Mon 24 Dec 00:53:00 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 1vqs-1.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vqs-1.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vqs-1.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vqs-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/1vqs-1.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vqs-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 ============================================================ Mon 24 Dec 00:53:04 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vqs-1.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vqs-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 723 and 0 Target number of residues in the AU: 723 Target solvent content: 0.4250 Checking the provided sequence file Detected sequence length: 116 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 5 Adjusted target number of residues: 580 Adjusted target solvent content: 0.54 Input MTZ file: 1vqs-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: 97 Cell parameters: 94.778 94.778 303.043 90.000 90.000 90.000 Input sequence file: 1vqs-1.8-parrot-mrncs.fasta_lf Building free atoms model in initial map for 4640 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: 29.971 1.800 Wilson plot Bfac: 11.04 64374 reflections ( 99.94 % complete ) and 0 restraints for refining 5117 atoms. Observations/parameters ratio is 3.15 ------------------------------------------------------ Starting model: R = 0.3215 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2680 (Rfree = 0.000) for 5117 atoms. Found 236 (236 requested) and removed 62 (118 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.57 1.49 NCS extension: 0 residues added, 5291 seeds are put forward Round 1: 483 peptides, 27 chains. Longest chain 46 peptides. Score 0.849 Round 2: 500 peptides, 15 chains. Longest chain 79 peptides. Score 0.902 Round 3: 516 peptides, 11 chains. Longest chain 104 peptides. Score 0.922 Round 4: 510 peptides, 14 chains. Longest chain 101 peptides. Score 0.910 Round 5: 516 peptides, 12 chains. Longest chain 104 peptides. Score 0.919 Taking the results from Round 3 Chains 11, Residues 505, Estimated correctness of the model 99.5 % 10 chains (497 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 36 A and 39 A Built loop between residues 57 C and 60 C Built loop between residues 91 C and 94 C Built loop between residues 46 B and 49 B Built loop between residues 91 D and 94 D 6 chains (515 residues) following loop building 5 chains (507 residues) in sequence following loop building ------------------------------------------------------ 64374 reflections ( 99.94 % complete ) and 5397 restraints for refining 5235 atoms. 1081 conditional restraints added. Observations/parameters ratio is 3.07 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2646 (Rfree = 0.000) for 5235 atoms. Found 233 (242 requested) and removed 61 (121 requested) atoms. Cycle 2: After refmac, R = 0.2206 (Rfree = 0.000) for 5401 atoms. Found 224 (249 requested) and removed 61 (124 requested) atoms. Cycle 3: After refmac, R = 0.2059 (Rfree = 0.000) for 5550 atoms. Found 200 (256 requested) and removed 64 (128 requested) atoms. Cycle 4: After refmac, R = 0.1965 (Rfree = 0.000) for 5671 atoms. Found 146 (262 requested) and removed 68 (131 requested) atoms. Cycle 5: After refmac, R = 0.1899 (Rfree = 0.000) for 5729 atoms. Found 179 (265 requested) and removed 62 (132 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.58 1.50 NCS extension: 2 residues added (3 deleted due to clashes), 5848 seeds are put forward Round 1: 519 peptides, 11 chains. Longest chain 104 peptides. Score 0.923 Round 2: 519 peptides, 9 chains. Longest chain 104 peptides. Score 0.928 Round 3: 519 peptides, 7 chains. Longest chain 104 peptides. Score 0.934 Round 4: 518 peptides, 10 chains. Longest chain 104 peptides. Score 0.925 Round 5: 516 peptides, 14 chains. Longest chain 104 peptides. Score 0.913 Taking the results from Round 3 Chains 7, Residues 512, Estimated correctness of the model 99.7 % 7 chains (512 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 45 A and 48 A Built loop between residues 56 C and 59 C 5 chains (516 residues) following loop building 5 chains (516 residues) in sequence following loop building ------------------------------------------------------ 64374 reflections ( 99.94 % complete ) and 5385 restraints for refining 5475 atoms. 1005 conditional restraints added. Observations/parameters ratio is 2.94 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2187 (Rfree = 0.000) for 5475 atoms. Found 226 (253 requested) and removed 40 (126 requested) atoms. Cycle 7: After refmac, R = 0.1979 (Rfree = 0.000) for 5654 atoms. Found 142 (261 requested) and removed 58 (130 requested) atoms. Cycle 8: After refmac, R = 0.1857 (Rfree = 0.000) for 5722 atoms. Found 158 (264 requested) and removed 37 (132 requested) atoms. Cycle 9: After refmac, R = 0.1826 (Rfree = 0.000) for 5825 atoms. Found 119 (269 requested) and removed 68 (134 requested) atoms. Cycle 10: After refmac, R = 0.1828 (Rfree = 0.000) for 5861 atoms. Found 136 (266 requested) and removed 61 (135 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.60 1.52 NCS extension: 0 residues added, 5936 seeds are put forward Round 1: 516 peptides, 13 chains. Longest chain 60 peptides. Score 0.916 Round 2: 521 peptides, 7 chains. Longest chain 104 peptides. Score 0.934 Round 3: 515 peptides, 12 chains. Longest chain 104 peptides. Score 0.918 Round 4: 519 peptides, 9 chains. Longest chain 103 peptides. Score 0.928 Round 5: 515 peptides, 12 chains. Longest chain 104 peptides. Score 0.918 Taking the results from Round 2 Chains 7, Residues 514, Estimated correctness of the model 99.7 % 7 chains (514 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 36 A and 39 A Built loop between residues 44 C and 47 C 5 chains (518 residues) following loop building 5 chains (518 residues) in sequence following loop building ------------------------------------------------------ 64374 reflections ( 99.94 % complete ) and 5433 restraints for refining 5540 atoms. 1033 conditional restraints added. Observations/parameters ratio is 2.90 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2102 (Rfree = 0.000) for 5540 atoms. Found 207 (251 requested) and removed 32 (128 requested) atoms. Cycle 12: After refmac, R = 0.1907 (Rfree = 0.000) for 5708 atoms. Found 165 (258 requested) and removed 52 (131 requested) atoms. Cycle 13: After refmac, R = 0.1825 (Rfree = 0.000) for 5796 atoms. Found 152 (263 requested) and removed 52 (134 requested) atoms. Cycle 14: After refmac, R = 0.1789 (Rfree = 0.000) for 5873 atoms. Found 142 (267 requested) and removed 66 (136 requested) atoms. Cycle 15: After refmac, R = 0.1757 (Rfree = 0.000) for 5932 atoms. Found 151 (269 requested) and removed 73 (137 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.59 1.51 NCS extension: 0 residues added, 6010 seeds are put forward Round 1: 514 peptides, 13 chains. Longest chain 60 peptides. Score 0.915 Round 2: 519 peptides, 8 chains. Longest chain 104 peptides. Score 0.931 Round 3: 518 peptides, 10 chains. Longest chain 103 peptides. Score 0.925 Round 4: 514 peptides, 12 chains. Longest chain 103 peptides. Score 0.918 Round 5: 516 peptides, 11 chains. Longest chain 104 peptides. Score 0.922 Taking the results from Round 2 Chains 8, Residues 511, Estimated correctness of the model 99.6 % 7 chains (505 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 37 A and 48 A Built loop between residues 35 E and 38 E 5 chains (517 residues) following loop building 5 chains (517 residues) in sequence following loop building ------------------------------------------------------ 64374 reflections ( 99.94 % complete ) and 5558 restraints for refining 5613 atoms. 1169 conditional restraints added. Observations/parameters ratio is 2.87 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2115 (Rfree = 0.000) for 5613 atoms. Found 244 (254 requested) and removed 46 (129 requested) atoms. Cycle 17: After refmac, R = 0.1933 (Rfree = 0.000) for 5796 atoms. Found 172 (263 requested) and removed 77 (134 requested) atoms. Cycle 18: After refmac, R = 0.1924 (Rfree = 0.000) for 5870 atoms. Found 155 (266 requested) and removed 71 (135 requested) atoms. Cycle 19: After refmac, R = 0.1836 (Rfree = 0.000) for 5949 atoms. Found 129 (269 requested) and removed 77 (137 requested) atoms. Cycle 20: After refmac, R = 0.1832 (Rfree = 0.000) for 5986 atoms. Found 151 (265 requested) and removed 70 (138 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.60 1.52 NCS extension: 0 residues added, 6067 seeds are put forward Round 1: 514 peptides, 14 chains. Longest chain 60 peptides. Score 0.912 Round 2: 520 peptides, 5 chains. Longest chain 108 peptides. Score 0.939 Round 3: 517 peptides, 11 chains. Longest chain 104 peptides. Score 0.922 Round 4: 519 peptides, 8 chains. Longest chain 109 peptides. Score 0.931 Round 5: 516 peptides, 11 chains. Longest chain 77 peptides. Score 0.922 Taking the results from Round 2 Chains 5, Residues 515, Estimated correctness of the model 99.7 % 5 chains (515 residues) have been docked in sequence Building loops using Loopy2018 5 chains (515 residues) following loop building 5 chains (515 residues) in sequence following loop building ------------------------------------------------------ 64374 reflections ( 99.94 % complete ) and 5583 restraints for refining 5636 atoms. 1213 conditional restraints added. Observations/parameters ratio is 2.86 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2123 (Rfree = 0.000) for 5636 atoms. Found 240 (250 requested) and removed 44 (130 requested) atoms. Cycle 22: After refmac, R = 0.1915 (Rfree = 0.000) for 5811 atoms. Found 161 (258 requested) and removed 60 (134 requested) atoms. Cycle 23: After refmac, R = 0.1823 (Rfree = 0.000) for 5892 atoms. Found 157 (261 requested) and removed 60 (136 requested) atoms. Cycle 24: After refmac, R = 0.1786 (Rfree = 0.000) for 5971 atoms. Found 125 (265 requested) and removed 88 (138 requested) atoms. Cycle 25: After refmac, R = 0.1753 (Rfree = 0.000) for 5983 atoms. Found 171 (260 requested) and removed 70 (138 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.59 1.51 NCS extension: 0 residues added, 6084 seeds are put forward Round 1: 517 peptides, 11 chains. Longest chain 104 peptides. Score 0.922 Round 2: 520 peptides, 8 chains. Longest chain 104 peptides. Score 0.931 Round 3: 514 peptides, 13 chains. Longest chain 78 peptides. Score 0.915 Round 4: 516 peptides, 7 chains. Longest chain 104 peptides. Score 0.933 Round 5: 513 peptides, 15 chains. Longest chain 74 peptides. Score 0.908 Taking the results from Round 4 Chains 7, Residues 509, Estimated correctness of the model 99.6 % 7 chains (509 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 45 A and 48 A Built loop between residues 54 C and 57 C 5 chains (513 residues) following loop building 5 chains (513 residues) in sequence following loop building ------------------------------------------------------ 64374 reflections ( 99.94 % complete ) and 5603 restraints for refining 5634 atoms. 1255 conditional restraints added. Observations/parameters ratio is 2.86 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2125 (Rfree = 0.000) for 5634 atoms. Found 241 (244 requested) and removed 39 (130 requested) atoms. Cycle 27: After refmac, R = 0.1912 (Rfree = 0.000) for 5814 atoms. Found 182 (253 requested) and removed 61 (134 requested) atoms. Cycle 28: After refmac, R = 0.1838 (Rfree = 0.000) for 5919 atoms. Found 150 (257 requested) and removed 75 (136 requested) atoms. Cycle 29: After refmac, R = 0.1789 (Rfree = 0.000) for 5974 atoms. Found 135 (259 requested) and removed 74 (138 requested) atoms. Cycle 30: After refmac, R = 0.1754 (Rfree = 0.000) for 6010 atoms. Found 147 (256 requested) and removed 61 (139 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.60 1.52 NCS extension: 0 residues added, 6096 seeds are put forward Round 1: 514 peptides, 13 chains. Longest chain 68 peptides. Score 0.915 Round 2: 518 peptides, 8 chains. Longest chain 104 peptides. Score 0.931 Round 3: 517 peptides, 10 chains. Longest chain 104 peptides. Score 0.925 Round 4: 518 peptides, 9 chains. Longest chain 103 peptides. Score 0.928 Round 5: 520 peptides, 8 chains. Longest chain 104 peptides. Score 0.931 Taking the results from Round 5 Chains 8, Residues 512, Estimated correctness of the model 99.6 % 8 chains (512 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 46 A and 49 A Built loop between residues 55 C and 58 C Built loop between residues 54 E and 57 E 5 chains (518 residues) following loop building 5 chains (518 residues) in sequence following loop building ------------------------------------------------------ 64374 reflections ( 99.94 % complete ) and 5583 restraints for refining 5644 atoms. 1183 conditional restraints added. Observations/parameters ratio is 2.85 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2140 (Rfree = 0.000) for 5644 atoms. Found 240 (240 requested) and removed 42 (130 requested) atoms. Cycle 32: After refmac, R = 0.1900 (Rfree = 0.000) for 5831 atoms. Found 178 (247 requested) and removed 47 (134 requested) atoms. Cycle 33: After refmac, R = 0.1837 (Rfree = 0.000) for 5932 atoms. Found 144 (253 requested) and removed 69 (137 requested) atoms. Cycle 34: After refmac, R = 0.1791 (Rfree = 0.000) for 5988 atoms. Found 146 (255 requested) and removed 64 (138 requested) atoms. Cycle 35: After refmac, R = 0.1761 (Rfree = 0.000) for 6052 atoms. Found 135 (258 requested) and removed 86 (140 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.59 1.51 NCS extension: 2 residues added (3 deleted due to clashes), 6103 seeds are put forward Round 1: 516 peptides, 12 chains. Longest chain 67 peptides. Score 0.919 Round 2: 519 peptides, 10 chains. Longest chain 104 peptides. Score 0.925 Round 3: 519 peptides, 8 chains. Longest chain 104 peptides. Score 0.931 Round 4: 516 peptides, 9 chains. Longest chain 108 peptides. Score 0.927 Round 5: 517 peptides, 12 chains. Longest chain 105 peptides. Score 0.919 Taking the results from Round 3 Chains 8, Residues 511, Estimated correctness of the model 99.6 % 8 chains (511 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 36 A and 39 A Built loop between residues 45 C and 48 C Built loop between residues 36 D and 39 D 5 chains (517 residues) following loop building 5 chains (517 residues) in sequence following loop building ------------------------------------------------------ 64374 reflections ( 99.94 % complete ) and 5569 restraints for refining 5643 atoms. 1180 conditional restraints added. Observations/parameters ratio is 2.85 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2098 (Rfree = 0.000) for 5643 atoms. Found 234 (234 requested) and removed 38 (130 requested) atoms. Cycle 37: After refmac, R = 0.2058 (Rfree = 0.000) for 5824 atoms. Found 135 (242 requested) and removed 64 (134 requested) atoms. Cycle 38: After refmac, R = 0.1861 (Rfree = 0.000) for 5887 atoms. Found 145 (244 requested) and removed 45 (135 requested) atoms. Cycle 39: After refmac, R = 0.1802 (Rfree = 0.000) for 5970 atoms. Found 117 (248 requested) and removed 58 (138 requested) atoms. Cycle 40: After refmac, R = 0.1815 (Rfree = 0.000) for 6011 atoms. Found 139 (249 requested) and removed 55 (138 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.59 1.51 NCS extension: 0 residues added, 6095 seeds are put forward Round 1: 514 peptides, 13 chains. Longest chain 69 peptides. Score 0.915 Round 2: 519 peptides, 7 chains. Longest chain 109 peptides. Score 0.934 Round 3: 516 peptides, 10 chains. Longest chain 103 peptides. Score 0.924 Round 4: 518 peptides, 9 chains. Longest chain 104 peptides. Score 0.928 Round 5: 514 peptides, 13 chains. Longest chain 80 peptides. Score 0.915 Taking the results from Round 2 Chains 7, Residues 512, Estimated correctness of the model 99.7 % 7 chains (512 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 36 A and 39 A Built loop between residues 36 E and 39 E 5 chains (516 residues) following loop building 5 chains (516 residues) in sequence following loop building ------------------------------------------------------ 64374 reflections ( 99.94 % complete ) and 5627 restraints for refining 5703 atoms. 1246 conditional restraints added. Observations/parameters ratio is 2.82 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2116 (Rfree = 0.000) for 5703 atoms. Found 234 (237 requested) and removed 40 (131 requested) atoms. Cycle 42: After refmac, R = 0.1915 (Rfree = 0.000) for 5881 atoms. Found 152 (245 requested) and removed 59 (136 requested) atoms. Cycle 43: After refmac, R = 0.1823 (Rfree = 0.000) for 5948 atoms. Found 142 (247 requested) and removed 58 (137 requested) atoms. Cycle 44: After refmac, R = 0.1787 (Rfree = 0.000) for 6020 atoms. Found 126 (250 requested) and removed 91 (139 requested) atoms. Cycle 45: After refmac, R = 0.1757 (Rfree = 0.000) for 6036 atoms. Found 157 (246 requested) and removed 66 (139 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.59 1.51 NCS extension: 0 residues added, 6127 seeds are put forward Round 1: 514 peptides, 13 chains. Longest chain 69 peptides. Score 0.915 Round 2: 519 peptides, 7 chains. Longest chain 108 peptides. Score 0.934 Round 3: 517 peptides, 9 chains. Longest chain 104 peptides. Score 0.928 Round 4: 515 peptides, 13 chains. Longest chain 80 peptides. Score 0.915 Round 5: 518 peptides, 10 chains. Longest chain 104 peptides. Score 0.925 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 7, Residues 512, Estimated correctness of the model 99.7 % 7 chains (512 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 35 A and 38 A Built loop between residues 36 E and 39 E 5 chains (516 residues) following loop building 5 chains (516 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 64374 reflections ( 99.94 % complete ) and 4378 restraints for refining 4268 atoms. Observations/parameters ratio is 3.77 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2805 (Rfree = 0.000) for 4268 atoms. Found 173 (173 requested) and removed 0 (173 requested) atoms. Cycle 47: After refmac, R = 0.2489 (Rfree = 0.000) for 4268 atoms. Found 180 (180 requested) and removed 0 (102 requested) atoms. Cycle 48: After refmac, R = 0.2325 (Rfree = 0.000) for 4268 atoms. Found 119 (187 requested) and removed 3 (106 requested) atoms. Cycle 49: After refmac, R = 0.2191 (Rfree = 0.000) for 4268 atoms. TimeTaking 89.23