Mon 24 Dec 00:42:13 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 2opl-1.5-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2opl-1.5-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2opl-1.5-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2opl-1.5-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/2opl-1.5-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2opl-1.5-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 ============================================================ Mon 24 Dec 00:42:18 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/2opl-1.5-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2opl-1.5-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 406 and 0 Target number of residues in the AU: 406 Target solvent content: 0.4115 Checking the provided sequence file Detected sequence length: 187 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 374 Adjusted target solvent content: 0.46 Input MTZ file: 2opl-1.5-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: 19 Cell parameters: 47.200 82.950 95.370 90.000 90.000 90.000 Input sequence file: 2opl-1.5-parrot-mrncs.fasta_lf Building free atoms model in initial map for 2992 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: 62.588 1.500 Wilson plot Bfac: 9.25 60683 reflections ( 99.87 % complete ) and 0 restraints for refining 3306 atoms. Observations/parameters ratio is 4.59 ------------------------------------------------------ Starting model: R = 0.3369 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2788 (Rfree = 0.000) for 3306 atoms. Found 257 (257 requested) and removed 138 (128 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.41 1.49 NCS extension: 0 residues added, 3425 seeds are put forward Round 1: 323 peptides, 14 chains. Longest chain 51 peptides. Score 0.912 Round 2: 343 peptides, 8 chains. Longest chain 119 peptides. Score 0.948 Round 3: 341 peptides, 9 chains. Longest chain 81 peptides. Score 0.944 Round 4: 345 peptides, 8 chains. Longest chain 78 peptides. Score 0.949 Round 5: 351 peptides, 4 chains. Longest chain 178 peptides. Score 0.965 Taking the results from Round 5 Chains 4, Residues 347, Estimated correctness of the model 99.9 % 4 chains (347 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 50 A and 56 A Built loop between residues 131 A and 136 A 2 chains (356 residues) following loop building 2 chains (356 residues) in sequence following loop building ------------------------------------------------------ 60683 reflections ( 99.87 % complete ) and 3100 restraints for refining 3214 atoms. 300 conditional restraints added. Observations/parameters ratio is 4.72 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2647 (Rfree = 0.000) for 3214 atoms. Found 154 (250 requested) and removed 62 (125 requested) atoms. Cycle 2: After refmac, R = 0.2402 (Rfree = 0.000) for 3304 atoms. Found 114 (257 requested) and removed 18 (128 requested) atoms. Cycle 3: After refmac, R = 0.2250 (Rfree = 0.000) for 3398 atoms. Found 92 (264 requested) and removed 9 (132 requested) atoms. Cycle 4: After refmac, R = 0.2012 (Rfree = 0.000) for 3476 atoms. Found 116 (270 requested) and removed 16 (135 requested) atoms. Cycle 5: After refmac, R = 0.1905 (Rfree = 0.000) for 3571 atoms. Found 102 (278 requested) and removed 27 (139 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.37 1.45 NCS extension: 2 residues added (176 deleted due to clashes), 3649 seeds are put forward Round 1: 352 peptides, 5 chains. Longest chain 125 peptides. Score 0.962 Round 2: 354 peptides, 3 chains. Longest chain 179 peptides. Score 0.969 Round 3: 348 peptides, 6 chains. Longest chain 113 peptides. Score 0.957 Round 4: 351 peptides, 5 chains. Longest chain 135 peptides. Score 0.962 Round 5: 354 peptides, 3 chains. Longest chain 179 peptides. Score 0.969 Taking the results from Round 5 Chains 3, Residues 351, Estimated correctness of the model 100.0 % 3 chains (351 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 131 A and 136 A 2 chains (355 residues) following loop building 2 chains (355 residues) in sequence following loop building ------------------------------------------------------ 60683 reflections ( 99.87 % complete ) and 3320 restraints for refining 3456 atoms. 526 conditional restraints added. Observations/parameters ratio is 4.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2237 (Rfree = 0.000) for 3456 atoms. Found 136 (268 requested) and removed 48 (134 requested) atoms. Cycle 7: After refmac, R = 0.1966 (Rfree = 0.000) for 3544 atoms. Found 134 (275 requested) and removed 18 (137 requested) atoms. Cycle 8: After refmac, R = 0.1870 (Rfree = 0.000) for 3656 atoms. Found 102 (284 requested) and removed 32 (142 requested) atoms. Cycle 9: After refmac, R = 0.1815 (Rfree = 0.000) for 3719 atoms. Found 103 (289 requested) and removed 39 (144 requested) atoms. Cycle 10: After refmac, R = 0.1782 (Rfree = 0.000) for 3780 atoms. Found 89 (294 requested) and removed 46 (147 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.37 1.45 NCS extension: 4 residues added (175 deleted due to clashes), 3828 seeds are put forward Round 1: 352 peptides, 5 chains. Longest chain 125 peptides. Score 0.962 Round 2: 351 peptides, 3 chains. Longest chain 179 peptides. Score 0.968 Round 3: 353 peptides, 6 chains. Longest chain 136 peptides. Score 0.959 Round 4: 353 peptides, 6 chains. Longest chain 114 peptides. Score 0.959 Round 5: 354 peptides, 5 chains. Longest chain 180 peptides. Score 0.963 Taking the results from Round 2 Chains 3, Residues 348, Estimated correctness of the model 99.9 % 3 chains (348 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 131 A and 139 A 2 chains (355 residues) following loop building 2 chains (355 residues) in sequence following loop building ------------------------------------------------------ 60683 reflections ( 99.87 % complete ) and 3417 restraints for refining 3529 atoms. 623 conditional restraints added. Observations/parameters ratio is 4.30 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2184 (Rfree = 0.000) for 3529 atoms. Found 147 (269 requested) and removed 45 (137 requested) atoms. Cycle 12: After refmac, R = 0.1942 (Rfree = 0.000) for 3625 atoms. Found 118 (276 requested) and removed 32 (141 requested) atoms. Cycle 13: After refmac, R = 0.1859 (Rfree = 0.000) for 3706 atoms. Found 111 (282 requested) and removed 39 (144 requested) atoms. Cycle 14: After refmac, R = 0.1815 (Rfree = 0.000) for 3769 atoms. Found 112 (287 requested) and removed 52 (146 requested) atoms. Cycle 15: After refmac, R = 0.1806 (Rfree = 0.000) for 3821 atoms. Found 99 (291 requested) and removed 64 (148 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.37 1.45 NCS extension: 3 residues added (176 deleted due to clashes), 3860 seeds are put forward Round 1: 349 peptides, 5 chains. Longest chain 125 peptides. Score 0.961 Round 2: 354 peptides, 3 chains. Longest chain 179 peptides. Score 0.969 Round 3: 354 peptides, 6 chains. Longest chain 136 peptides. Score 0.960 Round 4: 350 peptides, 5 chains. Longest chain 179 peptides. Score 0.961 Round 5: 354 peptides, 4 chains. Longest chain 127 peptides. Score 0.966 Taking the results from Round 2 Chains 3, Residues 351, Estimated correctness of the model 100.0 % 3 chains (351 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 131 A and 136 A 2 chains (355 residues) following loop building 2 chains (355 residues) in sequence following loop building ------------------------------------------------------ 60683 reflections ( 99.87 % complete ) and 3492 restraints for refining 3569 atoms. 698 conditional restraints added. Observations/parameters ratio is 4.25 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2184 (Rfree = 0.000) for 3569 atoms. Found 170 (266 requested) and removed 62 (138 requested) atoms. Cycle 17: After refmac, R = 0.1946 (Rfree = 0.000) for 3674 atoms. Found 99 (274 requested) and removed 42 (142 requested) atoms. Cycle 18: After refmac, R = 0.1847 (Rfree = 0.000) for 3722 atoms. Found 110 (278 requested) and removed 38 (145 requested) atoms. Cycle 19: After refmac, R = 0.1800 (Rfree = 0.000) for 3788 atoms. Found 80 (283 requested) and removed 50 (147 requested) atoms. Cycle 20: After refmac, R = 0.1758 (Rfree = 0.000) for 3807 atoms. Found 110 (278 requested) and removed 43 (148 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.37 1.45 NCS extension: 4 residues added (175 deleted due to clashes), 3879 seeds are put forward Round 1: 351 peptides, 4 chains. Longest chain 136 peptides. Score 0.965 Round 2: 355 peptides, 3 chains. Longest chain 180 peptides. Score 0.969 Round 3: 354 peptides, 4 chains. Longest chain 165 peptides. Score 0.966 Round 4: 352 peptides, 4 chains. Longest chain 137 peptides. Score 0.965 Round 5: 352 peptides, 6 chains. Longest chain 171 peptides. Score 0.959 Taking the results from Round 2 Chains 3, Residues 352, Estimated correctness of the model 100.0 % 3 chains (352 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 131 A and 136 A 2 chains (356 residues) following loop building 2 chains (356 residues) in sequence following loop building ------------------------------------------------------ 60683 reflections ( 99.87 % complete ) and 3484 restraints for refining 3590 atoms. 679 conditional restraints added. Observations/parameters ratio is 4.23 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2157 (Rfree = 0.000) for 3590 atoms. Found 151 (262 requested) and removed 44 (139 requested) atoms. Cycle 22: After refmac, R = 0.1915 (Rfree = 0.000) for 3691 atoms. Found 129 (270 requested) and removed 25 (143 requested) atoms. Cycle 23: After refmac, R = 0.1836 (Rfree = 0.000) for 3783 atoms. Found 89 (277 requested) and removed 41 (147 requested) atoms. Cycle 24: After refmac, R = 0.1789 (Rfree = 0.000) for 3820 atoms. Found 90 (279 requested) and removed 49 (148 requested) atoms. Cycle 25: After refmac, R = 0.1760 (Rfree = 0.000) for 3855 atoms. Found 109 (276 requested) and removed 46 (150 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.37 1.45 NCS extension: 4 residues added (176 deleted due to clashes), 3922 seeds are put forward Round 1: 355 peptides, 4 chains. Longest chain 137 peptides. Score 0.966 Round 2: 352 peptides, 3 chains. Longest chain 180 peptides. Score 0.968 Round 3: 354 peptides, 4 chains. Longest chain 165 peptides. Score 0.966 Round 4: 352 peptides, 4 chains. Longest chain 137 peptides. Score 0.965 Round 5: 354 peptides, 5 chains. Longest chain 181 peptides. Score 0.963 Taking the results from Round 2 Chains 3, Residues 349, Estimated correctness of the model 99.9 % 3 chains (349 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 131 A and 139 A 2 chains (356 residues) following loop building 2 chains (356 residues) in sequence following loop building ------------------------------------------------------ 60683 reflections ( 99.87 % complete ) and 3565 restraints for refining 3601 atoms. 760 conditional restraints added. Observations/parameters ratio is 4.21 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2158 (Rfree = 0.000) for 3601 atoms. Found 166 (258 requested) and removed 53 (140 requested) atoms. Cycle 27: After refmac, R = 0.1917 (Rfree = 0.000) for 3705 atoms. Found 99 (265 requested) and removed 26 (144 requested) atoms. Cycle 28: After refmac, R = 0.1823 (Rfree = 0.000) for 3774 atoms. Found 84 (270 requested) and removed 28 (146 requested) atoms. Cycle 29: After refmac, R = 0.1777 (Rfree = 0.000) for 3824 atoms. Found 97 (273 requested) and removed 41 (148 requested) atoms. Cycle 30: After refmac, R = 0.1758 (Rfree = 0.000) for 3868 atoms. Found 104 (277 requested) and removed 43 (150 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.37 1.45 NCS extension: 2 residues added (178 deleted due to clashes), 3932 seeds are put forward Round 1: 350 peptides, 4 chains. Longest chain 135 peptides. Score 0.965 Round 2: 353 peptides, 4 chains. Longest chain 163 peptides. Score 0.966 Round 3: 354 peptides, 3 chains. Longest chain 179 peptides. Score 0.969 Round 4: 352 peptides, 3 chains. Longest chain 180 peptides. Score 0.968 Round 5: 349 peptides, 6 chains. Longest chain 136 peptides. Score 0.958 Taking the results from Round 3 Chains 3, Residues 351, Estimated correctness of the model 100.0 % 3 chains (351 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 131 A and 136 A 2 chains (355 residues) following loop building 2 chains (355 residues) in sequence following loop building ------------------------------------------------------ 60683 reflections ( 99.87 % complete ) and 3541 restraints for refining 3611 atoms. 747 conditional restraints added. Observations/parameters ratio is 4.20 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2139 (Rfree = 0.000) for 3611 atoms. Found 153 (258 requested) and removed 48 (140 requested) atoms. Cycle 32: After refmac, R = 0.1908 (Rfree = 0.000) for 3712 atoms. Found 122 (266 requested) and removed 31 (144 requested) atoms. Cycle 33: After refmac, R = 0.1822 (Rfree = 0.000) for 3789 atoms. Found 91 (271 requested) and removed 32 (147 requested) atoms. Cycle 34: After refmac, R = 0.1771 (Rfree = 0.000) for 3838 atoms. Found 91 (275 requested) and removed 27 (149 requested) atoms. Cycle 35: After refmac, R = 0.1748 (Rfree = 0.000) for 3889 atoms. Found 78 (279 requested) and removed 39 (151 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.38 1.46 NCS extension: 2 residues added (177 deleted due to clashes), 3931 seeds are put forward Round 1: 354 peptides, 4 chains. Longest chain 135 peptides. Score 0.966 Round 2: 352 peptides, 3 chains. Longest chain 179 peptides. Score 0.968 Round 3: 354 peptides, 4 chains. Longest chain 165 peptides. Score 0.966 Round 4: 353 peptides, 5 chains. Longest chain 180 peptides. Score 0.963 Round 5: 354 peptides, 5 chains. Longest chain 136 peptides. Score 0.963 Taking the results from Round 2 Chains 3, Residues 349, Estimated correctness of the model 99.9 % 3 chains (349 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 131 A and 139 A 2 chains (356 residues) following loop building 2 chains (356 residues) in sequence following loop building ------------------------------------------------------ 60683 reflections ( 99.87 % complete ) and 3570 restraints for refining 3614 atoms. 769 conditional restraints added. Observations/parameters ratio is 4.20 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2166 (Rfree = 0.000) for 3614 atoms. Found 163 (259 requested) and removed 40 (140 requested) atoms. Cycle 37: After refmac, R = 0.1920 (Rfree = 0.000) for 3728 atoms. Found 113 (267 requested) and removed 20 (145 requested) atoms. Cycle 38: After refmac, R = 0.1839 (Rfree = 0.000) for 3814 atoms. Found 66 (273 requested) and removed 31 (148 requested) atoms. Cycle 39: After refmac, R = 0.1769 (Rfree = 0.000) for 3841 atoms. Found 70 (275 requested) and removed 29 (149 requested) atoms. Cycle 40: After refmac, R = 0.1744 (Rfree = 0.000) for 3870 atoms. Found 73 (277 requested) and removed 40 (150 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.37 1.45 NCS extension: 4 residues added (175 deleted due to clashes), 3908 seeds are put forward Round 1: 351 peptides, 5 chains. Longest chain 135 peptides. Score 0.962 Round 2: 351 peptides, 4 chains. Longest chain 164 peptides. Score 0.965 Round 3: 352 peptides, 5 chains. Longest chain 179 peptides. Score 0.962 Round 4: 350 peptides, 4 chains. Longest chain 135 peptides. Score 0.965 Round 5: 350 peptides, 7 chains. Longest chain 164 peptides. Score 0.955 Taking the results from Round 4 Chains 4, Residues 346, Estimated correctness of the model 99.9 % 4 chains (346 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 131 A and 139 A Built loop between residues 49 B and 52 B 2 chains (355 residues) following loop building 2 chains (355 residues) in sequence following loop building ------------------------------------------------------ 60683 reflections ( 99.87 % complete ) and 3546 restraints for refining 3596 atoms. 752 conditional restraints added. Observations/parameters ratio is 4.22 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2164 (Rfree = 0.000) for 3596 atoms. Found 172 (251 requested) and removed 49 (139 requested) atoms. Cycle 42: After refmac, R = 0.1928 (Rfree = 0.000) for 3712 atoms. Found 92 (260 requested) and removed 36 (144 requested) atoms. Cycle 43: After refmac, R = 0.1833 (Rfree = 0.000) for 3762 atoms. Found 93 (264 requested) and removed 28 (146 requested) atoms. Cycle 44: After refmac, R = 0.1796 (Rfree = 0.000) for 3819 atoms. Found 88 (267 requested) and removed 35 (148 requested) atoms. Cycle 45: After refmac, R = 0.1764 (Rfree = 0.000) for 3863 atoms. Found 78 (271 requested) and removed 38 (150 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.38 1.46 NCS extension: 3 residues added (176 deleted due to clashes), 3907 seeds are put forward Round 1: 350 peptides, 4 chains. Longest chain 135 peptides. Score 0.965 Round 2: 349 peptides, 4 chains. Longest chain 170 peptides. Score 0.964 Round 3: 348 peptides, 6 chains. Longest chain 164 peptides. Score 0.957 Round 4: 350 peptides, 4 chains. Longest chain 171 peptides. Score 0.965 Round 5: 352 peptides, 7 chains. Longest chain 171 peptides. Score 0.956 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 4, Residues 346, Estimated correctness of the model 99.9 % 3 chains (340 residues) have been docked in sequence Sequence coverage is 97 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 128 A and 136 A 3 chains (353 residues) following loop building 2 chains (347 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 60683 reflections ( 99.87 % complete ) and 2762 restraints for refining 2713 atoms. Observations/parameters ratio is 5.59 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2830 (Rfree = 0.000) for 2713 atoms. Found 167 (190 requested) and removed 0 (190 requested) atoms. Cycle 47: After refmac, R = 0.2307 (Rfree = 0.000) for 2713 atoms. Found 100 (201 requested) and removed 0 (111 requested) atoms. Cycle 48: After refmac, R = 0.2108 (Rfree = 0.000) for 2713 atoms. Found 50 (208 requested) and removed 4 (115 requested) atoms. Cycle 49: After refmac, R = 0.2000 (Rfree = 0.000) for 2713 atoms. TimeTaking 65.15