Sun 23 Dec 22:23:05 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vme-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vme-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vme-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vme-3.2-parrot-hancs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vme-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vme-3.2-parrot-hancs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Sun 23 Dec 22:23:15 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vme-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vme-3.2-parrot-hancs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 642 and 0 Target number of residues in the AU: 642 Target solvent content: 0.6343 Checking the provided sequence file Detected sequence length: 410 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 820 Adjusted target solvent content: 0.53 Input MTZ file: 1vme-3.2-parrot-hancs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 4 Cell parameters: 55.242 95.831 90.130 90.000 95.426 90.000 Input sequence file: 1vme-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 6560 target number of atoms Had to go as low as 0.70 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: 48.998 3.200 Wilson plot Bfac: 68.69 15542 reflections ( 99.87 % complete ) and 0 restraints for refining 7267 atoms. Observations/parameters ratio is 0.53 ------------------------------------------------------ Starting model: R = 0.3064 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2317 (Rfree = 0.000) for 7267 atoms. Found 36 (65 requested) and removed 56 (32 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.22 3.09 Search for helices and strands: 0 residues in 0 chains, 7407 seeds are put forward NCS extension: 0 residues added, 7407 seeds are put forward Round 1: 524 peptides, 82 chains. Longest chain 14 peptides. Score 0.507 Round 2: 580 peptides, 69 chains. Longest chain 20 peptides. Score 0.652 Round 3: 600 peptides, 62 chains. Longest chain 26 peptides. Score 0.706 Round 4: 605 peptides, 59 chains. Longest chain 27 peptides. Score 0.724 Round 5: 620 peptides, 54 chains. Longest chain 37 peptides. Score 0.757 Taking the results from Round 5 Chains 63, Residues 566, Estimated correctness of the model 76.3 % 9 chains (131 residues) have been docked in sequence Building loops using Loopy2018 63 chains (566 residues) following loop building 9 chains (131 residues) in sequence following loop building ------------------------------------------------------ 15542 reflections ( 99.87 % complete ) and 11105 restraints for refining 5986 atoms. 8373 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2602 (Rfree = 0.000) for 5986 atoms. Found 42 (53 requested) and removed 61 (26 requested) atoms. Cycle 2: After refmac, R = 0.2451 (Rfree = 0.000) for 5909 atoms. Found 20 (52 requested) and removed 43 (26 requested) atoms. Cycle 3: After refmac, R = 0.2416 (Rfree = 0.000) for 5852 atoms. Found 12 (50 requested) and removed 41 (26 requested) atoms. Cycle 4: After refmac, R = 0.2580 (Rfree = 0.000) for 5807 atoms. Found 44 (49 requested) and removed 46 (26 requested) atoms. Cycle 5: After refmac, R = 0.2443 (Rfree = 0.000) for 5795 atoms. Found 26 (48 requested) and removed 37 (26 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.20 3.07 Search for helices and strands: 0 residues in 0 chains, 5996 seeds are put forward NCS extension: 30 residues added (18 deleted due to clashes), 6026 seeds are put forward Round 1: 578 peptides, 61 chains. Longest chain 35 peptides. Score 0.689 Round 2: 602 peptides, 56 chains. Longest chain 27 peptides. Score 0.734 Round 3: 623 peptides, 56 chains. Longest chain 36 peptides. Score 0.752 Round 4: 635 peptides, 51 chains. Longest chain 56 peptides. Score 0.780 Round 5: 651 peptides, 47 chains. Longest chain 36 peptides. Score 0.806 Taking the results from Round 5 Chains 57, Residues 604, Estimated correctness of the model 84.3 % 13 chains (251 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 40 A and 48 A 55 chains (608 residues) following loop building 12 chains (258 residues) in sequence following loop building ------------------------------------------------------ 15542 reflections ( 99.87 % complete ) and 9849 restraints for refining 5988 atoms. 6436 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2682 (Rfree = 0.000) for 5988 atoms. Found 48 (48 requested) and removed 62 (26 requested) atoms. Cycle 7: After refmac, R = 0.2465 (Rfree = 0.000) for 5945 atoms. Found 18 (47 requested) and removed 38 (26 requested) atoms. Cycle 8: After refmac, R = 0.2379 (Rfree = 0.000) for 5904 atoms. Found 17 (46 requested) and removed 27 (26 requested) atoms. Cycle 9: After refmac, R = 0.2338 (Rfree = 0.000) for 5887 atoms. Found 8 (44 requested) and removed 26 (26 requested) atoms. Cycle 10: After refmac, R = 0.2330 (Rfree = 0.000) for 5854 atoms. Found 11 (43 requested) and removed 26 (26 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.21 3.08 Search for helices and strands: 0 residues in 0 chains, 6029 seeds are put forward NCS extension: 46 residues added (49 deleted due to clashes), 6075 seeds are put forward Round 1: 580 peptides, 60 chains. Longest chain 35 peptides. Score 0.695 Round 2: 598 peptides, 51 chains. Longest chain 29 peptides. Score 0.751 Round 3: 601 peptides, 53 chains. Longest chain 29 peptides. Score 0.746 Round 4: 609 peptides, 52 chains. Longest chain 33 peptides. Score 0.756 Round 5: 605 peptides, 52 chains. Longest chain 35 peptides. Score 0.753 Taking the results from Round 4 Chains 55, Residues 557, Estimated correctness of the model 76.1 % 7 chains (142 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 334 A and 344 A 54 chains (566 residues) following loop building 6 chains (151 residues) in sequence following loop building ------------------------------------------------------ 15542 reflections ( 99.87 % complete ) and 11265 restraints for refining 5989 atoms. 8422 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2507 (Rfree = 0.000) for 5989 atoms. Found 28 (42 requested) and removed 50 (26 requested) atoms. Cycle 12: After refmac, R = 0.2569 (Rfree = 0.000) for 5946 atoms. Found 41 (41 requested) and removed 45 (26 requested) atoms. Cycle 13: After refmac, R = 0.2306 (Rfree = 0.000) for 5927 atoms. Found 19 (40 requested) and removed 34 (26 requested) atoms. Cycle 14: After refmac, R = 0.2175 (Rfree = 0.000) for 5900 atoms. Found 13 (39 requested) and removed 35 (26 requested) atoms. Cycle 15: After refmac, R = 0.2153 (Rfree = 0.000) for 5874 atoms. Found 10 (37 requested) and removed 29 (26 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.21 3.08 Search for helices and strands: 0 residues in 0 chains, 6021 seeds are put forward NCS extension: 44 residues added (52 deleted due to clashes), 6065 seeds are put forward Round 1: 564 peptides, 60 chains. Longest chain 35 peptides. Score 0.679 Round 2: 587 peptides, 53 chains. Longest chain 23 peptides. Score 0.733 Round 3: 610 peptides, 50 chains. Longest chain 39 peptides. Score 0.765 Round 4: 614 peptides, 56 chains. Longest chain 30 peptides. Score 0.744 Round 5: 606 peptides, 53 chains. Longest chain 33 peptides. Score 0.750 Taking the results from Round 3 Chains 54, Residues 560, Estimated correctness of the model 77.7 % 6 chains (120 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 332 A and 343 A 51 chains (567 residues) following loop building 5 chains (130 residues) in sequence following loop building ------------------------------------------------------ 15542 reflections ( 99.87 % complete ) and 11410 restraints for refining 5987 atoms. 8682 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2480 (Rfree = 0.000) for 5987 atoms. Found 37 (37 requested) and removed 47 (26 requested) atoms. Cycle 17: After refmac, R = 0.2438 (Rfree = 0.000) for 5971 atoms. Found 24 (36 requested) and removed 43 (26 requested) atoms. Cycle 18: After refmac, R = 0.2545 (Rfree = 0.000) for 5947 atoms. Found 35 (35 requested) and removed 33 (26 requested) atoms. Cycle 19: After refmac, R = 0.2359 (Rfree = 0.000) for 5944 atoms. Found 12 (34 requested) and removed 27 (26 requested) atoms. Cycle 20: After refmac, R = 0.2288 (Rfree = 0.000) for 5925 atoms. Found 12 (33 requested) and removed 29 (26 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.19 3.06 Search for helices and strands: 0 residues in 0 chains, 6104 seeds are put forward NCS extension: 62 residues added (48 deleted due to clashes), 6166 seeds are put forward Round 1: 547 peptides, 64 chains. Longest chain 23 peptides. Score 0.640 Round 2: 603 peptides, 55 chains. Longest chain 26 peptides. Score 0.739 Round 3: 602 peptides, 51 chains. Longest chain 39 peptides. Score 0.755 Round 4: 597 peptides, 52 chains. Longest chain 33 peptides. Score 0.746 Round 5: 586 peptides, 56 chains. Longest chain 27 peptides. Score 0.719 Taking the results from Round 3 Chains 58, Residues 551, Estimated correctness of the model 76.0 % 11 chains (198 residues) have been docked in sequence Building loops using Loopy2018 58 chains (551 residues) following loop building 11 chains (198 residues) in sequence following loop building ------------------------------------------------------ 15542 reflections ( 99.87 % complete ) and 10726 restraints for refining 5989 atoms. 7770 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2455 (Rfree = 0.000) for 5989 atoms. Found 32 (32 requested) and removed 46 (26 requested) atoms. Cycle 22: After refmac, R = 0.2426 (Rfree = 0.000) for 5958 atoms. Found 31 (31 requested) and removed 41 (26 requested) atoms. Cycle 23: After refmac, R = 0.2537 (Rfree = 0.000) for 5927 atoms. Found 30 (30 requested) and removed 49 (26 requested) atoms. Cycle 24: After refmac, R = 0.2507 (Rfree = 0.000) for 5899 atoms. Found 29 (29 requested) and removed 34 (26 requested) atoms. Cycle 25: After refmac, R = 0.2484 (Rfree = 0.000) for 5880 atoms. Found 27 (27 requested) and removed 39 (26 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.19 3.06 Search for helices and strands: 0 residues in 0 chains, 6044 seeds are put forward NCS extension: 24 residues added (16 deleted due to clashes), 6068 seeds are put forward Round 1: 524 peptides, 57 chains. Longest chain 26 peptides. Score 0.651 Round 2: 548 peptides, 51 chains. Longest chain 33 peptides. Score 0.706 Round 3: 558 peptides, 57 chains. Longest chain 45 peptides. Score 0.687 Round 4: 576 peptides, 49 chains. Longest chain 25 peptides. Score 0.741 Round 5: 562 peptides, 56 chains. Longest chain 26 peptides. Score 0.696 Taking the results from Round 4 Chains 51, Residues 527, Estimated correctness of the model 73.4 % 8 chains (128 residues) have been docked in sequence Building loops using Loopy2018 51 chains (527 residues) following loop building 8 chains (128 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 15542 reflections ( 99.87 % complete ) and 11540 restraints for refining 5989 atoms. 8970 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2397 (Rfree = 0.000) for 5989 atoms. Found 26 (26 requested) and removed 43 (26 requested) atoms. Cycle 27: After refmac, R = 0.2497 (Rfree = 0.000) for 5952 atoms. Found 26 (26 requested) and removed 38 (26 requested) atoms. Cycle 28: After refmac, R = 0.2114 (Rfree = 0.000) for 5928 atoms. Found 26 (26 requested) and removed 39 (26 requested) atoms. Cycle 29: After refmac, R = 0.2331 (Rfree = 0.000) for 5908 atoms. Found 26 (26 requested) and removed 38 (26 requested) atoms. Cycle 30: After refmac, R = 0.2376 (Rfree = 0.000) for 5890 atoms. Found 26 (26 requested) and removed 39 (26 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.21 3.08 Search for helices and strands: 0 residues in 0 chains, 6057 seeds are put forward NCS extension: 11 residues added (14 deleted due to clashes), 6068 seeds are put forward Round 1: 515 peptides, 66 chains. Longest chain 24 peptides. Score 0.590 Round 2: 569 peptides, 54 chains. Longest chain 25 peptides. Score 0.712 Round 3: 557 peptides, 63 chains. Longest chain 25 peptides. Score 0.657 Round 4: 563 peptides, 54 chains. Longest chain 24 peptides. Score 0.706 Round 5: 559 peptides, 59 chains. Longest chain 28 peptides. Score 0.679 Taking the results from Round 2 Chains 56, Residues 515, Estimated correctness of the model 67.7 % 8 chains (146 residues) have been docked in sequence Building loops using Loopy2018 56 chains (515 residues) following loop building 8 chains (146 residues) in sequence following loop building ------------------------------------------------------ 15542 reflections ( 99.87 % complete ) and 11359 restraints for refining 5986 atoms. 8723 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2330 (Rfree = 0.000) for 5986 atoms. Found 26 (26 requested) and removed 39 (26 requested) atoms. Cycle 32: After refmac, R = 0.2121 (Rfree = 0.000) for 5964 atoms. Found 17 (26 requested) and removed 34 (26 requested) atoms. Cycle 33: After refmac, R = 0.2035 (Rfree = 0.000) for 5940 atoms. Found 14 (26 requested) and removed 27 (26 requested) atoms. Cycle 34: After refmac, R = 0.1945 (Rfree = 0.000) for 5923 atoms. Found 11 (26 requested) and removed 28 (26 requested) atoms. Cycle 35: After refmac, R = 0.1938 (Rfree = 0.000) for 5903 atoms. Found 10 (26 requested) and removed 27 (26 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.22 3.09 Search for helices and strands: 0 residues in 0 chains, 6042 seeds are put forward NCS extension: 18 residues added (8 deleted due to clashes), 6060 seeds are put forward Round 1: 515 peptides, 65 chains. Longest chain 21 peptides. Score 0.596 Round 2: 574 peptides, 58 chains. Longest chain 25 peptides. Score 0.699 Round 3: 563 peptides, 58 chains. Longest chain 26 peptides. Score 0.688 Round 4: 556 peptides, 59 chains. Longest chain 26 peptides. Score 0.676 Round 5: 560 peptides, 59 chains. Longest chain 25 peptides. Score 0.680 Taking the results from Round 2 Chains 61, Residues 516, Estimated correctness of the model 65.0 % 6 chains (96 residues) have been docked in sequence ------------------------------------------------------ 15542 reflections ( 99.87 % complete ) and 11797 restraints for refining 5986 atoms. 9384 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2190 (Rfree = 0.000) for 5986 atoms. Found 26 (26 requested) and removed 41 (26 requested) atoms. Cycle 37: After refmac, R = 0.2075 (Rfree = 0.000) for 5961 atoms. Found 15 (26 requested) and removed 30 (26 requested) atoms. Cycle 38: After refmac, R = 0.2039 (Rfree = 0.000) for 5931 atoms. Found 20 (26 requested) and removed 30 (26 requested) atoms. Cycle 39: After refmac, R = 0.1975 (Rfree = 0.000) for 5913 atoms. Found 11 (26 requested) and removed 26 (26 requested) atoms. Cycle 40: After refmac, R = 0.1916 (Rfree = 0.000) for 5895 atoms. Found 8 (26 requested) and removed 26 (26 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.22 3.09 Search for helices and strands: 0 residues in 0 chains, 6061 seeds are put forward NCS extension: 14 residues added (10 deleted due to clashes), 6075 seeds are put forward Round 1: 470 peptides, 60 chains. Longest chain 22 peptides. Score 0.567 Round 2: 534 peptides, 60 chains. Longest chain 27 peptides. Score 0.646 Round 3: 529 peptides, 60 chains. Longest chain 25 peptides. Score 0.641 Round 4: 535 peptides, 60 chains. Longest chain 24 peptides. Score 0.647 Round 5: 548 peptides, 56 chains. Longest chain 33 peptides. Score 0.682 Taking the results from Round 5 Chains 61, Residues 492, Estimated correctness of the model 61.3 % 6 chains (78 residues) have been docked in sequence ------------------------------------------------------ 15542 reflections ( 99.87 % complete ) and 12162 restraints for refining 5989 atoms. 9922 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2279 (Rfree = 0.000) for 5989 atoms. Found 26 (26 requested) and removed 37 (26 requested) atoms. Cycle 42: After refmac, R = 0.2108 (Rfree = 0.000) for 5972 atoms. Found 17 (26 requested) and removed 31 (26 requested) atoms. Cycle 43: After refmac, R = 0.2403 (Rfree = 0.000) for 5956 atoms. Found 26 (26 requested) and removed 31 (26 requested) atoms. Cycle 44: After refmac, R = 0.2118 (Rfree = 0.000) for 5944 atoms. Found 14 (26 requested) and removed 34 (26 requested) atoms. Cycle 45: After refmac, R = 0.2037 (Rfree = 0.000) for 5918 atoms. Found 18 (26 requested) and removed 33 (26 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.20 3.07 Search for helices and strands: 0 residues in 0 chains, 6067 seeds are put forward NCS extension: 17 residues added (3 deleted due to clashes), 6084 seeds are put forward Round 1: 463 peptides, 64 chains. Longest chain 23 peptides. Score 0.532 Round 2: 506 peptides, 60 chains. Longest chain 23 peptides. Score 0.613 Round 3: 513 peptides, 61 chains. Longest chain 20 peptides. Score 0.616 Round 4: 535 peptides, 59 chains. Longest chain 25 peptides. Score 0.653 Round 5: 516 peptides, 59 chains. Longest chain 25 peptides. Score 0.631 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 61, Residues 476, Estimated correctness of the model 54.6 % 4 chains (20 residues) have been docked in sequence Sequence coverage is 4 % Consider running further cycles of model building using 1vme-3_warpNtrace.pdb as input Building loops using Loopy2018 61 chains (476 residues) following loop building 4 chains (20 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 15542 reflections ( 99.87 % complete ) and 12853 restraints for refining 5989 atoms. 10952 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2229 (Rfree = 0.000) for 5989 atoms. Found 0 (26 requested) and removed 25 (26 requested) atoms. Cycle 47: After refmac, R = 0.2213 (Rfree = 0.000) for 5953 atoms. Found 0 (26 requested) and removed 26 (26 requested) atoms. Cycle 48: After refmac, R = 0.2168 (Rfree = 0.000) for 5914 atoms. Found 0 (26 requested) and removed 26 (26 requested) atoms. Cycle 49: After refmac, R = 0.2126 (Rfree = 0.000) for 5883 atoms. TimeTaking 83.1