Mon 24 Dec 00:54:06 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 2nuj-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2nuj-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2nuj-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2nuj-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/2nuj-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2nuj-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 00:54:10 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/2nuj-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2nuj-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 329 and 0 Target number of residues in the AU: 329 Target solvent content: 0.6174 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: 0.62 Input MTZ file: 2nuj-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: 91 Cell parameters: 78.401 78.401 151.418 90.000 90.000 90.000 Input sequence file: 2nuj-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 0.85 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: 78.401 3.400 Wilson plot Bfac: 59.74 6827 reflections ( 97.75 % complete ) and 0 restraints for refining 2889 atoms. Observations/parameters ratio is 0.59 ------------------------------------------------------ Starting model: R = 0.3209 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2637 (Rfree = 0.000) for 2889 atoms. Found 21 (21 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.19 2.71 Search for helices and strands: 0 residues in 0 chains, 2952 seeds are put forward NCS extension: 0 residues added, 2952 seeds are put forward Round 1: 208 peptides, 28 chains. Longest chain 19 peptides. Score 0.521 Round 2: 229 peptides, 26 chains. Longest chain 28 peptides. Score 0.605 Round 3: 247 peptides, 23 chains. Longest chain 31 peptides. Score 0.681 Round 4: 265 peptides, 23 chains. Longest chain 32 peptides. Score 0.718 Round 5: 250 peptides, 22 chains. Longest chain 27 peptides. Score 0.697 Taking the results from Round 4 Chains 27, Residues 242, Estimated correctness of the model 62.4 % 7 chains (106 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 46 B and 55 B 26 chains (241 residues) following loop building 6 chains (114 residues) in sequence following loop building ------------------------------------------------------ 6827 reflections ( 97.75 % complete ) and 4075 restraints for refining 2564 atoms. 2673 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2818 (Rfree = 0.000) for 2564 atoms. Found 19 (19 requested) and removed 29 (9 requested) atoms. Cycle 2: After refmac, R = 0.2779 (Rfree = 0.000) for 2503 atoms. Found 17 (19 requested) and removed 15 (9 requested) atoms. Cycle 3: After refmac, R = 0.2641 (Rfree = 0.000) for 2473 atoms. Found 12 (17 requested) and removed 12 (9 requested) atoms. Cycle 4: After refmac, R = 0.2545 (Rfree = 0.000) for 2451 atoms. Found 9 (17 requested) and removed 12 (9 requested) atoms. Cycle 5: After refmac, R = 0.2448 (Rfree = 0.000) for 2430 atoms. Found 5 (17 requested) and removed 14 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.22 2.74 Search for helices and strands: 0 residues in 0 chains, 2478 seeds are put forward NCS extension: 42 residues added (14 deleted due to clashes), 2520 seeds are put forward Round 1: 243 peptides, 26 chains. Longest chain 28 peptides. Score 0.640 Round 2: 247 peptides, 23 chains. Longest chain 37 peptides. Score 0.681 Round 3: 262 peptides, 21 chains. Longest chain 48 peptides. Score 0.731 Round 4: 259 peptides, 20 chains. Longest chain 37 peptides. Score 0.734 Round 5: 259 peptides, 20 chains. Longest chain 48 peptides. Score 0.734 Taking the results from Round 5 Chains 22, Residues 239, Estimated correctness of the model 66.2 % 6 chains (145 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 118 B and 122 B 21 chains (242 residues) following loop building 5 chains (148 residues) in sequence following loop building ------------------------------------------------------ 6827 reflections ( 97.75 % complete ) and 3630 restraints for refining 2435 atoms. 2058 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2835 (Rfree = 0.000) for 2435 atoms. Found 16 (16 requested) and removed 23 (9 requested) atoms. Cycle 7: After refmac, R = 0.2590 (Rfree = 0.000) for 2415 atoms. Found 13 (16 requested) and removed 13 (9 requested) atoms. Cycle 8: After refmac, R = 0.2488 (Rfree = 0.000) for 2405 atoms. Found 7 (15 requested) and removed 13 (9 requested) atoms. Cycle 9: After refmac, R = 0.2457 (Rfree = 0.000) for 2394 atoms. Found 4 (15 requested) and removed 10 (9 requested) atoms. Cycle 10: After refmac, R = 0.2418 (Rfree = 0.000) for 2385 atoms. Found 4 (15 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.24 2.75 Search for helices and strands: 0 residues in 0 chains, 2425 seeds are put forward NCS extension: 56 residues added (43 deleted due to clashes), 2481 seeds are put forward Round 1: 250 peptides, 24 chains. Longest chain 45 peptides. Score 0.677 Round 2: 259 peptides, 23 chains. Longest chain 51 peptides. Score 0.706 Round 3: 244 peptides, 20 chains. Longest chain 54 peptides. Score 0.705 Round 4: 260 peptides, 22 chains. Longest chain 47 peptides. Score 0.718 Round 5: 265 peptides, 25 chains. Longest chain 29 peptides. Score 0.699 Taking the results from Round 4 Chains 24, Residues 238, Estimated correctness of the model 62.4 % 5 chains (112 residues) have been docked in sequence Building loops using Loopy2018 24 chains (238 residues) following loop building 5 chains (112 residues) in sequence following loop building ------------------------------------------------------ 6827 reflections ( 97.75 % complete ) and 3864 restraints for refining 2383 atoms. 2451 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2689 (Rfree = 0.000) for 2383 atoms. Found 14 (14 requested) and removed 15 (9 requested) atoms. Cycle 12: After refmac, R = 0.2537 (Rfree = 0.000) for 2376 atoms. Found 6 (13 requested) and removed 11 (8 requested) atoms. Cycle 13: After refmac, R = 0.2473 (Rfree = 0.000) for 2363 atoms. Found 10 (13 requested) and removed 8 (8 requested) atoms. Cycle 14: After refmac, R = 0.2475 (Rfree = 0.000) for 2362 atoms. Found 12 (13 requested) and removed 9 (8 requested) atoms. Cycle 15: After refmac, R = 0.2335 (Rfree = 0.000) for 2360 atoms. Found 1 (12 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.24 2.75 Search for helices and strands: 0 residues in 0 chains, 2421 seeds are put forward NCS extension: 20 residues added (36 deleted due to clashes), 2441 seeds are put forward Round 1: 231 peptides, 25 chains. Longest chain 47 peptides. Score 0.622 Round 2: 256 peptides, 24 chains. Longest chain 46 peptides. Score 0.690 Round 3: 244 peptides, 23 chains. Longest chain 47 peptides. Score 0.674 Round 4: 243 peptides, 25 chains. Longest chain 36 peptides. Score 0.651 Round 5: 248 peptides, 23 chains. Longest chain 48 peptides. Score 0.683 Taking the results from Round 2 Chains 24, Residues 232, Estimated correctness of the model 55.3 % 4 chains (110 residues) have been docked in sequence ------------------------------------------------------ 6827 reflections ( 97.75 % complete ) and 3827 restraints for refining 2371 atoms. 2448 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2534 (Rfree = 0.000) for 2371 atoms. Found 12 (12 requested) and removed 11 (8 requested) atoms. Cycle 17: After refmac, R = 0.2392 (Rfree = 0.000) for 2361 atoms. Found 6 (12 requested) and removed 10 (8 requested) atoms. Cycle 18: After refmac, R = 0.2344 (Rfree = 0.000) for 2345 atoms. Found 12 (12 requested) and removed 9 (8 requested) atoms. Cycle 19: After refmac, R = 0.2315 (Rfree = 0.000) for 2342 atoms. Found 2 (12 requested) and removed 8 (8 requested) atoms. Cycle 20: After refmac, R = 0.2284 (Rfree = 0.000) for 2332 atoms. Found 3 (12 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.24 2.75 Search for helices and strands: 0 residues in 0 chains, 2400 seeds are put forward NCS extension: 27 residues added (10 deleted due to clashes), 2427 seeds are put forward Round 1: 235 peptides, 24 chains. Longest chain 44 peptides. Score 0.643 Round 2: 254 peptides, 21 chains. Longest chain 48 peptides. Score 0.715 Round 3: 254 peptides, 20 chains. Longest chain 47 peptides. Score 0.725 Round 4: 259 peptides, 25 chains. Longest chain 49 peptides. Score 0.686 Round 5: 246 peptides, 24 chains. Longest chain 47 peptides. Score 0.668 Taking the results from Round 3 Chains 21, Residues 234, Estimated correctness of the model 64.1 % 5 chains (132 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 118 A and 122 A 20 chains (237 residues) following loop building 4 chains (135 residues) in sequence following loop building ------------------------------------------------------ 6827 reflections ( 97.75 % complete ) and 3596 restraints for refining 2370 atoms. 2122 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2570 (Rfree = 0.000) for 2370 atoms. Found 12 (12 requested) and removed 12 (8 requested) atoms. Cycle 22: After refmac, R = 0.2492 (Rfree = 0.000) for 2365 atoms. Found 10 (12 requested) and removed 10 (8 requested) atoms. Cycle 23: After refmac, R = 0.2383 (Rfree = 0.000) for 2357 atoms. Found 7 (11 requested) and removed 11 (8 requested) atoms. Cycle 24: After refmac, R = 0.2331 (Rfree = 0.000) for 2346 atoms. Found 9 (11 requested) and removed 12 (8 requested) atoms. Cycle 25: After refmac, R = 0.2510 (Rfree = 0.000) for 2331 atoms. Found 11 (11 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.22 2.74 Search for helices and strands: 0 residues in 0 chains, 2392 seeds are put forward NCS extension: 70 residues added (19 deleted due to clashes), 2462 seeds are put forward Round 1: 232 peptides, 22 chains. Longest chain 48 peptides. Score 0.658 Round 2: 257 peptides, 19 chains. Longest chain 56 peptides. Score 0.740 Round 3: 255 peptides, 21 chains. Longest chain 59 peptides. Score 0.717 Round 4: 259 peptides, 21 chains. Longest chain 56 peptides. Score 0.725 Round 5: 260 peptides, 20 chains. Longest chain 58 peptides. Score 0.736 Taking the results from Round 2 Chains 21, Residues 238, Estimated correctness of the model 67.6 % 5 chains (151 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 117 A and 121 A 20 chains (241 residues) following loop building 4 chains (154 residues) in sequence following loop building ------------------------------------------------------ 6827 reflections ( 97.75 % complete ) and 3444 restraints for refining 2371 atoms. 1872 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2624 (Rfree = 0.000) for 2371 atoms. Found 10 (10 requested) and removed 27 (8 requested) atoms. Cycle 27: After refmac, R = 0.2414 (Rfree = 0.000) for 2342 atoms. Found 6 (10 requested) and removed 10 (8 requested) atoms. Cycle 28: After refmac, R = 0.2444 (Rfree = 0.000) for 2332 atoms. Found 10 (10 requested) and removed 9 (8 requested) atoms. Cycle 29: After refmac, R = 0.2364 (Rfree = 0.000) for 2331 atoms. Found 3 (9 requested) and removed 10 (8 requested) atoms. Cycle 30: After refmac, R = 0.2311 (Rfree = 0.000) for 2320 atoms. Found 5 (9 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.23 2.74 Search for helices and strands: 0 residues in 0 chains, 2361 seeds are put forward NCS extension: 49 residues added (17 deleted due to clashes), 2410 seeds are put forward Round 1: 241 peptides, 24 chains. Longest chain 49 peptides. Score 0.657 Round 2: 258 peptides, 18 chains. Longest chain 73 peptides. Score 0.751 Round 3: 256 peptides, 22 chains. Longest chain 54 peptides. Score 0.710 Round 4: 261 peptides, 19 chains. Longest chain 58 peptides. Score 0.747 Round 5: 261 peptides, 19 chains. Longest chain 53 peptides. Score 0.747 Taking the results from Round 2 Chains 19, Residues 240, Estimated correctness of the model 70.0 % 5 chains (169 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 39 A and 48 A Built loop between residues 119 A and 122 A 17 chains (250 residues) following loop building 3 chains (179 residues) in sequence following loop building ------------------------------------------------------ 6827 reflections ( 97.75 % complete ) and 3297 restraints for refining 2428 atoms. 1559 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2751 (Rfree = 0.000) for 2428 atoms. Found 9 (9 requested) and removed 20 (9 requested) atoms. Cycle 32: After refmac, R = 0.2647 (Rfree = 0.000) for 2404 atoms. Found 9 (9 requested) and removed 18 (9 requested) atoms. Cycle 33: After refmac, R = 0.2574 (Rfree = 0.000) for 2391 atoms. Found 7 (9 requested) and removed 11 (9 requested) atoms. Cycle 34: After refmac, R = 0.2493 (Rfree = 0.000) for 2383 atoms. Found 7 (9 requested) and removed 10 (9 requested) atoms. Cycle 35: After refmac, R = 0.2468 (Rfree = 0.000) for 2376 atoms. Found 7 (8 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.22 2.74 Search for helices and strands: 0 residues in 0 chains, 2435 seeds are put forward NCS extension: 65 residues added (107 deleted due to clashes), 2500 seeds are put forward Round 1: 251 peptides, 22 chains. Longest chain 57 peptides. Score 0.700 Round 2: 258 peptides, 18 chains. Longest chain 64 peptides. Score 0.751 Round 3: 264 peptides, 21 chains. Longest chain 57 peptides. Score 0.734 Round 4: 258 peptides, 22 chains. Longest chain 50 peptides. Score 0.714 Round 5: 261 peptides, 24 chains. Longest chain 43 peptides. Score 0.700 Taking the results from Round 2 Chains 22, Residues 240, Estimated correctness of the model 70.0 % 4 chains (138 residues) have been docked in sequence Building loops using Loopy2018 22 chains (240 residues) following loop building 4 chains (138 residues) in sequence following loop building ------------------------------------------------------ 6827 reflections ( 97.75 % complete ) and 3557 restraints for refining 2371 atoms. 2029 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2731 (Rfree = 0.000) for 2371 atoms. Found 8 (8 requested) and removed 12 (8 requested) atoms. Cycle 37: After refmac, R = 0.2596 (Rfree = 0.000) for 2360 atoms. Found 8 (8 requested) and removed 8 (8 requested) atoms. Cycle 38: After refmac, R = 0.2506 (Rfree = 0.000) for 2356 atoms. Found 8 (8 requested) and removed 9 (8 requested) atoms. Cycle 39: After refmac, R = 0.2454 (Rfree = 0.000) for 2346 atoms. Found 8 (8 requested) and removed 9 (8 requested) atoms. Cycle 40: After refmac, R = 0.2404 (Rfree = 0.000) for 2339 atoms. Found 8 (8 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.20 2.72 Search for helices and strands: 0 residues in 0 chains, 2387 seeds are put forward NCS extension: 51 residues added (9 deleted due to clashes), 2438 seeds are put forward Round 1: 241 peptides, 21 chains. Longest chain 48 peptides. Score 0.689 Round 2: 252 peptides, 17 chains. Longest chain 51 peptides. Score 0.749 Round 3: 253 peptides, 20 chains. Longest chain 49 peptides. Score 0.723 Round 4: 264 peptides, 18 chains. Longest chain 58 peptides. Score 0.761 Round 5: 254 peptides, 21 chains. Longest chain 55 peptides. Score 0.715 Taking the results from Round 4 Chains 21, Residues 246, Estimated correctness of the model 72.2 % 3 chains (111 residues) have been docked in sequence Building loops using Loopy2018 21 chains (246 residues) following loop building 3 chains (111 residues) in sequence following loop building ------------------------------------------------------ 6827 reflections ( 97.75 % complete ) and 3748 restraints for refining 2371 atoms. 2326 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2635 (Rfree = 0.000) for 2371 atoms. Found 8 (8 requested) and removed 13 (8 requested) atoms. Cycle 42: After refmac, R = 0.2546 (Rfree = 0.000) for 2361 atoms. Found 8 (8 requested) and removed 9 (8 requested) atoms. Cycle 43: After refmac, R = 0.2492 (Rfree = 0.000) for 2353 atoms. Found 7 (8 requested) and removed 9 (8 requested) atoms. Cycle 44: After refmac, R = 0.2517 (Rfree = 0.000) for 2345 atoms. Found 8 (8 requested) and removed 8 (8 requested) atoms. Cycle 45: After refmac, R = 0.2467 (Rfree = 0.000) for 2344 atoms. Found 4 (8 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.25 2.76 Search for helices and strands: 0 residues in 0 chains, 2379 seeds are put forward NCS extension: 48 residues added (17 deleted due to clashes), 2427 seeds are put forward Round 1: 239 peptides, 22 chains. Longest chain 47 peptides. Score 0.674 Round 2: 253 peptides, 21 chains. Longest chain 33 peptides. Score 0.713 Round 3: 246 peptides, 22 chains. Longest chain 46 peptides. Score 0.689 Round 4: 256 peptides, 23 chains. Longest chain 51 peptides. Score 0.700 Round 5: 253 peptides, 22 chains. Longest chain 51 peptides. Score 0.704 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 25, Residues 232, Estimated correctness of the model 61.1 % 6 chains (109 residues) have been docked in sequence Sequence coverage is 46 % Consider running further cycles of model building using 2nuj-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 96 A and 104 A Built loop between residues 118 A and 126 A 21 chains (236 residues) following loop building 4 chains (123 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6827 reflections ( 97.75 % complete ) and 3737 restraints for refining 2371 atoms. 2363 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2821 (Rfree = 0.000) for 2371 atoms. Found 0 (8 requested) and removed 5 (8 requested) atoms. Cycle 47: After refmac, R = 0.2719 (Rfree = 0.000) for 2353 atoms. Found 0 (8 requested) and removed 5 (8 requested) atoms. Cycle 48: After refmac, R = 0.2689 (Rfree = 0.000) for 2338 atoms. Found 0 (8 requested) and removed 2 (8 requested) atoms. Cycle 49: After refmac, R = 0.2701 (Rfree = 0.000) for 2335 atoms. TimeTaking 34.57