Sun 23 Dec 22:22:41 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 2otm-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2otm-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2otm-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2otm-3.2-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/2otm-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2otm-3.2-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 22:22:50 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/2otm-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2otm-3.2-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 396 and 0 Target number of residues in the AU: 396 Target solvent content: 0.6127 Checking the provided sequence file Detected sequence length: 154 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 3 Adjusted target number of residues: 462 Adjusted target solvent content: 0.55 Input MTZ file: 2otm-3.2-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: 5 Cell parameters: 112.035 62.893 78.663 90.000 93.262 90.000 Input sequence file: 2otm-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 3696 target number of atoms Had to go as low as 0.75 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: 78.536 3.200 Wilson plot Bfac: 57.84 9162 reflections ( 99.84 % complete ) and 0 restraints for refining 4138 atoms. Observations/parameters ratio is 0.55 ------------------------------------------------------ Starting model: R = 0.2996 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2559 (Rfree = 0.000) for 4138 atoms. Found 37 (37 requested) and removed 30 (18 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.08 2.88 Search for helices and strands: 0 residues in 0 chains, 4213 seeds are put forward NCS extension: 0 residues added, 4213 seeds are put forward Round 1: 292 peptides, 44 chains. Longest chain 15 peptides. Score 0.514 Round 2: 330 peptides, 38 chains. Longest chain 21 peptides. Score 0.656 Round 3: 348 peptides, 38 chains. Longest chain 29 peptides. Score 0.688 Round 4: 351 peptides, 37 chains. Longest chain 38 peptides. Score 0.701 Round 5: 358 peptides, 35 chains. Longest chain 25 peptides. Score 0.728 Taking the results from Round 5 Chains 37, Residues 323, Estimated correctness of the model 70.9 % 7 chains (112 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 45 A and 48 A 36 chains (324 residues) following loop building 6 chains (114 residues) in sequence following loop building ------------------------------------------------------ 9162 reflections ( 99.84 % complete ) and 6054 restraints for refining 3375 atoms. 4392 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2762 (Rfree = 0.000) for 3375 atoms. Found 30 (30 requested) and removed 37 (15 requested) atoms. Cycle 2: After refmac, R = 0.2478 (Rfree = 0.000) for 3327 atoms. Found 13 (29 requested) and removed 24 (15 requested) atoms. Cycle 3: After refmac, R = 0.2288 (Rfree = 0.000) for 3292 atoms. Found 9 (28 requested) and removed 18 (14 requested) atoms. Cycle 4: After refmac, R = 0.2238 (Rfree = 0.000) for 3275 atoms. Found 7 (27 requested) and removed 18 (14 requested) atoms. Cycle 5: After refmac, R = 0.2164 (Rfree = 0.000) for 3260 atoms. Found 11 (27 requested) and removed 18 (14 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.01 2.82 Search for helices and strands: 0 residues in 0 chains, 3367 seeds are put forward NCS extension: 16 residues added (27 deleted due to clashes), 3383 seeds are put forward Round 1: 333 peptides, 33 chains. Longest chain 27 peptides. Score 0.703 Round 2: 360 peptides, 32 chains. Longest chain 26 peptides. Score 0.752 Round 3: 352 peptides, 36 chains. Longest chain 36 peptides. Score 0.711 Round 4: 342 peptides, 32 chains. Longest chain 28 peptides. Score 0.725 Round 5: 362 peptides, 34 chains. Longest chain 27 peptides. Score 0.741 Taking the results from Round 2 Chains 37, Residues 328, Estimated correctness of the model 75.4 % 6 chains (104 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 113 A and 117 A 36 chains (331 residues) following loop building 5 chains (107 residues) in sequence following loop building ------------------------------------------------------ 9162 reflections ( 99.84 % complete ) and 6141 restraints for refining 3374 atoms. 4421 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2503 (Rfree = 0.000) for 3374 atoms. Found 13 (27 requested) and removed 19 (15 requested) atoms. Cycle 7: After refmac, R = 0.2282 (Rfree = 0.000) for 3355 atoms. Found 2 (26 requested) and removed 17 (15 requested) atoms. Cycle 8: After refmac, R = 0.2182 (Rfree = 0.000) for 3332 atoms. Found 6 (25 requested) and removed 20 (14 requested) atoms. Cycle 9: After refmac, R = 0.2092 (Rfree = 0.000) for 3313 atoms. Found 1 (24 requested) and removed 17 (14 requested) atoms. Cycle 10: After refmac, R = 0.2072 (Rfree = 0.000) for 3294 atoms. Found 5 (24 requested) and removed 15 (14 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.02 2.82 Search for helices and strands: 0 residues in 0 chains, 3383 seeds are put forward NCS extension: 17 residues added (28 deleted due to clashes), 3400 seeds are put forward Round 1: 334 peptides, 39 chains. Longest chain 26 peptides. Score 0.655 Round 2: 350 peptides, 32 chains. Longest chain 29 peptides. Score 0.737 Round 3: 359 peptides, 32 chains. Longest chain 29 peptides. Score 0.751 Round 4: 370 peptides, 31 chains. Longest chain 40 peptides. Score 0.772 Round 5: 355 peptides, 34 chains. Longest chain 42 peptides. Score 0.730 Taking the results from Round 4 Chains 35, Residues 339, Estimated correctness of the model 78.9 % 8 chains (162 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 43 A and 49 A 33 chains (343 residues) following loop building 7 chains (167 residues) in sequence following loop building ------------------------------------------------------ 9162 reflections ( 99.84 % complete ) and 5387 restraints for refining 3375 atoms. 3370 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2348 (Rfree = 0.000) for 3375 atoms. Found 16 (24 requested) and removed 29 (15 requested) atoms. Cycle 12: After refmac, R = 0.2108 (Rfree = 0.000) for 3347 atoms. Found 9 (23 requested) and removed 17 (15 requested) atoms. Cycle 13: After refmac, R = 0.2035 (Rfree = 0.000) for 3330 atoms. Found 7 (22 requested) and removed 17 (14 requested) atoms. Cycle 14: After refmac, R = 0.1983 (Rfree = 0.000) for 3317 atoms. Found 5 (21 requested) and removed 18 (14 requested) atoms. Cycle 15: After refmac, R = 0.1988 (Rfree = 0.000) for 3298 atoms. Found 2 (21 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.05 2.85 Search for helices and strands: 0 residues in 0 chains, 3390 seeds are put forward NCS extension: 25 residues added (24 deleted due to clashes), 3415 seeds are put forward Round 1: 334 peptides, 36 chains. Longest chain 37 peptides. Score 0.680 Round 2: 354 peptides, 27 chains. Longest chain 51 peptides. Score 0.777 Round 3: 344 peptides, 29 chains. Longest chain 50 peptides. Score 0.750 Round 4: 359 peptides, 29 chains. Longest chain 51 peptides. Score 0.771 Round 5: 361 peptides, 32 chains. Longest chain 29 peptides. Score 0.753 Taking the results from Round 2 Chains 27, Residues 327, Estimated correctness of the model 79.8 % 9 chains (202 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 113 A and 124 A 25 chains (332 residues) following loop building 8 chains (212 residues) in sequence following loop building ------------------------------------------------------ 9162 reflections ( 99.84 % complete ) and 5056 restraints for refining 3375 atoms. 2953 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2449 (Rfree = 0.000) for 3375 atoms. Found 21 (21 requested) and removed 35 (15 requested) atoms. Cycle 17: After refmac, R = 0.2497 (Rfree = 0.000) for 3342 atoms. Found 20 (20 requested) and removed 25 (15 requested) atoms. Cycle 18: After refmac, R = 0.2118 (Rfree = 0.000) for 3316 atoms. Found 16 (19 requested) and removed 17 (14 requested) atoms. Cycle 19: After refmac, R = 0.2016 (Rfree = 0.000) for 3307 atoms. Found 6 (19 requested) and removed 17 (14 requested) atoms. Cycle 20: After refmac, R = 0.1969 (Rfree = 0.000) for 3294 atoms. Found 10 (18 requested) and removed 18 (14 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.05 2.85 Search for helices and strands: 0 residues in 0 chains, 3389 seeds are put forward NCS extension: 60 residues added (33 deleted due to clashes), 3449 seeds are put forward Round 1: 329 peptides, 32 chains. Longest chain 51 peptides. Score 0.704 Round 2: 352 peptides, 28 chains. Longest chain 51 peptides. Score 0.768 Round 3: 357 peptides, 32 chains. Longest chain 47 peptides. Score 0.748 Round 4: 355 peptides, 30 chains. Longest chain 37 peptides. Score 0.759 Round 5: 357 peptides, 31 chains. Longest chain 38 peptides. Score 0.755 Taking the results from Round 2 Chains 31, Residues 324, Estimated correctness of the model 78.2 % 8 chains (152 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 114 A and 124 A 30 chains (333 residues) following loop building 7 chains (161 residues) in sequence following loop building ------------------------------------------------------ 9162 reflections ( 99.84 % complete ) and 5489 restraints for refining 3375 atoms. 3511 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2384 (Rfree = 0.000) for 3375 atoms. Found 18 (18 requested) and removed 32 (15 requested) atoms. Cycle 22: After refmac, R = 0.2189 (Rfree = 0.000) for 3346 atoms. Found 7 (17 requested) and removed 18 (15 requested) atoms. Cycle 23: After refmac, R = 0.2104 (Rfree = 0.000) for 3325 atoms. Found 8 (16 requested) and removed 20 (14 requested) atoms. Cycle 24: After refmac, R = 0.2105 (Rfree = 0.000) for 3310 atoms. Found 7 (16 requested) and removed 15 (14 requested) atoms. Cycle 25: After refmac, R = 0.2056 (Rfree = 0.000) for 3301 atoms. Found 5 (15 requested) and removed 15 (14 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.12 2.92 Search for helices and strands: 0 residues in 0 chains, 3395 seeds are put forward NCS extension: 29 residues added (47 deleted due to clashes), 3424 seeds are put forward Round 1: 323 peptides, 35 chains. Longest chain 21 peptides. Score 0.668 Round 2: 347 peptides, 29 chains. Longest chain 35 peptides. Score 0.754 Round 3: 341 peptides, 29 chains. Longest chain 30 peptides. Score 0.745 Round 4: 329 peptides, 29 chains. Longest chain 28 peptides. Score 0.727 Round 5: 338 peptides, 35 chains. Longest chain 27 peptides. Score 0.695 Taking the results from Round 2 Chains 32, Residues 318, Estimated correctness of the model 75.8 % 9 chains (140 residues) have been docked in sequence Building loops using Loopy2018 32 chains (318 residues) following loop building 9 chains (140 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 9162 reflections ( 99.84 % complete ) and 5809 restraints for refining 3374 atoms. 3983 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2317 (Rfree = 0.000) for 3374 atoms. Found 12 (15 requested) and removed 27 (15 requested) atoms. Cycle 27: After refmac, R = 0.2127 (Rfree = 0.000) for 3351 atoms. Found 8 (15 requested) and removed 16 (15 requested) atoms. Cycle 28: After refmac, R = 0.2075 (Rfree = 0.000) for 3334 atoms. Found 4 (14 requested) and removed 15 (14 requested) atoms. Cycle 29: After refmac, R = 0.2265 (Rfree = 0.000) for 3316 atoms. Found 8 (14 requested) and removed 14 (14 requested) atoms. Cycle 30: After refmac, R = 0.2403 (Rfree = 0.000) for 3308 atoms. Found 14 (14 requested) and removed 17 (14 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.07 2.87 Search for helices and strands: 0 residues in 0 chains, 3394 seeds are put forward NCS extension: 22 residues added (3 deleted due to clashes), 3416 seeds are put forward Round 1: 319 peptides, 37 chains. Longest chain 19 peptides. Score 0.643 Round 2: 332 peptides, 32 chains. Longest chain 24 peptides. Score 0.709 Round 3: 326 peptides, 37 chains. Longest chain 21 peptides. Score 0.657 Round 4: 338 peptides, 35 chains. Longest chain 32 peptides. Score 0.695 Round 5: 338 peptides, 33 chains. Longest chain 33 peptides. Score 0.711 Taking the results from Round 5 Chains 37, Residues 305, Estimated correctness of the model 67.5 % 6 chains (107 residues) have been docked in sequence Building loops using Loopy2018 37 chains (305 residues) following loop building 6 chains (107 residues) in sequence following loop building ------------------------------------------------------ 9162 reflections ( 99.84 % complete ) and 6202 restraints for refining 3375 atoms. 4602 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2408 (Rfree = 0.000) for 3375 atoms. Found 12 (15 requested) and removed 25 (15 requested) atoms. Cycle 32: After refmac, R = 0.2216 (Rfree = 0.000) for 3350 atoms. Found 4 (15 requested) and removed 16 (15 requested) atoms. Cycle 33: After refmac, R = 0.2133 (Rfree = 0.000) for 3333 atoms. Found 3 (14 requested) and removed 15 (14 requested) atoms. Cycle 34: After refmac, R = 0.2295 (Rfree = 0.000) for 3321 atoms. Found 14 (14 requested) and removed 14 (14 requested) atoms. Cycle 35: After refmac, R = 0.2084 (Rfree = 0.000) for 3316 atoms. Found 5 (14 requested) and removed 15 (14 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.08 2.88 Search for helices and strands: 0 residues in 0 chains, 3398 seeds are put forward NCS extension: 20 residues added (26 deleted due to clashes), 3418 seeds are put forward Round 1: 311 peptides, 35 chains. Longest chain 27 peptides. Score 0.646 Round 2: 325 peptides, 31 chains. Longest chain 32 peptides. Score 0.705 Round 3: 325 peptides, 28 chains. Longest chain 51 peptides. Score 0.729 Round 4: 327 peptides, 33 chains. Longest chain 32 peptides. Score 0.692 Round 5: 340 peptides, 34 chains. Longest chain 26 peptides. Score 0.706 Taking the results from Round 3 Chains 31, Residues 297, Estimated correctness of the model 71.1 % 9 chains (122 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 61 A and 70 A 29 chains (300 residues) following loop building 8 chains (130 residues) in sequence following loop building ------------------------------------------------------ 9162 reflections ( 99.84 % complete ) and 6058 restraints for refining 3375 atoms. 4431 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2456 (Rfree = 0.000) for 3375 atoms. Found 15 (15 requested) and removed 35 (15 requested) atoms. Cycle 37: After refmac, R = 0.2251 (Rfree = 0.000) for 3349 atoms. Found 9 (15 requested) and removed 18 (15 requested) atoms. Cycle 38: After refmac, R = 0.2171 (Rfree = 0.000) for 3339 atoms. Found 3 (14 requested) and removed 16 (14 requested) atoms. Cycle 39: After refmac, R = 0.2183 (Rfree = 0.000) for 3323 atoms. Found 2 (14 requested) and removed 15 (14 requested) atoms. Cycle 40: After refmac, R = 0.2512 (Rfree = 0.000) for 3309 atoms. Found 14 (14 requested) and removed 16 (14 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.08 2.88 Search for helices and strands: 0 residues in 0 chains, 3420 seeds are put forward NCS extension: 36 residues added (8 deleted due to clashes), 3456 seeds are put forward Round 1: 304 peptides, 40 chains. Longest chain 25 peptides. Score 0.584 Round 2: 324 peptides, 31 chains. Longest chain 27 peptides. Score 0.703 Round 3: 306 peptides, 33 chains. Longest chain 25 peptides. Score 0.654 Round 4: 319 peptides, 34 chains. Longest chain 27 peptides. Score 0.670 Round 5: 303 peptides, 36 chains. Longest chain 22 peptides. Score 0.620 Taking the results from Round 2 Chains 33, Residues 293, Estimated correctness of the model 65.8 % 8 chains (123 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 45 C and 50 C 32 chains (297 residues) following loop building 7 chains (127 residues) in sequence following loop building ------------------------------------------------------ 9162 reflections ( 99.84 % complete ) and 5978 restraints for refining 3375 atoms. 4311 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2411 (Rfree = 0.000) for 3375 atoms. Found 15 (15 requested) and removed 27 (15 requested) atoms. Cycle 42: After refmac, R = 0.2324 (Rfree = 0.000) for 3352 atoms. Found 7 (15 requested) and removed 15 (15 requested) atoms. Cycle 43: After refmac, R = 0.2297 (Rfree = 0.000) for 3336 atoms. Found 7 (15 requested) and removed 17 (15 requested) atoms. Cycle 44: After refmac, R = 0.2271 (Rfree = 0.000) for 3323 atoms. Found 2 (14 requested) and removed 14 (14 requested) atoms. Cycle 45: After refmac, R = 0.2280 (Rfree = 0.000) for 3311 atoms. Found 6 (14 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.04 2.84 Search for helices and strands: 0 residues in 0 chains, 3381 seeds are put forward NCS extension: 29 residues added (24 deleted due to clashes), 3410 seeds are put forward Round 1: 264 peptides, 36 chains. Longest chain 16 peptides. Score 0.532 Round 2: 298 peptides, 36 chains. Longest chain 20 peptides. Score 0.610 Round 3: 312 peptides, 34 chains. Longest chain 24 peptides. Score 0.657 Round 4: 323 peptides, 32 chains. Longest chain 24 peptides. Score 0.694 Round 5: 323 peptides, 33 chains. Longest chain 33 peptides. Score 0.685 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 36, Residues 291, Estimated correctness of the model 63.9 % 4 chains (55 residues) have been docked in sequence Sequence coverage is 18 % Consider running further cycles of model building using 2otm-3_warpNtrace.pdb as input Building loops using Loopy2018 36 chains (291 residues) following loop building 4 chains (55 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 9162 reflections ( 99.84 % complete ) and 6768 restraints for refining 3374 atoms. 5421 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2572 (Rfree = 0.000) for 3374 atoms. Found 0 (15 requested) and removed 14 (15 requested) atoms. Cycle 47: After refmac, R = 0.2516 (Rfree = 0.000) for 3355 atoms. Found 0 (15 requested) and removed 3 (15 requested) atoms. Cycle 48: After refmac, R = 0.2527 (Rfree = 0.000) for 3351 atoms. Found 0 (15 requested) and removed 9 (15 requested) atoms. Cycle 49: After refmac, R = 0.2479 (Rfree = 0.000) for 3340 atoms. TimeTaking 61.73