Tue 25 Dec 19:27:55 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 2opk-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2opk-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2opk-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2opk-3.6-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/2opk-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2opk-3.6-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 ============================================================ Tue 25 Dec 19:28:05 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/2opk-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2opk-3.6-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 409 and 0 Target number of residues in the AU: 409 Target solvent content: 0.6104 Checking the provided sequence file Detected sequence length: 112 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 448 Adjusted target solvent content: 0.57 Input MTZ file: 2opk-3.6-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: 96 Cell parameters: 75.570 75.570 198.970 90.000 90.000 90.000 Input sequence file: 2opk-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 3584 target number of atoms Had to go as low as 0.85 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: 28.177 3.600 Wilson plot Bfac: 56.81 7177 reflections ( 99.58 % complete ) and 0 restraints for refining 3972 atoms. Observations/parameters ratio is 0.45 ------------------------------------------------------ Starting model: R = 0.2915 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2706 (Rfree = 0.000) for 3972 atoms. Found 25 (25 requested) and removed 31 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.22 2.93 Search for helices and strands: 0 residues in 0 chains, 4009 seeds are put forward NCS extension: 0 residues added, 4009 seeds are put forward Round 1: 250 peptides, 41 chains. Longest chain 14 peptides. Score 0.434 Round 2: 315 peptides, 45 chains. Longest chain 14 peptides. Score 0.552 Round 3: 343 peptides, 39 chains. Longest chain 25 peptides. Score 0.664 Round 4: 355 peptides, 32 chains. Longest chain 42 peptides. Score 0.737 Round 5: 337 peptides, 29 chains. Longest chain 36 peptides. Score 0.732 Taking the results from Round 4 Chains 34, Residues 323, Estimated correctness of the model 60.4 % 5 chains (93 residues) have been docked in sequence Building loops using Loopy2018 34 chains (323 residues) following loop building 5 chains (93 residues) in sequence following loop building ------------------------------------------------------ 7177 reflections ( 99.58 % complete ) and 5566 restraints for refining 3247 atoms. 3934 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2490 (Rfree = 0.000) for 3247 atoms. Found 20 (20 requested) and removed 39 (10 requested) atoms. Cycle 2: After refmac, R = 0.2352 (Rfree = 0.000) for 3178 atoms. Found 18 (20 requested) and removed 19 (10 requested) atoms. Cycle 3: After refmac, R = 0.2288 (Rfree = 0.000) for 3143 atoms. Found 14 (19 requested) and removed 17 (10 requested) atoms. Cycle 4: After refmac, R = 0.2271 (Rfree = 0.000) for 3123 atoms. Found 12 (19 requested) and removed 15 (10 requested) atoms. Failed to save intermediate PDB Cycle 5: After refmac, R = 0.2226 (Rfree = 0.000) for 3111 atoms. Found 15 (18 requested) and removed 17 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.22 2.93 Search for helices and strands: 0 residues in 0 chains, 3156 seeds are put forward NCS extension: 21 residues added (3 deleted due to clashes), 3177 seeds are put forward Round 1: 329 peptides, 37 chains. Longest chain 29 peptides. Score 0.655 Round 2: 354 peptides, 32 chains. Longest chain 31 peptides. Score 0.736 Round 3: 333 peptides, 33 chains. Longest chain 36 peptides. Score 0.695 Round 4: 328 peptides, 32 chains. Longest chain 30 peptides. Score 0.695 Round 5: 351 peptides, 31 chains. Longest chain 30 peptides. Score 0.739 Taking the results from Round 5 Chains 36, Residues 320, Estimated correctness of the model 60.9 % 6 chains (76 residues) have been docked in sequence Building loops using Loopy2018 36 chains (320 residues) following loop building 6 chains (76 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 7177 reflections ( 99.58 % complete ) and 6134 restraints for refining 3249 atoms. 4600 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2543 (Rfree = 0.000) for 3249 atoms. Found 18 (18 requested) and removed 30 (10 requested) atoms. Failed to save intermediate PDB Cycle 7: After refmac, R = 0.2370 (Rfree = 0.000) for 3210 atoms. Found 8 (18 requested) and removed 25 (10 requested) atoms. Cycle 8: After refmac, R = 0.2317 (Rfree = 0.000) for 3187 atoms. Found 13 (17 requested) and removed 14 (10 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.2217 (Rfree = 0.000) for 3180 atoms. Found 11 (17 requested) and removed 13 (10 requested) atoms. Cycle 10: After refmac, R = 0.2167 (Rfree = 0.000) for 3178 atoms. Found 8 (16 requested) and removed 13 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.28 2.99 Search for helices and strands: 0 residues in 0 chains, 3242 seeds are put forward NCS extension: 22 residues added (3 deleted due to clashes), 3264 seeds are put forward Round 1: 305 peptides, 39 chains. Longest chain 23 peptides. Score 0.589 Round 2: 334 peptides, 35 chains. Longest chain 26 peptides. Score 0.681 Round 3: 333 peptides, 36 chains. Longest chain 24 peptides. Score 0.671 Round 4: 330 peptides, 35 chains. Longest chain 34 peptides. Score 0.674 Round 5: 339 peptides, 35 chains. Longest chain 35 peptides. Score 0.689 Taking the results from Round 5 Chains 37, Residues 304, Estimated correctness of the model 46.2 % 6 chains (62 residues) have been docked in sequence ------------------------------------------------------ 7177 reflections ( 99.58 % complete ) and 6308 restraints for refining 3249 atoms. 4910 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2552 (Rfree = 0.000) for 3249 atoms. Found 16 (16 requested) and removed 24 (10 requested) atoms. Failed to save intermediate PDB Cycle 12: After refmac, R = 0.2492 (Rfree = 0.000) for 3220 atoms. Found 11 (16 requested) and removed 19 (10 requested) atoms. Cycle 13: After refmac, R = 0.2316 (Rfree = 0.000) for 3206 atoms. Found 14 (16 requested) and removed 22 (10 requested) atoms. Cycle 14: After refmac, R = 0.2257 (Rfree = 0.000) for 3186 atoms. Found 4 (16 requested) and removed 19 (10 requested) atoms. Cycle 15: After refmac, R = 0.2180 (Rfree = 0.000) for 3170 atoms. Found 2 (16 requested) and removed 13 (10 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.25 2.96 Search for helices and strands: 0 residues in 0 chains, 3218 seeds are put forward NCS extension: 29 residues added (20 deleted due to clashes), 3247 seeds are put forward Round 1: 323 peptides, 42 chains. Longest chain 26 peptides. Score 0.599 Round 2: 342 peptides, 34 chains. Longest chain 36 peptides. Score 0.702 Round 3: 335 peptides, 33 chains. Longest chain 30 peptides. Score 0.699 Round 4: 334 peptides, 34 chains. Longest chain 26 peptides. Score 0.689 Round 5: 326 peptides, 36 chains. Longest chain 21 peptides. Score 0.658 Taking the results from Round 2 Chains 36, Residues 308, Estimated correctness of the model 50.2 % 5 chains (55 residues) have been docked in sequence Building loops using Loopy2018 36 chains (308 residues) following loop building 5 chains (55 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 7177 reflections ( 99.58 % complete ) and 6366 restraints for refining 3247 atoms. 4973 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2321 (Rfree = 0.000) for 3247 atoms. Found 16 (16 requested) and removed 22 (10 requested) atoms. Failed to save intermediate PDB Cycle 17: After refmac, R = 0.2204 (Rfree = 0.000) for 3222 atoms. Found 8 (16 requested) and removed 13 (10 requested) atoms. Cycle 18: After refmac, R = 0.2134 (Rfree = 0.000) for 3206 atoms. Found 3 (15 requested) and removed 16 (10 requested) atoms. Cycle 19: After refmac, R = 0.2090 (Rfree = 0.000) for 3186 atoms. Found 6 (15 requested) and removed 12 (10 requested) atoms. Cycle 20: After refmac, R = 0.2053 (Rfree = 0.000) for 3173 atoms. Found 4 (14 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.27 2.98 Search for helices and strands: 0 residues in 0 chains, 3238 seeds are put forward NCS extension: 39 residues added (14 deleted due to clashes), 3277 seeds are put forward Round 1: 296 peptides, 43 chains. Longest chain 21 peptides. Score 0.529 Round 2: 327 peptides, 35 chains. Longest chain 22 peptides. Score 0.668 Round 3: 343 peptides, 35 chains. Longest chain 25 peptides. Score 0.696 Round 4: 351 peptides, 40 chains. Longest chain 35 peptides. Score 0.670 Round 5: 355 peptides, 37 chains. Longest chain 27 peptides. Score 0.701 Taking the results from Round 5 Chains 41, Residues 318, Estimated correctness of the model 49.9 % 6 chains (67 residues) have been docked in sequence Building loops using Loopy2018 41 chains (318 residues) following loop building 6 chains (67 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 7177 reflections ( 99.58 % complete ) and 6179 restraints for refining 3249 atoms. 4670 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2636 (Rfree = 0.000) for 3249 atoms. Found 14 (14 requested) and removed 26 (10 requested) atoms. Cycle 22: After refmac, R = 0.2493 (Rfree = 0.000) for 3226 atoms. Found 14 (14 requested) and removed 16 (10 requested) atoms. Cycle 23: After refmac, R = 0.2416 (Rfree = 0.000) for 3215 atoms. Found 7 (13 requested) and removed 17 (10 requested) atoms. Cycle 24: After refmac, R = 0.2356 (Rfree = 0.000) for 3196 atoms. Found 12 (13 requested) and removed 18 (10 requested) atoms. Failed to save intermediate PDB Cycle 25: After refmac, R = 0.2352 (Rfree = 0.000) for 3188 atoms. Found 4 (12 requested) and removed 15 (10 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.28 2.99 Search for helices and strands: 0 residues in 0 chains, 3230 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 3255 seeds are put forward Round 1: 291 peptides, 38 chains. Longest chain 26 peptides. Score 0.568 Round 2: 318 peptides, 39 chains. Longest chain 24 peptides. Score 0.616 Round 3: 313 peptides, 34 chains. Longest chain 24 peptides. Score 0.651 Round 4: 315 peptides, 36 chains. Longest chain 21 peptides. Score 0.637 Round 5: 309 peptides, 36 chains. Longest chain 20 peptides. Score 0.625 Taking the results from Round 3 Chains 34, Residues 279, Estimated correctness of the model 33.5 % 3 chains (22 residues) have been docked in sequence ------------------------------------------------------ 7177 reflections ( 99.58 % complete ) and 6721 restraints for refining 3247 atoms. 5572 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2583 (Rfree = 0.000) for 3247 atoms. Found 12 (12 requested) and removed 33 (10 requested) atoms. Cycle 27: After refmac, R = 0.2332 (Rfree = 0.000) for 3216 atoms. Found 8 (12 requested) and removed 17 (10 requested) atoms. Cycle 28: After refmac, R = 0.2245 (Rfree = 0.000) for 3200 atoms. Found 6 (12 requested) and removed 11 (10 requested) atoms. Cycle 29: After refmac, R = 0.2210 (Rfree = 0.000) for 3191 atoms. Found 2 (12 requested) and removed 12 (10 requested) atoms. Cycle 30: After refmac, R = 0.2176 (Rfree = 0.000) for 3181 atoms. Found 3 (12 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.26 2.97 Search for helices and strands: 0 residues in 0 chains, 3235 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 3251 seeds are put forward Round 1: 272 peptides, 39 chains. Longest chain 16 peptides. Score 0.513 Round 2: 304 peptides, 40 chains. Longest chain 23 peptides. Score 0.577 Round 3: 280 peptides, 37 chains. Longest chain 16 peptides. Score 0.553 Round 4: 292 peptides, 33 chains. Longest chain 25 peptides. Score 0.619 Round 5: 285 peptides, 32 chains. Longest chain 31 peptides. Score 0.614 Taking the results from Round 4 Chains 39, Residues 259, Estimated correctness of the model 21.9 % 4 chains (56 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 7177 reflections ( 99.58 % complete ) and 6480 restraints for refining 3249 atoms. 5246 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2517 (Rfree = 0.000) for 3249 atoms. Found 12 (12 requested) and removed 23 (10 requested) atoms. Failed to save intermediate PDB Cycle 32: After refmac, R = 0.2378 (Rfree = 0.000) for 3215 atoms. Found 12 (12 requested) and removed 13 (10 requested) atoms. Cycle 33: After refmac, R = 0.2378 (Rfree = 0.000) for 3205 atoms. Found 12 (12 requested) and removed 16 (10 requested) atoms. Failed to save intermediate PDB Cycle 34: After refmac, R = 0.2224 (Rfree = 0.000) for 3198 atoms. Found 11 (12 requested) and removed 11 (10 requested) atoms. Failed to save intermediate PDB Cycle 35: After refmac, R = 0.2247 (Rfree = 0.000) for 3192 atoms. Found 8 (12 requested) and removed 13 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.25 2.96 Search for helices and strands: 0 residues in 0 chains, 3225 seeds are put forward NCS extension: 29 residues added (1 deleted due to clashes), 3254 seeds are put forward Round 1: 248 peptides, 39 chains. Longest chain 16 peptides. Score 0.452 Round 2: 275 peptides, 36 chains. Longest chain 16 peptides. Score 0.552 Round 3: 300 peptides, 40 chains. Longest chain 23 peptides. Score 0.568 Round 4: 291 peptides, 37 chains. Longest chain 21 peptides. Score 0.578 Round 5: 292 peptides, 38 chains. Longest chain 21 peptides. Score 0.570 Taking the results from Round 4 Chains 38, Residues 254, Estimated correctness of the model 5.9 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 7177 reflections ( 99.58 % complete ) and 7041 restraints for refining 3249 atoms. 6041 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2439 (Rfree = 0.000) for 3249 atoms. Found 12 (12 requested) and removed 15 (10 requested) atoms. Cycle 37: After refmac, R = 0.2387 (Rfree = 0.000) for 3238 atoms. Found 12 (12 requested) and removed 17 (10 requested) atoms. Cycle 38: After refmac, R = 0.2293 (Rfree = 0.000) for 3228 atoms. Found 12 (12 requested) and removed 14 (10 requested) atoms. Cycle 39: After refmac, R = 0.2208 (Rfree = 0.000) for 3220 atoms. Found 12 (12 requested) and removed 17 (10 requested) atoms. Cycle 40: After refmac, R = 0.2127 (Rfree = 0.000) for 3214 atoms. Found 7 (12 requested) and removed 12 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.25 2.96 Search for helices and strands: 0 residues in 0 chains, 3252 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 3269 seeds are put forward Round 1: 236 peptides, 40 chains. Longest chain 16 peptides. Score 0.407 Round 2: 270 peptides, 38 chains. Longest chain 18 peptides. Score 0.519 Round 3: 269 peptides, 38 chains. Longest chain 19 peptides. Score 0.517 Round 4: 255 peptides, 33 chains. Longest chain 19 peptides. Score 0.537 Round 5: 287 peptides, 38 chains. Longest chain 23 peptides. Score 0.559 Taking the results from Round 5 Chains 38, Residues 249, Estimated correctness of the model 0.0 % 2 chains (10 residues) have been docked in sequence ------------------------------------------------------ 7177 reflections ( 99.58 % complete ) and 7032 restraints for refining 3249 atoms. 6052 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2415 (Rfree = 0.000) for 3249 atoms. Found 12 (12 requested) and removed 18 (10 requested) atoms. Cycle 42: After refmac, R = 0.2284 (Rfree = 0.000) for 3234 atoms. Found 12 (12 requested) and removed 14 (10 requested) atoms. Cycle 43: After refmac, R = 0.2184 (Rfree = 0.000) for 3227 atoms. Found 10 (12 requested) and removed 20 (10 requested) atoms. Cycle 44: After refmac, R = 0.2163 (Rfree = 0.000) for 3216 atoms. Found 9 (12 requested) and removed 12 (10 requested) atoms. Failed to save intermediate PDB Cycle 45: After refmac, R = 0.2092 (Rfree = 0.000) for 3210 atoms. Found 9 (12 requested) and removed 14 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.20 2.91 Search for helices and strands: 0 residues in 0 chains, 3252 seeds are put forward NCS extension: 20 residues added (3 deleted due to clashes), 3272 seeds are put forward Round 1: 237 peptides, 42 chains. Longest chain 13 peptides. Score 0.386 Round 2: 261 peptides, 41 chains. Longest chain 15 peptides. Score 0.463 Round 3: 272 peptides, 38 chains. Longest chain 23 peptides. Score 0.524 Round 4: 280 peptides, 36 chains. Longest chain 23 peptides. Score 0.564 Round 5: 273 peptides, 39 chains. Longest chain 23 peptides. Score 0.516 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 37, Residues 244, Estimated correctness of the model 0.1 % 4 chains (29 residues) have been docked in sequence Sequence coverage is 11 % Consider running further cycles of model building using 2opk-3_warpNtrace.pdb as input Building loops using Loopy2018 37 chains (244 residues) following loop building 4 chains (29 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7177 reflections ( 99.58 % complete ) and 6978 restraints for refining 3249 atoms. 5958 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2447 (Rfree = 0.000) for 3249 atoms. Found 0 (12 requested) and removed 10 (10 requested) atoms. Failed to save intermediate PDB Cycle 47: After refmac, R = 0.2398 (Rfree = 0.000) for 3231 atoms. Found 0 (12 requested) and removed 10 (10 requested) atoms. Cycle 48: After refmac, R = 0.2374 (Rfree = 0.000) for 3221 atoms. Found 0 (12 requested) and removed 10 (10 requested) atoms. Cycle 49: After refmac, R = 0.2387 (Rfree = 0.000) for 3210 atoms. Found 0 (12 requested) and removed 6 (10 requested) atoms. Writing output files ... TimeTaking 61.48