Mon 24 Dec 00:16:24 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 2aml-1.5-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2aml-1.5-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2aml-1.5-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2aml-1.5-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/2aml-1.5-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2aml-1.5-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 00:16:29 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/2aml-1.5-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2aml-1.5-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 734 and 0 Target number of residues in the AU: 734 Target solvent content: 0.4210 Checking the provided sequence file Detected sequence length: 373 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 746 Adjusted target solvent content: 0.41 Input MTZ file: 2aml-1.5-parrot-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: 19 Cell parameters: 56.315 101.397 120.151 90.000 90.000 90.000 Input sequence file: 2aml-1.5-parrot-mrncs.fasta_lf Building free atoms model in initial map for 5968 target number of atoms Had to go as low as 0.30 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 1 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 77.491 1.500 Wilson plot Bfac: 10.52 110667 reflections ( 99.97 % complete ) and 0 restraints for refining 6567 atoms. Observations/parameters ratio is 4.21 ------------------------------------------------------ Starting model: R = 0.3340 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2841 (Rfree = 0.000) for 6567 atoms. Found 510 (510 requested) and removed 250 (255 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.42 1.60 NCS extension: 0 residues added, 6827 seeds are put forward Round 1: 656 peptides, 31 chains. Longest chain 78 peptides. Score 0.923 Round 2: 709 peptides, 12 chains. Longest chain 248 peptides. Score 0.968 Round 3: 705 peptides, 13 chains. Longest chain 91 peptides. Score 0.966 Round 4: 711 peptides, 9 chains. Longest chain 260 peptides. Score 0.973 Round 5: 713 peptides, 7 chains. Longest chain 194 peptides. Score 0.976 Taking the results from Round 5 Chains 7, Residues 706, Estimated correctness of the model 100.0 % 7 chains (706 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 46 A and 51 A Built loop between residues 210 A and 213 A Built loop between residues 263 A and 266 A Built loop between residues 202 B and 205 B Built loop between residues 308 B and 314 B 2 chains (721 residues) following loop building 2 chains (721 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 110667 reflections ( 99.97 % complete ) and 6437 restraints for refining 6666 atoms. 605 conditional restraints added. Observations/parameters ratio is 4.15 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2635 (Rfree = 0.000) for 6666 atoms. Found 305 (518 requested) and removed 102 (259 requested) atoms. Cycle 2: After refmac, R = 0.2378 (Rfree = 0.000) for 6865 atoms. Found 229 (534 requested) and removed 55 (267 requested) atoms. Cycle 3: After refmac, R = 0.2056 (Rfree = 0.000) for 7023 atoms. Found 242 (547 requested) and removed 75 (273 requested) atoms. Cycle 4: After refmac, R = 0.1924 (Rfree = 0.000) for 7176 atoms. Found 227 (559 requested) and removed 90 (279 requested) atoms. Cycle 5: After refmac, R = 0.1836 (Rfree = 0.000) for 7298 atoms. Found 225 (568 requested) and removed 76 (284 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.42 1.60 NCS extension: 15 residues added (349 deleted due to clashes), 7463 seeds are put forward Round 1: 716 peptides, 11 chains. Longest chain 124 peptides. Score 0.970 Round 2: 718 peptides, 4 chains. Longest chain 307 peptides. Score 0.980 Round 3: 719 peptides, 7 chains. Longest chain 162 peptides. Score 0.976 Round 4: 720 peptides, 6 chains. Longest chain 273 peptides. Score 0.978 Round 5: 719 peptides, 6 chains. Longest chain 197 peptides. Score 0.978 Taking the results from Round 2 Chains 5, Residues 714, Estimated correctness of the model 100.0 % 4 chains (713 residues) have been docked in sequence Building loops using Loopy2018 5 chains (714 residues) following loop building 4 chains (713 residues) in sequence following loop building ------------------------------------------------------ 110667 reflections ( 99.97 % complete ) and 6776 restraints for refining 7051 atoms. 968 conditional restraints added. Observations/parameters ratio is 3.92 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2267 (Rfree = 0.000) for 7051 atoms. Found 272 (548 requested) and removed 130 (274 requested) atoms. Cycle 7: After refmac, R = 0.2133 (Rfree = 0.000) for 7187 atoms. Found 185 (559 requested) and removed 48 (279 requested) atoms. Cycle 8: After refmac, R = 0.1908 (Rfree = 0.000) for 7307 atoms. Found 228 (569 requested) and removed 63 (284 requested) atoms. Cycle 9: After refmac, R = 0.1841 (Rfree = 0.000) for 7446 atoms. Found 229 (581 requested) and removed 94 (290 requested) atoms. Cycle 10: After refmac, R = 0.1872 (Rfree = 0.000) for 7571 atoms. Found 207 (589 requested) and removed 108 (294 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.43 1.61 NCS extension: 0 residues added (3 deleted due to clashes), 7670 seeds are put forward Round 1: 715 peptides, 11 chains. Longest chain 174 peptides. Score 0.970 Round 2: 718 peptides, 7 chains. Longest chain 246 peptides. Score 0.976 Round 3: 720 peptides, 5 chains. Longest chain 302 peptides. Score 0.979 Round 4: 719 peptides, 5 chains. Longest chain 301 peptides. Score 0.979 Round 5: 718 peptides, 6 chains. Longest chain 301 peptides. Score 0.977 Taking the results from Round 4 Chains 5, Residues 714, Estimated correctness of the model 100.0 % 5 chains (714 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 308 A and 314 A Built loop between residues 192 B and 195 B Built loop between residues 307 B and 310 B 2 chains (723 residues) following loop building 2 chains (723 residues) in sequence following loop building ------------------------------------------------------ 110667 reflections ( 99.97 % complete ) and 6822 restraints for refining 7177 atoms. 970 conditional restraints added. Observations/parameters ratio is 3.85 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2188 (Rfree = 0.000) for 7177 atoms. Found 297 (547 requested) and removed 97 (279 requested) atoms. Cycle 12: After refmac, R = 0.1930 (Rfree = 0.000) for 7363 atoms. Found 219 (562 requested) and removed 90 (286 requested) atoms. Cycle 13: After refmac, R = 0.1826 (Rfree = 0.000) for 7474 atoms. Found 232 (570 requested) and removed 71 (291 requested) atoms. Cycle 14: After refmac, R = 0.1785 (Rfree = 0.000) for 7615 atoms. Found 216 (581 requested) and removed 109 (296 requested) atoms. Cycle 15: After refmac, R = 0.1770 (Rfree = 0.000) for 7708 atoms. Found 220 (576 requested) and removed 129 (300 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.43 1.61 NCS extension: 4 residues added (1 deleted due to clashes), 7803 seeds are put forward Round 1: 720 peptides, 6 chains. Longest chain 360 peptides. Score 0.978 Round 2: 719 peptides, 5 chains. Longest chain 301 peptides. Score 0.979 Round 3: 720 peptides, 4 chains. Longest chain 301 peptides. Score 0.980 Round 4: 719 peptides, 5 chains. Longest chain 301 peptides. Score 0.979 Round 5: 714 peptides, 8 chains. Longest chain 285 peptides. Score 0.974 Taking the results from Round 3 Chains 4, Residues 716, Estimated correctness of the model 100.0 % 4 chains (716 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 308 A and 314 A Built loop between residues 212 B and 215 B 2 chains (723 residues) following loop building 2 chains (723 residues) in sequence following loop building ------------------------------------------------------ 110667 reflections ( 99.97 % complete ) and 6845 restraints for refining 7193 atoms. 993 conditional restraints added. Observations/parameters ratio is 3.85 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2147 (Rfree = 0.000) for 7193 atoms. Found 339 (525 requested) and removed 73 (279 requested) atoms. Cycle 17: After refmac, R = 0.1898 (Rfree = 0.000) for 7449 atoms. Found 223 (545 requested) and removed 90 (290 requested) atoms. Cycle 18: After refmac, R = 0.1812 (Rfree = 0.000) for 7557 atoms. Found 237 (554 requested) and removed 90 (294 requested) atoms. Cycle 19: After refmac, R = 0.1778 (Rfree = 0.000) for 7690 atoms. Found 212 (563 requested) and removed 136 (299 requested) atoms. Cycle 20: After refmac, R = 0.1747 (Rfree = 0.000) for 7750 atoms. Found 245 (555 requested) and removed 133 (301 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.43 1.61 NCS extension: 5 residues added (0 deleted due to clashes), 7867 seeds are put forward Round 1: 718 peptides, 6 chains. Longest chain 185 peptides. Score 0.977 Round 2: 718 peptides, 6 chains. Longest chain 301 peptides. Score 0.977 Round 3: 718 peptides, 6 chains. Longest chain 360 peptides. Score 0.977 Round 4: 720 peptides, 4 chains. Longest chain 360 peptides. Score 0.980 Round 5: 716 peptides, 8 chains. Longest chain 180 peptides. Score 0.974 Taking the results from Round 4 Chains 4, Residues 716, Estimated correctness of the model 100.0 % 4 chains (716 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 64 B and 67 B Built loop between residues 308 B and 314 B 2 chains (723 residues) following loop building 2 chains (723 residues) in sequence following loop building ------------------------------------------------------ 110667 reflections ( 99.97 % complete ) and 6888 restraints for refining 7213 atoms. 1036 conditional restraints added. Observations/parameters ratio is 3.84 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2149 (Rfree = 0.000) for 7213 atoms. Found 338 (504 requested) and removed 89 (280 requested) atoms. Cycle 22: After refmac, R = 0.1872 (Rfree = 0.000) for 7449 atoms. Found 257 (522 requested) and removed 84 (290 requested) atoms. Cycle 23: After refmac, R = 0.1801 (Rfree = 0.000) for 7597 atoms. Found 217 (533 requested) and removed 100 (296 requested) atoms. Cycle 24: After refmac, R = 0.1759 (Rfree = 0.000) for 7696 atoms. Found 220 (539 requested) and removed 105 (299 requested) atoms. Cycle 25: After refmac, R = 0.1746 (Rfree = 0.000) for 7793 atoms. Found 203 (546 requested) and removed 139 (303 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.43 1.61 NCS extension: 18 residues added (347 deleted due to clashes), 7875 seeds are put forward Round 1: 716 peptides, 10 chains. Longest chain 163 peptides. Score 0.972 Round 2: 717 peptides, 7 chains. Longest chain 225 peptides. Score 0.976 Round 3: 717 peptides, 6 chains. Longest chain 301 peptides. Score 0.977 Round 4: 719 peptides, 5 chains. Longest chain 304 peptides. Score 0.979 Round 5: 716 peptides, 8 chains. Longest chain 203 peptides. Score 0.974 Taking the results from Round 4 Chains 5, Residues 714, Estimated correctness of the model 100.0 % 5 chains (714 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 192 A and 195 A Built loop between residues 308 A and 314 A Built loop between residues 67 B and 70 B 2 chains (723 residues) following loop building 2 chains (723 residues) in sequence following loop building ------------------------------------------------------ 110667 reflections ( 99.97 % complete ) and 6863 restraints for refining 7264 atoms. 1011 conditional restraints added. Observations/parameters ratio is 3.81 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2137 (Rfree = 0.000) for 7264 atoms. Found 322 (496 requested) and removed 79 (282 requested) atoms. Cycle 27: After refmac, R = 0.1866 (Rfree = 0.000) for 7495 atoms. Found 234 (513 requested) and removed 74 (291 requested) atoms. Cycle 28: After refmac, R = 0.1793 (Rfree = 0.000) for 7627 atoms. Found 231 (524 requested) and removed 96 (297 requested) atoms. Cycle 29: After refmac, R = 0.1751 (Rfree = 0.000) for 7745 atoms. Found 250 (531 requested) and removed 120 (301 requested) atoms. Cycle 30: After refmac, R = 0.1734 (Rfree = 0.000) for 7860 atoms. Found 239 (539 requested) and removed 158 (306 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.43 1.61 NCS extension: 4 residues added (1 deleted due to clashes), 7945 seeds are put forward Round 1: 718 peptides, 7 chains. Longest chain 252 peptides. Score 0.976 Round 2: 717 peptides, 7 chains. Longest chain 245 peptides. Score 0.976 Round 3: 715 peptides, 7 chains. Longest chain 307 peptides. Score 0.976 Round 4: 720 peptides, 4 chains. Longest chain 304 peptides. Score 0.980 Round 5: 716 peptides, 8 chains. Longest chain 257 peptides. Score 0.974 Taking the results from Round 4 Chains 4, Residues 716, Estimated correctness of the model 100.0 % 4 chains (716 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 308 A and 314 A Built loop between residues 67 B and 70 B 2 chains (723 residues) following loop building 2 chains (723 residues) in sequence following loop building ------------------------------------------------------ 110667 reflections ( 99.97 % complete ) and 6939 restraints for refining 7264 atoms. 1087 conditional restraints added. Observations/parameters ratio is 3.81 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2151 (Rfree = 0.000) for 7264 atoms. Found 348 (485 requested) and removed 78 (282 requested) atoms. Cycle 32: After refmac, R = 0.1883 (Rfree = 0.000) for 7526 atoms. Found 235 (503 requested) and removed 74 (292 requested) atoms. Cycle 33: After refmac, R = 0.1801 (Rfree = 0.000) for 7665 atoms. Found 223 (513 requested) and removed 100 (298 requested) atoms. Failed to save intermediate PDB Cycle 34: After refmac, R = 0.1758 (Rfree = 0.000) for 7767 atoms. Found 228 (520 requested) and removed 109 (302 requested) atoms. Cycle 35: After refmac, R = 0.1738 (Rfree = 0.000) for 7874 atoms. Found 202 (527 requested) and removed 140 (306 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.43 1.61 NCS extension: 4 residues added (1 deleted due to clashes), 7940 seeds are put forward Round 1: 721 peptides, 5 chains. Longest chain 250 peptides. Score 0.979 Round 2: 722 peptides, 5 chains. Longest chain 301 peptides. Score 0.979 Round 3: 721 peptides, 6 chains. Longest chain 304 peptides. Score 0.978 Round 4: 721 peptides, 5 chains. Longest chain 365 peptides. Score 0.979 Round 5: 717 peptides, 7 chains. Longest chain 203 peptides. Score 0.976 Taking the results from Round 4 Chains 5, Residues 716, Estimated correctness of the model 100.0 % 5 chains (716 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 67 A and 70 A Built loop between residues 175 A and 178 A Built loop between residues 192 A and 196 A 2 chains (723 residues) following loop building 2 chains (723 residues) in sequence following loop building ------------------------------------------------------ 110667 reflections ( 99.97 % complete ) and 6967 restraints for refining 7308 atoms. 1115 conditional restraints added. Observations/parameters ratio is 3.79 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2154 (Rfree = 0.000) for 7308 atoms. Found 336 (477 requested) and removed 85 (284 requested) atoms. Cycle 37: After refmac, R = 0.1901 (Rfree = 0.000) for 7547 atoms. Found 224 (493 requested) and removed 79 (293 requested) atoms. Cycle 38: After refmac, R = 0.1812 (Rfree = 0.000) for 7659 atoms. Found 222 (502 requested) and removed 71 (299 requested) atoms. Cycle 39: After refmac, R = 0.1762 (Rfree = 0.000) for 7791 atoms. Found 222 (510 requested) and removed 85 (303 requested) atoms. Cycle 40: After refmac, R = 0.1749 (Rfree = 0.000) for 7907 atoms. Found 176 (517 requested) and removed 115 (308 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.44 1.63 NCS extension: 5 residues added (0 deleted due to clashes), 7973 seeds are put forward Round 1: 718 peptides, 7 chains. Longest chain 252 peptides. Score 0.976 Round 2: 719 peptides, 6 chains. Longest chain 245 peptides. Score 0.978 Round 3: 720 peptides, 5 chains. Longest chain 304 peptides. Score 0.979 Round 4: 718 peptides, 6 chains. Longest chain 281 peptides. Score 0.977 Round 5: 718 peptides, 7 chains. Longest chain 185 peptides. Score 0.976 Taking the results from Round 3 Chains 5, Residues 715, Estimated correctness of the model 100.0 % 5 chains (715 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 192 A and 195 A Built loop between residues 308 A and 313 A Built loop between residues 67 B and 70 B 2 chains (723 residues) following loop building 2 chains (723 residues) in sequence following loop building ------------------------------------------------------ 110667 reflections ( 99.97 % complete ) and 7059 restraints for refining 7343 atoms. 1207 conditional restraints added. Observations/parameters ratio is 3.77 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2162 (Rfree = 0.000) for 7343 atoms. Found 351 (468 requested) and removed 73 (285 requested) atoms. Cycle 42: After refmac, R = 0.1898 (Rfree = 0.000) for 7607 atoms. Found 227 (485 requested) and removed 77 (296 requested) atoms. Cycle 43: After refmac, R = 0.1807 (Rfree = 0.000) for 7732 atoms. Found 230 (494 requested) and removed 71 (301 requested) atoms. Cycle 44: After refmac, R = 0.1765 (Rfree = 0.000) for 7876 atoms. Found 191 (503 requested) and removed 90 (306 requested) atoms. Cycle 45: After refmac, R = 0.1729 (Rfree = 0.000) for 7949 atoms. Found 201 (508 requested) and removed 99 (310 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.43 1.61 NCS extension: 5 residues added (0 deleted due to clashes), 8056 seeds are put forward Round 1: 716 peptides, 9 chains. Longest chain 198 peptides. Score 0.973 Round 2: 720 peptides, 5 chains. Longest chain 360 peptides. Score 0.979 Round 3: 717 peptides, 8 chains. Longest chain 185 peptides. Score 0.975 Round 4: 720 peptides, 5 chains. Longest chain 304 peptides. Score 0.979 Round 5: 717 peptides, 8 chains. Longest chain 185 peptides. Score 0.975 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 5, Residues 715, Estimated correctness of the model 100.0 % 5 chains (715 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 288 A and 291 A Built loop between residues 309 A and 314 A Built loop between residues 67 B and 70 B 2 chains (723 residues) following loop building 2 chains (723 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 110667 reflections ( 99.97 % complete ) and 5852 restraints for refining 5729 atoms. Observations/parameters ratio is 4.83 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2803 (Rfree = 0.000) for 5729 atoms. Found 296 (365 requested) and removed 0 (365 requested) atoms. Cycle 47: After refmac, R = 0.2242 (Rfree = 0.000) for 5729 atoms. Found 200 (384 requested) and removed 0 (234 requested) atoms. Cycle 48: After refmac, R = 0.2024 (Rfree = 0.000) for 5729 atoms. Found 104 (397 requested) and removed 2 (242 requested) atoms. Cycle 49: After refmac, R = 0.1890 (Rfree = 0.000) for 5729 atoms. TimeTaking 89.93