Sun 23 Dec 22:23:05 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 2aml-1.5-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2aml-1.5-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2aml-1.5-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2aml-1.5-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/2aml-1.5-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2aml-1.5-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 22:23:14 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/hancs/ArpWArp/wArpResults/WorkingDir/2aml-1.5-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2aml-1.5-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 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-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: 19 Cell parameters: 56.315 101.397 120.151 90.000 90.000 90.000 Input sequence file: 2aml-1.5-parrot-hancs.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 6577 atoms. Observations/parameters ratio is 4.21 ------------------------------------------------------ Starting model: R = 0.3362 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2860 (Rfree = 0.000) for 6577 atoms. Found 511 (511 requested) and removed 226 (255 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.43 1.61 NCS extension: 0 residues added, 6862 seeds are put forward Round 1: 677 peptides, 26 chains. Longest chain 72 peptides. Score 0.939 Round 2: 706 peptides, 10 chains. Longest chain 260 peptides. Score 0.970 Round 3: 716 peptides, 7 chains. Longest chain 234 peptides. Score 0.976 Round 4: 715 peptides, 10 chains. Longest chain 150 peptides. Score 0.972 Round 5: 717 peptides, 6 chains. Longest chain 251 peptides. Score 0.977 Taking the results from Round 5 Chains 7, Residues 711, Estimated correctness of the model 100.0 % 6 chains (710 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 46 A and 50 A Built loop between residues 202 A and 205 A Built loop between residues 308 A and 313 A Built loop between residues 264 B and 267 B 3 chains (722 residues) following loop building 2 chains (721 residues) in sequence following loop building ------------------------------------------------------ 110667 reflections ( 99.97 % complete ) and 6421 restraints for refining 6660 atoms. 588 conditional restraints added. Observations/parameters ratio is 4.15 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2630 (Rfree = 0.000) for 6660 atoms. Found 288 (517 requested) and removed 101 (258 requested) atoms. Cycle 2: After refmac, R = 0.2378 (Rfree = 0.000) for 6842 atoms. Found 210 (532 requested) and removed 59 (266 requested) atoms. Cycle 3: After refmac, R = 0.2216 (Rfree = 0.000) for 6985 atoms. Found 182 (543 requested) and removed 62 (271 requested) atoms. Cycle 4: After refmac, R = 0.1974 (Rfree = 0.000) for 7092 atoms. Found 265 (552 requested) and removed 69 (276 requested) atoms. Cycle 5: After refmac, R = 0.1884 (Rfree = 0.000) for 7277 atoms. Found 224 (566 requested) and removed 114 (283 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.42 1.60 NCS extension: 15 residues added (378 deleted due to clashes), 7405 seeds are put forward Round 1: 717 peptides, 7 chains. Longest chain 247 peptides. Score 0.976 Round 2: 719 peptides, 7 chains. Longest chain 180 peptides. Score 0.976 Round 3: 718 peptides, 7 chains. Longest chain 304 peptides. Score 0.976 Round 4: 722 peptides, 5 chains. Longest chain 365 peptides. Score 0.979 Round 5: 721 peptides, 6 chains. Longest chain 304 peptides. Score 0.978 Taking the results from Round 4 Chains 5, Residues 717, Estimated correctness of the model 100.0 % 5 chains (717 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 209 A and 212 A 2 chains (723 residues) following loop building 2 chains (723 residues) in sequence following loop building ------------------------------------------------------ 110667 reflections ( 99.97 % complete ) and 6572 restraints for refining 7001 atoms. 720 conditional restraints added. Observations/parameters ratio is 3.95 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2211 (Rfree = 0.000) for 7001 atoms. Found 291 (533 requested) and removed 74 (272 requested) atoms. Cycle 7: After refmac, R = 0.1929 (Rfree = 0.000) for 7207 atoms. Found 243 (550 requested) and removed 91 (280 requested) atoms. Cycle 8: After refmac, R = 0.1831 (Rfree = 0.000) for 7343 atoms. Found 239 (561 requested) and removed 90 (286 requested) atoms. Cycle 9: After refmac, R = 0.1796 (Rfree = 0.000) for 7480 atoms. Found 205 (570 requested) and removed 117 (291 requested) atoms. Cycle 10: After refmac, R = 0.1757 (Rfree = 0.000) for 7553 atoms. Found 231 (564 requested) and removed 115 (294 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.43 1.61 NCS extension: 4 residues added (1 deleted due to clashes), 7673 seeds are put forward Round 1: 719 peptides, 8 chains. Longest chain 180 peptides. Score 0.975 Round 2: 722 peptides, 5 chains. Longest chain 306 peptides. Score 0.979 Round 3: 719 peptides, 8 chains. Longest chain 133 peptides. Score 0.975 Round 4: 721 peptides, 6 chains. Longest chain 301 peptides. Score 0.978 Round 5: 721 peptides, 6 chains. Longest chain 281 peptides. Score 0.978 Taking the results from Round 2 Chains 5, Residues 717, Estimated correctness of the model 100.0 % 5 chains (717 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 210 A and 213 A Built loop between residues 308 A and 311 A Built loop between residues 65 B and 68 B 2 chains (723 residues) following loop building 2 chains (723 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 110667 reflections ( 99.97 % complete ) and 6735 restraints for refining 7142 atoms. 883 conditional restraints added. Observations/parameters ratio is 3.87 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2164 (Rfree = 0.000) for 7142 atoms. Found 315 (533 requested) and removed 93 (277 requested) atoms. Cycle 12: After refmac, R = 0.1887 (Rfree = 0.000) for 7348 atoms. Found 242 (549 requested) and removed 94 (286 requested) atoms. Cycle 13: After refmac, R = 0.1814 (Rfree = 0.000) for 7472 atoms. Found 232 (559 requested) and removed 97 (291 requested) atoms. Cycle 14: After refmac, R = 0.1763 (Rfree = 0.000) for 7594 atoms. Found 225 (567 requested) and removed 130 (295 requested) atoms. Cycle 15: After refmac, R = 0.1743 (Rfree = 0.000) for 7673 atoms. Found 237 (562 requested) and removed 126 (299 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.43 1.61 NCS extension: 5 residues added (0 deleted due to clashes), 7789 seeds are put forward Round 1: 716 peptides, 10 chains. Longest chain 127 peptides. Score 0.972 Round 2: 720 peptides, 6 chains. Longest chain 247 peptides. Score 0.978 Round 3: 724 peptides, 3 chains. Longest chain 365 peptides. Score 0.982 Round 4: 720 peptides, 7 chains. Longest chain 301 peptides. Score 0.976 Round 5: 721 peptides, 6 chains. Longest chain 281 peptides. Score 0.978 Taking the results from Round 3 Chains 3, Residues 721, Estimated correctness of the model 100.0 % 3 chains (721 residues) have been docked in sequence Building loops using Loopy2018 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 6851 restraints for refining 7217 atoms. 999 conditional restraints added. Observations/parameters ratio is 3.83 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2137 (Rfree = 0.000) for 7217 atoms. Found 316 (516 requested) and removed 84 (280 requested) atoms. Cycle 17: After refmac, R = 0.1869 (Rfree = 0.000) for 7437 atoms. Found 227 (533 requested) and removed 90 (289 requested) atoms. Cycle 18: After refmac, R = 0.1797 (Rfree = 0.000) for 7556 atoms. Found 202 (542 requested) and removed 96 (294 requested) atoms. Cycle 19: After refmac, R = 0.1750 (Rfree = 0.000) for 7647 atoms. Found 215 (547 requested) and removed 122 (297 requested) atoms. Cycle 20: After refmac, R = 0.1733 (Rfree = 0.000) for 7715 atoms. Found 214 (541 requested) and removed 151 (300 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.42 1.60 NCS extension: 5 residues added (0 deleted due to clashes), 7783 seeds are put forward Round 1: 717 peptides, 9 chains. Longest chain 124 peptides. Score 0.973 Round 2: 722 peptides, 5 chains. Longest chain 307 peptides. Score 0.979 Round 3: 722 peptides, 5 chains. Longest chain 304 peptides. Score 0.979 Round 4: 720 peptides, 6 chains. Longest chain 365 peptides. Score 0.978 Round 5: 722 peptides, 5 chains. Longest chain 257 peptides. Score 0.979 Taking the results from Round 5 Chains 5, Residues 717, Estimated correctness of the model 100.0 % 5 chains (717 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 67 A and 70 A Built loop between residues 209 A and 212 A Built loop between residues 264 B and 267 B 2 chains (723 residues) following loop building 2 chains (723 residues) in sequence following loop building ------------------------------------------------------ 110667 reflections ( 99.97 % complete ) and 6848 restraints for refining 7226 atoms. 996 conditional restraints added. Observations/parameters ratio is 3.83 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2134 (Rfree = 0.000) for 7226 atoms. Found 329 (495 requested) and removed 92 (281 requested) atoms. Cycle 22: After refmac, R = 0.1868 (Rfree = 0.000) for 7449 atoms. Found 230 (510 requested) and removed 79 (290 requested) atoms. Cycle 23: After refmac, R = 0.1800 (Rfree = 0.000) for 7578 atoms. Found 208 (520 requested) and removed 111 (295 requested) atoms. Cycle 24: After refmac, R = 0.1747 (Rfree = 0.000) for 7659 atoms. Found 204 (513 requested) and removed 115 (298 requested) atoms. Cycle 25: After refmac, R = 0.1720 (Rfree = 0.000) for 7734 atoms. Found 206 (506 requested) and removed 129 (301 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.43 1.61 NCS extension: 5 residues added (0 deleted due to clashes), 7816 seeds are put forward Round 1: 718 peptides, 9 chains. Longest chain 185 peptides. Score 0.973 Round 2: 722 peptides, 5 chains. Longest chain 304 peptides. Score 0.979 Round 3: 720 peptides, 7 chains. Longest chain 196 peptides. Score 0.976 Round 4: 722 peptides, 5 chains. Longest chain 311 peptides. Score 0.979 Round 5: 720 peptides, 6 chains. Longest chain 289 peptides. Score 0.978 Taking the results from Round 4 Chains 5, Residues 717, Estimated correctness of the model 100.0 % 5 chains (717 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 67 A and 70 A Built loop between residues 192 A and 195 A Built loop between residues 60 B and 63 B 2 chains (723 residues) following loop building 2 chains (723 residues) in sequence following loop building ------------------------------------------------------ 110667 reflections ( 99.97 % complete ) and 6908 restraints for refining 7250 atoms. 1056 conditional restraints added. Observations/parameters ratio is 3.82 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2155 (Rfree = 0.000) for 7250 atoms. Found 306 (462 requested) and removed 97 (281 requested) atoms. Cycle 27: After refmac, R = 0.1874 (Rfree = 0.000) for 7447 atoms. Found 267 (476 requested) and removed 67 (290 requested) atoms. Cycle 28: After refmac, R = 0.1804 (Rfree = 0.000) for 7619 atoms. Found 229 (487 requested) and removed 105 (297 requested) atoms. Cycle 29: After refmac, R = 0.1770 (Rfree = 0.000) for 7725 atoms. Found 209 (494 requested) and removed 135 (301 requested) atoms. Cycle 30: After refmac, R = 0.1737 (Rfree = 0.000) for 7785 atoms. Found 260 (485 requested) and removed 120 (303 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.43 1.61 NCS extension: 4 residues added (1 deleted due to clashes), 7929 seeds are put forward Round 1: 716 peptides, 8 chains. Longest chain 180 peptides. Score 0.974 Round 2: 718 peptides, 7 chains. Longest chain 244 peptides. Score 0.976 Round 3: 719 peptides, 8 chains. Longest chain 196 peptides. Score 0.975 Round 4: 719 peptides, 8 chains. Longest chain 203 peptides. Score 0.975 Round 5: 718 peptides, 6 chains. Longest chain 301 peptides. Score 0.977 Taking the results from Round 5 Chains 6, Residues 712, Estimated correctness of the model 100.0 % 6 chains (712 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 67 A and 70 A Built loop between residues 264 A and 267 A Built loop between residues 315 A and 318 A 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 6878 restraints for refining 7255 atoms. 1026 conditional restraints added. Observations/parameters ratio is 3.81 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2152 (Rfree = 0.000) for 7255 atoms. Found 346 (451 requested) and removed 91 (282 requested) atoms. Cycle 32: After refmac, R = 0.1895 (Rfree = 0.000) for 7498 atoms. Found 253 (467 requested) and removed 62 (292 requested) atoms. Cycle 33: After refmac, R = 0.1812 (Rfree = 0.000) for 7673 atoms. Found 212 (478 requested) and removed 104 (299 requested) atoms. Cycle 34: After refmac, R = 0.1760 (Rfree = 0.000) for 7762 atoms. Found 206 (484 requested) and removed 97 (302 requested) atoms. Cycle 35: After refmac, R = 0.1722 (Rfree = 0.000) for 7850 atoms. Found 221 (490 requested) and removed 135 (306 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.43 1.61 NCS extension: 5 residues added (0 deleted due to clashes), 7941 seeds are put forward Round 1: 718 peptides, 9 chains. Longest chain 158 peptides. Score 0.973 Round 2: 718 peptides, 6 chains. Longest chain 243 peptides. Score 0.977 Round 3: 720 peptides, 6 chains. Longest chain 251 peptides. Score 0.978 Round 4: 718 peptides, 6 chains. Longest chain 301 peptides. Score 0.977 Round 5: 716 peptides, 8 chains. Longest chain 251 peptides. Score 0.974 Taking the results from Round 3 Chains 6, Residues 714, Estimated correctness of the model 100.0 % 6 chains (714 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 263 A and 267 A Built loop between residues 60 B and 63 B Built loop between residues 192 B and 195 B Built loop between residues 288 B and 291 B 2 chains (723 residues) following loop building 2 chains (723 residues) in sequence following loop building ------------------------------------------------------ 110667 reflections ( 99.97 % complete ) and 6970 restraints for refining 7286 atoms. 1118 conditional restraints added. Observations/parameters ratio is 3.80 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2145 (Rfree = 0.000) for 7286 atoms. Found 333 (441 requested) and removed 87 (283 requested) atoms. Cycle 37: After refmac, R = 0.1895 (Rfree = 0.000) for 7520 atoms. Found 225 (456 requested) and removed 65 (292 requested) atoms. Cycle 38: After refmac, R = 0.1805 (Rfree = 0.000) for 7657 atoms. Found 235 (466 requested) and removed 98 (298 requested) atoms. Cycle 39: After refmac, R = 0.1774 (Rfree = 0.000) for 7778 atoms. Found 185 (473 requested) and removed 134 (303 requested) atoms. Cycle 40: After refmac, R = 0.1730 (Rfree = 0.000) for 7816 atoms. Found 206 (462 requested) and removed 101 (304 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.43 1.61 NCS extension: 4 residues added (1 deleted due to clashes), 7925 seeds are put forward Round 1: 716 peptides, 8 chains. Longest chain 185 peptides. Score 0.974 Round 2: 721 peptides, 5 chains. Longest chain 242 peptides. Score 0.979 Round 3: 717 peptides, 9 chains. Longest chain 144 peptides. Score 0.973 Round 4: 717 peptides, 8 chains. Longest chain 203 peptides. Score 0.975 Round 5: 719 peptides, 7 chains. Longest chain 239 peptides. Score 0.976 Taking the results from Round 2 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 210 A and 213 A Built loop between residues 67 B and 70 B Built loop between residues 310 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 6989 restraints for refining 7317 atoms. 1137 conditional restraints added. Observations/parameters ratio is 3.78 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2149 (Rfree = 0.000) for 7317 atoms. Found 320 (432 requested) and removed 104 (284 requested) atoms. Cycle 42: After refmac, R = 0.1891 (Rfree = 0.000) for 7514 atoms. Found 242 (445 requested) and removed 60 (292 requested) atoms. Cycle 43: After refmac, R = 0.1803 (Rfree = 0.000) for 7677 atoms. Found 205 (454 requested) and removed 79 (299 requested) atoms. Cycle 44: After refmac, R = 0.1757 (Rfree = 0.000) for 7778 atoms. Found 203 (461 requested) and removed 110 (303 requested) atoms. Cycle 45: After refmac, R = 0.1734 (Rfree = 0.000) for 7846 atoms. Found 192 (453 requested) and removed 115 (306 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.43 1.61 NCS extension: 5 residues added (0 deleted due to clashes), 7928 seeds are put forward Round 1: 715 peptides, 8 chains. Longest chain 178 peptides. Score 0.974 Round 2: 717 peptides, 7 chains. Longest chain 243 peptides. Score 0.976 Round 3: 718 peptides, 7 chains. Longest chain 304 peptides. Score 0.976 Round 4: 719 peptides, 7 chains. Longest chain 303 peptides. Score 0.976 Round 5: 718 peptides, 7 chains. Longest chain 304 peptides. Score 0.976 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 7, Residues 711, Estimated correctness of the model 100.0 % 7 chains (711 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 210 A and 213 A Built loop between residues 262 A and 266 A Built loop between residues 310 A and 314 A Built loop between residues 338 A and 341 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 = 0.2790 (Rfree = 0.000) for 5729 atoms. Found 301 (320 requested) and removed 0 (320 requested) atoms. Cycle 47: After refmac, R = 0.2252 (Rfree = 0.000) for 5729 atoms. Found 202 (337 requested) and removed 1 (234 requested) atoms. Cycle 48: After refmac, R = 0.2022 (Rfree = 0.000) for 5729 atoms. Found 90 (348 requested) and removed 2 (242 requested) atoms. Cycle 49: After refmac, R = 0.1882 (Rfree = 0.000) for 5729 atoms. TimeTaking 115.35