null Mon 24 Dec 07:28:54 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 2aml-1.5-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2aml-1.5-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2aml-1.5-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2aml-1.5-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/2aml-1.5-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2aml-1.5-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 07:28:58 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/2aml-1.5-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2aml-1.5-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 734 and 0 Target number of residues in the AU: 734 Target solvent content: 0.4210 Checking the provided sequence file Detected sequence length: 373 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 746 Adjusted target solvent content: 0.41 Input MTZ file: 2aml-1.5-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: 19 Cell parameters: 56.315 101.397 120.151 90.000 90.000 90.000 Input sequence file: 2aml-1.5-parrot-noncs.fasta_lf Building free atoms model in initial map for 5968 target number of atoms Had to go as low as 0.25 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: 77.491 1.500 Wilson plot Bfac: 10.52 110667 reflections ( 99.97 % complete ) and 0 restraints for refining 6573 atoms. Observations/parameters ratio is 4.21 ------------------------------------------------------ Starting model: R = 0.3335 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2858 (Rfree = 0.000) for 6573 atoms. Found 511 (511 requested) and removed 264 (255 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.43 1.61 NCS extension: 0 residues added, 6820 seeds are put forward Round 1: 651 peptides, 32 chains. Longest chain 64 peptides. Score 0.919 Round 2: 698 peptides, 14 chains. Longest chain 105 peptides. Score 0.963 Round 3: 704 peptides, 14 chains. Longest chain 138 peptides. Score 0.964 Round 4: 711 peptides, 8 chains. Longest chain 323 peptides. Score 0.974 Round 5: 711 peptides, 9 chains. Longest chain 259 peptides. Score 0.973 Taking the results from Round 4 Chains 8, Residues 703, Estimated correctness of the model 100.0 % 7 chains (696 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 122 B and 126 B Built loop between residues 151 B and 154 B Built loop between residues 202 B and 205 B Built loop between residues 309 B and 313 B 4 chains (713 residues) following loop building 3 chains (706 residues) in sequence following loop building ------------------------------------------------------ 110667 reflections ( 99.97 % complete ) and 6535 restraints for refining 6635 atoms. 797 conditional restraints added. Observations/parameters ratio is 4.17 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2704 (Rfree = 0.000) for 6635 atoms. Found 280 (516 requested) and removed 108 (258 requested) atoms. Cycle 2: After refmac, R = 0.2418 (Rfree = 0.000) for 6804 atoms. Found 248 (529 requested) and removed 44 (264 requested) atoms. Cycle 3: After refmac, R = 0.2090 (Rfree = 0.000) for 6992 atoms. Found 264 (545 requested) and removed 78 (272 requested) atoms. Cycle 4: After refmac, R = 0.1960 (Rfree = 0.000) for 7160 atoms. Found 237 (558 requested) and removed 86 (279 requested) atoms. Cycle 5: After refmac, R = 0.1867 (Rfree = 0.000) for 7293 atoms. Found 263 (568 requested) and removed 77 (284 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.43 1.61 NCS extension: 16 residues added (348 deleted due to clashes), 7498 seeds are put forward Round 1: 713 peptides, 11 chains. Longest chain 174 peptides. Score 0.970 Round 2: 719 peptides, 6 chains. Longest chain 246 peptides. Score 0.978 Round 3: 716 peptides, 9 chains. Longest chain 194 peptides. Score 0.973 Round 4: 715 peptides, 7 chains. Longest chain 257 peptides. Score 0.976 Round 5: 717 peptides, 7 chains. Longest chain 195 peptides. Score 0.976 Taking the results from Round 2 Chains 6, Residues 713, Estimated correctness of the model 100.0 % 5 chains (709 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 210 A and 213 A Built loop between residues 62 B and 65 B Built loop between residues 309 B and 314 B 3 chains (721 residues) following loop building 2 chains (717 residues) in sequence following loop building ------------------------------------------------------ 110667 reflections ( 99.97 % complete ) and 6630 restraints for refining 6979 atoms. 810 conditional restraints added. Observations/parameters ratio is 3.96 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2212 (Rfree = 0.000) for 6979 atoms. Found 284 (542 requested) and removed 75 (271 requested) atoms. Cycle 7: After refmac, R = 0.1924 (Rfree = 0.000) for 7181 atoms. Found 254 (559 requested) and removed 70 (279 requested) atoms. Cycle 8: After refmac, R = 0.1827 (Rfree = 0.000) for 7346 atoms. Found 229 (572 requested) and removed 81 (286 requested) atoms. Cycle 9: After refmac, R = 0.1781 (Rfree = 0.000) for 7478 atoms. Found 237 (582 requested) and removed 118 (291 requested) atoms. Cycle 10: After refmac, R = 0.1756 (Rfree = 0.000) for 7581 atoms. Found 246 (590 requested) and removed 125 (295 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.43 1.61 NCS extension: 5 residues added (6 deleted due to clashes), 7707 seeds are put forward Round 1: 718 peptides, 9 chains. Longest chain 311 peptides. Score 0.973 Round 2: 715 peptides, 7 chains. Longest chain 307 peptides. Score 0.976 Round 3: 720 peptides, 7 chains. Longest chain 164 peptides. Score 0.976 Round 4: 720 peptides, 5 chains. Longest chain 307 peptides. Score 0.979 Round 5: 719 peptides, 7 chains. Longest chain 162 peptides. Score 0.976 Taking the results from Round 4 Chains 5, Residues 715, Estimated correctness of the model 100.0 % 5 chains (715 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 63 A and 67 A Built loop between residues 174 A and 177 A Built loop between residues 63 B and 67 B 2 chains (723 residues) following loop building 2 chains (723 residues) in sequence following loop building ------------------------------------------------------ 110667 reflections ( 99.97 % complete ) and 6712 restraints for refining 7123 atoms. 860 conditional restraints added. Observations/parameters ratio is 3.88 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2162 (Rfree = 0.000) for 7123 atoms. Found 324 (542 requested) and removed 65 (276 requested) atoms. Cycle 12: After refmac, R = 0.1895 (Rfree = 0.000) for 7372 atoms. Found 215 (563 requested) and removed 80 (287 requested) atoms. Cycle 13: After refmac, R = 0.1808 (Rfree = 0.000) for 7490 atoms. Found 215 (571 requested) and removed 99 (291 requested) atoms. Cycle 14: After refmac, R = 0.1765 (Rfree = 0.000) for 7591 atoms. Found 232 (579 requested) and removed 106 (295 requested) atoms. Cycle 15: After refmac, R = 0.1757 (Rfree = 0.000) for 7698 atoms. Found 223 (588 requested) and removed 141 (300 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.43 1.61 NCS extension: 5 residues added (0 deleted due to clashes), 7785 seeds are put forward Round 1: 719 peptides, 7 chains. Longest chain 244 peptides. Score 0.976 Round 2: 723 peptides, 4 chains. Longest chain 301 peptides. Score 0.981 Round 3: 722 peptides, 5 chains. Longest chain 304 peptides. Score 0.979 Round 4: 723 peptides, 3 chains. Longest chain 365 peptides. Score 0.982 Round 5: 721 peptides, 6 chains. Longest chain 281 peptides. Score 0.978 Taking the results from Round 4 Chains 3, Residues 720, Estimated correctness of the model 100.0 % 3 chains (720 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 88 B and 92 B 2 chains (723 residues) following loop building 2 chains (723 residues) in sequence following loop building ------------------------------------------------------ 110667 reflections ( 99.97 % complete ) and 6849 restraints for refining 7174 atoms. 997 conditional restraints added. Observations/parameters ratio is 3.86 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2157 (Rfree = 0.000) for 7174 atoms. Found 328 (535 requested) and removed 80 (278 requested) atoms. Cycle 17: After refmac, R = 0.1888 (Rfree = 0.000) for 7414 atoms. Found 236 (554 requested) and removed 91 (288 requested) atoms. Cycle 18: After refmac, R = 0.1814 (Rfree = 0.000) for 7538 atoms. Found 221 (564 requested) and removed 91 (293 requested) atoms. Cycle 19: After refmac, R = 0.1771 (Rfree = 0.000) for 7652 atoms. Found 205 (572 requested) and removed 105 (298 requested) atoms. Cycle 20: After refmac, R = 0.1742 (Rfree = 0.000) for 7731 atoms. Found 221 (566 requested) and removed 125 (301 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.43 1.61 NCS extension: 5 residues added (0 deleted due to clashes), 7832 seeds are put forward Round 1: 713 peptides, 10 chains. Longest chain 174 peptides. Score 0.971 Round 2: 717 peptides, 7 chains. Longest chain 240 peptides. Score 0.976 Round 3: 716 peptides, 8 chains. Longest chain 164 peptides. Score 0.974 Round 4: 718 peptides, 6 chains. Longest chain 247 peptides. Score 0.977 Round 5: 718 peptides, 5 chains. Longest chain 360 peptides. Score 0.979 Taking the results from Round 5 Chains 5, Residues 713, Estimated correctness of the model 100.0 % 5 chains (713 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 210 A and 213 A Built loop between residues 262 A and 266 A Built loop between residues 308 A and 314 A 2 chains (723 residues) following loop building 2 chains (723 residues) in sequence following loop building ------------------------------------------------------ 110667 reflections ( 99.97 % complete ) and 6876 restraints for refining 7199 atoms. 1024 conditional restraints added. Observations/parameters ratio is 3.84 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2168 (Rfree = 0.000) for 7199 atoms. Found 344 (514 requested) and removed 81 (279 requested) atoms. Cycle 22: After refmac, R = 0.1902 (Rfree = 0.000) for 7454 atoms. Found 223 (534 requested) and removed 75 (290 requested) atoms. Cycle 23: After refmac, R = 0.1810 (Rfree = 0.000) for 7581 atoms. Found 215 (544 requested) and removed 98 (295 requested) atoms. Cycle 24: After refmac, R = 0.1771 (Rfree = 0.000) for 7679 atoms. Found 233 (550 requested) and removed 126 (299 requested) atoms. Cycle 25: After refmac, R = 0.1761 (Rfree = 0.000) for 7764 atoms. Found 224 (544 requested) and removed 145 (302 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.43 1.61 NCS extension: 5 residues added (0 deleted due to clashes), 7848 seeds are put forward Round 1: 712 peptides, 11 chains. Longest chain 174 peptides. Score 0.970 Round 2: 718 peptides, 6 chains. Longest chain 240 peptides. Score 0.977 Round 3: 715 peptides, 9 chains. Longest chain 200 peptides. Score 0.973 Round 4: 718 peptides, 7 chains. Longest chain 246 peptides. Score 0.976 Round 5: 715 peptides, 9 chains. Longest chain 198 peptides. Score 0.973 Taking the results from Round 2 Chains 6, Residues 712, Estimated correctness of the model 100.0 % 6 chains (712 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 67 A and 70 A Built loop between residues 308 A and 314 A Built loop between residues 210 B and 213 B Built loop between residues 264 B and 267 B 2 chains (723 residues) following loop building 2 chains (723 residues) in sequence following loop building ------------------------------------------------------ 110667 reflections ( 99.97 % complete ) and 6983 restraints for refining 7271 atoms. 1131 conditional restraints added. Observations/parameters ratio is 3.81 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2153 (Rfree = 0.000) for 7271 atoms. Found 326 (497 requested) and removed 95 (282 requested) atoms. Cycle 27: After refmac, R = 0.1888 (Rfree = 0.000) for 7486 atoms. Found 245 (513 requested) and removed 89 (291 requested) atoms. Cycle 28: After refmac, R = 0.1824 (Rfree = 0.000) for 7625 atoms. Found 214 (523 requested) and removed 109 (297 requested) atoms. Cycle 29: After refmac, R = 0.1773 (Rfree = 0.000) for 7716 atoms. Found 244 (517 requested) and removed 116 (300 requested) atoms. Cycle 30: After refmac, R = 0.1757 (Rfree = 0.000) for 7818 atoms. Found 221 (525 requested) and removed 152 (305 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.43 1.61 NCS extension: 4 residues added (1 deleted due to clashes), 7893 seeds are put forward Round 1: 715 peptides, 9 chains. Longest chain 244 peptides. Score 0.973 Round 2: 719 peptides, 6 chains. Longest chain 244 peptides. Score 0.978 Round 3: 717 peptides, 8 chains. Longest chain 131 peptides. Score 0.975 Round 4: 715 peptides, 8 chains. Longest chain 203 peptides. Score 0.974 Round 5: 721 peptides, 4 chains. Longest chain 302 peptides. Score 0.980 Taking the results from Round 5 Chains 4, Residues 717, Estimated correctness of the model 100.0 % 4 chains (717 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 307 A and 310 A Built loop between residues 309 B and 314 B 2 chains (723 residues) following loop building 2 chains (723 residues) in sequence following loop building ------------------------------------------------------ 110667 reflections ( 99.97 % complete ) and 6954 restraints for refining 7261 atoms. 1102 conditional restraints added. Observations/parameters ratio is 3.81 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2158 (Rfree = 0.000) for 7261 atoms. Found 330 (474 requested) and removed 81 (282 requested) atoms. Cycle 32: After refmac, R = 0.1894 (Rfree = 0.000) for 7500 atoms. Found 225 (491 requested) and removed 89 (292 requested) atoms. Cycle 33: After refmac, R = 0.1808 (Rfree = 0.000) for 7615 atoms. Found 199 (498 requested) and removed 94 (296 requested) atoms. Cycle 34: After refmac, R = 0.1765 (Rfree = 0.000) for 7706 atoms. Found 229 (504 requested) and removed 100 (300 requested) atoms. Cycle 35: After refmac, R = 0.1747 (Rfree = 0.000) for 7821 atoms. Found 239 (512 requested) and removed 131 (304 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.43 1.61 NCS extension: 4 residues added (1 deleted due to clashes), 7933 seeds are put forward Round 1: 716 peptides, 8 chains. Longest chain 179 peptides. Score 0.974 Round 2: 711 peptides, 8 chains. Longest chain 259 peptides. Score 0.974 Round 3: 715 peptides, 8 chains. Longest chain 304 peptides. Score 0.974 Round 4: 716 peptides, 7 chains. Longest chain 203 peptides. Score 0.976 Round 5: 712 peptides, 10 chains. Longest chain 239 peptides. Score 0.971 Taking the results from Round 4 Chains 7, Residues 709, Estimated correctness of the model 100.0 % 7 chains (709 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 210 A and 213 A Built loop between residues 264 A and 267 A Built loop between residues 308 A and 314 A Built loop between residues 67 B and 70 B Built loop between residues 263 B and 267 B 2 chains (723 residues) following loop building 2 chains (723 residues) in sequence following loop building ------------------------------------------------------ 110667 reflections ( 99.97 % complete ) and 6991 restraints for refining 7277 atoms. 1139 conditional restraints added. Observations/parameters ratio is 3.80 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2166 (Rfree = 0.000) for 7277 atoms. Found 322 (463 requested) and removed 73 (282 requested) atoms. Cycle 37: After refmac, R = 0.1894 (Rfree = 0.000) for 7509 atoms. Found 260 (480 requested) and removed 88 (292 requested) atoms. Cycle 38: After refmac, R = 0.1809 (Rfree = 0.000) for 7662 atoms. Found 233 (490 requested) and removed 99 (298 requested) atoms. Cycle 39: After refmac, R = 0.1766 (Rfree = 0.000) for 7775 atoms. Found 220 (497 requested) and removed 132 (303 requested) atoms. Cycle 40: After refmac, R = 0.1738 (Rfree = 0.000) for 7845 atoms. Found 244 (489 requested) and removed 119 (305 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.43 1.61 NCS extension: 5 residues added (0 deleted due to clashes), 7975 seeds are put forward Round 1: 717 peptides, 8 chains. Longest chain 185 peptides. Score 0.975 Round 2: 712 peptides, 8 chains. Longest chain 240 peptides. Score 0.974 Round 3: 712 peptides, 8 chains. Longest chain 179 peptides. Score 0.974 Round 4: 712 peptides, 8 chains. Longest chain 227 peptides. Score 0.974 Round 5: 718 peptides, 7 chains. Longest chain 301 peptides. Score 0.976 Taking the results from Round 5 Chains 7, Residues 711, Estimated correctness of the model 100.0 % 7 chains (711 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 47 A and 50 A Built loop between residues 67 A and 70 A Built loop between residues 210 A and 213 A Built loop between residues 307 A and 310 A Built loop between residues 308 B and 313 B 2 chains (723 residues) following loop building 2 chains (723 residues) in sequence following loop building ------------------------------------------------------ 110667 reflections ( 99.97 % complete ) and 7054 restraints for refining 7309 atoms. 1202 conditional restraints added. Observations/parameters ratio is 3.79 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2144 (Rfree = 0.000) for 7309 atoms. Found 328 (454 requested) and removed 76 (284 requested) atoms. Cycle 42: After refmac, R = 0.1875 (Rfree = 0.000) for 7551 atoms. Found 225 (470 requested) and removed 88 (294 requested) atoms. Cycle 43: After refmac, R = 0.1806 (Rfree = 0.000) for 7664 atoms. Found 196 (478 requested) and removed 101 (298 requested) atoms. Cycle 44: After refmac, R = 0.1753 (Rfree = 0.000) for 7750 atoms. Found 222 (470 requested) and removed 106 (301 requested) atoms. Cycle 45: After refmac, R = 0.1752 (Rfree = 0.000) for 7846 atoms. Found 208 (477 requested) and removed 143 (305 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.43 1.61 NCS extension: 4 residues added (1 deleted due to clashes), 7915 seeds are put forward Round 1: 716 peptides, 8 chains. Longest chain 179 peptides. Score 0.974 Round 2: 714 peptides, 7 chains. Longest chain 246 peptides. Score 0.976 Round 3: 718 peptides, 7 chains. Longest chain 203 peptides. Score 0.976 Round 4: 718 peptides, 6 chains. Longest chain 304 peptides. Score 0.977 Round 5: 717 peptides, 6 chains. Longest chain 243 peptides. Score 0.977 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 7, Residues 711, Estimated correctness of the model 100.0 % 5 chains (656 residues) have been docked in sequence Sequence coverage is 92 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 308 A and 314 A Built loop between residues 209 B and 212 B 5 chains (718 residues) following loop building 3 chains (663 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 110667 reflections ( 99.97 % complete ) and 5605 restraints for refining 5491 atoms. Observations/parameters ratio is 5.04 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2994 (Rfree = 0.000) for 5491 atoms. Found 295 (325 requested) and removed 0 (325 requested) atoms. Cycle 47: After refmac, R = 0.2466 (Rfree = 0.000) for 5491 atoms. Found 193 (342 requested) and removed 0 (225 requested) atoms. Cycle 48: After refmac, R = 0.2241 (Rfree = 0.000) for 5491 atoms. Found 110 (353 requested) and removed 12 (232 requested) atoms. Cycle 49: After refmac, R = 0.2212 (Rfree = 0.000) for 5491 atoms. Found 34 (359 requested) and removed 9 (236 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 09:07:57 GMT 2018 Job finished. TimeTaking 99.06 Used memory is bytes: 12149320