Sun 23 Dec 23:43:57 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 1vmf-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vmf-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vmf-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vmf-3.2-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/1vmf-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vmf-3.2-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 ============================================================ Sun 23 Dec 23:44:02 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/1vmf-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vmf-3.2-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 335 and 0 Target number of residues in the AU: 335 Target solvent content: 0.6012 Checking the provided sequence file Detected sequence length: 145 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 3 Adjusted target number of residues: 435 Adjusted target solvent content: 0.48 Input MTZ file: 1vmf-3.2-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: 57.443 58.601 135.061 90.000 90.000 90.000 Input sequence file: 1vmf-3.2-parrot-mrncs.fasta_lf Building free atoms model in initial map for 3480 target number of atoms Had to go as low as 0.65 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: 67.531 3.200 Wilson plot Bfac: 53.00 7960 reflections ( 99.76 % complete ) and 0 restraints for refining 3864 atoms. Observations/parameters ratio is 0.52 ------------------------------------------------------ Starting model: R = 0.2931 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2792 (Rfree = 0.000) for 3864 atoms. Found 34 (34 requested) and removed 28 (17 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.05 3.13 Search for helices and strands: 0 residues in 0 chains, 3933 seeds are put forward NCS extension: 0 residues added, 3933 seeds are put forward Round 1: 258 peptides, 46 chains. Longest chain 11 peptides. Score 0.439 Round 2: 284 peptides, 35 chains. Longest chain 18 peptides. Score 0.646 Round 3: 324 peptides, 32 chains. Longest chain 27 peptides. Score 0.754 Round 4: 328 peptides, 32 chains. Longest chain 30 peptides. Score 0.760 Round 5: 335 peptides, 28 chains. Longest chain 39 peptides. Score 0.800 Taking the results from Round 5 Chains 30, Residues 307, Estimated correctness of the model 83.4 % 4 chains (103 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 69 B and 80 B 29 chains (317 residues) following loop building 3 chains (113 residues) in sequence following loop building ------------------------------------------------------ 7960 reflections ( 99.76 % complete ) and 5364 restraints for refining 3179 atoms. 3653 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2704 (Rfree = 0.000) for 3179 atoms. Found 27 (28 requested) and removed 35 (14 requested) atoms. Cycle 2: After refmac, R = 0.2491 (Rfree = 0.000) for 3133 atoms. Found 13 (27 requested) and removed 19 (14 requested) atoms. Cycle 3: After refmac, R = 0.2404 (Rfree = 0.000) for 3114 atoms. Found 11 (27 requested) and removed 17 (14 requested) atoms. Cycle 4: After refmac, R = 0.2329 (Rfree = 0.000) for 3101 atoms. Found 8 (25 requested) and removed 16 (13 requested) atoms. Cycle 5: After refmac, R = 0.2280 (Rfree = 0.000) for 3084 atoms. Found 10 (25 requested) and removed 15 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.99 3.07 Search for helices and strands: 0 residues in 0 chains, 3180 seeds are put forward NCS extension: 65 residues added (49 deleted due to clashes), 3245 seeds are put forward Round 1: 327 peptides, 34 chains. Longest chain 40 peptides. Score 0.743 Round 2: 337 peptides, 27 chains. Longest chain 42 peptides. Score 0.809 Round 3: 328 peptides, 28 chains. Longest chain 43 peptides. Score 0.790 Round 4: 336 peptides, 28 chains. Longest chain 46 peptides. Score 0.801 Round 5: 331 peptides, 30 chains. Longest chain 36 peptides. Score 0.780 Taking the results from Round 2 Chains 29, Residues 310, Estimated correctness of the model 84.8 % 4 chains (101 residues) have been docked in sequence Building loops using Loopy2018 29 chains (310 residues) following loop building 4 chains (101 residues) in sequence following loop building ------------------------------------------------------ 7960 reflections ( 99.76 % complete ) and 5779 restraints for refining 3177 atoms. 4161 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2550 (Rfree = 0.000) for 3177 atoms. Found 17 (25 requested) and removed 49 (14 requested) atoms. Cycle 7: After refmac, R = 0.2317 (Rfree = 0.000) for 3133 atoms. Found 12 (25 requested) and removed 25 (14 requested) atoms. Cycle 8: After refmac, R = 0.2303 (Rfree = 0.000) for 3116 atoms. Found 3 (24 requested) and removed 15 (14 requested) atoms. Cycle 9: After refmac, R = 0.2161 (Rfree = 0.000) for 3095 atoms. Found 10 (23 requested) and removed 14 (13 requested) atoms. Cycle 10: After refmac, R = 0.2102 (Rfree = 0.000) for 3085 atoms. Found 3 (22 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.98 3.06 Search for helices and strands: 0 residues in 0 chains, 3157 seeds are put forward NCS extension: 58 residues added (28 deleted due to clashes), 3215 seeds are put forward Round 1: 322 peptides, 33 chains. Longest chain 31 peptides. Score 0.742 Round 2: 332 peptides, 28 chains. Longest chain 35 peptides. Score 0.796 Round 3: 329 peptides, 27 chains. Longest chain 51 peptides. Score 0.799 Round 4: 338 peptides, 29 chains. Longest chain 35 peptides. Score 0.797 Round 5: 328 peptides, 30 chains. Longest chain 25 peptides. Score 0.775 Taking the results from Round 3 Chains 28, Residues 302, Estimated correctness of the model 83.3 % 3 chains (55 residues) have been docked in sequence Building loops using Loopy2018 28 chains (302 residues) following loop building 3 chains (55 residues) in sequence following loop building ------------------------------------------------------ 7960 reflections ( 99.76 % complete ) and 6384 restraints for refining 3177 atoms. 5017 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2458 (Rfree = 0.000) for 3177 atoms. Found 17 (22 requested) and removed 22 (14 requested) atoms. Cycle 12: After refmac, R = 0.2418 (Rfree = 0.000) for 3168 atoms. Found 12 (22 requested) and removed 17 (14 requested) atoms. Cycle 13: After refmac, R = 0.2222 (Rfree = 0.000) for 3155 atoms. Found 11 (21 requested) and removed 15 (14 requested) atoms. Cycle 14: After refmac, R = 0.2292 (Rfree = 0.000) for 3149 atoms. Found 8 (21 requested) and removed 15 (14 requested) atoms. Cycle 15: After refmac, R = 0.2207 (Rfree = 0.000) for 3138 atoms. Found 6 (20 requested) and removed 15 (14 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.98 3.06 Search for helices and strands: 0 residues in 0 chains, 3190 seeds are put forward NCS extension: 35 residues added (27 deleted due to clashes), 3225 seeds are put forward Round 1: 310 peptides, 34 chains. Longest chain 32 peptides. Score 0.711 Round 2: 330 peptides, 29 chains. Longest chain 34 peptides. Score 0.786 Round 3: 341 peptides, 29 chains. Longest chain 44 peptides. Score 0.801 Round 4: 331 peptides, 27 chains. Longest chain 33 peptides. Score 0.801 Round 5: 322 peptides, 27 chains. Longest chain 47 peptides. Score 0.788 Taking the results from Round 4 Chains 31, Residues 304, Estimated correctness of the model 83.6 % 3 chains (65 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 112 A and 122 A 31 chains (306 residues) following loop building 2 chains (74 residues) in sequence following loop building ------------------------------------------------------ 7960 reflections ( 99.76 % complete ) and 5857 restraints for refining 3176 atoms. 4390 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2518 (Rfree = 0.000) for 3176 atoms. Found 20 (20 requested) and removed 25 (14 requested) atoms. Cycle 17: After refmac, R = 0.2324 (Rfree = 0.000) for 3160 atoms. Found 14 (19 requested) and removed 19 (14 requested) atoms. Cycle 18: After refmac, R = 0.2299 (Rfree = 0.000) for 3153 atoms. Found 7 (18 requested) and removed 14 (14 requested) atoms. Cycle 19: After refmac, R = 0.2390 (Rfree = 0.000) for 3142 atoms. Found 17 (18 requested) and removed 17 (14 requested) atoms. Cycle 20: After refmac, R = 0.2473 (Rfree = 0.000) for 3139 atoms. Found 17 (17 requested) and removed 16 (14 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.03 3.11 Search for helices and strands: 0 residues in 0 chains, 3209 seeds are put forward NCS extension: 19 residues added (3 deleted due to clashes), 3228 seeds are put forward Round 1: 298 peptides, 37 chains. Longest chain 31 peptides. Score 0.657 Round 2: 324 peptides, 36 chains. Longest chain 17 peptides. Score 0.720 Round 3: 308 peptides, 31 chains. Longest chain 33 peptides. Score 0.734 Round 4: 311 peptides, 34 chains. Longest chain 32 peptides. Score 0.713 Round 5: 319 peptides, 33 chains. Longest chain 22 peptides. Score 0.737 Taking the results from Round 5 Chains 35, Residues 286, Estimated correctness of the model 72.6 % 3 chains (43 residues) have been docked in sequence Building loops using Loopy2018 35 chains (286 residues) following loop building 3 chains (43 residues) in sequence following loop building ------------------------------------------------------ 7960 reflections ( 99.76 % complete ) and 6350 restraints for refining 3177 atoms. 5062 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2482 (Rfree = 0.000) for 3177 atoms. Found 16 (17 requested) and removed 19 (14 requested) atoms. Cycle 22: After refmac, R = 0.2329 (Rfree = 0.000) for 3163 atoms. Found 11 (16 requested) and removed 21 (14 requested) atoms. Cycle 23: After refmac, R = 0.1996 (Rfree = 0.000) for 3147 atoms. Found 3 (16 requested) and removed 15 (14 requested) atoms. Cycle 24: After refmac, R = 0.2032 (Rfree = 0.000) for 3134 atoms. Found 6 (15 requested) and removed 14 (14 requested) atoms. Cycle 25: After refmac, R = 0.1943 (Rfree = 0.000) for 3126 atoms. Found 9 (15 requested) and removed 15 (14 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.00 3.08 Search for helices and strands: 0 residues in 0 chains, 3204 seeds are put forward NCS extension: 24 residues added (5 deleted due to clashes), 3228 seeds are put forward Round 1: 295 peptides, 41 chains. Longest chain 25 peptides. Score 0.608 Round 2: 287 peptides, 38 chains. Longest chain 25 peptides. Score 0.621 Round 3: 279 peptides, 31 chains. Longest chain 22 peptides. Score 0.676 Round 4: 296 peptides, 29 chains. Longest chain 23 peptides. Score 0.729 Round 5: 305 peptides, 32 chains. Longest chain 25 peptides. Score 0.720 Taking the results from Round 4 Chains 34, Residues 267, Estimated correctness of the model 71.1 % 4 chains (60 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 61 A and 70 A 33 chains (275 residues) following loop building 3 chains (68 residues) in sequence following loop building ------------------------------------------------------ 7960 reflections ( 99.76 % complete ) and 6125 restraints for refining 3177 atoms. 4775 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2355 (Rfree = 0.000) for 3177 atoms. Found 14 (14 requested) and removed 21 (14 requested) atoms. Cycle 27: After refmac, R = 0.2157 (Rfree = 0.000) for 3158 atoms. Found 14 (14 requested) and removed 16 (14 requested) atoms. Cycle 28: After refmac, R = 0.2121 (Rfree = 0.000) for 3148 atoms. Found 4 (14 requested) and removed 15 (14 requested) atoms. Cycle 29: After refmac, R = 0.1993 (Rfree = 0.000) for 3133 atoms. Found 3 (14 requested) and removed 14 (14 requested) atoms. Cycle 30: After refmac, R = 0.1907 (Rfree = 0.000) for 3118 atoms. Found 5 (14 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.01 3.09 Search for helices and strands: 0 residues in 0 chains, 3175 seeds are put forward NCS extension: 30 residues added (5 deleted due to clashes), 3205 seeds are put forward Round 1: 285 peptides, 37 chains. Longest chain 18 peptides. Score 0.627 Round 2: 294 peptides, 32 chains. Longest chain 19 peptides. Score 0.698 Round 3: 293 peptides, 31 chains. Longest chain 31 peptides. Score 0.705 Round 4: 302 peptides, 31 chains. Longest chain 31 peptides. Score 0.723 Round 5: 302 peptides, 29 chains. Longest chain 31 peptides. Score 0.740 Taking the results from Round 5 Chains 29, Residues 273, Estimated correctness of the model 73.2 % 2 chains (41 residues) have been docked in sequence Building loops using Loopy2018 29 chains (273 residues) following loop building 2 chains (41 residues) in sequence following loop building ------------------------------------------------------ 7960 reflections ( 99.76 % complete ) and 6488 restraints for refining 3177 atoms. 5293 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2122 (Rfree = 0.000) for 3177 atoms. Found 11 (14 requested) and removed 17 (14 requested) atoms. Cycle 32: After refmac, R = 0.2083 (Rfree = 0.000) for 3165 atoms. Found 8 (14 requested) and removed 15 (14 requested) atoms. Cycle 33: After refmac, R = 0.1984 (Rfree = 0.000) for 3154 atoms. Found 6 (14 requested) and removed 16 (14 requested) atoms. Cycle 34: After refmac, R = 0.2023 (Rfree = 0.000) for 3142 atoms. Found 6 (14 requested) and removed 14 (14 requested) atoms. Cycle 35: After refmac, R = 0.1954 (Rfree = 0.000) for 3132 atoms. Found 4 (14 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.00 3.08 Search for helices and strands: 0 residues in 0 chains, 3201 seeds are put forward NCS extension: 26 residues added (10 deleted due to clashes), 3227 seeds are put forward Round 1: 249 peptides, 36 chains. Longest chain 19 peptides. Score 0.543 Round 2: 291 peptides, 32 chains. Longest chain 25 peptides. Score 0.692 Round 3: 273 peptides, 33 chains. Longest chain 18 peptides. Score 0.641 Round 4: 283 peptides, 33 chains. Longest chain 18 peptides. Score 0.664 Round 5: 288 peptides, 32 chains. Longest chain 29 peptides. Score 0.685 Taking the results from Round 2 Chains 36, Residues 259, Estimated correctness of the model 63.5 % 2 chains (30 residues) have been docked in sequence ------------------------------------------------------ 7960 reflections ( 99.76 % complete ) and 6669 restraints for refining 3177 atoms. 5563 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2085 (Rfree = 0.000) for 3177 atoms. Found 14 (14 requested) and removed 15 (14 requested) atoms. Cycle 37: After refmac, R = 0.1994 (Rfree = 0.000) for 3172 atoms. Found 10 (14 requested) and removed 15 (14 requested) atoms. Cycle 38: After refmac, R = 0.1898 (Rfree = 0.000) for 3165 atoms. Found 0 (14 requested) and removed 14 (14 requested) atoms. Cycle 39: After refmac, R = 0.1889 (Rfree = 0.000) for 3151 atoms. Found 4 (14 requested) and removed 14 (14 requested) atoms. Cycle 40: After refmac, R = 0.1769 (Rfree = 0.000) for 3141 atoms. Found 6 (14 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.01 3.09 Search for helices and strands: 0 residues in 0 chains, 3210 seeds are put forward NCS extension: 17 residues added (5 deleted due to clashes), 3227 seeds are put forward Round 1: 247 peptides, 35 chains. Longest chain 20 peptides. Score 0.550 Round 2: 281 peptides, 32 chains. Longest chain 29 peptides. Score 0.670 Round 3: 275 peptides, 33 chains. Longest chain 19 peptides. Score 0.646 Round 4: 272 peptides, 29 chains. Longest chain 27 peptides. Score 0.681 Round 5: 274 peptides, 32 chains. Longest chain 26 peptides. Score 0.654 Taking the results from Round 4 Chains 31, Residues 243, Estimated correctness of the model 61.0 % 2 chains (38 residues) have been docked in sequence ------------------------------------------------------ 7960 reflections ( 99.76 % complete ) and 6520 restraints for refining 3177 atoms. 5380 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2280 (Rfree = 0.000) for 3177 atoms. Found 14 (14 requested) and removed 14 (14 requested) atoms. Cycle 42: After refmac, R = 0.2009 (Rfree = 0.000) for 3168 atoms. Found 8 (14 requested) and removed 16 (14 requested) atoms. Cycle 43: After refmac, R = 0.1886 (Rfree = 0.000) for 3159 atoms. Found 4 (14 requested) and removed 17 (14 requested) atoms. Cycle 44: After refmac, R = 0.2022 (Rfree = 0.000) for 3146 atoms. Found 11 (14 requested) and removed 15 (14 requested) atoms. Cycle 45: After refmac, R = 0.1880 (Rfree = 0.000) for 3140 atoms. Found 3 (14 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.98 3.06 Search for helices and strands: 0 residues in 0 chains, 3212 seeds are put forward NCS extension: 17 residues added (4 deleted due to clashes), 3229 seeds are put forward Round 1: 248 peptides, 33 chains. Longest chain 16 peptides. Score 0.578 Round 2: 277 peptides, 29 chains. Longest chain 24 peptides. Score 0.691 Round 3: 262 peptides, 29 chains. Longest chain 21 peptides. Score 0.658 Round 4: 256 peptides, 26 chains. Longest chain 26 peptides. Score 0.676 Round 5: 253 peptides, 30 chains. Longest chain 22 peptides. Score 0.626 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 31, Residues 248, Estimated correctness of the model 63.2 % 3 chains (53 residues) have been docked in sequence Sequence coverage is 21 % Consider running further cycles of model building using 1vmf-3_warpNtrace.pdb as input Building loops using Loopy2018 31 chains (248 residues) following loop building 3 chains (53 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7960 reflections ( 99.76 % complete ) and 6391 restraints for refining 3177 atoms. 5212 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2115 (Rfree = 0.000) for 3177 atoms. Found 0 (14 requested) and removed 13 (14 requested) atoms. Cycle 47: After refmac, R = 0.2094 (Rfree = 0.000) for 3160 atoms. Found 0 (14 requested) and removed 10 (14 requested) atoms. Cycle 48: After refmac, R = 0.2142 (Rfree = 0.000) for 3146 atoms. Found 0 (14 requested) and removed 11 (14 requested) atoms. Cycle 49: After refmac, R = 0.2001 (Rfree = 0.000) for 3130 atoms. TimeTaking 47.88