Mon 24 Dec 00:39:36 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 1vl5-1.9-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vl5-1.9-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vl5-1.9-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vl5-1.9-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/1vl5-1.9-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vl5-1.9-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 00:39:41 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/1vl5-1.9-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vl5-1.9-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 1137 and 0 Target number of residues in the AU: 1137 Target solvent content: 0.4688 Checking the provided sequence file Detected sequence length: 260 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1040 Adjusted target solvent content: 0.51 Input MTZ file: 1vl5-1.9-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: 64.006 87.475 105.236 90.000 100.573 90.000 Input sequence file: 1vl5-1.9-parrot-mrncs.fasta_lf Building free atoms model in initial map for 8320 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: 49.849 1.850 Wilson plot Bfac: 17.63 94468 reflections ( 97.09 % complete ) and 0 restraints for refining 9182 atoms. Observations/parameters ratio is 2.57 ------------------------------------------------------ Starting model: R = 0.3292 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2769 (Rfree = 0.000) for 9182 atoms. Found 392 (392 requested) and removed 203 (196 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.92 1.89 NCS extension: 0 residues added, 9371 seeds are put forward Round 1: 769 peptides, 47 chains. Longest chain 44 peptides. Score 0.821 Round 2: 813 peptides, 34 chains. Longest chain 75 peptides. Score 0.872 Round 3: 850 peptides, 23 chains. Longest chain 126 peptides. Score 0.907 Round 4: 859 peptides, 22 chains. Longest chain 109 peptides. Score 0.911 Round 5: 879 peptides, 16 chains. Longest chain 185 peptides. Score 0.926 Taking the results from Round 5 Chains 17, Residues 863, Estimated correctness of the model 99.5 % 13 chains (808 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 79 A and 88 A Built loop between residues 199 A and 203 A Built loop between residues 222 A and 230 A Built loop between residues 103 C and 106 C Built loop between residues 125 C and 129 C Built loop between residues 45 B and 50 B Built loop between residues 206 D and 209 D 9 chains (889 residues) following loop building 6 chains (837 residues) in sequence following loop building ------------------------------------------------------ 94468 reflections ( 97.09 % complete ) and 8817 restraints for refining 8565 atoms. 1611 conditional restraints added. Observations/parameters ratio is 2.76 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2826 (Rfree = 0.000) for 8565 atoms. Found 295 (366 requested) and removed 208 (183 requested) atoms. Cycle 2: After refmac, R = 0.2464 (Rfree = 0.000) for 8626 atoms. Found 259 (363 requested) and removed 73 (185 requested) atoms. Cycle 3: After refmac, R = 0.2297 (Rfree = 0.000) for 8777 atoms. Found 207 (368 requested) and removed 58 (188 requested) atoms. Cycle 4: After refmac, R = 0.2201 (Rfree = 0.000) for 8894 atoms. Found 168 (373 requested) and removed 60 (190 requested) atoms. Cycle 5: After refmac, R = 0.2139 (Rfree = 0.000) for 8972 atoms. Found 184 (377 requested) and removed 69 (192 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.89 1.86 NCS extension: 3 residues added (93 deleted due to clashes), 9097 seeds are put forward Round 1: 887 peptides, 10 chains. Longest chain 231 peptides. Score 0.938 Round 2: 894 peptides, 9 chains. Longest chain 191 peptides. Score 0.940 Round 3: 889 peptides, 12 chains. Longest chain 168 peptides. Score 0.935 Round 4: 882 peptides, 18 chains. Longest chain 188 peptides. Score 0.924 Round 5: 892 peptides, 13 chains. Longest chain 162 peptides. Score 0.934 Taking the results from Round 2 Chains 9, Residues 885, Estimated correctness of the model 99.7 % 9 chains (885 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 80 A and 87 A Built loop between residues 90 C and 93 C Built loop between residues 203 B and 206 B Built loop between residues 213 D and 216 D 5 chains (897 residues) following loop building 5 chains (897 residues) in sequence following loop building ------------------------------------------------------ 94468 reflections ( 97.09 % complete ) and 8450 restraints for refining 8761 atoms. 966 conditional restraints added. Observations/parameters ratio is 2.70 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2181 (Rfree = 0.000) for 8761 atoms. Found 326 (367 requested) and removed 145 (187 requested) atoms. Cycle 7: After refmac, R = 0.2094 (Rfree = 0.000) for 8929 atoms. Found 256 (374 requested) and removed 74 (191 requested) atoms. Cycle 8: After refmac, R = 0.2037 (Rfree = 0.000) for 9096 atoms. Found 225 (381 requested) and removed 73 (194 requested) atoms. Cycle 9: After refmac, R = 0.2007 (Rfree = 0.000) for 9230 atoms. Found 213 (387 requested) and removed 87 (197 requested) atoms. Cycle 10: After refmac, R = 0.1977 (Rfree = 0.000) for 9334 atoms. Found 195 (392 requested) and removed 84 (200 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.89 1.86 NCS extension: 45 residues added (24 deleted due to clashes), 9492 seeds are put forward Round 1: 884 peptides, 11 chains. Longest chain 162 peptides. Score 0.935 Round 2: 886 peptides, 8 chains. Longest chain 231 peptides. Score 0.940 Round 3: 889 peptides, 11 chains. Longest chain 168 peptides. Score 0.936 Round 4: 888 peptides, 9 chains. Longest chain 229 peptides. Score 0.939 Round 5: 879 peptides, 15 chains. Longest chain 137 peptides. Score 0.928 Taking the results from Round 2 Chains 8, Residues 878, Estimated correctness of the model 99.7 % 8 chains (878 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 129 B and 133 B Built loop between residues 213 B and 216 B 6 chains (883 residues) following loop building 6 chains (883 residues) in sequence following loop building ------------------------------------------------------ 94468 reflections ( 97.09 % complete ) and 8676 restraints for refining 8906 atoms. 1303 conditional restraints added. Observations/parameters ratio is 2.65 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2074 (Rfree = 0.000) for 8906 atoms. Found 373 (373 requested) and removed 110 (190 requested) atoms. Cycle 12: After refmac, R = 0.2038 (Rfree = 0.000) for 9151 atoms. Found 234 (384 requested) and removed 116 (196 requested) atoms. Cycle 13: After refmac, R = 0.1987 (Rfree = 0.000) for 9260 atoms. Found 230 (388 requested) and removed 87 (198 requested) atoms. Cycle 14: After refmac, R = 0.1960 (Rfree = 0.000) for 9390 atoms. Found 215 (394 requested) and removed 120 (201 requested) atoms. Cycle 15: After refmac, R = 0.1941 (Rfree = 0.000) for 9466 atoms. Found 245 (389 requested) and removed 113 (202 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.89 1.86 NCS extension: 45 residues added (24 deleted due to clashes), 9645 seeds are put forward Round 1: 887 peptides, 10 chains. Longest chain 231 peptides. Score 0.938 Round 2: 888 peptides, 11 chains. Longest chain 189 peptides. Score 0.936 Round 3: 885 peptides, 11 chains. Longest chain 231 peptides. Score 0.935 Round 4: 885 peptides, 11 chains. Longest chain 231 peptides. Score 0.935 Round 5: 884 peptides, 14 chains. Longest chain 229 peptides. Score 0.931 Taking the results from Round 1 Chains 12, Residues 877, Estimated correctness of the model 99.7 % 8 chains (851 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 45 A and 49 A 11 chains (880 residues) following loop building 7 chains (854 residues) in sequence following loop building ------------------------------------------------------ 94468 reflections ( 97.09 % complete ) and 8905 restraints for refining 8990 atoms. 1658 conditional restraints added. Observations/parameters ratio is 2.63 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2043 (Rfree = 0.000) for 8990 atoms. Found 350 (369 requested) and removed 94 (192 requested) atoms. Cycle 17: After refmac, R = 0.1995 (Rfree = 0.000) for 9222 atoms. Found 220 (379 requested) and removed 102 (197 requested) atoms. Cycle 18: After refmac, R = 0.1956 (Rfree = 0.000) for 9328 atoms. Found 207 (383 requested) and removed 82 (199 requested) atoms. Cycle 19: After refmac, R = 0.1925 (Rfree = 0.000) for 9442 atoms. Found 210 (388 requested) and removed 121 (202 requested) atoms. Cycle 20: After refmac, R = 0.1920 (Rfree = 0.000) for 9515 atoms. Found 225 (383 requested) and removed 124 (203 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.88 1.86 NCS extension: 170 residues added (137 deleted due to clashes), 9788 seeds are put forward Round 1: 887 peptides, 9 chains. Longest chain 231 peptides. Score 0.939 Round 2: 889 peptides, 12 chains. Longest chain 164 peptides. Score 0.935 Round 3: 891 peptides, 12 chains. Longest chain 154 peptides. Score 0.935 Round 4: 887 peptides, 16 chains. Longest chain 123 peptides. Score 0.928 Round 5: 888 peptides, 14 chains. Longest chain 162 peptides. Score 0.932 Taking the results from Round 1 Chains 10, Residues 878, Estimated correctness of the model 99.7 % 8 chains (872 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 45 C and 49 C Built loop between residues 203 C and 206 C 8 chains (883 residues) following loop building 6 chains (877 residues) in sequence following loop building ------------------------------------------------------ 94468 reflections ( 97.09 % complete ) and 8716 restraints for refining 9066 atoms. 1371 conditional restraints added. Observations/parameters ratio is 2.61 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2025 (Rfree = 0.000) for 9066 atoms. Found 356 (356 requested) and removed 105 (193 requested) atoms. Cycle 22: After refmac, R = 0.1989 (Rfree = 0.000) for 9299 atoms. Found 234 (366 requested) and removed 113 (199 requested) atoms. Cycle 23: After refmac, R = 0.1939 (Rfree = 0.000) for 9406 atoms. Found 224 (371 requested) and removed 78 (201 requested) atoms. Failed to save intermediate PDB Cycle 24: After refmac, R = 0.1916 (Rfree = 0.000) for 9540 atoms. Found 213 (375 requested) and removed 111 (204 requested) atoms. Failed to save intermediate PDB Cycle 25: After refmac, R = 0.1892 (Rfree = 0.000) for 9617 atoms. Found 220 (371 requested) and removed 116 (206 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.88 1.86 NCS extension: 100 residues added (150 deleted due to clashes), 9823 seeds are put forward Round 1: 884 peptides, 10 chains. Longest chain 229 peptides. Score 0.937 Round 2: 887 peptides, 10 chains. Longest chain 231 peptides. Score 0.938 Round 3: 881 peptides, 13 chains. Longest chain 155 peptides. Score 0.932 Round 4: 884 peptides, 12 chains. Longest chain 162 peptides. Score 0.934 Round 5: 887 peptides, 12 chains. Longest chain 179 peptides. Score 0.934 Taking the results from Round 2 Chains 10, Residues 877, Estimated correctness of the model 99.7 % 10 chains (877 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 167 A and 170 A Built loop between residues 213 A and 216 A Built loop between residues 79 C and 90 C Built loop between residues 45 B and 49 B Built loop between residues 169 B and 172 B 5 chains (896 residues) following loop building 5 chains (896 residues) in sequence following loop building ------------------------------------------------------ 94468 reflections ( 97.09 % complete ) and 8645 restraints for refining 9136 atoms. 1167 conditional restraints added. Observations/parameters ratio is 2.59 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2039 (Rfree = 0.000) for 9136 atoms. Found 343 (343 requested) and removed 109 (195 requested) atoms. Cycle 27: After refmac, R = 0.1979 (Rfree = 0.000) for 9352 atoms. Found 249 (352 requested) and removed 93 (200 requested) atoms. Cycle 28: After refmac, R = 0.1928 (Rfree = 0.000) for 9497 atoms. Found 219 (357 requested) and removed 92 (203 requested) atoms. Cycle 29: After refmac, R = 0.1899 (Rfree = 0.000) for 9611 atoms. Found 222 (362 requested) and removed 114 (205 requested) atoms. Cycle 30: After refmac, R = 0.1880 (Rfree = 0.000) for 9703 atoms. Found 229 (357 requested) and removed 137 (207 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.88 1.86 NCS extension: 42 residues added (21 deleted due to clashes), 9842 seeds are put forward Round 1: 884 peptides, 8 chains. Longest chain 231 peptides. Score 0.940 Round 2: 884 peptides, 11 chains. Longest chain 165 peptides. Score 0.935 Round 3: 884 peptides, 15 chains. Longest chain 143 peptides. Score 0.929 Round 4: 890 peptides, 9 chains. Longest chain 204 peptides. Score 0.940 Round 5: 888 peptides, 15 chains. Longest chain 168 peptides. Score 0.930 Taking the results from Round 4 Chains 10, Residues 881, Estimated correctness of the model 99.7 % 9 chains (880 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 79 A and 88 A Built loop between residues 76 C and 79 C Built loop between residues 46 B and 50 B Built loop between residues 228 D and 231 D 6 chains (896 residues) following loop building 6 chains (896 residues) in sequence following loop building ------------------------------------------------------ 94468 reflections ( 97.09 % complete ) and 8722 restraints for refining 9149 atoms. 1247 conditional restraints added. Observations/parameters ratio is 2.58 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2030 (Rfree = 0.000) for 9149 atoms. Found 328 (328 requested) and removed 116 (195 requested) atoms. Cycle 32: After refmac, R = 0.1974 (Rfree = 0.000) for 9346 atoms. Found 260 (336 requested) and removed 83 (200 requested) atoms. Cycle 33: After refmac, R = 0.1932 (Rfree = 0.000) for 9505 atoms. Found 254 (342 requested) and removed 104 (203 requested) atoms. Cycle 34: After refmac, R = 0.1902 (Rfree = 0.000) for 9644 atoms. Found 238 (347 requested) and removed 125 (206 requested) atoms. Cycle 35: After refmac, R = 0.1881 (Rfree = 0.000) for 9741 atoms. Found 227 (342 requested) and removed 132 (208 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.88 1.86 NCS extension: 41 residues added (22 deleted due to clashes), 9881 seeds are put forward Round 1: 877 peptides, 10 chains. Longest chain 228 peptides. Score 0.935 Round 2: 886 peptides, 9 chains. Longest chain 231 peptides. Score 0.939 Round 3: 883 peptides, 11 chains. Longest chain 175 peptides. Score 0.935 Round 4: 876 peptides, 12 chains. Longest chain 228 peptides. Score 0.932 Round 5: 885 peptides, 11 chains. Longest chain 228 peptides. Score 0.935 Taking the results from Round 2 Chains 11, Residues 877, Estimated correctness of the model 99.7 % 8 chains (805 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 213 A and 216 A Built loop between residues 46 C and 50 C 9 chains (882 residues) following loop building 6 chains (810 residues) in sequence following loop building ------------------------------------------------------ 94468 reflections ( 97.09 % complete ) and 9445 restraints for refining 9128 atoms. 2344 conditional restraints added. Observations/parameters ratio is 2.59 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2029 (Rfree = 0.000) for 9128 atoms. Found 312 (312 requested) and removed 90 (195 requested) atoms. Failed to save intermediate PDB Cycle 37: After refmac, R = 0.1977 (Rfree = 0.000) for 9333 atoms. Found 251 (320 requested) and removed 78 (200 requested) atoms. Cycle 38: After refmac, R = 0.1925 (Rfree = 0.000) for 9493 atoms. Found 229 (325 requested) and removed 82 (203 requested) atoms. Cycle 39: After refmac, R = 0.1908 (Rfree = 0.000) for 9629 atoms. Found 227 (330 requested) and removed 149 (206 requested) atoms. Cycle 40: After refmac, R = 0.1895 (Rfree = 0.000) for 9693 atoms. Found 233 (324 requested) and removed 131 (207 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.88 1.86 NCS extension: 152 residues added (143 deleted due to clashes), 9949 seeds are put forward Round 1: 882 peptides, 10 chains. Longest chain 231 peptides. Score 0.936 Round 2: 887 peptides, 9 chains. Longest chain 190 peptides. Score 0.939 Round 3: 875 peptides, 15 chains. Longest chain 168 peptides. Score 0.927 Round 4: 886 peptides, 11 chains. Longest chain 230 peptides. Score 0.936 Round 5: 881 peptides, 11 chains. Longest chain 230 peptides. Score 0.935 Taking the results from Round 2 Chains 10, Residues 878, Estimated correctness of the model 99.7 % 9 chains (877 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 90 C and 93 C Built loop between residues 45 B and 49 B Built loop between residues 213 D and 216 D 7 chains (885 residues) following loop building 7 chains (885 residues) in sequence following loop building ------------------------------------------------------ 94468 reflections ( 97.09 % complete ) and 8939 restraints for refining 9235 atoms. 1552 conditional restraints added. Observations/parameters ratio is 2.56 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1995 (Rfree = 0.000) for 9235 atoms. Found 300 (300 requested) and removed 105 (197 requested) atoms. Cycle 42: After refmac, R = 0.1951 (Rfree = 0.000) for 9412 atoms. Found 268 (306 requested) and removed 84 (201 requested) atoms. Cycle 43: After refmac, R = 0.1910 (Rfree = 0.000) for 9587 atoms. Found 237 (312 requested) and removed 111 (205 requested) atoms. Cycle 44: After refmac, R = 0.1896 (Rfree = 0.000) for 9703 atoms. Found 217 (315 requested) and removed 139 (207 requested) atoms. Cycle 45: After refmac, R = 0.1882 (Rfree = 0.000) for 9766 atoms. Found 253 (309 requested) and removed 133 (209 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.88 1.86 NCS extension: 41 residues added (22 deleted due to clashes), 9928 seeds are put forward Round 1: 881 peptides, 9 chains. Longest chain 231 peptides. Score 0.938 Round 2: 886 peptides, 9 chains. Longest chain 189 peptides. Score 0.939 Round 3: 884 peptides, 11 chains. Longest chain 229 peptides. Score 0.935 Round 4: 878 peptides, 16 chains. Longest chain 166 peptides. Score 0.926 Round 5: 877 peptides, 11 chains. Longest chain 229 peptides. Score 0.934 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 9, Residues 877, Estimated correctness of the model 99.7 % 9 chains (877 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 74 A and 88 A Built loop between residues 90 C and 93 C Built loop between residues 45 B and 49 B Built loop between residues 213 D and 216 D 5 chains (897 residues) following loop building 5 chains (897 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 94468 reflections ( 97.09 % complete ) and 7485 restraints for refining 7304 atoms. Observations/parameters ratio is 3.23 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2629 (Rfree = 0.000) for 7304 atoms. Found 225 (225 requested) and removed 0 (225 requested) atoms. Cycle 47: After refmac, R = 0.2412 (Rfree = 0.000) for 7304 atoms. Found 115 (232 requested) and removed 1 (161 requested) atoms. Cycle 48: After refmac, R = 0.2272 (Rfree = 0.000) for 7304 atoms. Found 65 (235 requested) and removed 5 (163 requested) atoms. Failed to save intermediate PDB Cycle 49: After refmac, R = 0.2205 (Rfree = 0.000) for 7304 atoms. Found 39 (237 requested) and removed 5 (164 requested) atoms. Writing output files ... TimeTaking 136.65