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 2o1q-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2o1q-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2o1q-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o1q-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/2o1q-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o1q-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 ============================================================ 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/2o1q-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o1q-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 186 and 0 Target number of residues in the AU: 186 Target solvent content: 0.6061 Checking the provided sequence file Detected sequence length: 145 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 290 Adjusted target solvent content: 0.39 Input MTZ file: 2o1q-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: 92 Cell parameters: 61.883 61.883 133.475 90.000 90.000 90.000 Input sequence file: 2o1q-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 2320 target number of atoms Had to go as low as 0.65 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: 56.142 3.200 Wilson plot Bfac: 54.88 4668 reflections ( 99.79 % complete ) and 0 restraints for refining 2559 atoms. Observations/parameters ratio is 0.46 ------------------------------------------------------ Starting model: R = 0.3240 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2805 (Rfree = 0.000) for 2559 atoms. Found 22 (22 requested) and removed 36 (11 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.04 3.53 Search for helices and strands: 0 residues in 0 chains, 2565 seeds are put forward NCS extension: 0 residues added, 2565 seeds are put forward Round 1: 149 peptides, 27 chains. Longest chain 14 peptides. Score 0.434 Round 2: 191 peptides, 25 chains. Longest chain 18 peptides. Score 0.675 Round 3: 198 peptides, 21 chains. Longest chain 22 peptides. Score 0.758 Round 4: 205 peptides, 24 chains. Longest chain 19 peptides. Score 0.738 Round 5: 210 peptides, 22 chains. Longest chain 30 peptides. Score 0.778 Taking the results from Round 5 Chains 26, Residues 188, Estimated correctness of the model 79.9 % 8 chains (87 residues) have been docked in sequence Building loops using Loopy2018 26 chains (188 residues) following loop building 8 chains (87 residues) in sequence following loop building ------------------------------------------------------ 4668 reflections ( 99.79 % complete ) and 3652 restraints for refining 2118 atoms. 2612 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2761 (Rfree = 0.000) for 2118 atoms. Found 16 (19 requested) and removed 29 (9 requested) atoms. Cycle 2: After refmac, R = 0.2672 (Rfree = 0.000) for 2077 atoms. Found 16 (18 requested) and removed 15 (9 requested) atoms. Cycle 3: After refmac, R = 0.2437 (Rfree = 0.000) for 2052 atoms. Found 11 (17 requested) and removed 13 (9 requested) atoms. Cycle 4: After refmac, R = 0.2620 (Rfree = 0.000) for 2041 atoms. Found 13 (17 requested) and removed 11 (9 requested) atoms. Cycle 5: After refmac, R = 0.2426 (Rfree = 0.000) for 2036 atoms. Found 4 (17 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.06 3.55 Search for helices and strands: 0 residues in 0 chains, 2079 seeds are put forward NCS extension: 34 residues added (8 deleted due to clashes), 2113 seeds are put forward Round 1: 181 peptides, 24 chains. Longest chain 17 peptides. Score 0.654 Round 2: 202 peptides, 19 chains. Longest chain 25 peptides. Score 0.794 Round 3: 209 peptides, 19 chains. Longest chain 35 peptides. Score 0.811 Round 4: 205 peptides, 19 chains. Longest chain 46 peptides. Score 0.801 Round 5: 220 peptides, 18 chains. Longest chain 48 peptides. Score 0.843 Taking the results from Round 5 Chains 19, Residues 202, Estimated correctness of the model 89.4 % 4 chains (106 residues) have been docked in sequence Building loops using Loopy2018 19 chains (202 residues) following loop building 4 chains (106 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 4668 reflections ( 99.79 % complete ) and 3418 restraints for refining 2117 atoms. 2224 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2906 (Rfree = 0.000) for 2117 atoms. Found 17 (17 requested) and removed 22 (9 requested) atoms. Failed to save intermediate PDB Cycle 7: After refmac, R = 0.2746 (Rfree = 0.000) for 2093 atoms. Found 16 (16 requested) and removed 14 (9 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.2424 (Rfree = 0.000) for 2075 atoms. Found 8 (15 requested) and removed 12 (9 requested) atoms. Cycle 9: After refmac, R = 0.2493 (Rfree = 0.000) for 2058 atoms. Found 15 (15 requested) and removed 11 (9 requested) atoms. Cycle 10: After refmac, R = 0.2435 (Rfree = 0.000) for 2054 atoms. Found 8 (15 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.08 3.57 Search for helices and strands: 0 residues in 0 chains, 2089 seeds are put forward NCS extension: 26 residues added (18 deleted due to clashes), 2115 seeds are put forward Round 1: 172 peptides, 26 chains. Longest chain 16 peptides. Score 0.577 Round 2: 213 peptides, 22 chains. Longest chain 34 peptides. Score 0.786 Round 3: 208 peptides, 22 chains. Longest chain 34 peptides. Score 0.773 Round 4: 176 peptides, 23 chains. Longest chain 19 peptides. Score 0.652 Round 5: 194 peptides, 22 chains. Longest chain 28 peptides. Score 0.732 Taking the results from Round 2 Chains 23, Residues 191, Estimated correctness of the model 81.2 % 5 chains (66 residues) have been docked in sequence Building loops using Loopy2018 23 chains (191 residues) following loop building 5 chains (66 residues) in sequence following loop building ------------------------------------------------------ 4668 reflections ( 99.79 % complete ) and 3893 restraints for refining 2116 atoms. 2928 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2760 (Rfree = 0.000) for 2116 atoms. Found 15 (15 requested) and removed 19 (9 requested) atoms. Failed to save intermediate PDB Cycle 12: After refmac, R = 0.2429 (Rfree = 0.000) for 2101 atoms. Found 14 (14 requested) and removed 12 (9 requested) atoms. Cycle 13: After refmac, R = 0.2211 (Rfree = 0.000) for 2100 atoms. Found 12 (14 requested) and removed 9 (9 requested) atoms. Cycle 14: After refmac, R = 0.2231 (Rfree = 0.000) for 2099 atoms. Found 13 (13 requested) and removed 11 (9 requested) atoms. Cycle 15: After refmac, R = 0.2138 (Rfree = 0.000) for 2101 atoms. Found 13 (13 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.03 3.52 Search for helices and strands: 0 residues in 0 chains, 2137 seeds are put forward NCS extension: 35 residues added (3 deleted due to clashes), 2172 seeds are put forward Round 1: 175 peptides, 27 chains. Longest chain 32 peptides. Score 0.571 Round 2: 179 peptides, 22 chains. Longest chain 39 peptides. Score 0.681 Round 3: 190 peptides, 24 chains. Longest chain 26 peptides. Score 0.688 Round 4: 189 peptides, 24 chains. Longest chain 20 peptides. Score 0.684 Round 5: 181 peptides, 25 chains. Longest chain 28 peptides. Score 0.636 Taking the results from Round 3 Chains 25, Residues 166, Estimated correctness of the model 62.6 % 4 chains (25 residues) have been docked in sequence ------------------------------------------------------ 4668 reflections ( 99.79 % complete ) and 4417 restraints for refining 2118 atoms. 3688 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3108 (Rfree = 0.000) for 2118 atoms. Found 13 (13 requested) and removed 19 (9 requested) atoms. Failed to save intermediate PDB Cycle 17: After refmac, R = 0.2540 (Rfree = 0.000) for 2099 atoms. Found 12 (13 requested) and removed 16 (9 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.2434 (Rfree = 0.000) for 2085 atoms. Found 13 (13 requested) and removed 14 (9 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.2629 (Rfree = 0.000) for 2077 atoms. Found 13 (13 requested) and removed 12 (9 requested) atoms. Cycle 20: After refmac, R = 0.2638 (Rfree = 0.000) for 2073 atoms. Found 13 (13 requested) and removed 13 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.07 3.56 Search for helices and strands: 0 residues in 0 chains, 2128 seeds are put forward NCS extension: 40 residues added (3 deleted due to clashes), 2168 seeds are put forward Round 1: 144 peptides, 25 chains. Longest chain 16 peptides. Score 0.453 Round 2: 157 peptides, 22 chains. Longest chain 24 peptides. Score 0.588 Round 3: 160 peptides, 21 chains. Longest chain 19 peptides. Score 0.622 Round 4: 172 peptides, 22 chains. Longest chain 24 peptides. Score 0.653 Round 5: 166 peptides, 23 chains. Longest chain 24 peptides. Score 0.609 Taking the results from Round 4 Chains 22, Residues 150, Estimated correctness of the model 54.6 % 5 chains (38 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 4668 reflections ( 99.79 % complete ) and 4319 restraints for refining 2118 atoms. 3622 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2883 (Rfree = 0.000) for 2118 atoms. Found 13 (13 requested) and removed 19 (9 requested) atoms. Failed to save intermediate PDB Cycle 22: After refmac, R = 0.2685 (Rfree = 0.000) for 2100 atoms. Found 13 (13 requested) and removed 10 (9 requested) atoms. Cycle 23: After refmac, R = 0.2111 (Rfree = 0.000) for 2096 atoms. Found 13 (13 requested) and removed 11 (9 requested) atoms. Failed to save intermediate PDB Cycle 24: After refmac, R = 0.2411 (Rfree = 0.000) for 2097 atoms. Found 13 (13 requested) and removed 13 (9 requested) atoms. Failed to save intermediate PDB Cycle 25: After refmac, R = 0.2262 (Rfree = 0.000) for 2090 atoms. Found 13 (13 requested) and removed 14 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.03 3.52 Search for helices and strands: 0 residues in 0 chains, 2123 seeds are put forward NCS extension: 17 residues added (8 deleted due to clashes), 2140 seeds are put forward Round 1: 130 peptides, 23 chains. Longest chain 19 peptides. Score 0.421 Round 2: 154 peptides, 23 chains. Longest chain 20 peptides. Score 0.553 Round 3: 143 peptides, 20 chains. Longest chain 25 peptides. Score 0.563 Round 4: 160 peptides, 22 chains. Longest chain 20 peptides. Score 0.602 Round 5: 152 peptides, 23 chains. Longest chain 19 peptides. Score 0.543 Taking the results from Round 4 Chains 22, Residues 138, Estimated correctness of the model 41.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4668 reflections ( 99.79 % complete ) and 4742 restraints for refining 2117 atoms. 4212 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2821 (Rfree = 0.000) for 2117 atoms. Found 13 (13 requested) and removed 14 (9 requested) atoms. Failed to save intermediate PDB Cycle 27: After refmac, R = 0.2809 (Rfree = 0.000) for 2107 atoms. Found 13 (13 requested) and removed 12 (9 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.2803 (Rfree = 0.000) for 2101 atoms. Found 13 (13 requested) and removed 9 (9 requested) atoms. Cycle 29: After refmac, R = 0.2124 (Rfree = 0.000) for 2096 atoms. Found 8 (13 requested) and removed 12 (9 requested) atoms. Cycle 30: After refmac, R = 0.2027 (Rfree = 0.000) for 2090 atoms. Found 7 (13 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.05 3.54 Search for helices and strands: 0 residues in 0 chains, 2144 seeds are put forward NCS extension: 34 residues added (5 deleted due to clashes), 2178 seeds are put forward Round 1: 123 peptides, 23 chains. Longest chain 15 peptides. Score 0.379 Round 2: 117 peptides, 18 chains. Longest chain 17 peptides. Score 0.471 Round 3: 120 peptides, 17 chains. Longest chain 16 peptides. Score 0.513 Round 4: 137 peptides, 22 chains. Longest chain 14 peptides. Score 0.486 Round 5: 134 peptides, 21 chains. Longest chain 17 peptides. Score 0.494 Taking the results from Round 3 Chains 17, Residues 103, Estimated correctness of the model 15.5 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 4668 reflections ( 99.79 % complete ) and 4622 restraints for refining 2074 atoms. 4220 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2701 (Rfree = 0.000) for 2074 atoms. Found 13 (13 requested) and removed 17 (9 requested) atoms. Cycle 32: After refmac, R = 0.2693 (Rfree = 0.000) for 2063 atoms. Found 13 (13 requested) and removed 13 (9 requested) atoms. Cycle 33: After refmac, R = 0.2646 (Rfree = 0.000) for 2058 atoms. Found 13 (13 requested) and removed 14 (9 requested) atoms. Cycle 34: After refmac, R = 0.2089 (Rfree = 0.000) for 2053 atoms. Found 3 (13 requested) and removed 32 (9 requested) atoms. Failed to save intermediate PDB Cycle 35: After refmac, R = 0.2053 (Rfree = 0.000) for 2020 atoms. Found 9 (13 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.05 3.54 Search for helices and strands: 0 residues in 0 chains, 2057 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 2079 seeds are put forward Round 1: 131 peptides, 23 chains. Longest chain 17 peptides. Score 0.427 Round 2: 144 peptides, 22 chains. Longest chain 13 peptides. Score 0.524 Round 3: 143 peptides, 21 chains. Longest chain 11 peptides. Score 0.541 Round 4: 146 peptides, 24 chains. Longest chain 15 peptides. Score 0.488 Round 5: 134 peptides, 23 chains. Longest chain 12 peptides. Score 0.445 Taking the results from Round 3 Chains 22, Residues 122, Estimated correctness of the model 24.2 % 3 chains (28 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 4668 reflections ( 99.79 % complete ) and 4222 restraints for refining 2035 atoms. 3683 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2714 (Rfree = 0.000) for 2035 atoms. Found 13 (13 requested) and removed 16 (9 requested) atoms. Cycle 37: After refmac, R = 0.2679 (Rfree = 0.000) for 2025 atoms. Found 13 (13 requested) and removed 12 (9 requested) atoms. Cycle 38: After refmac, R = 0.2534 (Rfree = 0.000) for 2020 atoms. Found 13 (13 requested) and removed 13 (9 requested) atoms. Cycle 39: After refmac, R = 0.2016 (Rfree = 0.000) for 2015 atoms. Found 12 (13 requested) and removed 11 (9 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.1996 (Rfree = 0.000) for 2013 atoms. Found 13 (13 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.07 3.56 Search for helices and strands: 0 residues in 0 chains, 2035 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 2046 seeds are put forward Round 1: 115 peptides, 22 chains. Longest chain 11 peptides. Score 0.355 Round 2: 126 peptides, 18 chains. Longest chain 13 peptides. Score 0.521 Round 3: 137 peptides, 21 chains. Longest chain 13 peptides. Score 0.510 Round 4: 136 peptides, 20 chains. Longest chain 13 peptides. Score 0.528 Round 5: 123 peptides, 19 chains. Longest chain 11 peptides. Score 0.481 Taking the results from Round 4 Chains 20, Residues 116, Estimated correctness of the model 20.2 % 3 chains (16 residues) have been docked in sequence ------------------------------------------------------ 4668 reflections ( 99.79 % complete ) and 4196 restraints for refining 2007 atoms. 3726 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2604 (Rfree = 0.000) for 2007 atoms. Found 13 (13 requested) and removed 11 (9 requested) atoms. Failed to save intermediate PDB Cycle 42: After refmac, R = 0.2611 (Rfree = 0.000) for 2004 atoms. Found 13 (13 requested) and removed 14 (9 requested) atoms. Cycle 43: After refmac, R = 0.2586 (Rfree = 0.000) for 2000 atoms. Found 12 (12 requested) and removed 13 (8 requested) atoms. Failed to save intermediate PDB Cycle 44: After refmac, R = 0.2568 (Rfree = 0.000) for 1996 atoms. Found 12 (12 requested) and removed 9 (8 requested) atoms. Cycle 45: After refmac, R = 0.2536 (Rfree = 0.000) for 1995 atoms. Found 12 (12 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.05 3.54 Search for helices and strands: 0 residues in 0 chains, 2047 seeds are put forward NCS extension: 0 residues added, 2047 seeds are put forward Round 1: 91 peptides, 18 chains. Longest chain 9 peptides. Score 0.307 Round 2: 103 peptides, 18 chains. Longest chain 10 peptides. Score 0.387 Round 3: 106 peptides, 18 chains. Longest chain 10 peptides. Score 0.406 Round 4: 101 peptides, 17 chains. Longest chain 13 peptides. Score 0.401 Round 5: 97 peptides, 16 chains. Longest chain 13 peptides. Score 0.404 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 18, Residues 88, Estimated correctness of the model 0.0 % 3 chains (10 residues) have been docked in sequence Sequence coverage is 11 % Consider running further cycles of model building using 2o1q-3_warpNtrace.pdb as input Building loops using Loopy2018 18 chains (88 residues) following loop building 3 chains (10 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4668 reflections ( 99.79 % complete ) and 4316 restraints for refining 1969 atoms. 3972 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2635 (Rfree = 0.000) for 1969 atoms. Found 0 (12 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2601 (Rfree = 0.000) for 1953 atoms. Found 0 (12 requested) and removed 8 (8 requested) atoms. Failed to save intermediate PDB Cycle 48: After refmac, R = 0.1917 (Rfree = 0.000) for 1944 atoms. Found 0 (12 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.2256 (Rfree = 0.000) for 1936 atoms. Found 0 (12 requested) and removed 8 (8 requested) atoms. Writing output files ... TimeTaking 45.84