Sun 23 Dec 22:22:56 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vjn-3.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vjn-3.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vjn-3.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjn-3.0-parrot-hancs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjn-3.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjn-3.0-parrot-hancs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Sun 23 Dec 22:23:06 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjn-3.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjn-3.0-parrot-hancs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 392 and 0 Target number of residues in the AU: 392 Target solvent content: 0.5070 Checking the provided sequence file Detected sequence length: 220 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 440 Adjusted target solvent content: 0.45 Input MTZ file: 1vjn-3.0-parrot-hancs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 1 Cell parameters: 43.059 45.719 63.384 73.681 89.271 64.860 Input sequence file: 1vjn-3.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 3520 target number of atoms Had to go as low as 0.55 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: 60.370 3.000 Wilson plot Bfac: 24.83 8199 reflections ( 98.22 % complete ) and 0 restraints for refining 3906 atoms. Observations/parameters ratio is 0.52 ------------------------------------------------------ Starting model: R = 0.2884 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2248 (Rfree = 0.000) for 3906 atoms. Found 42 (42 requested) and removed 46 (21 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.50 2.67 Search for helices and strands: 0 residues in 0 chains, 3960 seeds are put forward NCS extension: 0 residues added, 3960 seeds are put forward Round 1: 197 peptides, 35 chains. Longest chain 14 peptides. Score 0.400 Round 2: 242 peptides, 31 chains. Longest chain 20 peptides. Score 0.601 Round 3: 269 peptides, 34 chains. Longest chain 28 peptides. Score 0.637 Round 4: 287 peptides, 30 chains. Longest chain 29 peptides. Score 0.719 Round 5: 315 peptides, 28 chains. Longest chain 31 peptides. Score 0.786 Taking the results from Round 5 Chains 34, Residues 287, Estimated correctness of the model 84.7 % 6 chains (114 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 67 B and 77 B Built loop between residues 179 B and 187 B 29 chains (294 residues) following loop building 4 chains (130 residues) in sequence following loop building ------------------------------------------------------ 8199 reflections ( 98.22 % complete ) and 5223 restraints for refining 3228 atoms. 3541 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2644 (Rfree = 0.000) for 3228 atoms. Found 34 (34 requested) and removed 27 (17 requested) atoms. Cycle 2: After refmac, R = 0.2443 (Rfree = 0.000) for 3186 atoms. Found 24 (33 requested) and removed 21 (17 requested) atoms. Cycle 3: After refmac, R = 0.2337 (Rfree = 0.000) for 3147 atoms. Found 13 (33 requested) and removed 19 (17 requested) atoms. Cycle 4: After refmac, R = 0.2241 (Rfree = 0.000) for 3125 atoms. Found 15 (31 requested) and removed 19 (16 requested) atoms. Cycle 5: After refmac, R = 0.2164 (Rfree = 0.000) for 3104 atoms. Found 14 (30 requested) and removed 17 (16 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.42 2.59 Search for helices and strands: 0 residues in 0 chains, 3186 seeds are put forward NCS extension: 22 residues added (32 deleted due to clashes), 3208 seeds are put forward Round 1: 293 peptides, 30 chains. Longest chain 25 peptides. Score 0.731 Round 2: 308 peptides, 30 chains. Longest chain 34 peptides. Score 0.759 Round 3: 320 peptides, 27 chains. Longest chain 37 peptides. Score 0.801 Round 4: 308 peptides, 23 chains. Longest chain 39 peptides. Score 0.812 Round 5: 308 peptides, 27 chains. Longest chain 37 peptides. Score 0.783 Taking the results from Round 4 Chains 24, Residues 285, Estimated correctness of the model 87.9 % 7 chains (148 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 82 B and 86 B Built loop between residues 184 B and 187 B 22 chains (290 residues) following loop building 5 chains (153 residues) in sequence following loop building ------------------------------------------------------ 8199 reflections ( 98.22 % complete ) and 5200 restraints for refining 3229 atoms. 3396 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2496 (Rfree = 0.000) for 3229 atoms. Found 31 (31 requested) and removed 36 (17 requested) atoms. Cycle 7: After refmac, R = 0.2230 (Rfree = 0.000) for 3206 atoms. Found 22 (30 requested) and removed 19 (17 requested) atoms. Cycle 8: After refmac, R = 0.2129 (Rfree = 0.000) for 3198 atoms. Found 12 (29 requested) and removed 19 (17 requested) atoms. Cycle 9: After refmac, R = 0.2065 (Rfree = 0.000) for 3179 atoms. Found 11 (29 requested) and removed 17 (17 requested) atoms. Cycle 10: After refmac, R = 0.2039 (Rfree = 0.000) for 3160 atoms. Found 9 (28 requested) and removed 17 (17 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.45 2.62 Search for helices and strands: 0 residues in 0 chains, 3219 seeds are put forward NCS extension: 77 residues added (69 deleted due to clashes), 3296 seeds are put forward Round 1: 298 peptides, 29 chains. Longest chain 34 peptides. Score 0.749 Round 2: 308 peptides, 27 chains. Longest chain 28 peptides. Score 0.783 Round 3: 300 peptides, 26 chains. Longest chain 37 peptides. Score 0.778 Round 4: 302 peptides, 25 chains. Longest chain 51 peptides. Score 0.789 Round 5: 294 peptides, 25 chains. Longest chain 33 peptides. Score 0.776 Taking the results from Round 4 Chains 26, Residues 277, Estimated correctness of the model 85.1 % 5 chains (131 residues) have been docked in sequence Building loops using Loopy2018 26 chains (277 residues) following loop building 5 chains (131 residues) in sequence following loop building ------------------------------------------------------ 8199 reflections ( 98.22 % complete ) and 5417 restraints for refining 3231 atoms. 3741 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2393 (Rfree = 0.000) for 3231 atoms. Found 27 (27 requested) and removed 33 (17 requested) atoms. Cycle 12: After refmac, R = 0.2174 (Rfree = 0.000) for 3207 atoms. Found 18 (27 requested) and removed 19 (17 requested) atoms. Cycle 13: After refmac, R = 0.2067 (Rfree = 0.000) for 3199 atoms. Found 10 (26 requested) and removed 17 (17 requested) atoms. Cycle 14: After refmac, R = 0.2006 (Rfree = 0.000) for 3180 atoms. Found 13 (25 requested) and removed 17 (17 requested) atoms. Cycle 15: After refmac, R = 0.1945 (Rfree = 0.000) for 3168 atoms. Found 17 (24 requested) and removed 17 (17 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.45 2.62 Search for helices and strands: 0 residues in 0 chains, 3243 seeds are put forward NCS extension: 49 residues added (43 deleted due to clashes), 3292 seeds are put forward Round 1: 283 peptides, 31 chains. Longest chain 26 peptides. Score 0.701 Round 2: 299 peptides, 25 chains. Longest chain 35 peptides. Score 0.784 Round 3: 305 peptides, 27 chains. Longest chain 36 peptides. Score 0.778 Round 4: 292 peptides, 25 chains. Longest chain 32 peptides. Score 0.772 Round 5: 300 peptides, 28 chains. Longest chain 26 peptides. Score 0.761 Taking the results from Round 2 Chains 29, Residues 274, Estimated correctness of the model 84.4 % 7 chains (150 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 82 B and 86 B Built loop between residues 176 B and 186 B 25 chains (283 residues) following loop building 5 chains (162 residues) in sequence following loop building ------------------------------------------------------ 8199 reflections ( 98.22 % complete ) and 5115 restraints for refining 3231 atoms. 3330 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2348 (Rfree = 0.000) for 3231 atoms. Found 24 (24 requested) and removed 35 (17 requested) atoms. Cycle 17: After refmac, R = 0.2222 (Rfree = 0.000) for 3206 atoms. Found 14 (23 requested) and removed 19 (17 requested) atoms. Cycle 18: After refmac, R = 0.2186 (Rfree = 0.000) for 3186 atoms. Found 14 (22 requested) and removed 17 (17 requested) atoms. Cycle 19: After refmac, R = 0.2069 (Rfree = 0.000) for 3173 atoms. Found 17 (22 requested) and removed 17 (17 requested) atoms. Cycle 20: After refmac, R = 0.1995 (Rfree = 0.000) for 3168 atoms. Found 9 (21 requested) and removed 17 (17 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.43 2.60 Search for helices and strands: 0 residues in 0 chains, 3214 seeds are put forward NCS extension: 12 residues added (14 deleted due to clashes), 3226 seeds are put forward Round 1: 282 peptides, 24 chains. Longest chain 34 peptides. Score 0.764 Round 2: 293 peptides, 25 chains. Longest chain 32 peptides. Score 0.774 Round 3: 286 peptides, 27 chains. Longest chain 40 peptides. Score 0.745 Round 4: 278 peptides, 27 chains. Longest chain 26 peptides. Score 0.729 Round 5: 288 peptides, 26 chains. Longest chain 49 peptides. Score 0.757 Taking the results from Round 2 Chains 29, Residues 268, Estimated correctness of the model 83.1 % 6 chains (114 residues) have been docked in sequence Building loops using Loopy2018 29 chains (268 residues) following loop building 6 chains (114 residues) in sequence following loop building ------------------------------------------------------ 8199 reflections ( 98.22 % complete ) and 5655 restraints for refining 3231 atoms. 4102 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2206 (Rfree = 0.000) for 3231 atoms. Found 20 (20 requested) and removed 26 (17 requested) atoms. Cycle 22: After refmac, R = 0.2135 (Rfree = 0.000) for 3220 atoms. Found 11 (20 requested) and removed 19 (17 requested) atoms. Cycle 23: After refmac, R = 0.1979 (Rfree = 0.000) for 3201 atoms. Found 14 (19 requested) and removed 17 (17 requested) atoms. Cycle 24: After refmac, R = 0.1943 (Rfree = 0.000) for 3194 atoms. Found 7 (18 requested) and removed 17 (17 requested) atoms. Cycle 25: After refmac, R = 0.1915 (Rfree = 0.000) for 3183 atoms. Found 8 (18 requested) and removed 17 (17 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.41 2.58 Search for helices and strands: 0 residues in 0 chains, 3243 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 3266 seeds are put forward Round 1: 284 peptides, 28 chains. Longest chain 23 peptides. Score 0.732 Round 2: 297 peptides, 24 chains. Longest chain 35 peptides. Score 0.789 Round 3: 292 peptides, 25 chains. Longest chain 55 peptides. Score 0.772 Round 4: 291 peptides, 23 chains. Longest chain 55 peptides. Score 0.787 Round 5: 291 peptides, 26 chains. Longest chain 36 peptides. Score 0.762 Taking the results from Round 2 Chains 28, Residues 273, Estimated correctness of the model 85.1 % 5 chains (112 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 182 B and 187 B 25 chains (275 residues) following loop building 4 chains (116 residues) in sequence following loop building ------------------------------------------------------ 8199 reflections ( 98.22 % complete ) and 5472 restraints for refining 3231 atoms. 3890 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2187 (Rfree = 0.000) for 3231 atoms. Found 17 (17 requested) and removed 25 (17 requested) atoms. Cycle 27: After refmac, R = 0.2061 (Rfree = 0.000) for 3216 atoms. Found 17 (17 requested) and removed 18 (17 requested) atoms. Cycle 28: After refmac, R = 0.2016 (Rfree = 0.000) for 3210 atoms. Found 4 (17 requested) and removed 18 (17 requested) atoms. Cycle 29: After refmac, R = 0.2006 (Rfree = 0.000) for 3192 atoms. Found 8 (17 requested) and removed 17 (17 requested) atoms. Cycle 30: After refmac, R = 0.1974 (Rfree = 0.000) for 3179 atoms. Found 12 (17 requested) and removed 17 (17 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.40 2.57 Search for helices and strands: 0 residues in 0 chains, 3232 seeds are put forward NCS extension: 29 residues added (19 deleted due to clashes), 3261 seeds are put forward Round 1: 279 peptides, 29 chains. Longest chain 34 peptides. Score 0.712 Round 2: 292 peptides, 24 chains. Longest chain 34 peptides. Score 0.781 Round 3: 286 peptides, 28 chains. Longest chain 25 peptides. Score 0.736 Round 4: 299 peptides, 25 chains. Longest chain 34 peptides. Score 0.784 Round 5: 294 peptides, 28 chains. Longest chain 29 peptides. Score 0.751 Taking the results from Round 4 Chains 27, Residues 274, Estimated correctness of the model 84.4 % 4 chains (105 residues) have been docked in sequence Building loops using Loopy2018 27 chains (274 residues) following loop building 4 chains (105 residues) in sequence following loop building ------------------------------------------------------ 8199 reflections ( 98.22 % complete ) and 5642 restraints for refining 3231 atoms. 4112 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2316 (Rfree = 0.000) for 3231 atoms. Found 17 (17 requested) and removed 22 (17 requested) atoms. Cycle 32: After refmac, R = 0.2114 (Rfree = 0.000) for 3219 atoms. Found 16 (17 requested) and removed 17 (17 requested) atoms. Cycle 33: After refmac, R = 0.2015 (Rfree = 0.000) for 3215 atoms. Found 8 (17 requested) and removed 17 (17 requested) atoms. Cycle 34: After refmac, R = 0.1976 (Rfree = 0.000) for 3204 atoms. Found 7 (17 requested) and removed 17 (17 requested) atoms. Cycle 35: After refmac, R = 0.1968 (Rfree = 0.000) for 3194 atoms. Found 5 (17 requested) and removed 18 (17 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.41 2.58 Search for helices and strands: 0 residues in 0 chains, 3251 seeds are put forward NCS extension: 27 residues added (3 deleted due to clashes), 3278 seeds are put forward Round 1: 280 peptides, 29 chains. Longest chain 28 peptides. Score 0.714 Round 2: 291 peptides, 27 chains. Longest chain 30 peptides. Score 0.754 Round 3: 297 peptides, 28 chains. Longest chain 30 peptides. Score 0.756 Round 4: 297 peptides, 31 chains. Longest chain 26 peptides. Score 0.730 Round 5: 290 peptides, 30 chains. Longest chain 26 peptides. Score 0.725 Taking the results from Round 3 Chains 30, Residues 269, Estimated correctness of the model 80.5 % 3 chains (66 residues) have been docked in sequence Building loops using Loopy2018 30 chains (269 residues) following loop building 3 chains (66 residues) in sequence following loop building ------------------------------------------------------ 8199 reflections ( 98.22 % complete ) and 6202 restraints for refining 3231 atoms. 4871 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2117 (Rfree = 0.000) for 3231 atoms. Found 17 (17 requested) and removed 20 (17 requested) atoms. Cycle 37: After refmac, R = 0.1978 (Rfree = 0.000) for 3223 atoms. Found 11 (17 requested) and removed 17 (17 requested) atoms. Cycle 38: After refmac, R = 0.1923 (Rfree = 0.000) for 3212 atoms. Found 10 (17 requested) and removed 17 (17 requested) atoms. Cycle 39: After refmac, R = 0.1899 (Rfree = 0.000) for 3202 atoms. Found 9 (17 requested) and removed 18 (17 requested) atoms. Cycle 40: After refmac, R = 0.1881 (Rfree = 0.000) for 3192 atoms. Found 7 (17 requested) and removed 17 (17 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.38 2.54 Search for helices and strands: 0 residues in 0 chains, 3236 seeds are put forward NCS extension: 26 residues added (9 deleted due to clashes), 3262 seeds are put forward Round 1: 258 peptides, 26 chains. Longest chain 27 peptides. Score 0.697 Round 2: 274 peptides, 25 chains. Longest chain 28 peptides. Score 0.740 Round 3: 266 peptides, 25 chains. Longest chain 29 peptides. Score 0.724 Round 4: 267 peptides, 25 chains. Longest chain 34 peptides. Score 0.726 Round 5: 267 peptides, 26 chains. Longest chain 28 peptides. Score 0.717 Taking the results from Round 2 Chains 27, Residues 249, Estimated correctness of the model 78.1 % 4 chains (60 residues) have been docked in sequence Building loops using Loopy2018 27 chains (249 residues) following loop building 4 chains (60 residues) in sequence following loop building ------------------------------------------------------ 8199 reflections ( 98.22 % complete ) and 6180 restraints for refining 3231 atoms. 4944 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2085 (Rfree = 0.000) for 3231 atoms. Found 17 (17 requested) and removed 21 (17 requested) atoms. Failed to save intermediate PDB Cycle 42: After refmac, R = 0.1942 (Rfree = 0.000) for 3223 atoms. Found 17 (17 requested) and removed 17 (17 requested) atoms. Cycle 43: After refmac, R = 0.1861 (Rfree = 0.000) for 3220 atoms. Found 9 (17 requested) and removed 17 (17 requested) atoms. Cycle 44: After refmac, R = 0.1822 (Rfree = 0.000) for 3209 atoms. Found 6 (17 requested) and removed 17 (17 requested) atoms. Cycle 45: After refmac, R = 0.1786 (Rfree = 0.000) for 3195 atoms. Found 9 (17 requested) and removed 17 (17 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.44 2.61 Search for helices and strands: 0 residues in 0 chains, 3231 seeds are put forward NCS extension: 25 residues added (7 deleted due to clashes), 3256 seeds are put forward Round 1: 245 peptides, 29 chains. Longest chain 24 peptides. Score 0.633 Round 2: 244 peptides, 25 chains. Longest chain 33 peptides. Score 0.676 Round 3: 245 peptides, 24 chains. Longest chain 30 peptides. Score 0.690 Round 4: 249 peptides, 24 chains. Longest chain 34 peptides. Score 0.698 Round 5: 252 peptides, 25 chains. Longest chain 28 peptides. Score 0.695 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 24, Residues 225, Estimated correctness of the model 71.2 % 3 chains (55 residues) have been docked in sequence Sequence coverage is 24 % Consider running further cycles of model building using 1vjn-3_warpNtrace.pdb as input Building loops using Loopy2018 24 chains (225 residues) following loop building 3 chains (55 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8199 reflections ( 98.22 % complete ) and 6384 restraints for refining 3231 atoms. 5273 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1984 (Rfree = 0.000) for 3231 atoms. Found 0 (17 requested) and removed 8 (17 requested) atoms. Cycle 47: After refmac, R = 0.1879 (Rfree = 0.000) for 3220 atoms. Found 0 (17 requested) and removed 6 (17 requested) atoms. Cycle 48: After refmac, R = 0.1851 (Rfree = 0.000) for 3208 atoms. Found 0 (17 requested) and removed 6 (17 requested) atoms. Cycle 49: After refmac, R = 0.1811 (Rfree = 0.000) for 3198 atoms. TimeTaking 57.3