Sun 23 Dec 22:22:43 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 2opl-1.5-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2opl-1.5-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2opl-1.5-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2opl-1.5-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/2opl-1.5-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2opl-1.5-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 22:22:53 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/2opl-1.5-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2opl-1.5-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 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-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: 19 Cell parameters: 47.200 82.950 95.370 90.000 90.000 90.000 Input sequence file: 2opl-1.5-parrot-hancs.fasta_lf Building free atoms model in initial map for 2992 target number of atoms Had to go as low as 0.35 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 3316 atoms. Observations/parameters ratio is 4.58 ------------------------------------------------------ Starting model: R = 0.3353 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2790 (Rfree = 0.000) for 3316 atoms. Found 257 (257 requested) and removed 139 (128 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.41 1.49 NCS extension: 0 residues added, 3434 seeds are put forward Round 1: 319 peptides, 14 chains. Longest chain 48 peptides. Score 0.909 Round 2: 341 peptides, 7 chains. Longest chain 120 peptides. Score 0.951 Round 3: 339 peptides, 7 chains. Longest chain 130 peptides. Score 0.950 Round 4: 350 peptides, 5 chains. Longest chain 123 peptides. Score 0.961 Round 5: 349 peptides, 6 chains. Longest chain 163 peptides. Score 0.958 Taking the results from Round 4 Chains 5, Residues 345, Estimated correctness of the model 99.9 % 4 chains (337 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 128 A and 136 A Built loop between residues 69 B and 72 B 3 chains (354 residues) following loop building 2 chains (346 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 60683 reflections ( 99.87 % complete ) and 3192 restraints for refining 3206 atoms. 434 conditional restraints added. Observations/parameters ratio is 4.73 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2662 (Rfree = 0.000) for 3206 atoms. Found 157 (249 requested) and removed 61 (124 requested) atoms. Cycle 2: After refmac, R = 0.2415 (Rfree = 0.000) for 3302 atoms. Found 127 (256 requested) and removed 17 (128 requested) atoms. Cycle 3: After refmac, R = 0.2261 (Rfree = 0.000) for 3409 atoms. Found 86 (265 requested) and removed 15 (132 requested) atoms. Cycle 4: After refmac, R = 0.2042 (Rfree = 0.000) for 3477 atoms. Found 91 (270 requested) and removed 17 (135 requested) atoms. Cycle 5: After refmac, R = 0.1931 (Rfree = 0.000) for 3543 atoms. Found 81 (276 requested) and removed 16 (138 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.37 1.45 NCS extension: 6 residues added (173 deleted due to clashes), 3615 seeds are put forward Round 1: 358 peptides, 3 chains. Longest chain 179 peptides. Score 0.970 Round 2: 359 peptides, 2 chains. Longest chain 180 peptides. Score 0.973 Round 3: 356 peptides, 6 chains. Longest chain 164 peptides. Score 0.960 Round 4: 355 peptides, 4 chains. Longest chain 179 peptides. Score 0.966 Round 5: 358 peptides, 3 chains. Longest chain 179 peptides. Score 0.970 Taking the results from Round 2 Chains 2, Residues 357, Estimated correctness of the model 100.0 % 2 chains (357 residues) have been docked in sequence Building loops using Loopy2018 2 chains (357 residues) following loop building 2 chains (357 residues) in sequence following loop building ------------------------------------------------------ 60683 reflections ( 99.87 % complete ) and 3235 restraints for refining 3421 atoms. 426 conditional restraints added. Observations/parameters ratio is 4.43 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2212 (Rfree = 0.000) for 3421 atoms. Found 147 (266 requested) and removed 36 (133 requested) atoms. Failed to save intermediate PDB Cycle 7: After refmac, R = 0.1962 (Rfree = 0.000) for 3530 atoms. Found 137 (274 requested) and removed 39 (137 requested) atoms. Cycle 8: After refmac, R = 0.1875 (Rfree = 0.000) for 3626 atoms. Found 112 (282 requested) and removed 38 (141 requested) atoms. Cycle 9: After refmac, R = 0.1841 (Rfree = 0.000) for 3695 atoms. Found 101 (287 requested) and removed 41 (143 requested) atoms. Cycle 10: After refmac, R = 0.1803 (Rfree = 0.000) for 3748 atoms. Found 104 (292 requested) and removed 45 (146 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.36 1.43 NCS extension: 4 residues added (176 deleted due to clashes), 3813 seeds are put forward Round 1: 359 peptides, 3 chains. Longest chain 180 peptides. Score 0.970 Round 2: 359 peptides, 2 chains. Longest chain 180 peptides. Score 0.973 Round 3: 358 peptides, 5 chains. Longest chain 165 peptides. Score 0.964 Round 4: 359 peptides, 3 chains. Longest chain 181 peptides. Score 0.970 Round 5: 355 peptides, 7 chains. Longest chain 132 peptides. Score 0.957 Taking the results from Round 2 Chains 2, Residues 357, Estimated correctness of the model 100.0 % 2 chains (357 residues) have been docked in sequence Building loops using Loopy2018 2 chains (357 residues) following loop building 2 chains (357 residues) in sequence following loop building ------------------------------------------------------ 60683 reflections ( 99.87 % complete ) and 3296 restraints for refining 3503 atoms. 487 conditional restraints added. Observations/parameters ratio is 4.33 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2171 (Rfree = 0.000) for 3503 atoms. Found 170 (272 requested) and removed 45 (136 requested) atoms. Cycle 12: After refmac, R = 0.1949 (Rfree = 0.000) for 3624 atoms. Found 112 (282 requested) and removed 32 (141 requested) atoms. Cycle 13: After refmac, R = 0.1853 (Rfree = 0.000) for 3699 atoms. Found 102 (288 requested) and removed 23 (144 requested) atoms. Cycle 14: After refmac, R = 0.1816 (Rfree = 0.000) for 3775 atoms. Found 63 (293 requested) and removed 43 (146 requested) atoms. Cycle 15: After refmac, R = 0.1762 (Rfree = 0.000) for 3791 atoms. Found 102 (289 requested) and removed 28 (147 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.37 1.45 NCS extension: 4 residues added (176 deleted due to clashes), 3872 seeds are put forward Round 1: 357 peptides, 4 chains. Longest chain 136 peptides. Score 0.967 Round 2: 354 peptides, 3 chains. Longest chain 180 peptides. Score 0.969 Round 3: 353 peptides, 4 chains. Longest chain 180 peptides. Score 0.966 Round 4: 351 peptides, 6 chains. Longest chain 125 peptides. Score 0.959 Round 5: 352 peptides, 4 chains. Longest chain 171 peptides. Score 0.965 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 139 A 2 chains (358 residues) following loop building 2 chains (358 residues) in sequence following loop building ------------------------------------------------------ 60683 reflections ( 99.87 % complete ) and 3398 restraints for refining 3544 atoms. 578 conditional restraints added. Observations/parameters ratio is 4.28 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2162 (Rfree = 0.000) for 3544 atoms. Found 164 (269 requested) and removed 47 (137 requested) atoms. Cycle 17: After refmac, R = 0.1920 (Rfree = 0.000) for 3658 atoms. Found 110 (278 requested) and removed 31 (142 requested) atoms. Cycle 18: After refmac, R = 0.1826 (Rfree = 0.000) for 3730 atoms. Found 94 (284 requested) and removed 29 (145 requested) atoms. Cycle 19: After refmac, R = 0.1801 (Rfree = 0.000) for 3787 atoms. Found 89 (289 requested) and removed 41 (147 requested) atoms. Cycle 20: After refmac, R = 0.1767 (Rfree = 0.000) for 3827 atoms. Found 93 (292 requested) and removed 49 (149 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.37 1.45 NCS extension: 5 residues added (175 deleted due to clashes), 3878 seeds are put forward Round 1: 357 peptides, 4 chains. Longest chain 137 peptides. Score 0.967 Round 2: 354 peptides, 3 chains. Longest chain 180 peptides. Score 0.969 Round 3: 352 peptides, 5 chains. Longest chain 114 peptides. Score 0.962 Round 4: 353 peptides, 7 chains. Longest chain 130 peptides. Score 0.956 Round 5: 356 peptides, 3 chains. Longest chain 180 peptides. Score 0.970 Taking the results from Round 5 Chains 3, Residues 353, Estimated correctness of the model 100.0 % 3 chains (353 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 131 A and 136 A 2 chains (357 residues) following loop building 2 chains (357 residues) in sequence following loop building ------------------------------------------------------ 60683 reflections ( 99.87 % complete ) and 3422 restraints for refining 3565 atoms. 609 conditional restraints added. Observations/parameters ratio is 4.26 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2163 (Rfree = 0.000) for 3565 atoms. Found 168 (266 requested) and removed 44 (138 requested) atoms. Cycle 22: After refmac, R = 0.1909 (Rfree = 0.000) for 3681 atoms. Found 111 (275 requested) and removed 23 (143 requested) atoms. Cycle 23: After refmac, R = 0.1826 (Rfree = 0.000) for 3757 atoms. Found 81 (281 requested) and removed 29 (146 requested) atoms. Cycle 24: After refmac, R = 0.1775 (Rfree = 0.000) for 3801 atoms. Found 98 (284 requested) and removed 27 (148 requested) atoms. Cycle 25: After refmac, R = 0.1752 (Rfree = 0.000) for 3862 atoms. Found 82 (289 requested) and removed 45 (150 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.37 1.45 NCS extension: 8 residues added (172 deleted due to clashes), 3909 seeds are put forward Round 1: 355 peptides, 5 chains. Longest chain 136 peptides. Score 0.963 Round 2: 353 peptides, 4 chains. Longest chain 180 peptides. Score 0.966 Round 3: 352 peptides, 7 chains. Longest chain 136 peptides. Score 0.956 Round 4: 356 peptides, 3 chains. Longest chain 180 peptides. Score 0.970 Round 5: 350 peptides, 6 chains. Longest chain 145 peptides. Score 0.958 Taking the results from Round 4 Chains 3, Residues 353, Estimated correctness of the model 100.0 % 3 chains (353 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 131 A and 136 A 2 chains (357 residues) following loop building 2 chains (357 residues) in sequence following loop building ------------------------------------------------------ 60683 reflections ( 99.87 % complete ) and 3464 restraints for refining 3600 atoms. 651 conditional restraints added. Observations/parameters ratio is 4.21 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2168 (Rfree = 0.000) for 3600 atoms. Found 159 (262 requested) and removed 39 (139 requested) atoms. Cycle 27: After refmac, R = 0.1898 (Rfree = 0.000) for 3712 atoms. Found 131 (272 requested) and removed 19 (144 requested) atoms. Cycle 28: After refmac, R = 0.1820 (Rfree = 0.000) for 3816 atoms. Found 96 (279 requested) and removed 34 (148 requested) atoms. Cycle 29: After refmac, R = 0.1769 (Rfree = 0.000) for 3872 atoms. Found 86 (283 requested) and removed 28 (150 requested) atoms. Cycle 30: After refmac, R = 0.1746 (Rfree = 0.000) for 3915 atoms. Found 109 (287 requested) and removed 34 (152 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.38 1.46 NCS extension: 4 residues added (176 deleted due to clashes), 3995 seeds are put forward Round 1: 358 peptides, 4 chains. Longest chain 180 peptides. Score 0.967 Round 2: 359 peptides, 3 chains. Longest chain 180 peptides. Score 0.970 Round 3: 356 peptides, 6 chains. Longest chain 131 peptides. Score 0.960 Round 4: 351 peptides, 5 chains. Longest chain 145 peptides. Score 0.962 Round 5: 356 peptides, 5 chains. Longest chain 128 peptides. Score 0.964 Taking the results from Round 2 Chains 3, Residues 356, Estimated correctness of the model 100.0 % 3 chains (356 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 137 A and 140 A 2 chains (358 residues) following loop building 2 chains (358 residues) in sequence following loop building ------------------------------------------------------ 60683 reflections ( 99.87 % complete ) and 3492 restraints for refining 3636 atoms. 672 conditional restraints added. Observations/parameters ratio is 4.17 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2138 (Rfree = 0.000) for 3636 atoms. Found 170 (265 requested) and removed 50 (141 requested) atoms. Cycle 32: After refmac, R = 0.1910 (Rfree = 0.000) for 3751 atoms. Found 111 (274 requested) and removed 25 (146 requested) atoms. Cycle 33: After refmac, R = 0.1834 (Rfree = 0.000) for 3827 atoms. Found 87 (280 requested) and removed 34 (149 requested) atoms. Cycle 34: After refmac, R = 0.1780 (Rfree = 0.000) for 3872 atoms. Found 92 (283 requested) and removed 27 (150 requested) atoms. Cycle 35: After refmac, R = 0.1768 (Rfree = 0.000) for 3926 atoms. Found 79 (288 requested) and removed 45 (153 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.38 1.46 NCS extension: 5 residues added (175 deleted due to clashes), 3966 seeds are put forward Round 1: 352 peptides, 5 chains. Longest chain 137 peptides. Score 0.962 Round 2: 354 peptides, 4 chains. Longest chain 171 peptides. Score 0.966 Round 3: 352 peptides, 6 chains. Longest chain 114 peptides. Score 0.959 Round 4: 351 peptides, 5 chains. Longest chain 165 peptides. Score 0.962 Round 5: 352 peptides, 7 chains. Longest chain 114 peptides. Score 0.956 Taking the results from Round 2 Chains 4, Residues 350, Estimated correctness of the model 99.9 % 3 chains (344 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 131 A and 136 A 3 chains (354 residues) following loop building 2 chains (348 residues) in sequence following loop building ------------------------------------------------------ 60683 reflections ( 99.87 % complete ) and 3581 restraints for refining 3626 atoms. 811 conditional restraints added. Observations/parameters ratio is 4.18 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2165 (Rfree = 0.000) for 3626 atoms. Found 157 (259 requested) and removed 50 (141 requested) atoms. Cycle 37: After refmac, R = 0.1918 (Rfree = 0.000) for 3730 atoms. Found 126 (267 requested) and removed 25 (145 requested) atoms. Cycle 38: After refmac, R = 0.1838 (Rfree = 0.000) for 3825 atoms. Found 118 (273 requested) and removed 33 (148 requested) atoms. Cycle 39: After refmac, R = 0.1798 (Rfree = 0.000) for 3899 atoms. Found 90 (280 requested) and removed 48 (152 requested) atoms. Cycle 40: After refmac, R = 0.1772 (Rfree = 0.000) for 3928 atoms. Found 94 (275 requested) and removed 39 (153 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.37 1.45 NCS extension: 5 residues added (175 deleted due to clashes), 3989 seeds are put forward Round 1: 352 peptides, 6 chains. Longest chain 126 peptides. Score 0.959 Round 2: 351 peptides, 4 chains. Longest chain 171 peptides. Score 0.965 Round 3: 352 peptides, 7 chains. Longest chain 136 peptides. Score 0.956 Round 4: 353 peptides, 4 chains. Longest chain 170 peptides. Score 0.966 Round 5: 355 peptides, 4 chains. Longest chain 180 peptides. Score 0.966 Taking the results from Round 5 Chains 4, Residues 351, Estimated correctness of the model 99.9 % 4 chains (351 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 54 A and 58 A Built loop between residues 131 A and 136 A 2 chains (358 residues) following loop building 2 chains (358 residues) in sequence following loop building ------------------------------------------------------ 60683 reflections ( 99.87 % complete ) and 3522 restraints for refining 3657 atoms. 702 conditional restraints added. Observations/parameters ratio is 4.15 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2169 (Rfree = 0.000) for 3657 atoms. Found 163 (256 requested) and removed 51 (142 requested) atoms. Cycle 42: After refmac, R = 0.1923 (Rfree = 0.000) for 3765 atoms. Found 133 (264 requested) and removed 30 (146 requested) atoms. Cycle 43: After refmac, R = 0.1840 (Rfree = 0.000) for 3860 atoms. Found 98 (270 requested) and removed 49 (150 requested) atoms. Cycle 44: After refmac, R = 0.1802 (Rfree = 0.000) for 3902 atoms. Found 86 (274 requested) and removed 42 (152 requested) atoms. Cycle 45: After refmac, R = 0.1773 (Rfree = 0.000) for 3928 atoms. Found 100 (275 requested) and removed 39 (153 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.38 1.46 NCS extension: 6 residues added (174 deleted due to clashes), 3997 seeds are put forward Round 1: 352 peptides, 4 chains. Longest chain 136 peptides. Score 0.965 Round 2: 355 peptides, 4 chains. Longest chain 171 peptides. Score 0.966 Round 3: 355 peptides, 4 chains. Longest chain 171 peptides. Score 0.966 Round 4: 350 peptides, 8 chains. Longest chain 136 peptides. Score 0.951 Round 5: 355 peptides, 4 chains. Longest chain 171 peptides. Score 0.966 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 4, Residues 351, Estimated correctness of the model 99.9 % 3 chains (344 residues) have been docked in sequence Sequence coverage is 97 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 131 A and 136 A 3 chains (355 residues) following loop building 2 chains (348 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 60683 reflections ( 99.87 % complete ) and 2774 restraints for refining 2725 atoms. Observations/parameters ratio is 5.57 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2798 (Rfree = 0.000) for 2725 atoms. Found 172 (190 requested) and removed 0 (190 requested) atoms. Cycle 47: After refmac, R = 0.2306 (Rfree = 0.000) for 2725 atoms. Found 95 (202 requested) and removed 1 (112 requested) atoms. Cycle 48: After refmac, R = 0.2101 (Rfree = 0.000) for 2725 atoms. Found 52 (209 requested) and removed 2 (116 requested) atoms. Cycle 49: After refmac, R = 0.1988 (Rfree = 0.000) for 2725 atoms. Found 20 (212 requested) and removed 3 (118 requested) atoms. Writing output files ... TimeTaking 72.6