Mon 24 Dec 00:19:42 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 2aj7-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2aj7-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2aj7-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2aj7-3.4-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/2aj7-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2aj7-3.4-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 00:19:46 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/2aj7-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2aj7-3.4-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 401 and 0 Target number of residues in the AU: 401 Target solvent content: 0.6165 Checking the provided sequence file Detected sequence length: 163 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 326 Adjusted target solvent content: 0.69 Input MTZ file: 2aj7-3.4-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: 173 Cell parameters: 108.801 108.801 82.811 90.000 90.000 120.000 Input sequence file: 2aj7-3.4-parrot-mrncs.fasta_lf Building free atoms model in initial map for 2608 target number of atoms Had to go as low as 1.15 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: 94.224 3.400 Wilson plot Bfac: 59.71 7776 reflections ( 99.94 % complete ) and 0 restraints for refining 2890 atoms. Observations/parameters ratio is 0.67 ------------------------------------------------------ Starting model: R = 0.3185 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2791 (Rfree = 0.000) for 2890 atoms. Found 21 (21 requested) and removed 23 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.24 2.48 Search for helices and strands: 0 residues in 0 chains, 2941 seeds are put forward NCS extension: 0 residues added, 2941 seeds are put forward Round 1: 198 peptides, 24 chains. Longest chain 17 peptides. Score 0.499 Round 2: 228 peptides, 19 chains. Longest chain 30 peptides. Score 0.625 Round 3: 221 peptides, 24 chains. Longest chain 23 peptides. Score 0.556 Round 4: 223 peptides, 21 chains. Longest chain 28 peptides. Score 0.593 Round 5: 242 peptides, 19 chains. Longest chain 33 peptides. Score 0.654 Taking the results from Round 5 Chains 22, Residues 223, Estimated correctness of the model 45.3 % 4 chains (66 residues) have been docked in sequence ------------------------------------------------------ 7776 reflections ( 99.94 % complete ) and 4405 restraints for refining 2442 atoms. 3264 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2673 (Rfree = 0.000) for 2442 atoms. Found 18 (18 requested) and removed 20 (9 requested) atoms. Cycle 2: After refmac, R = 0.2616 (Rfree = 0.000) for 2372 atoms. Found 18 (18 requested) and removed 16 (9 requested) atoms. Cycle 3: After refmac, R = 0.2483 (Rfree = 0.000) for 2349 atoms. Found 17 (17 requested) and removed 14 (8 requested) atoms. Cycle 4: After refmac, R = 0.2409 (Rfree = 0.000) for 2324 atoms. Found 17 (17 requested) and removed 11 (8 requested) atoms. Cycle 5: After refmac, R = 0.2380 (Rfree = 0.000) for 2314 atoms. Found 17 (17 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.21 2.46 Search for helices and strands: 0 residues in 0 chains, 2373 seeds are put forward NCS extension: 33 residues added (7 deleted due to clashes), 2406 seeds are put forward Round 1: 235 peptides, 22 chains. Longest chain 30 peptides. Score 0.609 Round 2: 242 peptides, 18 chains. Longest chain 32 peptides. Score 0.663 Round 3: 238 peptides, 21 chains. Longest chain 24 peptides. Score 0.626 Round 4: 262 peptides, 17 chains. Longest chain 47 peptides. Score 0.709 Round 5: 252 peptides, 19 chains. Longest chain 30 peptides. Score 0.673 Taking the results from Round 4 Chains 19, Residues 245, Estimated correctness of the model 60.2 % 3 chains (92 residues) have been docked in sequence Building loops using Loopy2018 19 chains (245 residues) following loop building 3 chains (92 residues) in sequence following loop building ------------------------------------------------------ 7776 reflections ( 99.94 % complete ) and 3876 restraints for refining 2369 atoms. 2516 conditional restraints added. Observations/parameters ratio is 0.82 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2609 (Rfree = 0.000) for 2369 atoms. Found 17 (17 requested) and removed 31 (8 requested) atoms. Cycle 7: After refmac, R = 0.2428 (Rfree = 0.000) for 2343 atoms. Found 15 (17 requested) and removed 11 (8 requested) atoms. Cycle 8: After refmac, R = 0.2372 (Rfree = 0.000) for 2333 atoms. Found 12 (16 requested) and removed 9 (8 requested) atoms. Cycle 9: After refmac, R = 0.2332 (Rfree = 0.000) for 2333 atoms. Found 7 (16 requested) and removed 9 (8 requested) atoms. Cycle 10: After refmac, R = 0.2280 (Rfree = 0.000) for 2321 atoms. Found 8 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.17 2.43 Search for helices and strands: 0 residues in 0 chains, 2381 seeds are put forward NCS extension: 24 residues added (34 deleted due to clashes), 2405 seeds are put forward Round 1: 237 peptides, 21 chains. Longest chain 39 peptides. Score 0.624 Round 2: 258 peptides, 20 chains. Longest chain 38 peptides. Score 0.675 Round 3: 263 peptides, 16 chains. Longest chain 39 peptides. Score 0.719 Round 4: 263 peptides, 13 chains. Longest chain 39 peptides. Score 0.744 Round 5: 266 peptides, 15 chains. Longest chain 46 peptides. Score 0.732 Taking the results from Round 4 Chains 16, Residues 250, Estimated correctness of the model 68.5 % 5 chains (140 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 47 A and 56 A 14 chains (253 residues) following loop building 4 chains (148 residues) in sequence following loop building ------------------------------------------------------ 7776 reflections ( 99.94 % complete ) and 3452 restraints for refining 2410 atoms. 1821 conditional restraints added. Observations/parameters ratio is 0.81 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2640 (Rfree = 0.000) for 2410 atoms. Found 16 (16 requested) and removed 26 (9 requested) atoms. Cycle 12: After refmac, R = 0.2362 (Rfree = 0.000) for 2393 atoms. Found 11 (16 requested) and removed 22 (9 requested) atoms. Cycle 13: After refmac, R = 0.2387 (Rfree = 0.000) for 2377 atoms. Found 12 (15 requested) and removed 17 (8 requested) atoms. Cycle 14: After refmac, R = 0.2201 (Rfree = 0.000) for 2365 atoms. Found 5 (14 requested) and removed 14 (8 requested) atoms. Cycle 15: After refmac, R = 0.2153 (Rfree = 0.000) for 2349 atoms. Found 6 (14 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.12 2.39 Search for helices and strands: 0 residues in 0 chains, 2390 seeds are put forward NCS extension: 35 residues added (39 deleted due to clashes), 2425 seeds are put forward Round 1: 252 peptides, 22 chains. Longest chain 28 peptides. Score 0.644 Round 2: 267 peptides, 19 chains. Longest chain 39 peptides. Score 0.700 Round 3: 259 peptides, 19 chains. Longest chain 42 peptides. Score 0.686 Round 4: 261 peptides, 19 chains. Longest chain 40 peptides. Score 0.689 Round 5: 263 peptides, 20 chains. Longest chain 40 peptides. Score 0.684 Taking the results from Round 2 Chains 19, Residues 248, Estimated correctness of the model 57.9 % 4 chains (97 residues) have been docked in sequence ------------------------------------------------------ 7776 reflections ( 99.94 % complete ) and 3931 restraints for refining 2371 atoms. 2562 conditional restraints added. Observations/parameters ratio is 0.82 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2448 (Rfree = 0.000) for 2371 atoms. Found 14 (14 requested) and removed 19 (8 requested) atoms. Cycle 17: After refmac, R = 0.2206 (Rfree = 0.000) for 2360 atoms. Found 14 (14 requested) and removed 15 (8 requested) atoms. Cycle 18: After refmac, R = 0.2127 (Rfree = 0.000) for 2351 atoms. Found 13 (14 requested) and removed 11 (8 requested) atoms. Cycle 19: After refmac, R = 0.2023 (Rfree = 0.000) for 2347 atoms. Found 5 (14 requested) and removed 11 (8 requested) atoms. Cycle 20: After refmac, R = 0.2042 (Rfree = 0.000) for 2338 atoms. Found 6 (14 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.18 2.44 Search for helices and strands: 0 residues in 0 chains, 2410 seeds are put forward NCS extension: 18 residues added (39 deleted due to clashes), 2428 seeds are put forward Round 1: 261 peptides, 17 chains. Longest chain 48 peptides. Score 0.707 Round 2: 265 peptides, 15 chains. Longest chain 53 peptides. Score 0.731 Round 3: 262 peptides, 18 chains. Longest chain 35 peptides. Score 0.700 Round 4: 270 peptides, 18 chains. Longest chain 51 peptides. Score 0.713 Round 5: 261 peptides, 17 chains. Longest chain 41 peptides. Score 0.707 Taking the results from Round 2 Chains 16, Residues 250, Estimated correctness of the model 65.5 % 6 chains (170 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 54 A and 62 A Built loop between residues 90 B and 96 B 14 chains (262 residues) following loop building 4 chains (182 residues) in sequence following loop building ------------------------------------------------------ 7776 reflections ( 99.94 % complete ) and 3214 restraints for refining 2417 atoms. 1444 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2432 (Rfree = 0.000) for 2417 atoms. Found 14 (14 requested) and removed 28 (9 requested) atoms. Cycle 22: After refmac, R = 0.2299 (Rfree = 0.000) for 2392 atoms. Found 13 (14 requested) and removed 19 (9 requested) atoms. Failed to save intermediate PDB Cycle 23: After refmac, R = 0.2259 (Rfree = 0.000) for 2377 atoms. Found 10 (14 requested) and removed 16 (9 requested) atoms. Cycle 24: After refmac, R = 0.2208 (Rfree = 0.000) for 2362 atoms. Found 13 (13 requested) and removed 17 (8 requested) atoms. Cycle 25: After refmac, R = 0.2169 (Rfree = 0.000) for 2346 atoms. Found 12 (12 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.15 2.41 Search for helices and strands: 0 residues in 0 chains, 2417 seeds are put forward NCS extension: 33 residues added (29 deleted due to clashes), 2450 seeds are put forward Round 1: 256 peptides, 21 chains. Longest chain 38 peptides. Score 0.662 Round 2: 267 peptides, 15 chains. Longest chain 55 peptides. Score 0.734 Round 3: 276 peptides, 15 chains. Longest chain 64 peptides. Score 0.748 Round 4: 263 peptides, 14 chains. Longest chain 50 peptides. Score 0.736 Round 5: 268 peptides, 18 chains. Longest chain 50 peptides. Score 0.710 Taking the results from Round 3 Chains 19, Residues 261, Estimated correctness of the model 69.4 % 5 chains (146 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 33 B and 38 B Built loop between residues 51 B and 54 B 15 chains (265 residues) following loop building 3 chains (152 residues) in sequence following loop building ------------------------------------------------------ 7776 reflections ( 99.94 % complete ) and 3323 restraints for refining 2371 atoms. 1634 conditional restraints added. Observations/parameters ratio is 0.82 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2350 (Rfree = 0.000) for 2371 atoms. Found 12 (12 requested) and removed 28 (8 requested) atoms. Cycle 27: After refmac, R = 0.2239 (Rfree = 0.000) for 2348 atoms. Found 12 (12 requested) and removed 19 (8 requested) atoms. Cycle 28: After refmac, R = 0.2218 (Rfree = 0.000) for 2331 atoms. Found 7 (11 requested) and removed 12 (8 requested) atoms. Cycle 29: After refmac, R = 0.2054 (Rfree = 0.000) for 2322 atoms. Found 4 (11 requested) and removed 9 (8 requested) atoms. Cycle 30: After refmac, R = 0.1941 (Rfree = 0.000) for 2316 atoms. Found 4 (11 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.14 2.41 Search for helices and strands: 0 residues in 0 chains, 2372 seeds are put forward NCS extension: 8 residues added (25 deleted due to clashes), 2380 seeds are put forward Round 1: 260 peptides, 16 chains. Longest chain 50 peptides. Score 0.714 Round 2: 271 peptides, 15 chains. Longest chain 54 peptides. Score 0.740 Round 3: 269 peptides, 15 chains. Longest chain 55 peptides. Score 0.737 Round 4: 263 peptides, 15 chains. Longest chain 47 peptides. Score 0.727 Round 5: 266 peptides, 13 chains. Longest chain 54 peptides. Score 0.748 Taking the results from Round 5 Chains 14, Residues 253, Estimated correctness of the model 69.4 % 4 chains (132 residues) have been docked in sequence Building loops using Loopy2018 14 chains (253 residues) following loop building 4 chains (132 residues) in sequence following loop building ------------------------------------------------------ 7776 reflections ( 99.94 % complete ) and 3561 restraints for refining 2371 atoms. 2006 conditional restraints added. Observations/parameters ratio is 0.82 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2603 (Rfree = 0.000) for 2371 atoms. Found 10 (10 requested) and removed 30 (8 requested) atoms. Cycle 32: After refmac, R = 0.2392 (Rfree = 0.000) for 2346 atoms. Found 10 (10 requested) and removed 25 (8 requested) atoms. Cycle 33: After refmac, R = 0.2310 (Rfree = 0.000) for 2329 atoms. Found 10 (10 requested) and removed 13 (8 requested) atoms. Cycle 34: After refmac, R = 0.2311 (Rfree = 0.000) for 2324 atoms. Found 9 (9 requested) and removed 14 (8 requested) atoms. Cycle 35: After refmac, R = 0.2154 (Rfree = 0.000) for 2318 atoms. Found 4 (9 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.15 2.41 Search for helices and strands: 0 residues in 0 chains, 2362 seeds are put forward NCS extension: 38 residues added (37 deleted due to clashes), 2400 seeds are put forward Round 1: 258 peptides, 20 chains. Longest chain 40 peptides. Score 0.675 Round 2: 262 peptides, 18 chains. Longest chain 37 peptides. Score 0.700 Round 3: 253 peptides, 20 chains. Longest chain 29 peptides. Score 0.665 Round 4: 266 peptides, 17 chains. Longest chain 44 peptides. Score 0.715 Round 5: 269 peptides, 16 chains. Longest chain 39 peptides. Score 0.729 Taking the results from Round 5 Chains 17, Residues 253, Estimated correctness of the model 65.0 % 6 chains (149 residues) have been docked in sequence Building loops using Loopy2018 17 chains (253 residues) following loop building 6 chains (149 residues) in sequence following loop building ------------------------------------------------------ 7776 reflections ( 99.94 % complete ) and 3373 restraints for refining 2371 atoms. 1748 conditional restraints added. Observations/parameters ratio is 0.82 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2587 (Rfree = 0.000) for 2371 atoms. Found 8 (8 requested) and removed 31 (8 requested) atoms. Cycle 37: After refmac, R = 0.2503 (Rfree = 0.000) for 2338 atoms. Found 8 (8 requested) and removed 22 (8 requested) atoms. Cycle 38: After refmac, R = 0.2292 (Rfree = 0.000) for 2319 atoms. Found 8 (8 requested) and removed 12 (8 requested) atoms. Cycle 39: After refmac, R = 0.2199 (Rfree = 0.000) for 2312 atoms. Found 7 (8 requested) and removed 12 (8 requested) atoms. Cycle 40: After refmac, R = 0.2197 (Rfree = 0.000) for 2307 atoms. Found 8 (8 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.19 2.44 Search for helices and strands: 0 residues in 0 chains, 2383 seeds are put forward NCS extension: 2 residues added (12 deleted due to clashes), 2385 seeds are put forward Round 1: 249 peptides, 20 chains. Longest chain 25 peptides. Score 0.658 Round 2: 254 peptides, 18 chains. Longest chain 48 peptides. Score 0.686 Round 3: 271 peptides, 18 chains. Longest chain 44 peptides. Score 0.715 Round 4: 263 peptides, 16 chains. Longest chain 40 peptides. Score 0.719 Round 5: 250 peptides, 16 chains. Longest chain 44 peptides. Score 0.697 Taking the results from Round 4 Chains 18, Residues 247, Estimated correctness of the model 62.6 % 4 chains (116 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 75 B and 78 B 17 chains (249 residues) following loop building 3 chains (118 residues) in sequence following loop building ------------------------------------------------------ 7776 reflections ( 99.94 % complete ) and 3686 restraints for refining 2370 atoms. 2208 conditional restraints added. Observations/parameters ratio is 0.82 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2594 (Rfree = 0.000) for 2370 atoms. Found 8 (8 requested) and removed 22 (8 requested) atoms. Cycle 42: After refmac, R = 0.2440 (Rfree = 0.000) for 2346 atoms. Found 8 (8 requested) and removed 9 (8 requested) atoms. Cycle 43: After refmac, R = 0.2389 (Rfree = 0.000) for 2341 atoms. Found 7 (8 requested) and removed 10 (8 requested) atoms. Cycle 44: After refmac, R = 0.2382 (Rfree = 0.000) for 2337 atoms. Found 1 (8 requested) and removed 9 (8 requested) atoms. Cycle 45: After refmac, R = 0.2376 (Rfree = 0.000) for 2327 atoms. Found 1 (8 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.21 2.46 Search for helices and strands: 0 residues in 0 chains, 2391 seeds are put forward NCS extension: 11 residues added (8 deleted due to clashes), 2402 seeds are put forward Round 1: 235 peptides, 21 chains. Longest chain 36 peptides. Score 0.619 Round 2: 254 peptides, 19 chains. Longest chain 29 peptides. Score 0.676 Round 3: 256 peptides, 19 chains. Longest chain 49 peptides. Score 0.680 Round 4: 248 peptides, 16 chains. Longest chain 41 peptides. Score 0.693 Round 5: 251 peptides, 16 chains. Longest chain 75 peptides. Score 0.698 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 19, Residues 235, Estimated correctness of the model 57.4 % 3 chains (114 residues) have been docked in sequence Sequence coverage is 48 % Consider running further cycles of model building using 2aj7-3_warpNtrace.pdb as input Building loops using Loopy2018 19 chains (235 residues) following loop building 3 chains (114 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7776 reflections ( 99.94 % complete ) and 3842 restraints for refining 2371 atoms. 2459 conditional restraints added. Observations/parameters ratio is 0.82 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2583 (Rfree = 0.000) for 2371 atoms. Found 0 (8 requested) and removed 5 (8 requested) atoms. Cycle 47: After refmac, R = 0.2494 (Rfree = 0.000) for 2361 atoms. Found 0 (8 requested) and removed 1 (8 requested) atoms. Cycle 48: After refmac, R = 0.2465 (Rfree = 0.000) for 2359 atoms. Found 0 (8 requested) and removed 1 (8 requested) atoms. Cycle 49: After refmac, R = 0.2445 (Rfree = 0.000) for 2355 atoms. TimeTaking 41.83