Tue 25 Dec 19:27:55 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 2nuj-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2nuj-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2nuj-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2nuj-3.4-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/2nuj-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2nuj-3.4-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 ============================================================ Tue 25 Dec 19:28:04 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/2nuj-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2nuj-3.4-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 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-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: 91 Cell parameters: 78.401 78.401 151.418 90.000 90.000 90.000 Input sequence file: 2nuj-3.4-parrot-hancs.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 2885 atoms. Observations/parameters ratio is 0.59 ------------------------------------------------------ Starting model: R = 0.3227 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2749 (Rfree = 0.000) for 2885 atoms. Found 19 (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, 2935 seeds are put forward NCS extension: 0 residues added, 2935 seeds are put forward Round 1: 197 peptides, 34 chains. Longest chain 16 peptides. Score 0.401 Round 2: 237 peptides, 30 chains. Longest chain 30 peptides. Score 0.578 Round 3: 253 peptides, 29 chains. Longest chain 25 peptides. Score 0.630 Round 4: 258 peptides, 26 chains. Longest chain 33 peptides. Score 0.674 Round 5: 265 peptides, 24 chains. Longest chain 27 peptides. Score 0.708 Taking the results from Round 5 Chains 27, Residues 241, Estimated correctness of the model 59.9 % 5 chains (72 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 92 A and 103 A 24 chains (245 residues) following loop building 4 chains (82 residues) in sequence following loop building ------------------------------------------------------ 6827 reflections ( 97.75 % complete ) and 4338 restraints for refining 2536 atoms. 3049 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2668 (Rfree = 0.000) for 2536 atoms. Found 19 (19 requested) and removed 23 (9 requested) atoms. Cycle 2: After refmac, R = 0.2483 (Rfree = 0.000) for 2485 atoms. Found 12 (19 requested) and removed 11 (9 requested) atoms. Cycle 3: After refmac, R = 0.2418 (Rfree = 0.000) for 2466 atoms. Found 9 (17 requested) and removed 10 (9 requested) atoms. Cycle 4: After refmac, R = 0.2363 (Rfree = 0.000) for 2453 atoms. Found 12 (17 requested) and removed 12 (9 requested) atoms. Failed to save intermediate PDB Cycle 5: After refmac, R = 0.2311 (Rfree = 0.000) for 2449 atoms. Found 6 (17 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.23 2.74 Search for helices and strands: 0 residues in 0 chains, 2517 seeds are put forward NCS extension: 60 residues added (31 deleted due to clashes), 2577 seeds are put forward Round 1: 239 peptides, 24 chains. Longest chain 21 peptides. Score 0.652 Round 2: 241 peptides, 21 chains. Longest chain 26 peptides. Score 0.689 Round 3: 247 peptides, 23 chains. Longest chain 27 peptides. Score 0.681 Round 4: 241 peptides, 21 chains. Longest chain 24 peptides. Score 0.689 Round 5: 248 peptides, 20 chains. Longest chain 37 peptides. Score 0.713 Taking the results from Round 5 Chains 23, Residues 228, Estimated correctness of the model 61.1 % 6 chains (102 residues) have been docked in sequence Building loops using Loopy2018 23 chains (228 residues) following loop building 6 chains (102 residues) in sequence following loop building ------------------------------------------------------ 6827 reflections ( 97.75 % complete ) and 4075 restraints for refining 2414 atoms. 2782 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2658 (Rfree = 0.000) for 2414 atoms. Found 16 (16 requested) and removed 20 (9 requested) atoms. Cycle 7: After refmac, R = 0.2499 (Rfree = 0.000) for 2386 atoms. Found 9 (16 requested) and removed 10 (9 requested) atoms. Cycle 8: After refmac, R = 0.2419 (Rfree = 0.000) for 2377 atoms. Found 8 (15 requested) and removed 9 (8 requested) atoms. Cycle 9: After refmac, R = 0.2369 (Rfree = 0.000) for 2369 atoms. Found 6 (14 requested) and removed 9 (8 requested) atoms. Cycle 10: After refmac, R = 0.2321 (Rfree = 0.000) for 2363 atoms. Found 3 (14 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.23 2.74 Search for helices and strands: 0 residues in 0 chains, 2408 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 2427 seeds are put forward Round 1: 244 peptides, 22 chains. Longest chain 28 peptides. Score 0.685 Round 2: 254 peptides, 25 chains. Longest chain 30 peptides. Score 0.675 Round 3: 259 peptides, 28 chains. Longest chain 48 peptides. Score 0.655 Round 4: 258 peptides, 24 chains. Longest chain 44 peptides. Score 0.694 Round 5: 255 peptides, 23 chains. Longest chain 49 peptides. Score 0.698 Taking the results from Round 5 Chains 24, Residues 232, Estimated correctness of the model 57.4 % 5 chains (126 residues) have been docked in sequence ------------------------------------------------------ 6827 reflections ( 97.75 % complete ) and 3757 restraints for refining 2371 atoms. 2357 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2687 (Rfree = 0.000) for 2371 atoms. Found 14 (14 requested) and removed 20 (8 requested) atoms. Cycle 12: After refmac, R = 0.2540 (Rfree = 0.000) for 2348 atoms. Found 9 (14 requested) and removed 13 (8 requested) atoms. Cycle 13: After refmac, R = 0.2458 (Rfree = 0.000) for 2330 atoms. Found 7 (14 requested) and removed 10 (8 requested) atoms. Cycle 14: After refmac, R = 0.2375 (Rfree = 0.000) for 2316 atoms. Found 9 (14 requested) and removed 8 (8 requested) atoms. Cycle 15: After refmac, R = 0.2365 (Rfree = 0.000) for 2311 atoms. Found 9 (14 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.19 2.71 Search for helices and strands: 0 residues in 0 chains, 2359 seeds are put forward NCS extension: 68 residues added (18 deleted due to clashes), 2427 seeds are put forward Round 1: 246 peptides, 24 chains. Longest chain 48 peptides. Score 0.668 Round 2: 262 peptides, 25 chains. Longest chain 48 peptides. Score 0.692 Round 3: 264 peptides, 20 chains. Longest chain 48 peptides. Score 0.744 Round 4: 258 peptides, 20 chains. Longest chain 44 peptides. Score 0.732 Round 5: 249 peptides, 19 chains. Longest chain 46 peptides. Score 0.725 Taking the results from Round 3 Chains 20, Residues 244, Estimated correctness of the model 68.5 % 4 chains (114 residues) have been docked in sequence Building loops using Loopy2018 20 chains (244 residues) following loop building 4 chains (114 residues) in sequence following loop building ------------------------------------------------------ 6827 reflections ( 97.75 % complete ) and 3714 restraints for refining 2370 atoms. 2275 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2613 (Rfree = 0.000) for 2370 atoms. Found 14 (14 requested) and removed 13 (8 requested) atoms. Cycle 17: After refmac, R = 0.2418 (Rfree = 0.000) for 2356 atoms. Found 7 (13 requested) and removed 10 (8 requested) atoms. Cycle 18: After refmac, R = 0.2416 (Rfree = 0.000) for 2342 atoms. Found 10 (13 requested) and removed 10 (8 requested) atoms. Cycle 19: After refmac, R = 0.2347 (Rfree = 0.000) for 2326 atoms. Found 8 (13 requested) and removed 15 (8 requested) atoms. Cycle 20: After refmac, R = 0.2227 (Rfree = 0.000) for 2311 atoms. Found 11 (12 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.24 2.75 Search for helices and strands: 0 residues in 0 chains, 2364 seeds are put forward NCS extension: 65 residues added (4 deleted due to clashes), 2429 seeds are put forward Round 1: 236 peptides, 24 chains. Longest chain 46 peptides. Score 0.645 Round 2: 257 peptides, 16 chains. Longest chain 66 peptides. Score 0.767 Round 3: 254 peptides, 20 chains. Longest chain 46 peptides. Score 0.725 Round 4: 258 peptides, 16 chains. Longest chain 75 peptides. Score 0.768 Round 5: 248 peptides, 21 chains. Longest chain 48 peptides. Score 0.703 Taking the results from Round 4 Chains 17, Residues 242, Estimated correctness of the model 73.7 % 5 chains (141 residues) have been docked in sequence Building loops using Loopy2018 17 chains (242 residues) following loop building 5 chains (141 residues) in sequence following loop building ------------------------------------------------------ 6827 reflections ( 97.75 % complete ) and 3610 restraints for refining 2371 atoms. 2095 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2679 (Rfree = 0.000) for 2371 atoms. Found 12 (12 requested) and removed 23 (8 requested) atoms. Cycle 22: After refmac, R = 0.2561 (Rfree = 0.000) for 2348 atoms. Found 12 (12 requested) and removed 11 (8 requested) atoms. Cycle 23: After refmac, R = 0.2380 (Rfree = 0.000) for 2337 atoms. Found 7 (11 requested) and removed 9 (8 requested) atoms. Cycle 24: After refmac, R = 0.2293 (Rfree = 0.000) for 2328 atoms. Found 7 (11 requested) and removed 8 (8 requested) atoms. Cycle 25: After refmac, R = 0.2285 (Rfree = 0.000) for 2319 atoms. Found 7 (11 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.22 2.74 Search for helices and strands: 0 residues in 0 chains, 2352 seeds are put forward NCS extension: 112 residues added (24 deleted due to clashes), 2464 seeds are put forward Round 1: 231 peptides, 23 chains. Longest chain 46 peptides. Score 0.644 Round 2: 258 peptides, 17 chains. Longest chain 72 peptides. Score 0.760 Round 3: 256 peptides, 21 chains. Longest chain 66 peptides. Score 0.719 Round 4: 255 peptides, 18 chains. Longest chain 51 peptides. Score 0.745 Round 5: 254 peptides, 22 chains. Longest chain 39 peptides. Score 0.706 Taking the results from Round 2 Chains 19, Residues 241, Estimated correctness of the model 72.0 % 5 chains (163 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 118 A and 126 A 17 chains (243 residues) following loop building 4 chains (170 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 6827 reflections ( 97.75 % complete ) and 3311 restraints for refining 2370 atoms. 1695 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2635 (Rfree = 0.000) for 2370 atoms. Found 10 (10 requested) and removed 24 (8 requested) atoms. Cycle 27: After refmac, R = 0.2381 (Rfree = 0.000) for 2340 atoms. Found 10 (10 requested) and removed 9 (8 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.2306 (Rfree = 0.000) for 2332 atoms. Found 5 (10 requested) and removed 10 (8 requested) atoms. Cycle 29: After refmac, R = 0.2279 (Rfree = 0.000) for 2323 atoms. Found 4 (9 requested) and removed 9 (8 requested) atoms. Failed to save intermediate PDB Cycle 30: After refmac, R = 0.2256 (Rfree = 0.000) for 2312 atoms. Found 7 (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, 2385 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 2397 seeds are put forward Round 1: 239 peptides, 22 chains. Longest chain 51 peptides. Score 0.674 Round 2: 251 peptides, 18 chains. Longest chain 48 peptides. Score 0.738 Round 3: 258 peptides, 22 chains. Longest chain 50 peptides. Score 0.714 Round 4: 256 peptides, 20 chains. Longest chain 55 peptides. Score 0.729 Round 5: 249 peptides, 23 chains. Longest chain 49 peptides. Score 0.685 Taking the results from Round 2 Chains 20, Residues 233, Estimated correctness of the model 67.1 % 4 chains (127 residues) have been docked in sequence Building loops using Loopy2018 20 chains (233 residues) following loop building 4 chains (127 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 6827 reflections ( 97.75 % complete ) and 3717 restraints for refining 2371 atoms. 2271 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2633 (Rfree = 0.000) for 2371 atoms. Found 8 (8 requested) and removed 15 (8 requested) atoms. Cycle 32: After refmac, R = 0.2598 (Rfree = 0.000) for 2359 atoms. Found 8 (8 requested) and removed 12 (8 requested) atoms. Cycle 33: After refmac, R = 0.2630 (Rfree = 0.000) for 2343 atoms. Found 8 (8 requested) and removed 13 (8 requested) atoms. Failed to save intermediate PDB Cycle 34: After refmac, R = 0.2664 (Rfree = 0.000) for 2325 atoms. Found 8 (8 requested) and removed 14 (8 requested) atoms. Cycle 35: After refmac, R = 0.2650 (Rfree = 0.000) for 2314 atoms. Found 8 (8 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.17 2.69 Search for helices and strands: 0 residues in 0 chains, 2384 seeds are put forward NCS extension: 62 residues added (8 deleted due to clashes), 2446 seeds are put forward Round 1: 234 peptides, 23 chains. Longest chain 45 peptides. Score 0.652 Round 2: 248 peptides, 19 chains. Longest chain 51 peptides. Score 0.723 Round 3: 259 peptides, 21 chains. Longest chain 48 peptides. Score 0.725 Round 4: 249 peptides, 20 chains. Longest chain 29 peptides. Score 0.715 Round 5: 258 peptides, 19 chains. Longest chain 49 peptides. Score 0.742 Taking the results from Round 5 Chains 22, Residues 239, Estimated correctness of the model 68.0 % 3 chains (67 residues) have been docked in sequence Building loops using Loopy2018 22 chains (239 residues) following loop building 3 chains (67 residues) in sequence following loop building ------------------------------------------------------ 6827 reflections ( 97.75 % complete ) and 4267 restraints for refining 2371 atoms. 3057 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2529 (Rfree = 0.000) for 2371 atoms. Found 8 (8 requested) and removed 10 (8 requested) atoms. Cycle 37: After refmac, R = 0.2440 (Rfree = 0.000) for 2362 atoms. Found 8 (8 requested) and removed 9 (8 requested) atoms. Cycle 38: After refmac, R = 0.2322 (Rfree = 0.000) for 2357 atoms. Found 8 (8 requested) and removed 9 (8 requested) atoms. Failed to save intermediate PDB Cycle 39: After refmac, R = 0.2258 (Rfree = 0.000) for 2352 atoms. Found 3 (8 requested) and removed 9 (8 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.2198 (Rfree = 0.000) for 2344 atoms. Found 2 (8 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.22 2.74 Search for helices and strands: 0 residues in 0 chains, 2415 seeds are put forward NCS extension: 25 residues added (20 deleted due to clashes), 2440 seeds are put forward Round 1: 227 peptides, 22 chains. Longest chain 29 peptides. Score 0.646 Round 2: 255 peptides, 22 chains. Longest chain 29 peptides. Score 0.708 Round 3: 247 peptides, 24 chains. Longest chain 43 peptides. Score 0.670 Round 4: 252 peptides, 21 chains. Longest chain 45 peptides. Score 0.711 Round 5: 255 peptides, 22 chains. Longest chain 46 peptides. Score 0.708 Taking the results from Round 4 Chains 25, Residues 231, Estimated correctness of the model 60.7 % 6 chains (111 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 41 A and 52 A Built loop between residues 67 A and 74 A 22 chains (244 residues) following loop building 4 chains (127 residues) in sequence following loop building ------------------------------------------------------ 6827 reflections ( 97.75 % complete ) and 3633 restraints for refining 2369 atoms. 2116 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2664 (Rfree = 0.000) for 2369 atoms. Found 8 (8 requested) and removed 16 (8 requested) atoms. Failed to save intermediate PDB Cycle 42: After refmac, R = 0.2554 (Rfree = 0.000) for 2348 atoms. Found 8 (8 requested) and removed 9 (8 requested) atoms. Cycle 43: After refmac, R = 0.2404 (Rfree = 0.000) for 2338 atoms. Found 8 (8 requested) and removed 11 (8 requested) atoms. Cycle 44: After refmac, R = 0.2330 (Rfree = 0.000) for 2331 atoms. Found 8 (8 requested) and removed 8 (8 requested) atoms. Cycle 45: After refmac, R = 0.2275 (Rfree = 0.000) for 2326 atoms. Found 4 (8 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.25 2.76 Search for helices and strands: 0 residues in 0 chains, 2361 seeds are put forward NCS extension: 89 residues added (74 deleted due to clashes), 2450 seeds are put forward Round 1: 230 peptides, 20 chains. Longest chain 44 peptides. Score 0.675 Round 2: 252 peptides, 20 chains. Longest chain 45 peptides. Score 0.721 Round 3: 241 peptides, 22 chains. Longest chain 29 peptides. Score 0.678 Round 4: 258 peptides, 21 chains. Longest chain 45 peptides. Score 0.723 Round 5: 246 peptides, 21 chains. Longest chain 35 peptides. Score 0.699 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 23, Residues 237, Estimated correctness of the model 63.6 % 7 chains (118 residues) have been docked in sequence Sequence coverage is 49 % Consider running further cycles of model building using 2nuj-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 39 B and 52 B Built loop between residues 68 B and 74 B Built loop between residues 117 B and 126 B 17 chains (254 residues) following loop building 4 chains (143 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6827 reflections ( 97.75 % complete ) and 3440 restraints for refining 2371 atoms. 1853 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2705 (Rfree = 0.000) for 2371 atoms. Found 0 (8 requested) and removed 8 (8 requested) atoms. Failed to save intermediate PDB Cycle 47: After refmac, R = 0.2541 (Rfree = 0.000) for 2353 atoms. Found 0 (8 requested) and removed 1 (8 requested) atoms. Cycle 48: After refmac, R = 0.2458 (Rfree = 0.000) for 2346 atoms. Found 0 (8 requested) and removed 2 (8 requested) atoms. Cycle 49: After refmac, R = 0.2429 (Rfree = 0.000) for 2344 atoms. Found 0 (8 requested) and removed 2 (8 requested) atoms. Writing output files ... Failed to save intermediate PDB TimeTaking 50.37