null Tue 25 Dec 19:27:57 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-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2o8q-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2o8q-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o8q-3.4-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-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o8q-3.4-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 19:28:06 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-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o8q-3.4-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 274 and 0 Target number of residues in the AU: 274 Target solvent content: 0.6269 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-3.4-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-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 2144 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: 29.026 3.400 Wilson plot Bfac: 64.56 5837 reflections ( 98.66 % complete ) and 0 restraints for refining 2363 atoms. Observations/parameters ratio is 0.62 ------------------------------------------------------ Starting model: R = 0.3016 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2292 (Rfree = 0.000) for 2363 atoms. Found 10 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.30 2.72 Search for helices and strands: 0 residues in 0 chains, 2386 seeds are put forward NCS extension: 0 residues added, 2386 seeds are put forward Round 1: 179 peptides, 24 chains. Longest chain 29 peptides. Score 0.524 Round 2: 204 peptides, 19 chains. Longest chain 41 peptides. Score 0.671 Round 3: 195 peptides, 14 chains. Longest chain 39 peptides. Score 0.709 Round 4: 195 peptides, 18 chains. Longest chain 23 peptides. Score 0.660 Round 5: 194 peptides, 14 chains. Longest chain 51 peptides. Score 0.707 Taking the results from Round 3 Chains 15, Residues 181, Estimated correctness of the model 60.2 % 4 chains (93 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 50 A and 55 A Built loop between residues 82 A and 89 A 13 chains (191 residues) following loop building 2 chains (103 residues) in sequence following loop building ------------------------------------------------------ 5837 reflections ( 98.66 % complete ) and 3234 restraints for refining 2071 atoms. 2035 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2678 (Rfree = 0.000) for 2071 atoms. Found 13 (15 requested) and removed 27 (7 requested) atoms. Cycle 2: After refmac, R = 0.2429 (Rfree = 0.000) for 2004 atoms. Found 12 (15 requested) and removed 14 (7 requested) atoms. Cycle 3: After refmac, R = 0.2358 (Rfree = 0.000) for 1984 atoms. Found 14 (14 requested) and removed 18 (7 requested) atoms. Cycle 4: After refmac, R = 0.2367 (Rfree = 0.000) for 1972 atoms. Found 13 (13 requested) and removed 9 (7 requested) atoms. Cycle 5: After refmac, R = 0.2245 (Rfree = 0.000) for 1959 atoms. Found 13 (13 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.25 2.68 Search for helices and strands: 0 residues in 0 chains, 1995 seeds are put forward NCS extension: 43 residues added (15 deleted due to clashes), 2038 seeds are put forward Round 1: 188 peptides, 17 chains. Longest chain 33 peptides. Score 0.654 Round 2: 207 peptides, 12 chains. Longest chain 36 peptides. Score 0.759 Round 3: 212 peptides, 16 chains. Longest chain 55 peptides. Score 0.726 Round 4: 208 peptides, 14 chains. Longest chain 38 peptides. Score 0.739 Round 5: 211 peptides, 17 chains. Longest chain 25 peptides. Score 0.712 Taking the results from Round 2 Chains 14, Residues 195, Estimated correctness of the model 71.8 % 5 chains (124 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 51 B and 55 B 14 chains (196 residues) following loop building 4 chains (127 residues) in sequence following loop building ------------------------------------------------------ 5837 reflections ( 98.66 % complete ) and 2737 restraints for refining 1949 atoms. 1467 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2756 (Rfree = 0.000) for 1949 atoms. Found 13 (13 requested) and removed 36 (7 requested) atoms. Cycle 7: After refmac, R = 0.2503 (Rfree = 0.000) for 1910 atoms. Found 7 (12 requested) and removed 14 (7 requested) atoms. Cycle 8: After refmac, R = 0.2418 (Rfree = 0.000) for 1893 atoms. Found 11 (12 requested) and removed 11 (7 requested) atoms. Cycle 9: After refmac, R = 0.2355 (Rfree = 0.000) for 1884 atoms. Found 12 (12 requested) and removed 9 (7 requested) atoms. Cycle 10: After refmac, R = 0.2321 (Rfree = 0.000) for 1881 atoms. Found 7 (11 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.30 2.72 Search for helices and strands: 0 residues in 0 chains, 1918 seeds are put forward NCS extension: 23 residues added (26 deleted due to clashes), 1941 seeds are put forward Round 1: 188 peptides, 17 chains. Longest chain 33 peptides. Score 0.654 Round 2: 202 peptides, 13 chains. Longest chain 67 peptides. Score 0.737 Round 3: 209 peptides, 10 chains. Longest chain 70 peptides. Score 0.783 Round 4: 203 peptides, 12 chains. Longest chain 62 peptides. Score 0.750 Round 5: 207 peptides, 13 chains. Longest chain 60 peptides. Score 0.748 Taking the results from Round 3 Chains 11, Residues 199, Estimated correctness of the model 76.7 % 3 chains (120 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 53 A and 57 A 10 chains (202 residues) following loop building 2 chains (123 residues) in sequence following loop building ------------------------------------------------------ 5837 reflections ( 98.66 % complete ) and 2831 restraints for refining 1950 atoms. 1501 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2544 (Rfree = 0.000) for 1950 atoms. Found 11 (11 requested) and removed 22 (7 requested) atoms. Cycle 12: After refmac, R = 0.2457 (Rfree = 0.000) for 1930 atoms. Found 11 (11 requested) and removed 22 (7 requested) atoms. Cycle 13: After refmac, R = 0.2350 (Rfree = 0.000) for 1914 atoms. Found 3 (11 requested) and removed 8 (7 requested) atoms. Cycle 14: After refmac, R = 0.2299 (Rfree = 0.000) for 1908 atoms. Found 2 (10 requested) and removed 7 (7 requested) atoms. Cycle 15: After refmac, R = 0.2287 (Rfree = 0.000) for 1901 atoms. Found 3 (10 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.26 2.69 Search for helices and strands: 0 residues in 0 chains, 1939 seeds are put forward NCS extension: 45 residues added (76 deleted due to clashes), 1984 seeds are put forward Round 1: 192 peptides, 14 chains. Longest chain 43 peptides. Score 0.702 Round 2: 203 peptides, 17 chains. Longest chain 41 peptides. Score 0.693 Round 3: 191 peptides, 13 chains. Longest chain 41 peptides. Score 0.712 Round 4: 189 peptides, 16 chains. Longest chain 37 peptides. Score 0.669 Round 5: 193 peptides, 15 chains. Longest chain 34 peptides. Score 0.692 Taking the results from Round 3 Chains 15, Residues 178, Estimated correctness of the model 60.9 % 5 chains (95 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 48 B and 57 B 13 chains (182 residues) following loop building 4 chains (103 residues) in sequence following loop building ------------------------------------------------------ 5837 reflections ( 98.66 % complete ) and 3160 restraints for refining 1950 atoms. 2016 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2464 (Rfree = 0.000) for 1950 atoms. Found 10 (10 requested) and removed 16 (7 requested) atoms. Cycle 17: After refmac, R = 0.2574 (Rfree = 0.000) for 1931 atoms. Found 10 (10 requested) and removed 13 (7 requested) atoms. Cycle 18: After refmac, R = 0.2426 (Rfree = 0.000) for 1914 atoms. Found 9 (9 requested) and removed 14 (7 requested) atoms. Cycle 19: After refmac, R = 0.2437 (Rfree = 0.000) for 1904 atoms. Found 9 (9 requested) and removed 12 (7 requested) atoms. Cycle 20: After refmac, R = 0.2550 (Rfree = 0.000) for 1896 atoms. Found 9 (9 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.24 2.68 Search for helices and strands: 0 residues in 0 chains, 1925 seeds are put forward NCS extension: 53 residues added (11 deleted due to clashes), 1978 seeds are put forward Round 1: 192 peptides, 16 chains. Longest chain 33 peptides. Score 0.677 Round 2: 200 peptides, 15 chains. Longest chain 51 peptides. Score 0.709 Round 3: 208 peptides, 15 chains. Longest chain 38 peptides. Score 0.728 Round 4: 215 peptides, 16 chains. Longest chain 55 peptides. Score 0.732 Round 5: 203 peptides, 15 chains. Longest chain 56 peptides. Score 0.717 Taking the results from Round 4 Chains 17, Residues 199, Estimated correctness of the model 65.7 % 4 chains (64 residues) have been docked in sequence Building loops using Loopy2018 17 chains (199 residues) following loop building 4 chains (64 residues) in sequence following loop building ------------------------------------------------------ 5837 reflections ( 98.66 % complete ) and 3471 restraints for refining 1950 atoms. 2434 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2998 (Rfree = 0.000) for 1950 atoms. Found 8 (8 requested) and removed 43 (7 requested) atoms. Cycle 22: After refmac, R = 0.2568 (Rfree = 0.000) for 1905 atoms. Found 8 (8 requested) and removed 24 (7 requested) atoms. Cycle 23: After refmac, R = 0.2497 (Rfree = 0.000) for 1883 atoms. Found 8 (8 requested) and removed 10 (7 requested) atoms. Cycle 24: After refmac, R = 0.2419 (Rfree = 0.000) for 1880 atoms. Found 6 (8 requested) and removed 10 (7 requested) atoms. Cycle 25: After refmac, R = 0.2376 (Rfree = 0.000) for 1875 atoms. Found 7 (7 requested) and removed 13 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.22 2.66 Search for helices and strands: 0 residues in 0 chains, 1899 seeds are put forward NCS extension: 18 residues added (7 deleted due to clashes), 1917 seeds are put forward Round 1: 189 peptides, 19 chains. Longest chain 40 peptides. Score 0.629 Round 2: 207 peptides, 14 chains. Longest chain 35 peptides. Score 0.737 Round 3: 203 peptides, 17 chains. Longest chain 28 peptides. Score 0.693 Round 4: 219 peptides, 14 chains. Longest chain 42 peptides. Score 0.762 Round 5: 208 peptides, 14 chains. Longest chain 56 peptides. Score 0.739 Taking the results from Round 4 Chains 18, Residues 205, Estimated correctness of the model 72.4 % 4 chains (81 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 107 A and 118 A 17 chains (207 residues) following loop building 3 chains (91 residues) in sequence following loop building ------------------------------------------------------ 5837 reflections ( 98.66 % complete ) and 3025 restraints for refining 1950 atoms. 1873 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2731 (Rfree = 0.000) for 1950 atoms. Found 7 (7 requested) and removed 28 (7 requested) atoms. Cycle 27: After refmac, R = 0.2550 (Rfree = 0.000) for 1923 atoms. Found 7 (7 requested) and removed 16 (7 requested) atoms. Cycle 28: After refmac, R = 0.2453 (Rfree = 0.000) for 1906 atoms. Found 7 (7 requested) and removed 10 (7 requested) atoms. Cycle 29: After refmac, R = 0.2597 (Rfree = 0.000) for 1901 atoms. Found 7 (7 requested) and removed 10 (7 requested) atoms. Cycle 30: After refmac, R = 0.2445 (Rfree = 0.000) for 1892 atoms. Found 7 (7 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.29 2.72 Search for helices and strands: 0 residues in 0 chains, 1928 seeds are put forward NCS extension: 90 residues added (6 deleted due to clashes), 2018 seeds are put forward Round 1: 179 peptides, 18 chains. Longest chain 33 peptides. Score 0.614 Round 2: 192 peptides, 18 chains. Longest chain 38 peptides. Score 0.651 Round 3: 186 peptides, 15 chains. Longest chain 58 peptides. Score 0.674 Round 4: 180 peptides, 15 chains. Longest chain 28 peptides. Score 0.658 Round 5: 194 peptides, 17 chains. Longest chain 27 peptides. Score 0.670 Taking the results from Round 3 Chains 18, Residues 171, Estimated correctness of the model 50.9 % 3 chains (47 residues) have been docked in sequence ------------------------------------------------------ 5837 reflections ( 98.66 % complete ) and 3714 restraints for refining 1950 atoms. 2838 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2888 (Rfree = 0.000) for 1950 atoms. Found 7 (7 requested) and removed 14 (7 requested) atoms. Cycle 32: After refmac, R = 0.2522 (Rfree = 0.000) for 1938 atoms. Found 7 (7 requested) and removed 10 (7 requested) atoms. Cycle 33: After refmac, R = 0.2367 (Rfree = 0.000) for 1926 atoms. Found 4 (7 requested) and removed 9 (7 requested) atoms. Cycle 34: After refmac, R = 0.2348 (Rfree = 0.000) for 1920 atoms. Found 7 (7 requested) and removed 9 (7 requested) atoms. Cycle 35: After refmac, R = 0.2396 (Rfree = 0.000) for 1917 atoms. Found 7 (7 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.28 2.71 Search for helices and strands: 0 residues in 0 chains, 1953 seeds are put forward NCS extension: 49 residues added (1 deleted due to clashes), 2002 seeds are put forward Round 1: 176 peptides, 22 chains. Longest chain 28 peptides. Score 0.545 Round 2: 195 peptides, 17 chains. Longest chain 30 peptides. Score 0.672 Round 3: 182 peptides, 19 chains. Longest chain 27 peptides. Score 0.609 Round 4: 195 peptides, 20 chains. Longest chain 29 peptides. Score 0.633 Round 5: 198 peptides, 15 chains. Longest chain 41 peptides. Score 0.705 Taking the results from Round 5 Chains 17, Residues 183, Estimated correctness of the model 59.1 % 3 chains (43 residues) have been docked in sequence Building loops using Loopy2018 17 chains (183 residues) following loop building 3 chains (43 residues) in sequence following loop building ------------------------------------------------------ 5837 reflections ( 98.66 % complete ) and 3716 restraints for refining 1949 atoms. 2838 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2639 (Rfree = 0.000) for 1949 atoms. Found 7 (7 requested) and removed 42 (7 requested) atoms. Cycle 37: After refmac, R = 0.2451 (Rfree = 0.000) for 1910 atoms. Found 7 (7 requested) and removed 11 (7 requested) atoms. Cycle 38: After refmac, R = 0.2475 (Rfree = 0.000) for 1902 atoms. Found 7 (7 requested) and removed 11 (7 requested) atoms. Cycle 39: After refmac, R = 0.2321 (Rfree = 0.000) for 1895 atoms. Found 7 (7 requested) and removed 8 (7 requested) atoms. Cycle 40: After refmac, R = 0.2192 (Rfree = 0.000) for 1893 atoms. Found 5 (7 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.26 2.69 Search for helices and strands: 0 residues in 0 chains, 1940 seeds are put forward NCS extension: 33 residues added (9 deleted due to clashes), 1973 seeds are put forward Round 1: 175 peptides, 20 chains. Longest chain 23 peptides. Score 0.572 Round 2: 188 peptides, 19 chains. Longest chain 35 peptides. Score 0.627 Round 3: 202 peptides, 15 chains. Longest chain 48 peptides. Score 0.714 Round 4: 186 peptides, 18 chains. Longest chain 41 peptides. Score 0.634 Round 5: 186 peptides, 20 chains. Longest chain 33 peptides. Score 0.607 Taking the results from Round 3 Chains 16, Residues 187, Estimated correctness of the model 61.4 % 1 chains (24 residues) have been docked in sequence ------------------------------------------------------ 5837 reflections ( 98.66 % complete ) and 3804 restraints for refining 1950 atoms. 2964 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2527 (Rfree = 0.000) for 1950 atoms. Found 7 (7 requested) and removed 9 (7 requested) atoms. Cycle 42: After refmac, R = 0.2401 (Rfree = 0.000) for 1939 atoms. Found 7 (7 requested) and removed 9 (7 requested) atoms. Cycle 43: After refmac, R = 0.2407 (Rfree = 0.000) for 1932 atoms. Found 7 (7 requested) and removed 11 (7 requested) atoms. Cycle 44: After refmac, R = 0.2305 (Rfree = 0.000) for 1925 atoms. Found 7 (7 requested) and removed 9 (7 requested) atoms. Cycle 45: After refmac, R = 0.2331 (Rfree = 0.000) for 1921 atoms. Found 7 (7 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.27 2.70 Search for helices and strands: 0 residues in 0 chains, 1950 seeds are put forward NCS extension: 33 residues added (9 deleted due to clashes), 1983 seeds are put forward Round 1: 181 peptides, 18 chains. Longest chain 35 peptides. Score 0.620 Round 2: 195 peptides, 16 chains. Longest chain 39 peptides. Score 0.685 Round 3: 195 peptides, 16 chains. Longest chain 42 peptides. Score 0.685 Round 4: 195 peptides, 17 chains. Longest chain 34 peptides. Score 0.672 Round 5: 186 peptides, 21 chains. Longest chain 21 peptides. Score 0.592 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 18, Residues 179, Estimated correctness of the model 53.9 % 2 chains (51 residues) have been docked in sequence Sequence coverage is 28 % Consider running further cycles of model building using 2o8q-3_warpNtrace.pdb as input Building loops using Loopy2018 18 chains (179 residues) following loop building 2 chains (51 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5837 reflections ( 98.66 % complete ) and 3620 restraints for refining 1950 atoms. 2707 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2747 (Rfree = 0.000) for 1950 atoms. Found 0 (7 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.2509 (Rfree = 0.000) for 1939 atoms. Found 0 (7 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.2458 (Rfree = 0.000) for 1927 atoms. Found 0 (7 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.2373 (Rfree = 0.000) for 1917 atoms. Found 0 (7 requested) and removed 7 (7 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:17:26 GMT 2018 Job finished. TimeTaking 49.48 Used memory is bytes: 7407096