Mon 24 Dec 00:20:31 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 2itb-2.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2itb-2.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2itb-2.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2itb-2.0-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/2itb-2.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2itb-2.0-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 00:20:36 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/2itb-2.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2itb-2.0-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 326 and 0 Target number of residues in the AU: 326 Target solvent content: 0.5125 Checking the provided sequence file Detected sequence length: 206 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 412 Adjusted target solvent content: 0.38 Input MTZ file: 2itb-2.0-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: 19 Cell parameters: 61.232 70.168 84.235 90.000 90.000 90.000 Input sequence file: 2itb-2.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 3296 target number of atoms Had to go as low as 0.45 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 1 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 53.913 2.050 Wilson plot Bfac: 26.09 23366 reflections ( 99.87 % complete ) and 0 restraints for refining 3635 atoms. Observations/parameters ratio is 1.61 ------------------------------------------------------ Starting model: R = 0.3368 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2842 (Rfree = 0.000) for 3635 atoms. Found 56 (116 requested) and removed 62 (58 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.17 2.55 NCS extension: 0 residues added, 3629 seeds are put forward Round 1: 271 peptides, 36 chains. Longest chain 19 peptides. Score 0.670 Round 2: 326 peptides, 23 chains. Longest chain 37 peptides. Score 0.875 Round 3: 339 peptides, 15 chains. Longest chain 70 peptides. Score 0.924 Round 4: 339 peptides, 20 chains. Longest chain 47 peptides. Score 0.902 Round 5: 352 peptides, 10 chains. Longest chain 103 peptides. Score 0.949 Taking the results from Round 5 Chains 13, Residues 342, Estimated correctness of the model 99.7 % 8 chains (316 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 89 A and 92 A Built loop between residues 108 A and 113 A Built loop between residues 108 B and 111 B Built loop between residues 160 B and 165 B 8 chains (353 residues) following loop building 4 chains (328 residues) in sequence following loop building ------------------------------------------------------ 23366 reflections ( 99.87 % complete ) and 3752 restraints for refining 3336 atoms. 1023 conditional restraints added. Observations/parameters ratio is 1.75 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2939 (Rfree = 0.000) for 3336 atoms. Found 62 (106 requested) and removed 59 (53 requested) atoms. Cycle 2: After refmac, R = 0.2692 (Rfree = 0.000) for 3314 atoms. Found 52 (104 requested) and removed 53 (53 requested) atoms. Cycle 3: After refmac, R = 0.2531 (Rfree = 0.000) for 3299 atoms. Found 39 (101 requested) and removed 52 (52 requested) atoms. Cycle 4: After refmac, R = 0.2441 (Rfree = 0.000) for 3277 atoms. Found 35 (98 requested) and removed 28 (52 requested) atoms. Cycle 5: After refmac, R = 0.2371 (Rfree = 0.000) for 3271 atoms. Found 28 (96 requested) and removed 19 (52 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.12 2.50 NCS extension: 7 residues added (5 deleted due to clashes), 3292 seeds are put forward Round 1: 365 peptides, 8 chains. Longest chain 92 peptides. Score 0.960 Round 2: 369 peptides, 9 chains. Longest chain 102 peptides. Score 0.959 Round 3: 369 peptides, 8 chains. Longest chain 101 peptides. Score 0.962 Round 4: 369 peptides, 10 chains. Longest chain 101 peptides. Score 0.956 Round 5: 369 peptides, 10 chains. Longest chain 101 peptides. Score 0.956 Taking the results from Round 3 Chains 10, Residues 361, Estimated correctness of the model 99.8 % 6 chains (342 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 107 A and 113 A Built loop between residues 136 A and 144 A Built loop between residues 107 B and 110 B 7 chains (375 residues) following loop building 3 chains (356 residues) in sequence following loop building ------------------------------------------------------ 23366 reflections ( 99.87 % complete ) and 3546 restraints for refining 3381 atoms. 590 conditional restraints added. Observations/parameters ratio is 1.73 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2470 (Rfree = 0.000) for 3381 atoms. Found 56 (96 requested) and removed 59 (53 requested) atoms. Cycle 7: After refmac, R = 0.2290 (Rfree = 0.000) for 3377 atoms. Found 40 (94 requested) and removed 51 (53 requested) atoms. Cycle 8: After refmac, R = 0.2214 (Rfree = 0.000) for 3363 atoms. Found 45 (92 requested) and removed 14 (53 requested) atoms. Cycle 9: After refmac, R = 0.2121 (Rfree = 0.000) for 3388 atoms. Found 37 (93 requested) and removed 18 (54 requested) atoms. Cycle 10: After refmac, R = 0.2084 (Rfree = 0.000) for 3400 atoms. Found 39 (93 requested) and removed 17 (54 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.11 2.48 NCS extension: 6 residues added (36 deleted due to clashes), 3428 seeds are put forward Round 1: 373 peptides, 8 chains. Longest chain 92 peptides. Score 0.963 Round 2: 377 peptides, 7 chains. Longest chain 103 peptides. Score 0.967 Round 3: 376 peptides, 8 chains. Longest chain 101 peptides. Score 0.964 Round 4: 376 peptides, 10 chains. Longest chain 90 peptides. Score 0.958 Round 5: 380 peptides, 5 chains. Longest chain 103 peptides. Score 0.973 Taking the results from Round 5 Chains 6, Residues 375, Estimated correctness of the model 99.9 % 5 chains (372 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 107 A and 110 A Built loop between residues 105 B and 111 B Built loop between residues 138 B and 146 B 2 chains (386 residues) following loop building 2 chains (386 residues) in sequence following loop building ------------------------------------------------------ 23366 reflections ( 99.87 % complete ) and 3441 restraints for refining 3476 atoms. 314 conditional restraints added. Observations/parameters ratio is 1.68 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2262 (Rfree = 0.000) for 3476 atoms. Found 54 (95 requested) and removed 60 (55 requested) atoms. Cycle 12: After refmac, R = 0.2107 (Rfree = 0.000) for 3465 atoms. Found 41 (92 requested) and removed 55 (55 requested) atoms. Cycle 13: After refmac, R = 0.2025 (Rfree = 0.000) for 3447 atoms. Found 41 (90 requested) and removed 33 (55 requested) atoms. Cycle 14: After refmac, R = 0.1974 (Rfree = 0.000) for 3451 atoms. Found 45 (88 requested) and removed 33 (55 requested) atoms. Cycle 15: After refmac, R = 0.1932 (Rfree = 0.000) for 3460 atoms. Found 42 (86 requested) and removed 19 (55 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.10 2.47 NCS extension: 0 residues added, 3484 seeds are put forward Round 1: 383 peptides, 6 chains. Longest chain 102 peptides. Score 0.971 Round 2: 384 peptides, 4 chains. Longest chain 122 peptides. Score 0.976 Round 3: 382 peptides, 6 chains. Longest chain 100 peptides. Score 0.971 Round 4: 382 peptides, 7 chains. Longest chain 103 peptides. Score 0.968 Round 5: 376 peptides, 9 chains. Longest chain 91 peptides. Score 0.961 Taking the results from Round 2 Chains 4, Residues 380, Estimated correctness of the model 99.9 % 4 chains (380 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 77 A and 80 A Built loop between residues 107 B and 110 B 2 chains (384 residues) following loop building 2 chains (384 residues) in sequence following loop building ------------------------------------------------------ 23366 reflections ( 99.87 % complete ) and 3412 restraints for refining 3467 atoms. 302 conditional restraints added. Observations/parameters ratio is 1.68 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2099 (Rfree = 0.000) for 3467 atoms. Found 50 (86 requested) and removed 57 (55 requested) atoms. Cycle 17: After refmac, R = 0.1982 (Rfree = 0.000) for 3455 atoms. Found 44 (84 requested) and removed 39 (55 requested) atoms. Cycle 18: After refmac, R = 0.1946 (Rfree = 0.000) for 3454 atoms. Found 39 (81 requested) and removed 27 (55 requested) atoms. Cycle 19: After refmac, R = 0.1905 (Rfree = 0.000) for 3463 atoms. Found 31 (79 requested) and removed 32 (55 requested) atoms. Cycle 20: After refmac, R = 0.1897 (Rfree = 0.000) for 3459 atoms. Found 44 (77 requested) and removed 28 (55 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.12 2.50 NCS extension: 0 residues added, 3476 seeds are put forward Round 1: 385 peptides, 5 chains. Longest chain 102 peptides. Score 0.974 Round 2: 381 peptides, 8 chains. Longest chain 91 peptides. Score 0.965 Round 3: 383 peptides, 5 chains. Longest chain 102 peptides. Score 0.974 Round 4: 382 peptides, 8 chains. Longest chain 103 peptides. Score 0.965 Round 5: 377 peptides, 7 chains. Longest chain 92 peptides. Score 0.967 Taking the results from Round 3 Chains 6, Residues 378, Estimated correctness of the model 99.9 % 5 chains (376 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 105 A and 109 A Built loop between residues 71 B and 77 B Built loop between residues 107 B and 110 B 2 chains (386 residues) following loop building 2 chains (386 residues) in sequence following loop building ------------------------------------------------------ 23366 reflections ( 99.87 % complete ) and 3397 restraints for refining 3462 atoms. 270 conditional restraints added. Observations/parameters ratio is 1.69 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2093 (Rfree = 0.000) for 3462 atoms. Found 64 (75 requested) and removed 59 (55 requested) atoms. Cycle 22: After refmac, R = 0.1970 (Rfree = 0.000) for 3466 atoms. Found 36 (73 requested) and removed 36 (55 requested) atoms. Cycle 23: After refmac, R = 0.1921 (Rfree = 0.000) for 3466 atoms. Found 29 (70 requested) and removed 27 (55 requested) atoms. Cycle 24: After refmac, R = 0.1888 (Rfree = 0.000) for 3465 atoms. Found 40 (68 requested) and removed 27 (55 requested) atoms. Cycle 25: After refmac, R = 0.1864 (Rfree = 0.000) for 3475 atoms. Found 45 (67 requested) and removed 24 (55 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.11 2.48 NCS extension: 0 residues added, 3498 seeds are put forward Round 1: 384 peptides, 6 chains. Longest chain 102 peptides. Score 0.971 Round 2: 386 peptides, 4 chains. Longest chain 122 peptides. Score 0.977 Round 3: 382 peptides, 7 chains. Longest chain 90 peptides. Score 0.968 Round 4: 386 peptides, 4 chains. Longest chain 194 peptides. Score 0.977 Round 5: 381 peptides, 9 chains. Longest chain 103 peptides. Score 0.962 Taking the results from Round 4 Chains 4, Residues 382, Estimated correctness of the model 99.9 % 3 chains (322 residues) have been docked in sequence Building loops using Loopy2018 4 chains (382 residues) following loop building 3 chains (322 residues) in sequence following loop building ------------------------------------------------------ 23366 reflections ( 99.87 % complete ) and 3869 restraints for refining 3472 atoms. 1000 conditional restraints added. Observations/parameters ratio is 1.68 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2272 (Rfree = 0.000) for 3472 atoms. Found 64 (64 requested) and removed 74 (55 requested) atoms. Cycle 27: After refmac, R = 0.2093 (Rfree = 0.000) for 3457 atoms. Found 40 (62 requested) and removed 55 (55 requested) atoms. Cycle 28: After refmac, R = 0.1993 (Rfree = 0.000) for 3439 atoms. Found 31 (59 requested) and removed 20 (54 requested) atoms. Cycle 29: After refmac, R = 0.1945 (Rfree = 0.000) for 3445 atoms. Found 29 (57 requested) and removed 18 (55 requested) atoms. Cycle 30: After refmac, R = 0.1911 (Rfree = 0.000) for 3451 atoms. Found 26 (55 requested) and removed 16 (55 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.11 2.48 NCS extension: 36 residues added (200 deleted due to clashes), 3497 seeds are put forward Round 1: 382 peptides, 7 chains. Longest chain 102 peptides. Score 0.968 Round 2: 381 peptides, 6 chains. Longest chain 101 peptides. Score 0.971 Round 3: 380 peptides, 8 chains. Longest chain 103 peptides. Score 0.965 Round 4: 382 peptides, 8 chains. Longest chain 90 peptides. Score 0.965 Round 5: 377 peptides, 9 chains. Longest chain 86 peptides. Score 0.961 Taking the results from Round 2 Chains 6, Residues 375, Estimated correctness of the model 99.9 % 6 chains (375 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 71 A and 74 A Built loop between residues 108 A and 111 A Built loop between residues 107 B and 112 B Built loop between residues 161 B and 165 B 2 chains (386 residues) following loop building 2 chains (386 residues) in sequence following loop building ------------------------------------------------------ 23366 reflections ( 99.87 % complete ) and 3409 restraints for refining 3476 atoms. 282 conditional restraints added. Observations/parameters ratio is 1.68 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2090 (Rfree = 0.000) for 3476 atoms. Found 55 (55 requested) and removed 59 (55 requested) atoms. Cycle 32: After refmac, R = 0.1943 (Rfree = 0.000) for 3468 atoms. Found 44 (55 requested) and removed 36 (55 requested) atoms. Cycle 33: After refmac, R = 0.1902 (Rfree = 0.000) for 3472 atoms. Found 36 (55 requested) and removed 30 (55 requested) atoms. Cycle 34: After refmac, R = 0.1860 (Rfree = 0.000) for 3477 atoms. Found 38 (55 requested) and removed 25 (55 requested) atoms. Cycle 35: After refmac, R = 0.1845 (Rfree = 0.000) for 3488 atoms. Found 37 (55 requested) and removed 33 (55 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.11 2.48 NCS extension: 0 residues added, 3492 seeds are put forward Round 1: 384 peptides, 6 chains. Longest chain 102 peptides. Score 0.971 Round 2: 387 peptides, 3 chains. Longest chain 194 peptides. Score 0.979 Round 3: 382 peptides, 6 chains. Longest chain 113 peptides. Score 0.971 Round 4: 380 peptides, 10 chains. Longest chain 81 peptides. Score 0.959 Round 5: 378 peptides, 9 chains. Longest chain 90 peptides. Score 0.962 Taking the results from Round 2 Chains 3, Residues 384, Estimated correctness of the model 99.9 % 3 chains (384 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 107 B and 110 B 2 chains (386 residues) following loop building 2 chains (386 residues) in sequence following loop building ------------------------------------------------------ 23366 reflections ( 99.87 % complete ) and 3420 restraints for refining 3470 atoms. 293 conditional restraints added. Observations/parameters ratio is 1.68 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2017 (Rfree = 0.000) for 3470 atoms. Found 55 (55 requested) and removed 57 (55 requested) atoms. Cycle 37: After refmac, R = 0.1904 (Rfree = 0.000) for 3462 atoms. Found 43 (55 requested) and removed 44 (55 requested) atoms. Cycle 38: After refmac, R = 0.1879 (Rfree = 0.000) for 3458 atoms. Found 39 (55 requested) and removed 28 (55 requested) atoms. Cycle 39: After refmac, R = 0.1830 (Rfree = 0.000) for 3468 atoms. Found 35 (55 requested) and removed 31 (55 requested) atoms. Cycle 40: After refmac, R = 0.1822 (Rfree = 0.000) for 3471 atoms. Found 37 (55 requested) and removed 23 (55 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.11 2.48 NCS extension: 0 residues added, 3485 seeds are put forward Round 1: 384 peptides, 6 chains. Longest chain 102 peptides. Score 0.971 Round 2: 386 peptides, 4 chains. Longest chain 102 peptides. Score 0.977 Round 3: 379 peptides, 8 chains. Longest chain 103 peptides. Score 0.965 Round 4: 384 peptides, 6 chains. Longest chain 101 peptides. Score 0.971 Round 5: 379 peptides, 10 chains. Longest chain 78 peptides. Score 0.959 Taking the results from Round 2 Chains 4, Residues 382, Estimated correctness of the model 99.9 % 4 chains (382 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 108 A and 111 A Built loop between residues 107 B and 110 B 2 chains (386 residues) following loop building 2 chains (386 residues) in sequence following loop building ------------------------------------------------------ 23366 reflections ( 99.87 % complete ) and 3387 restraints for refining 3457 atoms. 260 conditional restraints added. Observations/parameters ratio is 1.69 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1998 (Rfree = 0.000) for 3457 atoms. Found 55 (55 requested) and removed 57 (55 requested) atoms. Cycle 42: After refmac, R = 0.1902 (Rfree = 0.000) for 3452 atoms. Found 48 (55 requested) and removed 26 (55 requested) atoms. Cycle 43: After refmac, R = 0.1852 (Rfree = 0.000) for 3473 atoms. Found 37 (55 requested) and removed 27 (55 requested) atoms. Cycle 44: After refmac, R = 0.1826 (Rfree = 0.000) for 3478 atoms. Found 45 (55 requested) and removed 21 (55 requested) atoms. Cycle 45: After refmac, R = 0.1806 (Rfree = 0.000) for 3499 atoms. Found 41 (55 requested) and removed 30 (55 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.11 2.48 NCS extension: 0 residues added, 3512 seeds are put forward Round 1: 385 peptides, 5 chains. Longest chain 102 peptides. Score 0.974 Round 2: 383 peptides, 6 chains. Longest chain 103 peptides. Score 0.971 Round 3: 384 peptides, 6 chains. Longest chain 103 peptides. Score 0.971 Round 4: 380 peptides, 9 chains. Longest chain 90 peptides. Score 0.962 Round 5: 381 peptides, 9 chains. Longest chain 90 peptides. Score 0.962 Taking the results from Round 1 Last building cycle: Chain fragments will be rearranged Chains 5, Residues 380, Estimated correctness of the model 99.9 % 5 chains (380 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 107 A and 110 A Built loop between residues 71 B and 74 B Built loop between residues 107 B and 110 B 2 chains (386 residues) following loop building 2 chains (386 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 23366 reflections ( 99.87 % complete ) and 3127 restraints for refining 3067 atoms. Observations/parameters ratio is 1.90 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2555 (Rfree = 0.000) for 3067 atoms. Found 34 (48 requested) and removed 0 (48 requested) atoms. Cycle 47: After refmac, R = 0.2380 (Rfree = 0.000) for 3067 atoms. Found 16 (49 requested) and removed 2 (49 requested) atoms. Cycle 48: After refmac, R = 0.2281 (Rfree = 0.000) for 3067 atoms. Found 5 (49 requested) and removed 2 (49 requested) atoms. Cycle 49: After refmac, R = 0.2273 (Rfree = 0.000) for 3067 atoms. TimeTaking 43.4