides, 4 chains. Longest chain 99 peptides. Score 0.950 Taking the results from Round 4 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 1854 restraints for refining 1900 atoms. 269 conditional restraints added. Observations/parameters ratio is 2.95 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1948 (Rfree = 0.000) for 1900 atoms. Found 82 (95 requested) and removed 21 (51 requested) atoms. Cycle 17: After refmac, R = 0.1878 (Rfree = 0.000) for 1957 atoms. Found 45 (98 requested) and removed 14 (53 requested) atoms. Cycle 18: After refmac, R = 0.1817 (Rfree = 0.000) for 1986 atoms. Found 38 (99 requested) and removed 13 (54 requested) atoms. Cycle 19: After refmac, R = 0.1772 (Rfree = 0.000) for 2005 atoms. Found 39 (100 requested) and removed 10 (54 requested) atoms. Cycle 20: After refmac, R = 0.1753 (Rfree = 0.000) for 2033 atoms. Found 34 (101 requested) and removed 17 (55 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.73 1.78 NCS extension: 4 residues added (0 deleted due to clashes), 2054 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: 193 peptides, 3 chains. Longest chain 99 peptides. Score 0.957 Round 4: 191 peptides, 3 chains. Longest chain 97 peptides. Score 0.955 Round 5: 193 peptides, 3 chains. Longest chain 99 peptides. Score 0.957 Taking the results from Round 2 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 1899 restraints for refining 1919 atoms. 331 conditional restraints added. Observations/parameters ratio is 2.92 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1908 (Rfree = 0.000) for 1919 atoms. Found 92 (96 requested) and removed 27 (52 requested) atoms. Cycle 22: After refmac, R = 0.1863 (Rfree = 0.000) for 1977 atoms. Found 58 (99 requested) and removed 22 (54 requested) atoms. Cycle 23: After refmac, R = 0.1812 (Rfree = 0.000) for 2009 atoms. Found 59 (100 requested) and removed 24 (54 requested) atoms. Cycle 24: After refmac, R = 0.1789 (Rfree = 0.000) for 2042 atoms. Found 35 (102 requested) and removed 31 (55 requested) atoms. Cycle 25: After refmac, R = 0.1742 (Rfree = 0.000) for 2042 atoms. Found 57 (100 requested) and removed 21 (55 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.72 1.77 NCS extension: 0 residues added, 2078 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 97 peptides. Score 0.955 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 1863 restraints for refining 1930 atoms. 278 conditional restraints added. Observations/parameters ratio is 2.91 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1904 (Rfree = 0.000) for 1930 atoms. Found 94 (94 requested) and removed 16 (52 requested) atoms. Cycle 27: After refmac, R = 0.1854 (Rfree = 0.000) for 2001 atoms. Found 54 (98 requested) and removed 31 (54 requested) atoms. Cycle 28: After refmac, R = 0.1808 (Rfree = 0.000) for 2018 atoms. Found 49 (97 requested) and removed 22 (55 requested) atoms. Cycle 29: After refmac, R = 0.1764 (Rfree = 0.000) for 2042 atoms. Found 54 (98 requested) and removed 23 (55 requested) atoms. Cycle 30: After refmac, R = 0.1765 (Rfree = 0.000) for 2069 atoms. Found 58 (99 requested) and removed 35 (56 requested) atoms. ------------------------------------------------------ Building Cycle 7 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: 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: 194 peptides, 2 chains. Longest chain 99 peptides. Score 0.963 Round 5: 192 peptides, 2 chains. Longest chain 97 peptides. Score 0.962 Taking the results from Round 4 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 1902 restraints for refining 1948 atoms. 317 conditional restraints added. Observations/parameters ratio is 2.88 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1899 (Rfree = 0.000) for 1948 atoms. Found 91 (91 requested) and removed 21 (53 requested) atoms. Cycle 32: After refmac, R = 0.1871 (Rfree = 0.000) for 2011 atoms. Found 65 (94 requested) and removed 21 (54 requested) atoms. Cycle 33: After refmac, R = 0.1816 (Rfree = 0.000) for 2050 atoms. Found 51 (95 requested) and removed 21 (55 requested) atoms. Cycle 34: After refmac, R = 0.1780 (Rfree = 0.000) for 2077 atoms. Found 43 (97 requested) and removed 23 (56 requested) atoms. Cycle 35: After refmac, R = 0.1750 (Rfree = 0.000) for 2087 atoms. Found 60 (96 requested) and removed 26 (57 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.71 1.76 NCS extension: 4 residues added (0 deleted due to clashes), 2125 seeds are put forward Round 1: 193 peptides, 3 chains. Longest chain 99 peptides. Score 0.957 Round 2: 190 peptides, 3 chains. Longest chain 97 peptides. Score 0.954 Round 3: 193 peptides, 2 chains. Longest chain 99 peptides. Score 0.963 Round 4: 191 peptides, 4 chains. Longest chain 99 peptides. Score 0.949 Round 5: 190 peptides, 3 chains. Longest chain 97 peptides. Score 0.954 Taking the results from Round 3 Chains 2, Residues 191, Estimated correctness of the model 99.9 % 2 chains (191 residues) have been docked in sequence Building loops using Loopy2018 2 chains (191 residues) following loop building 2 chains (191 residues) in sequence following loop building ------------------------------------------------------ 22446 reflections ( 97.68 % complete ) and 1928 restraints for refining 1960 atoms. 351 conditional restraints added. Observations/parameters ratio is 2.86 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1884 (Rfree = 0.000) for 1960 atoms. Found 89 (89 requested) and removed 18 (53 requested) atoms. Cycle 37: After refmac, R = 0.1826 (Rfree = 0.000) for 2027 atoms. Found 56 (92 requested) and removed 17 (55 requested) atoms. Cycle 38: After refmac, R = 0.1781 (Rfree = 0.000) for 2059 atoms. Found 59 (94 requested) and removed 14 (56 requested) atoms. Cycle 39: After refmac, R = 0.1761 (Rfree = 0.000) for 2097 atoms. Found 47 (96 requested) and removed 26 (57 requested) atoms. Cycle 40: After refmac, R = 0.1734 (Rfree = 0.000) for 2113 atoms. Found 49 (94 requested) and removed 23 (57 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.72 1.77 NCS extension: 5 residues added (0 deleted due to clashes), 2144 seeds are put forward Round 1: 192 peptides, 3 chains. Longest chain 99 peptides. Score 0.956 Round 2: 192 peptides, 3 chains. Longest chain 99 peptides. Score 0.956 Round 3: 190 peptides, 3 chains. Longest chain 97 peptides. Score 0.954 Round 4: 191 peptides, 4 chains. Longest chain 80 peptides. Score 0.949 Round 5: 193 peptides, 2 chains. Longest chain 99 peptides. Score 0.963 Taking the results from Round 5 Chains 2, Residues 191, Estimated correctness of the model 99.9 % 2 chains (191 residues) have been docked in sequence Building loops using Loopy2018 2 chains (191 residues) following loop building 2 chains (191 residues) in sequence following loop building ------------------------------------------------------ 22446 reflections ( 97.68 % complete ) and 1964 restraints for refining 1981 atoms. 387 conditional restraints added. Observations/parameters ratio is 2.83 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1886 (Rfree = 0.000) for 1981 atoms. Found 88 (88 requested) and removed 21 (53 requested) atoms. Cycle 42: After refmac, R = 0.1840 (Rfree = 0.000) for 2044 atoms. Found 56 (91 requested) and removed 30 (55 requested) atoms. Cycle 43: After refmac, R = 0.1797 (Rfree = 0.000) for 2067 atoms. Found 56 (90 requested) and removed 22 (56 requested) atoms. Cycle 44: After refmac, R = 0.1783 (Rfree = 0.000) for 2100 atoms. Found 50 (91 requested) and removed 35 (57 requested) atoms. Cycle 45: After refmac, R = 0.1767 (Rfree = 0.000) for 2113 atoms. Found 48 (90 requested) and removed 28 (57 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.71 1.76 NCS extension: 5 residues added (0 deleted due to clashes), 2138 seeds are put forward Round 1: 193 peptides, 2 chains. Longest chain 99 peptides. Score 0.963 Round 2: 192 peptides, 3 chains. Longest chain 99 peptides. Score 0.956 Round 3: 193 peptides, 2 chains. Longest chain 99 peptides. Score 0.963 Round 4: 189 peptides, 4 chains. Longest chain 99 peptides. Score 0.947 Round 5: 193 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 191, Estimated correctness of the model 99.9 % 2 chains (191 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 2 chains (191 residues) following loop building 2 chains (191 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 22446 reflections ( 97.68 % complete ) and 1577 restraints for refining 1546 atoms. Observations/parameters ratio is 3.63 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2512 (Rfree = 0.000) for 1546 atoms. Found 42 (64 requested) and removed 0 (64 requested) atoms. Cycle 47: After refmac, R = 0.2272 (Rfree = 0.000) for 1546 atoms. Found 18 (65 requested) and removed 0 (43 requested) atoms. Cycle 48: After refmac, R = 0.2149 (Rfree = 0.000) for 1546 atoms. Found 15 (66 requested) and removed 1 (43 requested) atoms. Cycle 49: After refmac, R = 0.2077 (Rfree = 0.000) for 1546 atoms. TimeTaking 30.77