null 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 2o8q-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2o8q-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2o8q-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o8q-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/2o8q-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o8q-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/2o8q-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o8q-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 287 and 0 Target number of residues in the AU: 287 Target solvent content: 0.6092 Checking the provided sequence file Detected sequence length: 134 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 268 Adjusted target solvent content: 0.64 Input MTZ file: 2o8q-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: 94 Cell parameters: 103.170 103.170 74.680 90.000 90.000 90.000 Input sequence file: 2o8q-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 2144 target number of atoms Had to go as low as 0.80 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: 29.026 3.200 Wilson plot Bfac: 56.34 6965 reflections ( 98.78 % complete ) and 0 restraints for refining 2368 atoms. Observations/parameters ratio is 0.74 ------------------------------------------------------ Starting model: R = 0.2949 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2738 (Rfree = 0.000) for 2368 atoms. Found 21 (21 requested) and removed 16 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.08 2.54 Search for helices and strands: 0 residues in 0 chains, 2406 seeds are put forward NCS extension: 0 residues added, 2406 seeds are put forward Round 1: 178 peptides, 23 chains. Longest chain 22 peptides. Score 0.537 Round 2: 192 peptides, 21 chains. Longest chain 23 peptides. Score 0.611 Round 3: 200 peptides, 19 chains. Longest chain 22 peptides. Score 0.660 Round 4: 213 peptides, 17 chains. Longest chain 28 peptides. Score 0.717 Round 5: 207 peptides, 20 chains. Longest chain 27 peptides. Score 0.666 Taking the results from Round 4 Chains 20, Residues 196, Estimated correctness of the model 68.7 % 4 chains (70 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 36 A and 40 A 18 chains (197 residues) following loop building 3 chains (73 residues) in sequence following loop building ------------------------------------------------------ 6965 reflections ( 98.78 % complete ) and 3318 restraints for refining 1996 atoms. 2261 conditional restraints added. Observations/parameters ratio is 0.87 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2746 (Rfree = 0.000) for 1996 atoms. Found 17 (17 requested) and removed 15 (8 requested) atoms. Cycle 2: After refmac, R = 0.2546 (Rfree = 0.000) for 1967 atoms. Found 15 (17 requested) and removed 11 (8 requested) atoms. Cycle 3: After refmac, R = 0.2407 (Rfree = 0.000) for 1955 atoms. Found 16 (16 requested) and removed 10 (8 requested) atoms. Cycle 4: After refmac, R = 0.2301 (Rfree = 0.000) for 1955 atoms. Found 6 (16 requested) and removed 9 (8 requested) atoms. Cycle 5: After refmac, R = 0.2333 (Rfree = 0.000) for 1943 atoms. Found 14 (16 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.10 2.56 Search for helices and strands: 0 residues in 0 chains, 1981 seeds are put forward NCS extension: 27 residues added (9 deleted due to clashes), 2008 seeds are put forward Round 1: 195 peptides, 17 chains. Longest chain 24 peptides. Score 0.672 Round 2: 208 peptides, 16 chains. Longest chain 29 peptides. Score 0.717 Round 3: 210 peptides, 17 chains. Longest chain 35 peptides. Score 0.710 Round 4: 204 peptides, 16 chains. Longest chain 32 peptides. Score 0.707 Round 5: 219 peptides, 16 chains. Longest chain 37 peptides. Score 0.741 Taking the results from Round 5 Chains 17, Residues 203, Estimated correctness of the model 73.4 % 3 chains (66 residues) have been docked in sequence Building loops using Loopy2018 17 chains (203 residues) following loop building 3 chains (66 residues) in sequence following loop building ------------------------------------------------------ 6965 reflections ( 98.78 % complete ) and 3299 restraints for refining 1957 atoms. 2203 conditional restraints added. Observations/parameters ratio is 0.89 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2720 (Rfree = 0.000) for 1957 atoms. Found 15 (15 requested) and removed 13 (8 requested) atoms. Cycle 7: After refmac, R = 0.2512 (Rfree = 0.000) for 1940 atoms. Found 13 (15 requested) and removed 11 (8 requested) atoms. Cycle 8: After refmac, R = 0.2453 (Rfree = 0.000) for 1934 atoms. Found 15 (15 requested) and removed 14 (8 requested) atoms. Cycle 9: After refmac, R = 0.2457 (Rfree = 0.000) for 1922 atoms. Found 14 (14 requested) and removed 11 (8 requested) atoms. Cycle 10: After refmac, R = 0.2437 (Rfree = 0.000) for 1918 atoms. Found 9 (14 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.08 2.54 Search for helices and strands: 0 residues in 0 chains, 1951 seeds are put forward NCS extension: 50 residues added (6 deleted due to clashes), 2001 seeds are put forward Round 1: 207 peptides, 17 chains. Longest chain 38 peptides. Score 0.703 Round 2: 213 peptides, 15 chains. Longest chain 57 peptides. Score 0.739 Round 3: 209 peptides, 17 chains. Longest chain 29 peptides. Score 0.707 Round 4: 210 peptides, 18 chains. Longest chain 37 peptides. Score 0.698 Round 5: 213 peptides, 17 chains. Longest chain 27 peptides. Score 0.717 Taking the results from Round 2 Chains 17, Residues 198, Estimated correctness of the model 73.0 % 3 chains (92 residues) have been docked in sequence Building loops using Loopy2018 17 chains (198 residues) following loop building 3 chains (92 residues) in sequence following loop building ------------------------------------------------------ 6965 reflections ( 98.78 % complete ) and 3173 restraints for refining 1957 atoms. 2007 conditional restraints added. Observations/parameters ratio is 0.89 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2681 (Rfree = 0.000) for 1957 atoms. Found 14 (14 requested) and removed 25 (8 requested) atoms. Cycle 12: After refmac, R = 0.2453 (Rfree = 0.000) for 1931 atoms. Found 13 (13 requested) and removed 13 (8 requested) atoms. Cycle 13: After refmac, R = 0.2374 (Rfree = 0.000) for 1920 atoms. Found 7 (13 requested) and removed 14 (8 requested) atoms. Cycle 14: After refmac, R = 0.2293 (Rfree = 0.000) for 1903 atoms. Found 13 (13 requested) and removed 14 (8 requested) atoms. Cycle 15: After refmac, R = 0.2307 (Rfree = 0.000) for 1895 atoms. Found 12 (12 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.11 2.57 Search for helices and strands: 0 residues in 0 chains, 1943 seeds are put forward NCS extension: 50 residues added (45 deleted due to clashes), 1993 seeds are put forward Round 1: 205 peptides, 17 chains. Longest chain 39 peptides. Score 0.698 Round 2: 216 peptides, 15 chains. Longest chain 51 peptides. Score 0.745 Round 3: 214 peptides, 15 chains. Longest chain 46 peptides. Score 0.741 Round 4: 223 peptides, 11 chains. Longest chain 53 peptides. Score 0.799 Round 5: 218 peptides, 15 chains. Longest chain 46 peptides. Score 0.750 Taking the results from Round 4 Chains 14, Residues 212, Estimated correctness of the model 83.3 % 4 chains (119 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 80 A and 91 A 11 chains (214 residues) following loop building 3 chains (129 residues) in sequence following loop building ------------------------------------------------------ 6965 reflections ( 98.78 % complete ) and 2660 restraints for refining 1957 atoms. 1264 conditional restraints added. Observations/parameters ratio is 0.89 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2775 (Rfree = 0.000) for 1957 atoms. Found 12 (12 requested) and removed 28 (8 requested) atoms. Cycle 17: After refmac, R = 0.2488 (Rfree = 0.000) for 1927 atoms. Found 12 (12 requested) and removed 14 (8 requested) atoms. Cycle 18: After refmac, R = 0.2332 (Rfree = 0.000) for 1914 atoms. Found 11 (11 requested) and removed 19 (8 requested) atoms. Cycle 19: After refmac, R = 0.2244 (Rfree = 0.000) for 1898 atoms. Found 11 (11 requested) and removed 12 (8 requested) atoms. Cycle 20: After refmac, R = 0.2401 (Rfree = 0.000) for 1895 atoms. Found 11 (11 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.06 2.53 Search for helices and strands: 0 residues in 0 chains, 1941 seeds are put forward NCS extension: 87 residues added (13 deleted due to clashes), 2028 seeds are put forward Round 1: 209 peptides, 17 chains. Longest chain 30 peptides. Score 0.707 Round 2: 213 peptides, 13 chains. Longest chain 65 peptides. Score 0.760 Round 3: 210 peptides, 16 chains. Longest chain 37 peptides. Score 0.721 Round 4: 223 peptides, 15 chains. Longest chain 42 peptides. Score 0.760 Round 5: 224 peptides, 14 chains. Longest chain 42 peptides. Score 0.772 Taking the results from Round 5 Chains 19, Residues 210, Estimated correctness of the model 78.9 % 5 chains (107 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 83 A and 88 A Built loop between residues 81 B and 85 B 16 chains (215 residues) following loop building 3 chains (114 residues) in sequence following loop building ------------------------------------------------------ 6965 reflections ( 98.78 % complete ) and 2873 restraints for refining 1957 atoms. 1519 conditional restraints added. Observations/parameters ratio is 0.89 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2685 (Rfree = 0.000) for 1957 atoms. Found 10 (10 requested) and removed 18 (8 requested) atoms. Cycle 22: After refmac, R = 0.2505 (Rfree = 0.000) for 1942 atoms. Found 10 (10 requested) and removed 12 (8 requested) atoms. Cycle 23: After refmac, R = 0.2477 (Rfree = 0.000) for 1934 atoms. Found 10 (10 requested) and removed 16 (8 requested) atoms. Cycle 24: After refmac, R = 0.2497 (Rfree = 0.000) for 1921 atoms. Found 9 (9 requested) and removed 11 (8 requested) atoms. Cycle 25: After refmac, R = 0.2353 (Rfree = 0.000) for 1912 atoms. Found 9 (9 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.08 2.54 Search for helices and strands: 0 residues in 0 chains, 1954 seeds are put forward NCS extension: 37 residues added (12 deleted due to clashes), 1991 seeds are put forward Round 1: 215 peptides, 18 chains. Longest chain 50 peptides. Score 0.710 Round 2: 212 peptides, 15 chains. Longest chain 34 peptides. Score 0.737 Round 3: 209 peptides, 17 chains. Longest chain 30 peptides. Score 0.707 Round 4: 215 peptides, 18 chains. Longest chain 27 peptides. Score 0.710 Round 5: 224 peptides, 14 chains. Longest chain 54 peptides. Score 0.772 Taking the results from Round 5 Chains 16, Residues 210, Estimated correctness of the model 78.9 % 3 chains (114 residues) have been docked in sequence Building loops using Loopy2018 16 chains (210 residues) following loop building 3 chains (114 residues) in sequence following loop building ------------------------------------------------------ 6965 reflections ( 98.78 % complete ) and 2870 restraints for refining 1957 atoms. 1527 conditional restraints added. Observations/parameters ratio is 0.89 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2586 (Rfree = 0.000) for 1957 atoms. Found 8 (8 requested) and removed 22 (8 requested) atoms. Cycle 27: After refmac, R = 0.2367 (Rfree = 0.000) for 1932 atoms. Found 8 (8 requested) and removed 12 (8 requested) atoms. Cycle 28: After refmac, R = 0.2280 (Rfree = 0.000) for 1921 atoms. Found 2 (8 requested) and removed 10 (8 requested) atoms. Cycle 29: After refmac, R = 0.2263 (Rfree = 0.000) for 1903 atoms. Found 8 (8 requested) and removed 8 (8 requested) atoms. Cycle 30: After refmac, R = 0.2211 (Rfree = 0.000) for 1901 atoms. Found 6 (8 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.08 2.54 Search for helices and strands: 0 residues in 0 chains, 1933 seeds are put forward NCS extension: 36 residues added (12 deleted due to clashes), 1969 seeds are put forward Round 1: 197 peptides, 17 chains. Longest chain 27 peptides. Score 0.678 Round 2: 200 peptides, 14 chains. Longest chain 43 peptides. Score 0.721 Round 3: 203 peptides, 12 chains. Longest chain 51 peptides. Score 0.750 Round 4: 212 peptides, 14 chains. Longest chain 51 peptides. Score 0.748 Round 5: 201 peptides, 17 chains. Longest chain 41 peptides. Score 0.688 Taking the results from Round 3 Chains 14, Residues 191, Estimated correctness of the model 75.1 % 5 chains (131 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 82 A and 85 A 13 chains (192 residues) following loop building 4 chains (133 residues) in sequence following loop building ------------------------------------------------------ 6965 reflections ( 98.78 % complete ) and 2816 restraints for refining 1957 atoms. 1465 conditional restraints added. Observations/parameters ratio is 0.89 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2610 (Rfree = 0.000) for 1957 atoms. Found 8 (8 requested) and removed 29 (8 requested) atoms. Cycle 32: After refmac, R = 0.2637 (Rfree = 0.000) for 1930 atoms. Found 8 (8 requested) and removed 13 (8 requested) atoms. Cycle 33: After refmac, R = 0.2386 (Rfree = 0.000) for 1911 atoms. Found 8 (8 requested) and removed 18 (8 requested) atoms. Cycle 34: After refmac, R = 0.2297 (Rfree = 0.000) for 1893 atoms. Found 8 (8 requested) and removed 13 (8 requested) atoms. Cycle 35: After refmac, R = 0.2224 (Rfree = 0.000) for 1880 atoms. Found 8 (8 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.10 2.56 Search for helices and strands: 0 residues in 0 chains, 1916 seeds are put forward NCS extension: 82 residues added (2 deleted due to clashes), 1998 seeds are put forward Round 1: 193 peptides, 19 chains. Longest chain 43 peptides. Score 0.641 Round 2: 206 peptides, 16 chains. Longest chain 30 peptides. Score 0.712 Round 3: 211 peptides, 16 chains. Longest chain 43 peptides. Score 0.723 Round 4: 207 peptides, 15 chains. Longest chain 40 peptides. Score 0.726 Round 5: 200 peptides, 18 chains. Longest chain 29 peptides. Score 0.673 Taking the results from Round 4 Chains 15, Residues 192, Estimated correctness of the model 70.5 % 3 chains (83 residues) have been docked in sequence Building loops using Loopy2018 15 chains (192 residues) following loop building 3 chains (83 residues) in sequence following loop building ------------------------------------------------------ 6965 reflections ( 98.78 % complete ) and 3285 restraints for refining 1957 atoms. 2155 conditional restraints added. Observations/parameters ratio is 0.89 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2610 (Rfree = 0.000) for 1957 atoms. Found 8 (8 requested) and removed 19 (8 requested) atoms. Cycle 37: After refmac, R = 0.2461 (Rfree = 0.000) for 1936 atoms. Found 8 (8 requested) and removed 16 (8 requested) atoms. Cycle 38: After refmac, R = 0.2414 (Rfree = 0.000) for 1917 atoms. Found 8 (8 requested) and removed 15 (8 requested) atoms. Cycle 39: After refmac, R = 0.2368 (Rfree = 0.000) for 1905 atoms. Found 8 (8 requested) and removed 15 (8 requested) atoms. Cycle 40: After refmac, R = 0.2221 (Rfree = 0.000) for 1893 atoms. Found 8 (8 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.06 2.53 Search for helices and strands: 0 residues in 0 chains, 1932 seeds are put forward NCS extension: 14 residues added (11 deleted due to clashes), 1946 seeds are put forward Round 1: 202 peptides, 13 chains. Longest chain 41 peptides. Score 0.737 Round 2: 206 peptides, 15 chains. Longest chain 41 peptides. Score 0.723 Round 3: 211 peptides, 13 chains. Longest chain 48 peptides. Score 0.756 Round 4: 214 peptides, 13 chains. Longest chain 41 peptides. Score 0.762 Round 5: 205 peptides, 12 chains. Longest chain 65 peptides. Score 0.755 Taking the results from Round 4 Chains 13, Residues 201, Estimated correctness of the model 77.2 % 6 chains (145 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 88 A and 91 A 12 chains (203 residues) following loop building 5 chains (147 residues) in sequence following loop building ------------------------------------------------------ 6965 reflections ( 98.78 % complete ) and 2635 restraints for refining 1956 atoms. 1206 conditional restraints added. Observations/parameters ratio is 0.89 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2401 (Rfree = 0.000) for 1956 atoms. Found 8 (8 requested) and removed 22 (8 requested) atoms. Cycle 42: After refmac, R = 0.2282 (Rfree = 0.000) for 1938 atoms. Found 8 (8 requested) and removed 13 (8 requested) atoms. Cycle 43: After refmac, R = 0.2288 (Rfree = 0.000) for 1928 atoms. Found 8 (8 requested) and removed 12 (8 requested) atoms. Cycle 44: After refmac, R = 0.2205 (Rfree = 0.000) for 1921 atoms. Found 8 (8 requested) and removed 8 (8 requested) atoms. Cycle 45: After refmac, R = 0.2221 (Rfree = 0.000) for 1916 atoms. Found 8 (8 requested) and removed 14 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.13 2.58 Search for helices and strands: 0 residues in 0 chains, 1965 seeds are put forward NCS extension: 34 residues added (35 deleted due to clashes), 1999 seeds are put forward Round 1: 201 peptides, 13 chains. Longest chain 51 peptides. Score 0.735 Round 2: 211 peptides, 14 chains. Longest chain 35 peptides. Score 0.746 Round 3: 213 peptides, 12 chains. Longest chain 54 peptides. Score 0.771 Round 4: 209 peptides, 14 chains. Longest chain 42 peptides. Score 0.741 Round 5: 203 peptides, 14 chains. Longest chain 41 peptides. Score 0.728 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 17, Residues 201, Estimated correctness of the model 78.8 % 6 chains (109 residues) have been docked in sequence Sequence coverage is 53 % Consider running further cycles of model building using 2o8q-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 81 A and 88 A 15 chains (201 residues) following loop building 5 chains (115 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6965 reflections ( 98.78 % complete ) and 2859 restraints for refining 1957 atoms. 1587 conditional restraints added. Observations/parameters ratio is 0.89 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2546 (Rfree = 0.000) for 1957 atoms. Found 0 (8 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2340 (Rfree = 0.000) for 1941 atoms. Found 0 (8 requested) and removed 4 (8 requested) atoms. Cycle 48: After refmac, R = 0.2219 (Rfree = 0.000) for 1932 atoms. Found 0 (8 requested) and removed 5 (8 requested) atoms. Cycle 49: After refmac, R = 0.2160 (Rfree = 0.000) for 1925 atoms. Found 0 (8 requested) and removed 3 (8 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:11:26 GMT 2018 Job finished. TimeTaking 48.36 Used memory is bytes: 21147760