Mon 24 Dec 00:20:03 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 2a6a-2.5-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2a6a-2.5-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2a6a-2.5-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2a6a-2.5-parrot-mrncs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2a6a-2.5-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2a6a-2.5-parrot-mrncs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Mon 24 Dec 00:20:08 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/2a6a-2.5-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2a6a-2.5-parrot-mrncs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 380 and 0 Target number of residues in the AU: 380 Target solvent content: 0.6095 Checking the provided sequence file Detected sequence length: 218 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 436 Adjusted target solvent content: 0.55 Input MTZ file: 2a6a-2.5-parrot-mrncs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 21 Cell parameters: 93.313 217.176 51.977 90.000 90.000 90.000 Input sequence file: 2a6a-2.5-parrot-mrncs.fasta_lf Building free atoms model in initial map for 3488 target number of atoms Had to go as low as 0.65 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 3 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: 108.588 2.500 Wilson plot Bfac: 56.36 16883 reflections ( 98.49 % complete ) and 0 restraints for refining 3934 atoms. Observations/parameters ratio is 1.07 ------------------------------------------------------ Starting model: R = 0.3543 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2680 (Rfree = 0.000) for 3934 atoms. Found 45 (71 requested) and removed 60 (35 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.83 2.65 NCS extension: 0 residues added, 3919 seeds are put forward Round 1: 246 peptides, 37 chains. Longest chain 17 peptides. Score 0.486 Round 2: 281 peptides, 31 chains. Longest chain 26 peptides. Score 0.637 Round 3: 299 peptides, 26 chains. Longest chain 41 peptides. Score 0.716 Round 4: 298 peptides, 24 chains. Longest chain 47 peptides. Score 0.731 Round 5: 299 peptides, 24 chains. Longest chain 44 peptides. Score 0.733 Taking the results from Round 5 Chains 25, Residues 275, Estimated correctness of the model 87.1 % 5 chains (147 residues) have been docked in sequence Building loops using Loopy2018 25 chains (275 residues) following loop building 5 chains (147 residues) in sequence following loop building ------------------------------------------------------ 16883 reflections ( 98.49 % complete ) and 5326 restraints for refining 3267 atoms. 3650 conditional restraints added. Observations/parameters ratio is 1.29 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2849 (Rfree = 0.000) for 3267 atoms. Found 58 (59 requested) and removed 43 (29 requested) atoms. Cycle 2: After refmac, R = 0.2575 (Rfree = 0.000) for 3260 atoms. Found 34 (58 requested) and removed 33 (29 requested) atoms. Cycle 3: After refmac, R = 0.2457 (Rfree = 0.000) for 3234 atoms. Found 35 (57 requested) and removed 30 (29 requested) atoms. Cycle 4: After refmac, R = 0.2364 (Rfree = 0.000) for 3229 atoms. Found 23 (55 requested) and removed 29 (29 requested) atoms. Cycle 5: After refmac, R = 0.2339 (Rfree = 0.000) for 3203 atoms. Found 24 (53 requested) and removed 30 (29 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.86 2.68 NCS extension: 0 residues added, 3210 seeds are put forward Round 1: 295 peptides, 29 chains. Longest chain 42 peptides. Score 0.683 Round 2: 313 peptides, 20 chains. Longest chain 44 peptides. Score 0.784 Round 3: 306 peptides, 23 chains. Longest chain 42 peptides. Score 0.752 Round 4: 311 peptides, 22 chains. Longest chain 34 peptides. Score 0.767 Round 5: 309 peptides, 23 chains. Longest chain 35 peptides. Score 0.757 Taking the results from Round 2 Chains 20, Residues 293, Estimated correctness of the model 91.3 % 6 chains (156 residues) have been docked in sequence Building loops using Loopy2018 20 chains (293 residues) following loop building 6 chains (156 residues) in sequence following loop building ------------------------------------------------------ 16883 reflections ( 98.49 % complete ) and 5212 restraints for refining 3268 atoms. 3424 conditional restraints added. Observations/parameters ratio is 1.29 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2432 (Rfree = 0.000) for 3268 atoms. Found 43 (53 requested) and removed 35 (29 requested) atoms. Cycle 7: After refmac, R = 0.2309 (Rfree = 0.000) for 3262 atoms. Found 23 (52 requested) and removed 33 (29 requested) atoms. Cycle 8: After refmac, R = 0.2229 (Rfree = 0.000) for 3250 atoms. Found 19 (50 requested) and removed 32 (29 requested) atoms. Cycle 9: After refmac, R = 0.2248 (Rfree = 0.000) for 3233 atoms. Found 31 (49 requested) and removed 33 (29 requested) atoms. Cycle 10: After refmac, R = 0.2197 (Rfree = 0.000) for 3230 atoms. Found 21 (48 requested) and removed 31 (29 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.86 2.68 NCS extension: 30 residues added (43 deleted due to clashes), 3259 seeds are put forward Round 1: 307 peptides, 21 chains. Longest chain 53 peptides. Score 0.769 Round 2: 328 peptides, 20 chains. Longest chain 55 peptides. Score 0.804 Round 3: 322 peptides, 21 chains. Longest chain 45 peptides. Score 0.789 Round 4: 314 peptides, 24 chains. Longest chain 40 peptides. Score 0.757 Round 5: 322 peptides, 22 chains. Longest chain 43 peptides. Score 0.783 Taking the results from Round 2 Chains 21, Residues 308, Estimated correctness of the model 92.7 % 6 chains (189 residues) have been docked in sequence Building loops using Loopy2018 21 chains (308 residues) following loop building 6 chains (189 residues) in sequence following loop building ------------------------------------------------------ 16883 reflections ( 98.49 % complete ) and 4875 restraints for refining 3268 atoms. 2941 conditional restraints added. Observations/parameters ratio is 1.29 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2404 (Rfree = 0.000) for 3268 atoms. Found 36 (47 requested) and removed 38 (29 requested) atoms. Cycle 12: After refmac, R = 0.2286 (Rfree = 0.000) for 3257 atoms. Found 26 (46 requested) and removed 32 (29 requested) atoms. Failed to save intermediate PDB Cycle 13: After refmac, R = 0.2286 (Rfree = 0.000) for 3248 atoms. Found 26 (44 requested) and removed 35 (29 requested) atoms. Cycle 14: After refmac, R = 0.2252 (Rfree = 0.000) for 3233 atoms. Found 32 (43 requested) and removed 32 (29 requested) atoms. Cycle 15: After refmac, R = 0.2253 (Rfree = 0.000) for 3231 atoms. Found 22 (42 requested) and removed 33 (29 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.84 2.66 NCS extension: 20 residues added (23 deleted due to clashes), 3250 seeds are put forward Round 1: 319 peptides, 21 chains. Longest chain 55 peptides. Score 0.785 Round 2: 327 peptides, 19 chains. Longest chain 45 peptides. Score 0.809 Round 3: 318 peptides, 21 chains. Longest chain 56 peptides. Score 0.784 Round 4: 331 peptides, 19 chains. Longest chain 56 peptides. Score 0.814 Round 5: 324 peptides, 21 chains. Longest chain 38 peptides. Score 0.792 Taking the results from Round 4 Chains 20, Residues 312, Estimated correctness of the model 93.3 % 8 chains (233 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 55 A and 65 A Built loop between residues 74 A and 79 A Built loop between residues 74 B and 77 B Built loop between residues 89 B and 100 B Built loop between residues 154 B and 159 B 14 chains (335 residues) following loop building 3 chains (262 residues) in sequence following loop building ------------------------------------------------------ 16883 reflections ( 98.49 % complete ) and 4185 restraints for refining 3267 atoms. 1885 conditional restraints added. Observations/parameters ratio is 1.29 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2421 (Rfree = 0.000) for 3267 atoms. Found 41 (41 requested) and removed 43 (29 requested) atoms. Cycle 17: After refmac, R = 0.2216 (Rfree = 0.000) for 3255 atoms. Found 24 (40 requested) and removed 36 (29 requested) atoms. Cycle 18: After refmac, R = 0.2117 (Rfree = 0.000) for 3240 atoms. Found 28 (38 requested) and removed 32 (29 requested) atoms. Cycle 19: After refmac, R = 0.2046 (Rfree = 0.000) for 3234 atoms. Found 20 (37 requested) and removed 31 (29 requested) atoms. Cycle 20: After refmac, R = 0.2020 (Rfree = 0.000) for 3221 atoms. Found 16 (36 requested) and removed 32 (29 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.83 2.65 NCS extension: 100 residues added (211 deleted due to clashes), 3314 seeds are put forward Round 1: 337 peptides, 19 chains. Longest chain 60 peptides. Score 0.821 Round 2: 340 peptides, 17 chains. Longest chain 60 peptides. Score 0.836 Round 3: 329 peptides, 19 chains. Longest chain 56 peptides. Score 0.811 Round 4: 337 peptides, 16 chains. Longest chain 83 peptides. Score 0.839 Round 5: 331 peptides, 20 chains. Longest chain 46 peptides. Score 0.808 Taking the results from Round 4 Chains 16, Residues 321, Estimated correctness of the model 94.9 % 6 chains (273 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 84 A and 87 A Built loop between residues 93 B and 96 B Built loop between residues 151 B and 154 B 13 chains (327 residues) following loop building 3 chains (279 residues) in sequence following loop building ------------------------------------------------------ 16883 reflections ( 98.49 % complete ) and 4128 restraints for refining 3268 atoms. 1772 conditional restraints added. Observations/parameters ratio is 1.29 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2271 (Rfree = 0.000) for 3268 atoms. Found 35 (35 requested) and removed 39 (29 requested) atoms. Cycle 22: After refmac, R = 0.2086 (Rfree = 0.000) for 3257 atoms. Found 33 (34 requested) and removed 31 (29 requested) atoms. Cycle 23: After refmac, R = 0.2025 (Rfree = 0.000) for 3254 atoms. Found 22 (33 requested) and removed 31 (29 requested) atoms. Cycle 24: After refmac, R = 0.2016 (Rfree = 0.000) for 3239 atoms. Found 20 (31 requested) and removed 32 (29 requested) atoms. Cycle 25: After refmac, R = 0.2031 (Rfree = 0.000) for 3225 atoms. Found 26 (30 requested) and removed 29 (29 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.84 2.66 NCS extension: 184 residues added (261 deleted due to clashes), 3414 seeds are put forward Round 1: 335 peptides, 16 chains. Longest chain 51 peptides. Score 0.837 Round 2: 336 peptides, 13 chains. Longest chain 54 peptides. Score 0.855 Round 3: 327 peptides, 15 chains. Longest chain 58 peptides. Score 0.834 Round 4: 332 peptides, 16 chains. Longest chain 59 peptides. Score 0.833 Round 5: 327 peptides, 17 chains. Longest chain 51 peptides. Score 0.822 Taking the results from Round 2 Chains 13, Residues 323, Estimated correctness of the model 95.8 % 8 chains (290 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 57 A and 60 A Built loop between residues 74 A and 77 A Built loop between residues 48 B and 59 B Built loop between residues 89 B and 97 B Built loop between residues 149 B and 154 B 7 chains (343 residues) following loop building 3 chains (315 residues) in sequence following loop building ------------------------------------------------------ 16883 reflections ( 98.49 % complete ) and 3694 restraints for refining 3268 atoms. 1139 conditional restraints added. Observations/parameters ratio is 1.29 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2208 (Rfree = 0.000) for 3268 atoms. Found 29 (29 requested) and removed 39 (29 requested) atoms. Cycle 27: After refmac, R = 0.2014 (Rfree = 0.000) for 3242 atoms. Found 29 (29 requested) and removed 30 (29 requested) atoms. Cycle 28: After refmac, R = 0.1970 (Rfree = 0.000) for 3238 atoms. Found 21 (29 requested) and removed 32 (29 requested) atoms. Cycle 29: After refmac, R = 0.1924 (Rfree = 0.000) for 3227 atoms. Found 29 (29 requested) and removed 29 (29 requested) atoms. Cycle 30: After refmac, R = 0.1906 (Rfree = 0.000) for 3226 atoms. Found 18 (29 requested) and removed 32 (29 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.84 2.66 NCS extension: 68 residues added (170 deleted due to clashes), 3285 seeds are put forward Round 1: 341 peptides, 16 chains. Longest chain 51 peptides. Score 0.843 Round 2: 351 peptides, 12 chains. Longest chain 124 peptides. Score 0.874 Round 3: 344 peptides, 14 chains. Longest chain 105 peptides. Score 0.857 Round 4: 355 peptides, 13 chains. Longest chain 83 peptides. Score 0.872 Round 5: 344 peptides, 17 chains. Longest chain 51 peptides. Score 0.840 Taking the results from Round 2 Chains 12, Residues 339, Estimated correctness of the model 96.7 % 6 chains (301 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 57 A and 65 A Built loop between residues 74 A and 77 A Built loop between residues 126 A and 129 A Built loop between residues 74 B and 77 B 7 chains (349 residues) following loop building 2 chains (314 residues) in sequence following loop building ------------------------------------------------------ 16883 reflections ( 98.49 % complete ) and 3741 restraints for refining 3267 atoms. 1144 conditional restraints added. Observations/parameters ratio is 1.29 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2073 (Rfree = 0.000) for 3267 atoms. Found 29 (29 requested) and removed 33 (29 requested) atoms. Cycle 32: After refmac, R = 0.1919 (Rfree = 0.000) for 3255 atoms. Found 29 (29 requested) and removed 32 (29 requested) atoms. Cycle 33: After refmac, R = 0.1887 (Rfree = 0.000) for 3249 atoms. Found 26 (29 requested) and removed 36 (29 requested) atoms. Cycle 34: After refmac, R = 0.1859 (Rfree = 0.000) for 3237 atoms. Found 29 (29 requested) and removed 34 (29 requested) atoms. Cycle 35: After refmac, R = 0.1819 (Rfree = 0.000) for 3232 atoms. Found 24 (29 requested) and removed 37 (29 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.84 2.66 NCS extension: 18 residues added (44 deleted due to clashes), 3243 seeds are put forward Round 1: 351 peptides, 12 chains. Longest chain 75 peptides. Score 0.874 Round 2: 354 peptides, 14 chains. Longest chain 59 peptides. Score 0.866 Round 3: 348 peptides, 15 chains. Longest chain 69 peptides. Score 0.855 Round 4: 356 peptides, 13 chains. Longest chain 51 peptides. Score 0.873 Round 5: 350 peptides, 15 chains. Longest chain 51 peptides. Score 0.857 Taking the results from Round 1 Chains 13, Residues 339, Estimated correctness of the model 96.7 % 8 chains (314 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 90 A and 95 A Built loop between residues 48 B and 56 B Built loop between residues 74 B and 77 B Built loop between residues 123 B and 126 B 9 chains (354 residues) following loop building 4 chains (329 residues) in sequence following loop building ------------------------------------------------------ 16883 reflections ( 98.49 % complete ) and 3604 restraints for refining 3268 atoms. 910 conditional restraints added. Observations/parameters ratio is 1.29 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2004 (Rfree = 0.000) for 3268 atoms. Found 29 (29 requested) and removed 36 (29 requested) atoms. Cycle 37: After refmac, R = 0.1829 (Rfree = 0.000) for 3251 atoms. Found 29 (29 requested) and removed 32 (29 requested) atoms. Cycle 38: After refmac, R = 0.1754 (Rfree = 0.000) for 3245 atoms. Found 28 (29 requested) and removed 37 (29 requested) atoms. Cycle 39: After refmac, R = 0.1747 (Rfree = 0.000) for 3234 atoms. Found 29 (29 requested) and removed 36 (29 requested) atoms. Cycle 40: After refmac, R = 0.1724 (Rfree = 0.000) for 3225 atoms. Found 29 (29 requested) and removed 35 (29 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.83 2.65 NCS extension: 53 residues added (166 deleted due to clashes), 3274 seeds are put forward Round 1: 342 peptides, 18 chains. Longest chain 62 peptides. Score 0.832 Round 2: 359 peptides, 11 chains. Longest chain 115 peptides. Score 0.885 Round 3: 353 peptides, 16 chains. Longest chain 51 peptides. Score 0.855 Round 4: 350 peptides, 16 chains. Longest chain 46 peptides. Score 0.852 Round 5: 353 peptides, 16 chains. Longest chain 69 peptides. Score 0.855 Taking the results from Round 2 Chains 11, Residues 348, Estimated correctness of the model 97.2 % 9 chains (334 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 57 A and 65 A Built loop between residues 73 A and 77 A Built loop between residues 88 A and 91 A Built loop between residues 126 B and 129 B Built loop between residues 150 B and 153 B Built loop between residues 175 B and 178 B 4 chains (363 residues) following loop building 3 chains (352 residues) in sequence following loop building ------------------------------------------------------ 16883 reflections ( 98.49 % complete ) and 3377 restraints for refining 3268 atoms. 555 conditional restraints added. Observations/parameters ratio is 1.29 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2047 (Rfree = 0.000) for 3268 atoms. Found 29 (29 requested) and removed 41 (29 requested) atoms. Cycle 42: After refmac, R = 0.1845 (Rfree = 0.000) for 3252 atoms. Found 29 (29 requested) and removed 31 (29 requested) atoms. Cycle 43: After refmac, R = 0.1817 (Rfree = 0.000) for 3249 atoms. Found 28 (29 requested) and removed 37 (29 requested) atoms. Cycle 44: After refmac, R = 0.1800 (Rfree = 0.000) for 3238 atoms. Found 26 (29 requested) and removed 35 (29 requested) atoms. Cycle 45: After refmac, R = 0.1785 (Rfree = 0.000) for 3229 atoms. Found 29 (29 requested) and removed 39 (29 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.83 2.65 NCS extension: 33 residues added (176 deleted due to clashes), 3261 seeds are put forward Round 1: 361 peptides, 9 chains. Longest chain 75 peptides. Score 0.896 Round 2: 358 peptides, 9 chains. Longest chain 76 peptides. Score 0.893 Round 3: 354 peptides, 15 chains. Longest chain 43 peptides. Score 0.861 Round 4: 364 peptides, 9 chains. Longest chain 100 peptides. Score 0.898 Round 5: 347 peptides, 12 chains. Longest chain 49 peptides. Score 0.870 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 11, Residues 355, Estimated correctness of the model 97.8 % 9 chains (333 residues) have been docked in sequence Sequence coverage is 93 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 57 A and 60 A Built loop between residues 73 A and 76 A Built loop between residues 48 B and 60 B Built loop between residues 158 B and 161 B Built loop between residues 174 B and 177 B 5 chains (368 residues) following loop building 4 chains (352 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 16883 reflections ( 98.49 % complete ) and 2852 restraints for refining 2809 atoms. Observations/parameters ratio is 1.50 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2614 (Rfree = 0.000) for 2809 atoms. Found 16 (25 requested) and removed 0 (25 requested) atoms. Cycle 47: After refmac, R = 0.2330 (Rfree = 0.000) for 2809 atoms. Found 10 (25 requested) and removed 2 (25 requested) atoms. Cycle 48: After refmac, R = 0.2242 (Rfree = 0.000) for 2809 atoms. Found 4 (25 requested) and removed 2 (25 requested) atoms. Cycle 49: After refmac, R = 0.2209 (Rfree = 0.000) for 2809 atoms. TimeTaking 50.27