Mon 24 Dec 07:26:09 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 1vl5-1.9-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vl5-1.9-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vl5-1.9-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vl5-1.9-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/1vl5-1.9-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vl5-1.9-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 07:26:14 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/1vl5-1.9-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vl5-1.9-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 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-noncs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 4 Cell parameters: 64.006 87.475 105.236 90.000 100.573 90.000 Input sequence file: 1vl5-1.9-parrot-noncs.fasta_lf Building free atoms model in initial map for 8320 target number of atoms Had to go as low as 0.50 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 Failed to save intermediate PDB 94468 reflections ( 97.09 % complete ) and 0 restraints for refining 9161 atoms. Observations/parameters ratio is 2.58 ------------------------------------------------------ Starting model: R = 0.3496 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3030 (Rfree = 0.000) for 9161 atoms. Found 311 (391 requested) and removed 204 (195 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.92 1.89 NCS extension: 0 residues added, 9268 seeds are put forward Round 1: 643 peptides, 80 chains. Longest chain 34 peptides. Score 0.608 Round 2: 732 peptides, 60 chains. Longest chain 34 peptides. Score 0.761 Round 3: 767 peptides, 39 chains. Longest chain 75 peptides. Score 0.841 Round 4: 788 peptides, 33 chains. Longest chain 85 peptides. Score 0.865 Round 5: 801 peptides, 38 chains. Longest chain 87 peptides. Score 0.858 Taking the results from Round 4 Chains 41, Residues 755, Estimated correctness of the model 98.6 % 19 chains (591 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 233 A and 236 A Built loop between residues 95 C and 101 C Built loop between residues 157 C and 166 C Built loop between residues 174 B and 178 B Built loop between residues 179 D and 182 D 34 chains (771 residues) following loop building 14 chains (611 residues) in sequence following loop building ------------------------------------------------------ 94468 reflections ( 97.09 % complete ) and 10425 restraints for refining 8489 atoms. 4593 conditional restraints added. Observations/parameters ratio is 2.78 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3223 (Rfree = 0.000) for 8489 atoms. Found 342 (363 requested) and removed 191 (181 requested) atoms. Cycle 2: After refmac, R = 0.2900 (Rfree = 0.000) for 8601 atoms. Found 274 (362 requested) and removed 109 (184 requested) atoms. Cycle 3: After refmac, R = 0.2733 (Rfree = 0.000) for 8712 atoms. Found 224 (367 requested) and removed 50 (187 requested) atoms. Cycle 4: After refmac, R = 0.2608 (Rfree = 0.000) for 8842 atoms. Found 221 (372 requested) and removed 54 (190 requested) atoms. Cycle 5: After refmac, R = 0.2511 (Rfree = 0.000) for 8970 atoms. Found 203 (377 requested) and removed 29 (192 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.89 1.86 NCS extension: 4 residues added (84 deleted due to clashes), 9156 seeds are put forward Round 1: 834 peptides, 24 chains. Longest chain 161 peptides. Score 0.900 Round 2: 851 peptides, 16 chains. Longest chain 231 peptides. Score 0.919 Round 3: 854 peptides, 18 chains. Longest chain 183 peptides. Score 0.917 Round 4: 861 peptides, 15 chains. Longest chain 231 peptides. Score 0.924 Round 5: 857 peptides, 20 chains. Longest chain 101 peptides. Score 0.914 Taking the results from Round 4 Chains 17, Residues 846, Estimated correctness of the model 99.5 % 11 chains (805 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 137 A and 140 A Built loop between residues 203 A and 209 A Built loop between residues 45 C and 50 C Built loop between residues 38 B and 41 B Built loop between residues 109 B and 112 B 12 chains (861 residues) following loop building 6 chains (820 residues) in sequence following loop building ------------------------------------------------------ 94468 reflections ( 97.09 % complete ) and 8675 restraints for refining 8642 atoms. 1629 conditional restraints added. Observations/parameters ratio is 2.73 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2511 (Rfree = 0.000) for 8642 atoms. Found 356 (362 requested) and removed 170 (184 requested) atoms. Cycle 7: After refmac, R = 0.2360 (Rfree = 0.000) for 8809 atoms. Found 253 (369 requested) and removed 68 (188 requested) atoms. Cycle 8: After refmac, R = 0.2248 (Rfree = 0.000) for 8974 atoms. Found 211 (376 requested) and removed 58 (192 requested) atoms. Cycle 9: After refmac, R = 0.2172 (Rfree = 0.000) for 9093 atoms. Found 205 (382 requested) and removed 59 (195 requested) atoms. Cycle 10: After refmac, R = 0.2105 (Rfree = 0.000) for 9220 atoms. Found 168 (387 requested) and removed 71 (197 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.88 1.86 NCS extension: 110 residues added (45 deleted due to clashes), 9433 seeds are put forward Round 1: 873 peptides, 9 chains. Longest chain 231 peptides. Score 0.936 Round 2: 868 peptides, 13 chains. Longest chain 162 peptides. Score 0.929 Round 3: 873 peptides, 10 chains. Longest chain 185 peptides. Score 0.935 Round 4: 878 peptides, 14 chains. Longest chain 166 peptides. Score 0.929 Round 5: 883 peptides, 12 chains. Longest chain 168 peptides. Score 0.934 Taking the results from Round 1 Chains 10, Residues 864, Estimated correctness of the model 99.6 % 6 chains (828 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 45 A and 49 A 9 chains (867 residues) following loop building 5 chains (831 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 94468 reflections ( 97.09 % complete ) and 8766 restraints for refining 8813 atoms. 1646 conditional restraints added. Observations/parameters ratio is 2.68 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2171 (Rfree = 0.000) for 8813 atoms. Found 358 (369 requested) and removed 101 (188 requested) atoms. Cycle 12: After refmac, R = 0.2120 (Rfree = 0.000) for 9050 atoms. Found 209 (380 requested) and removed 117 (194 requested) atoms. Failed to save intermediate PDB Cycle 13: After refmac, R = 0.2049 (Rfree = 0.000) for 9131 atoms. Found 210 (375 requested) and removed 79 (195 requested) atoms. Cycle 14: After refmac, R = 0.2013 (Rfree = 0.000) for 9249 atoms. Found 198 (380 requested) and removed 104 (198 requested) atoms. Cycle 15: After refmac, R = 0.1988 (Rfree = 0.000) for 9327 atoms. Found 196 (375 requested) and removed 104 (199 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.88 1.86 NCS extension: 47 residues added (22 deleted due to clashes), 9470 seeds are put forward Round 1: 874 peptides, 13 chains. Longest chain 231 peptides. Score 0.930 Round 2: 878 peptides, 12 chains. Longest chain 185 peptides. Score 0.932 Round 3: 878 peptides, 10 chains. Longest chain 228 peptides. Score 0.936 Round 4: 880 peptides, 11 chains. Longest chain 231 peptides. Score 0.934 Round 5: 880 peptides, 15 chains. Longest chain 166 peptides. Score 0.928 Taking the results from Round 3 Chains 12, Residues 868, Estimated correctness of the model 99.6 % 9 chains (860 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 147 A and 150 A Built loop between residues 45 B and 49 B Built loop between residues 148 B and 152 B 8 chains (875 residues) following loop building 6 chains (868 residues) in sequence following loop building ------------------------------------------------------ 94468 reflections ( 97.09 % complete ) and 8730 restraints for refining 8945 atoms. 1444 conditional restraints added. Observations/parameters ratio is 2.64 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2100 (Rfree = 0.000) for 8945 atoms. Found 351 (351 requested) and removed 129 (191 requested) atoms. Cycle 17: After refmac, R = 0.2072 (Rfree = 0.000) for 9145 atoms. Found 233 (361 requested) and removed 137 (196 requested) atoms. Cycle 18: After refmac, R = 0.2015 (Rfree = 0.000) for 9232 atoms. Found 220 (355 requested) and removed 86 (197 requested) atoms. Cycle 19: After refmac, R = 0.1981 (Rfree = 0.000) for 9354 atoms. Found 194 (360 requested) and removed 130 (200 requested) atoms. Cycle 20: After refmac, R = 0.1948 (Rfree = 0.000) for 9407 atoms. Found 216 (354 requested) and removed 118 (201 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.88 1.86 NCS extension: 120 residues added (144 deleted due to clashes), 9626 seeds are put forward Round 1: 885 peptides, 9 chains. Longest chain 230 peptides. Score 0.939 Round 2: 885 peptides, 10 chains. Longest chain 231 peptides. Score 0.937 Round 3: 882 peptides, 11 chains. Longest chain 166 peptides. Score 0.935 Round 4: 880 peptides, 12 chains. Longest chain 206 peptides. Score 0.933 Round 5: 882 peptides, 12 chains. Longest chain 166 peptides. Score 0.933 Taking the results from Round 1 Chains 10, Residues 876, Estimated correctness of the model 99.7 % 9 chains (875 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 96 B and 99 B 7 chains (883 residues) following loop building 6 chains (882 residues) in sequence following loop building ------------------------------------------------------ 94468 reflections ( 97.09 % complete ) and 8528 restraints for refining 8963 atoms. 1160 conditional restraints added. Observations/parameters ratio is 2.63 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2045 (Rfree = 0.000) for 8963 atoms. Found 329 (329 requested) and removed 109 (191 requested) atoms. Cycle 22: After refmac, R = 0.2019 (Rfree = 0.000) for 9161 atoms. Found 222 (337 requested) and removed 120 (196 requested) atoms. Cycle 23: After refmac, R = 0.1970 (Rfree = 0.000) for 9256 atoms. Found 272 (333 requested) and removed 96 (198 requested) atoms. Cycle 24: After refmac, R = 0.1960 (Rfree = 0.000) for 9424 atoms. Found 201 (339 requested) and removed 156 (201 requested) atoms. Failed to save intermediate PDB Cycle 25: After refmac, R = 0.1926 (Rfree = 0.000) for 9454 atoms. Found 272 (332 requested) and removed 135 (202 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.88 1.86 NCS extension: 85 residues added (63 deleted due to clashes), 9678 seeds are put forward Round 1: 888 peptides, 10 chains. Longest chain 230 peptides. Score 0.938 Round 2: 895 peptides, 12 chains. Longest chain 231 peptides. Score 0.936 Round 3: 892 peptides, 12 chains. Longest chain 231 peptides. Score 0.935 Round 4: 895 peptides, 13 chains. Longest chain 206 peptides. Score 0.934 Round 5: 896 peptides, 10 chains. Longest chain 191 peptides. Score 0.939 Taking the results from Round 5 Chains 10, Residues 886, Estimated correctness of the model 99.7 % 8 chains (880 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 90 C and 93 C Built loop between residues 77 B and 87 B Built loop between residues 213 D and 216 D 7 chains (898 residues) following loop building 5 chains (893 residues) in sequence following loop building ------------------------------------------------------ 94468 reflections ( 97.09 % complete ) and 8516 restraints for refining 9001 atoms. 1048 conditional restraints added. Observations/parameters ratio is 2.62 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2071 (Rfree = 0.000) for 9001 atoms. Found 316 (316 requested) and removed 163 (192 requested) atoms. Cycle 27: After refmac, R = 0.2012 (Rfree = 0.000) for 9131 atoms. Found 276 (313 requested) and removed 120 (195 requested) atoms. Cycle 28: After refmac, R = 0.1961 (Rfree = 0.000) for 9276 atoms. Found 270 (318 requested) and removed 110 (198 requested) atoms. Cycle 29: After refmac, R = 0.1940 (Rfree = 0.000) for 9432 atoms. Found 213 (322 requested) and removed 169 (201 requested) atoms. Cycle 30: After refmac, R = 0.1918 (Rfree = 0.000) for 9464 atoms. Found 247 (316 requested) and removed 157 (202 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.88 1.86 NCS extension: 47 residues added (22 deleted due to clashes), 9614 seeds are put forward Round 1: 889 peptides, 10 chains. Longest chain 230 peptides. Score 0.938 Round 2: 892 peptides, 10 chains. Longest chain 231 peptides. Score 0.938 Round 3: 894 peptides, 13 chains. Longest chain 231 peptides. Score 0.934 Round 4: 889 peptides, 15 chains. Longest chain 162 peptides. Score 0.930 Round 5: 896 peptides, 13 chains. Longest chain 166 peptides. Score 0.935 Taking the results from Round 2 Chains 11, Residues 882, Estimated correctness of the model 99.7 % 9 chains (876 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 90 C and 93 C Built loop between residues 213 C and 216 C Built loop between residues 46 B and 50 B 8 chains (889 residues) following loop building 6 chains (883 residues) in sequence following loop building ------------------------------------------------------ 94468 reflections ( 97.09 % complete ) and 8571 restraints for refining 8956 atoms. 1176 conditional restraints added. Observations/parameters ratio is 2.64 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2041 (Rfree = 0.000) for 8956 atoms. Found 291 (291 requested) and removed 103 (191 requested) atoms. Cycle 32: After refmac, R = 0.1986 (Rfree = 0.000) for 9129 atoms. Found 245 (297 requested) and removed 74 (195 requested) atoms. Cycle 33: After refmac, R = 0.1953 (Rfree = 0.000) for 9292 atoms. Found 222 (302 requested) and removed 122 (198 requested) atoms. Cycle 34: After refmac, R = 0.1934 (Rfree = 0.000) for 9376 atoms. Found 239 (297 requested) and removed 143 (200 requested) atoms. Cycle 35: After refmac, R = 0.1919 (Rfree = 0.000) for 9460 atoms. Found 238 (292 requested) and removed 150 (202 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.88 1.86 NCS extension: 134 residues added (169 deleted due to clashes), 9684 seeds are put forward Round 1: 897 peptides, 11 chains. Longest chain 166 peptides. Score 0.938 Round 2: 896 peptides, 12 chains. Longest chain 191 peptides. Score 0.936 Round 3: 899 peptides, 11 chains. Longest chain 168 peptides. Score 0.938 Round 4: 891 peptides, 17 chains. Longest chain 159 peptides. Score 0.927 Round 5: 889 peptides, 16 chains. Longest chain 231 peptides. Score 0.929 Taking the results from Round 3 Chains 13, Residues 888, Estimated correctness of the model 99.7 % 9 chains (863 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 130 A and 133 A Built loop between residues 127 C and 137 C Built loop between residues 46 B and 49 B 9 chains (893 residues) following loop building 6 chains (876 residues) in sequence following loop building ------------------------------------------------------ 94468 reflections ( 97.09 % complete ) and 8653 restraints for refining 8944 atoms. 1268 conditional restraints added. Observations/parameters ratio is 2.64 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2029 (Rfree = 0.000) for 8944 atoms. Found 267 (267 requested) and removed 99 (191 requested) atoms. Cycle 37: After refmac, R = 0.1992 (Rfree = 0.000) for 9097 atoms. Found 272 (272 requested) and removed 90 (194 requested) atoms. Cycle 38: After refmac, R = 0.1955 (Rfree = 0.000) for 9269 atoms. Found 277 (277 requested) and removed 127 (198 requested) atoms. Failed to save intermediate PDB Cycle 39: After refmac, R = 0.1936 (Rfree = 0.000) for 9409 atoms. Found 269 (281 requested) and removed 156 (201 requested) atoms. Cycle 40: After refmac, R = 0.1924 (Rfree = 0.000) for 9512 atoms. Found 270 (277 requested) and removed 160 (203 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.88 1.86 NCS extension: 87 residues added (156 deleted due to clashes), 9712 seeds are put forward Round 1: 897 peptides, 11 chains. Longest chain 231 peptides. Score 0.938 Round 2: 896 peptides, 12 chains. Longest chain 231 peptides. Score 0.936 Round 3: 900 peptides, 11 chains. Longest chain 231 peptides. Score 0.939 Round 4: 891 peptides, 17 chains. Longest chain 145 peptides. Score 0.927 Round 5: 893 peptides, 10 chains. Longest chain 231 peptides. Score 0.939 Taking the results from Round 5 Chains 10, Residues 883, Estimated correctness of the model 99.7 % 9 chains (878 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 46 A and 50 A Built loop between residues 203 C and 206 C Built loop between residues 192 B and 195 B 7 chains (890 residues) following loop building 6 chains (885 residues) in sequence following loop building ------------------------------------------------------ 94468 reflections ( 97.09 % complete ) and 8520 restraints for refining 8969 atoms. 1114 conditional restraints added. Observations/parameters ratio is 2.63 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2036 (Rfree = 0.000) for 8969 atoms. Found 253 (253 requested) and removed 110 (191 requested) atoms. Cycle 42: After refmac, R = 0.1987 (Rfree = 0.000) for 9094 atoms. Found 257 (257 requested) and removed 57 (194 requested) atoms. Cycle 43: After refmac, R = 0.1954 (Rfree = 0.000) for 9279 atoms. Found 228 (262 requested) and removed 98 (198 requested) atoms. Cycle 44: After refmac, R = 0.1937 (Rfree = 0.000) for 9397 atoms. Found 204 (265 requested) and removed 111 (201 requested) atoms. Cycle 45: After refmac, R = 0.1909 (Rfree = 0.000) for 9478 atoms. Found 226 (259 requested) and removed 113 (202 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.88 1.86 NCS extension: 43 residues added (29 deleted due to clashes), 9639 seeds are put forward Round 1: 894 peptides, 11 chains. Longest chain 231 peptides. Score 0.937 Round 2: 891 peptides, 11 chains. Longest chain 191 peptides. Score 0.937 Round 3: 892 peptides, 10 chains. Longest chain 231 peptides. Score 0.938 Round 4: 889 peptides, 15 chains. Longest chain 161 peptides. Score 0.930 Round 5: 895 peptides, 12 chains. Longest chain 167 peptides. Score 0.936 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 11, Residues 882, Estimated correctness of the model 99.7 % 9 chains (868 residues) have been docked in sequence Sequence coverage is 98 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 68 A and 81 A Built loop between residues 90 A and 93 A Built loop between residues 46 C and 50 C 9 chains (894 residues) following loop building 6 chains (885 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 94468 reflections ( 97.09 % complete ) and 7426 restraints for refining 7250 atoms. Observations/parameters ratio is 3.26 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2657 (Rfree = 0.000) for 7250 atoms. Found 198 (198 requested) and removed 0 (198 requested) atoms. Cycle 47: After refmac, R = 0.2454 (Rfree = 0.000) for 7250 atoms. Found 108 (204 requested) and removed 1 (159 requested) atoms. Cycle 48: After refmac, R = 0.2320 (Rfree = 0.000) for 7250 atoms. Found 80 (207 requested) and removed 0 (161 requested) atoms. Cycle 49: After refmac, R = 0.2237 (Rfree = 0.000) for 7250 atoms. Found 52 (209 requested) and removed 5 (163 requested) atoms. Writing output files ... TimeTaking 107.13