Sun 23 Dec 23:56:48 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 2pke-1.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2pke-1.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2pke-1.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pke-1.8-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/2pke-1.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pke-1.8-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 23:56:53 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/2pke-1.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pke-1.8-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 424 and 0 Target number of residues in the AU: 424 Target solvent content: 0.4894 Checking the provided sequence file Detected sequence length: 251 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 502 Adjusted target solvent content: 0.40 Input MTZ file: 2pke-1.8-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: 4 Cell parameters: 34.220 107.280 62.650 90.000 102.296 90.000 Input sequence file: 2pke-1.8-parrot-mrncs.fasta_lf Building free atoms model in initial map for 4016 target number of atoms Had to go as low as 0.35 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: 61.213 1.810 Wilson plot Bfac: 21.23 33222 reflections ( 85.82 % complete ) and 0 restraints for refining 4431 atoms. Observations/parameters ratio is 1.87 ------------------------------------------------------ Starting model: R = 0.3142 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2624 (Rfree = 0.000) for 4431 atoms. Found 146 (201 requested) and removed 108 (100 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.99 2.28 NCS extension: 0 residues added, 4469 seeds are put forward Round 1: 335 peptides, 30 chains. Longest chain 36 peptides. Score 0.789 Round 2: 382 peptides, 18 chains. Longest chain 37 peptides. Score 0.903 Round 3: 396 peptides, 13 chains. Longest chain 71 peptides. Score 0.930 Round 4: 411 peptides, 13 chains. Longest chain 51 peptides. Score 0.937 Round 5: 416 peptides, 10 chains. Longest chain 96 peptides. Score 0.948 Taking the results from Round 5 Chains 11, Residues 406, Estimated correctness of the model 99.8 % 9 chains (400 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 115 A and 119 A Built loop between residues 207 A and 218 A Built loop between residues 153 B and 157 B Built loop between residues 174 B and 177 B 6 chains (423 residues) following loop building 5 chains (418 residues) in sequence following loop building ------------------------------------------------------ 33222 reflections ( 85.82 % complete ) and 4103 restraints for refining 3960 atoms. 757 conditional restraints added. Observations/parameters ratio is 2.10 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2897 (Rfree = 0.000) for 3960 atoms. Found 106 (180 requested) and removed 93 (90 requested) atoms. Failed to save intermediate PDB Cycle 2: After refmac, R = 0.2565 (Rfree = 0.000) for 3961 atoms. Found 88 (176 requested) and removed 59 (90 requested) atoms. Cycle 3: After refmac, R = 0.2387 (Rfree = 0.000) for 3970 atoms. Found 73 (174 requested) and removed 25 (90 requested) atoms. Cycle 4: After refmac, R = 0.2278 (Rfree = 0.000) for 4006 atoms. Found 81 (175 requested) and removed 28 (91 requested) atoms. Cycle 5: After refmac, R = 0.2190 (Rfree = 0.000) for 4050 atoms. Found 69 (177 requested) and removed 23 (92 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.90 2.17 NCS extension: 24 residues added (3 deleted due to clashes), 4128 seeds are put forward Round 1: 421 peptides, 7 chains. Longest chain 150 peptides. Score 0.959 Round 2: 424 peptides, 8 chains. Longest chain 128 peptides. Score 0.957 Round 3: 426 peptides, 8 chains. Longest chain 138 peptides. Score 0.957 Round 4: 429 peptides, 7 chains. Longest chain 152 peptides. Score 0.961 Round 5: 430 peptides, 8 chains. Longest chain 153 peptides. Score 0.959 Taking the results from Round 4 Chains 7, Residues 422, Estimated correctness of the model 99.9 % 7 chains (422 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 104 A and 107 A Built loop between residues 208 A and 218 A 5 chains (433 residues) following loop building 5 chains (433 residues) in sequence following loop building ------------------------------------------------------ 33222 reflections ( 85.82 % complete ) and 4077 restraints for refining 4029 atoms. 644 conditional restraints added. Observations/parameters ratio is 2.06 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2291 (Rfree = 0.000) for 4029 atoms. Found 127 (176 requested) and removed 91 (91 requested) atoms. Cycle 7: After refmac, R = 0.2167 (Rfree = 0.000) for 4061 atoms. Found 90 (174 requested) and removed 29 (92 requested) atoms. Cycle 8: After refmac, R = 0.2089 (Rfree = 0.000) for 4120 atoms. Found 76 (176 requested) and removed 31 (93 requested) atoms. Cycle 9: After refmac, R = 0.2036 (Rfree = 0.000) for 4161 atoms. Found 77 (178 requested) and removed 40 (94 requested) atoms. Cycle 10: After refmac, R = 0.2001 (Rfree = 0.000) for 4195 atoms. Found 79 (176 requested) and removed 49 (95 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.90 2.17 NCS extension: 41 residues added (21 deleted due to clashes), 4267 seeds are put forward Round 1: 429 peptides, 7 chains. Longest chain 137 peptides. Score 0.961 Round 2: 431 peptides, 6 chains. Longest chain 153 peptides. Score 0.964 Round 3: 430 peptides, 9 chains. Longest chain 132 peptides. Score 0.956 Round 4: 431 peptides, 8 chains. Longest chain 155 peptides. Score 0.959 Round 5: 433 peptides, 8 chains. Longest chain 155 peptides. Score 0.960 Taking the results from Round 2 Chains 6, Residues 425, Estimated correctness of the model 99.9 % 6 chains (425 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 207 A and 218 A Built loop between residues 45 B and 56 B 4 chains (445 residues) following loop building 4 chains (445 residues) in sequence following loop building ------------------------------------------------------ 33222 reflections ( 85.82 % complete ) and 4155 restraints for refining 4177 atoms. 623 conditional restraints added. Observations/parameters ratio is 1.99 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2195 (Rfree = 0.000) for 4177 atoms. Found 129 (171 requested) and removed 97 (95 requested) atoms. Cycle 12: After refmac, R = 0.2063 (Rfree = 0.000) for 4205 atoms. Found 97 (168 requested) and removed 42 (95 requested) atoms. Cycle 13: After refmac, R = 0.2009 (Rfree = 0.000) for 4258 atoms. Found 69 (170 requested) and removed 36 (96 requested) atoms. Cycle 14: After refmac, R = 0.1947 (Rfree = 0.000) for 4289 atoms. Found 75 (168 requested) and removed 32 (97 requested) atoms. Cycle 15: After refmac, R = 0.1925 (Rfree = 0.000) for 4327 atoms. Found 77 (169 requested) and removed 45 (98 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.90 2.17 NCS extension: 97 residues added (134 deleted due to clashes), 4456 seeds are put forward Round 1: 432 peptides, 6 chains. Longest chain 153 peptides. Score 0.964 Round 2: 431 peptides, 8 chains. Longest chain 132 peptides. Score 0.959 Round 3: 431 peptides, 9 chains. Longest chain 101 peptides. Score 0.956 Round 4: 430 peptides, 10 chains. Longest chain 117 peptides. Score 0.953 Round 5: 431 peptides, 9 chains. Longest chain 84 peptides. Score 0.956 Taking the results from Round 1 Chains 6, Residues 426, Estimated correctness of the model 99.9 % 6 chains (426 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 207 A and 217 A Built loop between residues 46 B and 56 B 4 chains (444 residues) following loop building 4 chains (444 residues) in sequence following loop building ------------------------------------------------------ 33222 reflections ( 85.82 % complete ) and 4168 restraints for refining 4207 atoms. 645 conditional restraints added. Observations/parameters ratio is 1.97 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2126 (Rfree = 0.000) for 4207 atoms. Found 142 (160 requested) and removed 99 (95 requested) atoms. Cycle 17: After refmac, R = 0.2032 (Rfree = 0.000) for 4244 atoms. Found 92 (158 requested) and removed 38 (96 requested) atoms. Cycle 18: After refmac, R = 0.1951 (Rfree = 0.000) for 4295 atoms. Found 69 (160 requested) and removed 28 (97 requested) atoms. Cycle 19: After refmac, R = 0.1885 (Rfree = 0.000) for 4334 atoms. Found 53 (162 requested) and removed 37 (98 requested) atoms. Cycle 20: After refmac, R = 0.1850 (Rfree = 0.000) for 4346 atoms. Found 80 (158 requested) and removed 34 (99 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.90 2.17 NCS extension: 33 residues added (2 deleted due to clashes), 4429 seeds are put forward Round 1: 429 peptides, 6 chains. Longest chain 153 peptides. Score 0.964 Round 2: 430 peptides, 8 chains. Longest chain 153 peptides. Score 0.959 Round 3: 432 peptides, 8 chains. Longest chain 132 peptides. Score 0.959 Round 4: 432 peptides, 8 chains. Longest chain 138 peptides. Score 0.959 Round 5: 432 peptides, 7 chains. Longest chain 154 peptides. Score 0.962 Taking the results from Round 1 Chains 6, Residues 423, Estimated correctness of the model 99.9 % 6 chains (423 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 46 B and 56 B 5 chains (432 residues) following loop building 5 chains (432 residues) in sequence following loop building ------------------------------------------------------ 33222 reflections ( 85.82 % complete ) and 4336 restraints for refining 4207 atoms. 919 conditional restraints added. Observations/parameters ratio is 1.97 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2040 (Rfree = 0.000) for 4207 atoms. Found 133 (153 requested) and removed 80 (95 requested) atoms. Cycle 22: After refmac, R = 0.1979 (Rfree = 0.000) for 4256 atoms. Found 91 (151 requested) and removed 40 (96 requested) atoms. Cycle 23: After refmac, R = 0.1889 (Rfree = 0.000) for 4306 atoms. Found 87 (153 requested) and removed 28 (98 requested) atoms. Cycle 24: After refmac, R = 0.1841 (Rfree = 0.000) for 4362 atoms. Found 61 (154 requested) and removed 45 (99 requested) atoms. Cycle 25: After refmac, R = 0.1810 (Rfree = 0.000) for 4375 atoms. Found 92 (151 requested) and removed 52 (99 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.90 2.17 NCS extension: 26 residues added (3 deleted due to clashes), 4444 seeds are put forward Round 1: 432 peptides, 6 chains. Longest chain 153 peptides. Score 0.964 Round 2: 428 peptides, 9 chains. Longest chain 105 peptides. Score 0.955 Round 3: 427 peptides, 10 chains. Longest chain 103 peptides. Score 0.952 Round 4: 430 peptides, 7 chains. Longest chain 138 peptides. Score 0.961 Round 5: 426 peptides, 8 chains. Longest chain 135 peptides. Score 0.957 Taking the results from Round 1 Chains 6, Residues 426, Estimated correctness of the model 99.9 % 6 chains (426 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 208 A and 217 A Built loop between residues 45 B and 56 B 4 chains (444 residues) following loop building 4 chains (444 residues) in sequence following loop building ------------------------------------------------------ 33222 reflections ( 85.82 % complete ) and 4242 restraints for refining 4291 atoms. 719 conditional restraints added. Observations/parameters ratio is 1.94 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2032 (Rfree = 0.000) for 4291 atoms. Found 133 (144 requested) and removed 101 (97 requested) atoms. Cycle 27: After refmac, R = 0.1952 (Rfree = 0.000) for 4317 atoms. Found 88 (141 requested) and removed 47 (98 requested) atoms. Cycle 28: After refmac, R = 0.1877 (Rfree = 0.000) for 4357 atoms. Found 90 (139 requested) and removed 43 (99 requested) atoms. Cycle 29: After refmac, R = 0.1829 (Rfree = 0.000) for 4401 atoms. Found 93 (140 requested) and removed 54 (100 requested) atoms. Cycle 30: After refmac, R = 0.1796 (Rfree = 0.000) for 4436 atoms. Found 90 (137 requested) and removed 57 (101 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.89 2.16 NCS extension: 149 residues added (120 deleted due to clashes), 4619 seeds are put forward Round 1: 427 peptides, 8 chains. Longest chain 138 peptides. Score 0.958 Round 2: 432 peptides, 6 chains. Longest chain 153 peptides. Score 0.964 Round 3: 422 peptides, 12 chains. Longest chain 96 peptides. Score 0.945 Round 4: 422 peptides, 11 chains. Longest chain 85 peptides. Score 0.948 Round 5: 426 peptides, 9 chains. Longest chain 149 peptides. Score 0.955 Taking the results from Round 2 Chains 6, Residues 426, Estimated correctness of the model 99.9 % 6 chains (426 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 208 A and 218 A Built loop between residues 45 B and 56 B 4 chains (445 residues) following loop building 4 chains (445 residues) in sequence following loop building ------------------------------------------------------ 33222 reflections ( 85.82 % complete ) and 4247 restraints for refining 4293 atoms. 715 conditional restraints added. Observations/parameters ratio is 1.93 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2024 (Rfree = 0.000) for 4293 atoms. Found 129 (129 requested) and removed 94 (97 requested) atoms. Cycle 32: After refmac, R = 0.1916 (Rfree = 0.000) for 4326 atoms. Found 110 (126 requested) and removed 31 (98 requested) atoms. Cycle 33: After refmac, R = 0.1843 (Rfree = 0.000) for 4403 atoms. Found 84 (128 requested) and removed 44 (100 requested) atoms. Cycle 34: After refmac, R = 0.1792 (Rfree = 0.000) for 4438 atoms. Found 89 (125 requested) and removed 52 (101 requested) atoms. Cycle 35: After refmac, R = 0.1776 (Rfree = 0.000) for 4471 atoms. Found 93 (122 requested) and removed 63 (101 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.90 2.17 NCS extension: 45 residues added (24 deleted due to clashes), 4547 seeds are put forward Round 1: 430 peptides, 6 chains. Longest chain 153 peptides. Score 0.964 Round 2: 427 peptides, 8 chains. Longest chain 153 peptides. Score 0.958 Round 3: 426 peptides, 10 chains. Longest chain 102 peptides. Score 0.952 Round 4: 431 peptides, 7 chains. Longest chain 153 peptides. Score 0.962 Round 5: 426 peptides, 12 chains. Longest chain 153 peptides. Score 0.946 Taking the results from Round 1 Chains 6, Residues 424, Estimated correctness of the model 99.9 % 6 chains (424 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 207 A and 218 A 5 chains (434 residues) following loop building 5 chains (434 residues) in sequence following loop building ------------------------------------------------------ 33222 reflections ( 85.82 % complete ) and 4417 restraints for refining 4314 atoms. 978 conditional restraints added. Observations/parameters ratio is 1.93 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1995 (Rfree = 0.000) for 4314 atoms. Found 114 (114 requested) and removed 83 (98 requested) atoms. Cycle 37: After refmac, R = 0.1903 (Rfree = 0.000) for 4342 atoms. Found 86 (110 requested) and removed 34 (98 requested) atoms. Cycle 38: After refmac, R = 0.1827 (Rfree = 0.000) for 4388 atoms. Found 95 (112 requested) and removed 33 (100 requested) atoms. Cycle 39: After refmac, R = 0.1782 (Rfree = 0.000) for 4447 atoms. Found 78 (113 requested) and removed 44 (101 requested) atoms. Cycle 40: After refmac, R = 0.1732 (Rfree = 0.000) for 4477 atoms. Found 81 (110 requested) and removed 36 (102 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.90 2.17 NCS extension: 42 residues added (22 deleted due to clashes), 4565 seeds are put forward Round 1: 427 peptides, 7 chains. Longest chain 153 peptides. Score 0.960 Round 2: 427 peptides, 8 chains. Longest chain 139 peptides. Score 0.958 Round 3: 426 peptides, 8 chains. Longest chain 153 peptides. Score 0.957 Round 4: 426 peptides, 9 chains. Longest chain 153 peptides. Score 0.955 Round 5: 427 peptides, 10 chains. Longest chain 99 peptides. Score 0.952 Taking the results from Round 1 Chains 7, Residues 420, Estimated correctness of the model 99.9 % 7 chains (420 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 18 A and 21 A Built loop between residues 208 B and 218 B 5 chains (431 residues) following loop building 5 chains (431 residues) in sequence following loop building ------------------------------------------------------ 33222 reflections ( 85.82 % complete ) and 4447 restraints for refining 4320 atoms. 1031 conditional restraints added. Observations/parameters ratio is 1.92 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1949 (Rfree = 0.000) for 4320 atoms. Found 106 (106 requested) and removed 78 (98 requested) atoms. Cycle 42: After refmac, R = 0.1843 (Rfree = 0.000) for 4342 atoms. Found 102 (102 requested) and removed 19 (98 requested) atoms. Cycle 43: After refmac, R = 0.1786 (Rfree = 0.000) for 4422 atoms. Found 77 (105 requested) and removed 34 (100 requested) atoms. Cycle 44: After refmac, R = 0.1740 (Rfree = 0.000) for 4464 atoms. Found 73 (106 requested) and removed 40 (101 requested) atoms. Cycle 45: After refmac, R = 0.1723 (Rfree = 0.000) for 4493 atoms. Found 75 (102 requested) and removed 41 (102 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.91 2.19 NCS extension: 20 residues added (2 deleted due to clashes), 4549 seeds are put forward Round 1: 420 peptides, 8 chains. Longest chain 139 peptides. Score 0.956 Round 2: 425 peptides, 6 chains. Longest chain 148 peptides. Score 0.962 Round 3: 424 peptides, 9 chains. Longest chain 103 peptides. Score 0.954 Round 4: 434 peptides, 6 chains. Longest chain 153 peptides. Score 0.965 Round 5: 431 peptides, 9 chains. Longest chain 153 peptides. Score 0.956 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 6, Residues 428, Estimated correctness of the model 99.9 % 6 chains (428 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 208 B and 218 B 5 chains (437 residues) following loop building 5 chains (437 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 33222 reflections ( 85.82 % complete ) and 3470 restraints for refining 3405 atoms. Observations/parameters ratio is 2.44 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2551 (Rfree = 0.000) for 3405 atoms. Found 44 (77 requested) and removed 0 (77 requested) atoms. Cycle 47: After refmac, R = 0.2377 (Rfree = 0.000) for 3405 atoms. Found 15 (78 requested) and removed 0 (78 requested) atoms. Cycle 48: After refmac, R = 0.2286 (Rfree = 0.000) for 3405 atoms. Found 10 (78 requested) and removed 0 (78 requested) atoms. Cycle 49: After refmac, R = 0.2226 (Rfree = 0.000) for 3405 atoms. Found 7 (79 requested) and removed 0 (79 requested) atoms. Writing output files ... TimeTaking 63.85