Sun 23 Dec 22:22:55 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 1vl4-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vl4-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vl4-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vl4-3.2-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/1vl4-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vl4-3.2-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 22:23:04 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/hancs/ArpWArp/wArpResults/WorkingDir/1vl4-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vl4-3.2-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 752 and 0 Target number of residues in the AU: 752 Target solvent content: 0.6045 Checking the provided sequence file Detected sequence length: 447 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 894 Adjusted target solvent content: 0.53 Input MTZ file: 1vl4-3.2-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: 19 Cell parameters: 80.171 107.117 119.834 90.000 90.000 90.000 Input sequence file: 1vl4-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 7152 target number of atoms Had to go as low as 0.60 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: 79.862 3.200 Wilson plot Bfac: 54.38 17516 reflections ( 99.52 % complete ) and 0 restraints for refining 7875 atoms. Observations/parameters ratio is 0.56 ------------------------------------------------------ Starting model: R = 0.3008 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2637 (Rfree = 0.000) for 7875 atoms. Found 70 (70 requested) and removed 78 (35 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.96 2.84 Search for helices and strands: 0 residues in 0 chains, 7983 seeds are put forward NCS extension: 0 residues added, 7983 seeds are put forward Round 1: 505 peptides, 84 chains. Longest chain 17 peptides. Score 0.449 Round 2: 604 peptides, 74 chains. Longest chain 20 peptides. Score 0.630 Round 3: 643 peptides, 64 chains. Longest chain 38 peptides. Score 0.713 Round 4: 652 peptides, 62 chains. Longest chain 33 peptides. Score 0.729 Round 5: 660 peptides, 64 chains. Longest chain 29 peptides. Score 0.727 Taking the results from Round 4 Chains 71, Residues 590, Estimated correctness of the model 71.1 % 12 chains (189 residues) have been docked in sequence Building loops using Loopy2018 71 chains (590 residues) following loop building 12 chains (189 residues) in sequence following loop building ------------------------------------------------------ 17516 reflections ( 99.52 % complete ) and 11940 restraints for refining 6525 atoms. 8935 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2723 (Rfree = 0.000) for 6525 atoms. Found 58 (58 requested) and removed 90 (29 requested) atoms. Cycle 2: After refmac, R = 0.2546 (Rfree = 0.000) for 6386 atoms. Found 35 (57 requested) and removed 44 (29 requested) atoms. Cycle 3: After refmac, R = 0.2437 (Rfree = 0.000) for 6340 atoms. Found 34 (55 requested) and removed 40 (28 requested) atoms. Cycle 4: After refmac, R = 0.2403 (Rfree = 0.000) for 6311 atoms. Found 19 (53 requested) and removed 45 (28 requested) atoms. Cycle 5: After refmac, R = 0.2333 (Rfree = 0.000) for 6273 atoms. Found 17 (52 requested) and removed 43 (28 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.00 2.88 Search for helices and strands: 0 residues in 0 chains, 6416 seeds are put forward NCS extension: 16 residues added (16 deleted due to clashes), 6432 seeds are put forward Round 1: 603 peptides, 72 chains. Longest chain 29 peptides. Score 0.639 Round 2: 679 peptides, 64 chains. Longest chain 34 peptides. Score 0.743 Round 3: 678 peptides, 54 chains. Longest chain 46 peptides. Score 0.778 Round 4: 664 peptides, 63 chains. Longest chain 35 peptides. Score 0.735 Round 5: 651 peptides, 61 chains. Longest chain 43 peptides. Score 0.732 Taking the results from Round 3 Chains 60, Residues 624, Estimated correctness of the model 79.9 % 8 chains (206 residues) have been docked in sequence Building loops using Loopy2018 60 chains (624 residues) following loop building 8 chains (206 residues) in sequence following loop building ------------------------------------------------------ 17516 reflections ( 99.52 % complete ) and 11704 restraints for refining 6529 atoms. 8418 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2805 (Rfree = 0.000) for 6529 atoms. Found 47 (52 requested) and removed 78 (29 requested) atoms. Cycle 7: After refmac, R = 0.2588 (Rfree = 0.000) for 6435 atoms. Found 38 (51 requested) and removed 45 (29 requested) atoms. Cycle 8: After refmac, R = 0.2490 (Rfree = 0.000) for 6401 atoms. Found 18 (49 requested) and removed 39 (28 requested) atoms. Cycle 9: After refmac, R = 0.2393 (Rfree = 0.000) for 6360 atoms. Found 16 (48 requested) and removed 34 (28 requested) atoms. Cycle 10: After refmac, R = 0.2336 (Rfree = 0.000) for 6333 atoms. Found 12 (46 requested) and removed 35 (28 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.05 2.93 Search for helices and strands: 0 residues in 0 chains, 6448 seeds are put forward NCS extension: 18 residues added (9 deleted due to clashes), 6466 seeds are put forward Round 1: 621 peptides, 69 chains. Longest chain 32 peptides. Score 0.671 Round 2: 684 peptides, 59 chains. Longest chain 42 peptides. Score 0.765 Round 3: 689 peptides, 59 chains. Longest chain 47 peptides. Score 0.768 Round 4: 668 peptides, 63 chains. Longest chain 29 peptides. Score 0.738 Round 5: 675 peptides, 62 chains. Longest chain 33 peptides. Score 0.747 Taking the results from Round 3 Chains 68, Residues 630, Estimated correctness of the model 78.2 % 10 chains (188 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 178 A and 181 A 67 chains (632 residues) following loop building 9 chains (190 residues) in sequence following loop building ------------------------------------------------------ 17516 reflections ( 99.52 % complete ) and 11993 restraints for refining 6529 atoms. 8806 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2537 (Rfree = 0.000) for 6529 atoms. Found 45 (46 requested) and removed 56 (29 requested) atoms. Cycle 12: After refmac, R = 0.2311 (Rfree = 0.000) for 6502 atoms. Found 19 (45 requested) and removed 42 (29 requested) atoms. Cycle 13: After refmac, R = 0.2256 (Rfree = 0.000) for 6464 atoms. Found 14 (44 requested) and removed 32 (29 requested) atoms. Cycle 14: After refmac, R = 0.2387 (Rfree = 0.000) for 6438 atoms. Found 31 (42 requested) and removed 35 (28 requested) atoms. Cycle 15: After refmac, R = 0.2124 (Rfree = 0.000) for 6426 atoms. Found 8 (41 requested) and removed 33 (28 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.99 2.87 Search for helices and strands: 0 residues in 0 chains, 6555 seeds are put forward NCS extension: 46 residues added (11 deleted due to clashes), 6601 seeds are put forward Round 1: 617 peptides, 68 chains. Longest chain 37 peptides. Score 0.672 Round 2: 660 peptides, 54 chains. Longest chain 74 peptides. Score 0.765 Round 3: 649 peptides, 64 chains. Longest chain 72 peptides. Score 0.718 Round 4: 654 peptides, 61 chains. Longest chain 39 peptides. Score 0.734 Round 5: 646 peptides, 60 chains. Longest chain 31 peptides. Score 0.732 Taking the results from Round 2 Chains 61, Residues 606, Estimated correctness of the model 77.7 % 12 chains (216 residues) have been docked in sequence Building loops using Loopy2018 61 chains (606 residues) following loop building 12 chains (216 residues) in sequence following loop building ------------------------------------------------------ 17516 reflections ( 99.52 % complete ) and 11655 restraints for refining 6529 atoms. 8475 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2492 (Rfree = 0.000) for 6529 atoms. Found 41 (41 requested) and removed 51 (29 requested) atoms. Cycle 17: After refmac, R = 0.2319 (Rfree = 0.000) for 6495 atoms. Found 13 (39 requested) and removed 32 (29 requested) atoms. Cycle 18: After refmac, R = 0.2264 (Rfree = 0.000) for 6463 atoms. Found 13 (38 requested) and removed 31 (29 requested) atoms. Cycle 19: After refmac, R = 0.2193 (Rfree = 0.000) for 6437 atoms. Found 7 (36 requested) and removed 29 (28 requested) atoms. Cycle 20: After refmac, R = 0.2151 (Rfree = 0.000) for 6407 atoms. Found 17 (35 requested) and removed 28 (28 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.01 2.89 Search for helices and strands: 0 residues in 0 chains, 6541 seeds are put forward NCS extension: 103 residues added (22 deleted due to clashes), 6644 seeds are put forward Round 1: 589 peptides, 65 chains. Longest chain 36 peptides. Score 0.657 Round 2: 643 peptides, 57 chains. Longest chain 68 peptides. Score 0.741 Round 3: 638 peptides, 64 chains. Longest chain 57 peptides. Score 0.709 Round 4: 659 peptides, 63 chains. Longest chain 48 peptides. Score 0.731 Round 5: 651 peptides, 64 chains. Longest chain 37 peptides. Score 0.720 Taking the results from Round 2 Chains 62, Residues 586, Estimated correctness of the model 73.4 % 12 chains (232 residues) have been docked in sequence Building loops using Loopy2018 62 chains (586 residues) following loop building 12 chains (232 residues) in sequence following loop building ------------------------------------------------------ 17516 reflections ( 99.52 % complete ) and 11563 restraints for refining 6528 atoms. 8382 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2436 (Rfree = 0.000) for 6528 atoms. Found 34 (35 requested) and removed 48 (29 requested) atoms. Cycle 22: After refmac, R = 0.2318 (Rfree = 0.000) for 6481 atoms. Found 18 (34 requested) and removed 34 (29 requested) atoms. Cycle 23: After refmac, R = 0.2224 (Rfree = 0.000) for 6443 atoms. Found 17 (32 requested) and removed 38 (29 requested) atoms. Cycle 24: After refmac, R = 0.2291 (Rfree = 0.000) for 6406 atoms. Found 28 (31 requested) and removed 33 (28 requested) atoms. Cycle 25: After refmac, R = 0.2127 (Rfree = 0.000) for 6389 atoms. Found 13 (30 requested) and removed 33 (28 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.00 2.88 Search for helices and strands: 0 residues in 0 chains, 6522 seeds are put forward NCS extension: 55 residues added (50 deleted due to clashes), 6577 seeds are put forward Round 1: 578 peptides, 73 chains. Longest chain 32 peptides. Score 0.606 Round 2: 639 peptides, 61 chains. Longest chain 63 peptides. Score 0.722 Round 3: 650 peptides, 60 chains. Longest chain 48 peptides. Score 0.735 Round 4: 647 peptides, 60 chains. Longest chain 31 peptides. Score 0.732 Round 5: 633 peptides, 63 chains. Longest chain 49 peptides. Score 0.708 Taking the results from Round 3 Chains 64, Residues 590, Estimated correctness of the model 72.3 % 9 chains (194 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 190 A and 193 A 62 chains (590 residues) following loop building 8 chains (196 residues) in sequence following loop building ------------------------------------------------------ 17516 reflections ( 99.52 % complete ) and 11958 restraints for refining 6529 atoms. 8959 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2492 (Rfree = 0.000) for 6529 atoms. Found 29 (29 requested) and removed 54 (29 requested) atoms. Cycle 27: After refmac, R = 0.2340 (Rfree = 0.000) for 6485 atoms. Found 29 (29 requested) and removed 41 (29 requested) atoms. Cycle 28: After refmac, R = 0.2207 (Rfree = 0.000) for 6447 atoms. Found 24 (29 requested) and removed 31 (29 requested) atoms. Cycle 29: After refmac, R = 0.2130 (Rfree = 0.000) for 6431 atoms. Found 9 (28 requested) and removed 29 (28 requested) atoms. Cycle 30: After refmac, R = 0.2069 (Rfree = 0.000) for 6405 atoms. Found 12 (28 requested) and removed 28 (28 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.00 2.88 Search for helices and strands: 0 residues in 0 chains, 6585 seeds are put forward NCS extension: 110 residues added (38 deleted due to clashes), 6695 seeds are put forward Round 1: 556 peptides, 68 chains. Longest chain 27 peptides. Score 0.607 Round 2: 607 peptides, 60 chains. Longest chain 39 peptides. Score 0.698 Round 3: 609 peptides, 61 chains. Longest chain 32 peptides. Score 0.695 Round 4: 614 peptides, 63 chains. Longest chain 35 peptides. Score 0.691 Round 5: 615 peptides, 58 chains. Longest chain 43 peptides. Score 0.713 Taking the results from Round 5 Chains 62, Residues 557, Estimated correctness of the model 67.9 % 10 chains (169 residues) have been docked in sequence Building loops using Loopy2018 62 chains (557 residues) following loop building 10 chains (169 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 17516 reflections ( 99.52 % complete ) and 12197 restraints for refining 6529 atoms. 9349 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2458 (Rfree = 0.000) for 6529 atoms. Found 29 (29 requested) and removed 41 (29 requested) atoms. Cycle 32: After refmac, R = 0.2379 (Rfree = 0.000) for 6499 atoms. Found 21 (29 requested) and removed 38 (29 requested) atoms. Cycle 33: After refmac, R = 0.2283 (Rfree = 0.000) for 6465 atoms. Found 24 (29 requested) and removed 37 (29 requested) atoms. Cycle 34: After refmac, R = 0.2155 (Rfree = 0.000) for 6440 atoms. Found 11 (28 requested) and removed 30 (28 requested) atoms. Cycle 35: After refmac, R = 0.2110 (Rfree = 0.000) for 6411 atoms. Found 16 (28 requested) and removed 29 (28 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.03 2.91 Search for helices and strands: 0 residues in 0 chains, 6543 seeds are put forward NCS extension: 28 residues added (14 deleted due to clashes), 6571 seeds are put forward Round 1: 532 peptides, 63 chains. Longest chain 26 peptides. Score 0.605 Round 2: 583 peptides, 63 chains. Longest chain 27 peptides. Score 0.661 Round 3: 573 peptides, 61 chains. Longest chain 37 peptides. Score 0.660 Round 4: 569 peptides, 63 chains. Longest chain 29 peptides. Score 0.646 Round 5: 575 peptides, 63 chains. Longest chain 27 peptides. Score 0.652 Taking the results from Round 2 Chains 68, Residues 520, Estimated correctness of the model 56.5 % 9 chains (133 residues) have been docked in sequence ------------------------------------------------------ 17516 reflections ( 99.52 % complete ) and 13021 restraints for refining 6529 atoms. 10508 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2382 (Rfree = 0.000) for 6529 atoms. Found 29 (29 requested) and removed 38 (29 requested) atoms. Cycle 37: After refmac, R = 0.2349 (Rfree = 0.000) for 6508 atoms. Found 29 (29 requested) and removed 33 (29 requested) atoms. Cycle 38: After refmac, R = 0.2136 (Rfree = 0.000) for 6494 atoms. Found 15 (29 requested) and removed 30 (29 requested) atoms. Cycle 39: After refmac, R = 0.2101 (Rfree = 0.000) for 6468 atoms. Found 15 (29 requested) and removed 29 (29 requested) atoms. Cycle 40: After refmac, R = 0.2057 (Rfree = 0.000) for 6451 atoms. Found 9 (28 requested) and removed 28 (28 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.01 2.89 Search for helices and strands: 0 residues in 0 chains, 6553 seeds are put forward NCS extension: 22 residues added (14 deleted due to clashes), 6575 seeds are put forward Round 1: 520 peptides, 61 chains. Longest chain 28 peptides. Score 0.602 Round 2: 576 peptides, 59 chains. Longest chain 30 peptides. Score 0.672 Round 3: 566 peptides, 59 chains. Longest chain 27 peptides. Score 0.662 Round 4: 574 peptides, 63 chains. Longest chain 39 peptides. Score 0.651 Round 5: 541 peptides, 60 chains. Longest chain 27 peptides. Score 0.631 Taking the results from Round 2 Chains 68, Residues 517, Estimated correctness of the model 59.0 % 8 chains (129 residues) have been docked in sequence ------------------------------------------------------ 17516 reflections ( 99.52 % complete ) and 12664 restraints for refining 6529 atoms. 10141 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2309 (Rfree = 0.000) for 6529 atoms. Found 29 (29 requested) and removed 38 (29 requested) atoms. Cycle 42: After refmac, R = 0.2412 (Rfree = 0.000) for 6501 atoms. Found 29 (29 requested) and removed 35 (29 requested) atoms. Cycle 43: After refmac, R = 0.2246 (Rfree = 0.000) for 6479 atoms. Found 23 (29 requested) and removed 35 (29 requested) atoms. Cycle 44: After refmac, R = 0.2385 (Rfree = 0.000) for 6455 atoms. Found 29 (29 requested) and removed 38 (29 requested) atoms. Cycle 45: After refmac, R = 0.2155 (Rfree = 0.000) for 6435 atoms. Found 17 (28 requested) and removed 29 (28 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.03 2.91 Search for helices and strands: 0 residues in 0 chains, 6616 seeds are put forward NCS extension: 22 residues added (5 deleted due to clashes), 6638 seeds are put forward Round 1: 512 peptides, 70 chains. Longest chain 27 peptides. Score 0.542 Round 2: 570 peptides, 62 chains. Longest chain 30 peptides. Score 0.652 Round 3: 566 peptides, 65 chains. Longest chain 27 peptides. Score 0.633 Round 4: 574 peptides, 60 chains. Longest chain 41 peptides. Score 0.666 Round 5: 558 peptides, 61 chains. Longest chain 38 peptides. Score 0.644 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 64, Residues 514, Estimated correctness of the model 57.6 % 9 chains (124 residues) have been docked in sequence Sequence coverage is 24 % Consider running further cycles of model building using 1vl4-3_warpNtrace.pdb as input Building loops using Loopy2018 64 chains (514 residues) following loop building 9 chains (124 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 17516 reflections ( 99.52 % complete ) and 12969 restraints for refining 6529 atoms. 10513 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2387 (Rfree = 0.000) for 6529 atoms. Found 0 (29 requested) and removed 23 (29 requested) atoms. Cycle 47: After refmac, R = 0.2258 (Rfree = 0.000) for 6500 atoms. Found 0 (29 requested) and removed 13 (29 requested) atoms. Cycle 48: After refmac, R = 0.2174 (Rfree = 0.000) for 6477 atoms. Found 0 (29 requested) and removed 18 (29 requested) atoms. Cycle 49: After refmac, R = 0.2165 (Rfree = 0.000) for 6452 atoms. TimeTaking 92.77