null Sun 23 Dec 23:42:49 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2o8q-2.5-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2o8q-2.5-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2o8q-2.5-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2o8q-2.5-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2o8q-2.5-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2o8q-2.5-parrot-mrncs ############### 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 23:42:54 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/mrncs/ArpWArp/wArpResults/WorkingDir/2o8q-2.5-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2o8q-2.5-parrot-mrncs/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 347 and 0 Target number of residues in the AU: 347 Target solvent content: 0.5275 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-2.5-parrot-mrncs.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-2.5-parrot-mrncs.fasta_lf Building free atoms model in initial map for 2144 target number of atoms Had to go as low as 0.75 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 2.501 Wilson plot Bfac: 29.54 14305 reflections ( 98.97 % complete ) and 0 restraints for refining 2395 atoms. Observations/parameters ratio is 1.49 ------------------------------------------------------ Starting model: R = 0.3021 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2237 (Rfree = 0.000) for 2395 atoms. Found 34 (43 requested) and removed 23 (21 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.51 2.07 NCS extension: 0 residues added, 2406 seeds are put forward Round 1: 192 peptides, 21 chains. Longest chain 32 peptides. Score 0.611 Round 2: 205 peptides, 16 chains. Longest chain 47 peptides. Score 0.709 Round 3: 221 peptides, 12 chains. Longest chain 56 peptides. Score 0.786 Round 4: 222 peptides, 15 chains. Longest chain 35 peptides. Score 0.758 Round 5: 231 peptides, 12 chains. Longest chain 53 peptides. Score 0.803 Taking the results from Round 5 Chains 13, Residues 219, Estimated correctness of the model 92.6 % 8 chains (196 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 76 A and 84 A Built loop between residues 116 A and 120 A Built loop between residues 19 B and 25 B Built loop between residues 62 B and 66 B Built loop between residues 117 B and 120 B 7 chains (236 residues) following loop building 3 chains (216 residues) in sequence following loop building ------------------------------------------------------ 14305 reflections ( 98.97 % complete ) and 2458 restraints for refining 2218 atoms. 635 conditional restraints added. Observations/parameters ratio is 1.61 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2603 (Rfree = 0.000) for 2218 atoms. Found 40 (40 requested) and removed 26 (20 requested) atoms. Cycle 2: After refmac, R = 0.2381 (Rfree = 0.000) for 2196 atoms. Found 29 (39 requested) and removed 20 (20 requested) atoms. Cycle 3: After refmac, R = 0.2279 (Rfree = 0.000) for 2189 atoms. Found 28 (37 requested) and removed 21 (19 requested) atoms. Cycle 4: After refmac, R = 0.2197 (Rfree = 0.000) for 2187 atoms. Found 28 (37 requested) and removed 20 (19 requested) atoms. Cycle 5: After refmac, R = 0.2119 (Rfree = 0.000) for 2187 atoms. Found 25 (36 requested) and removed 20 (19 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.45 2.02 NCS extension: 40 residues added (80 deleted due to clashes), 2242 seeds are put forward Round 1: 225 peptides, 8 chains. Longest chain 68 peptides. Score 0.829 Round 2: 227 peptides, 9 chains. Longest chain 65 peptides. Score 0.824 Round 3: 227 peptides, 9 chains. Longest chain 70 peptides. Score 0.824 Round 4: 229 peptides, 9 chains. Longest chain 68 peptides. Score 0.827 Round 5: 232 peptides, 6 chains. Longest chain 84 peptides. Score 0.856 Taking the results from Round 5 Chains 8, Residues 226, Estimated correctness of the model 95.8 % 4 chains (200 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 19 A and 26 A Built loop between residues 47 B and 57 B 5 chains (240 residues) following loop building 2 chains (215 residues) in sequence following loop building ------------------------------------------------------ 14305 reflections ( 98.97 % complete ) and 2445 restraints for refining 2174 atoms. 592 conditional restraints added. Observations/parameters ratio is 1.65 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2368 (Rfree = 0.000) for 2174 atoms. Found 35 (35 requested) and removed 24 (19 requested) atoms. Cycle 7: After refmac, R = 0.2154 (Rfree = 0.000) for 2182 atoms. Found 34 (34 requested) and removed 20 (19 requested) atoms. Cycle 8: After refmac, R = 0.2045 (Rfree = 0.000) for 2185 atoms. Found 25 (34 requested) and removed 19 (19 requested) atoms. Cycle 9: After refmac, R = 0.1964 (Rfree = 0.000) for 2188 atoms. Found 15 (33 requested) and removed 19 (19 requested) atoms. Cycle 10: After refmac, R = 0.1947 (Rfree = 0.000) for 2177 atoms. Found 21 (32 requested) and removed 19 (19 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.45 2.02 NCS extension: 20 residues added (49 deleted due to clashes), 2203 seeds are put forward Round 1: 231 peptides, 10 chains. Longest chain 72 peptides. Score 0.821 Round 2: 238 peptides, 8 chains. Longest chain 97 peptides. Score 0.848 Round 3: 234 peptides, 10 chains. Longest chain 95 peptides. Score 0.826 Round 4: 240 peptides, 8 chains. Longest chain 70 peptides. Score 0.850 Round 5: 233 peptides, 9 chains. Longest chain 92 peptides. Score 0.833 Taking the results from Round 4 Chains 8, Residues 232, Estimated correctness of the model 95.5 % 5 chains (214 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 49 A and 57 A Built loop between residues 48 B and 51 B 5 chains (238 residues) following loop building 3 chains (223 residues) in sequence following loop building ------------------------------------------------------ 14305 reflections ( 98.97 % complete ) and 2393 restraints for refining 2157 atoms. 533 conditional restraints added. Observations/parameters ratio is 1.66 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2160 (Rfree = 0.000) for 2157 atoms. Found 31 (31 requested) and removed 21 (19 requested) atoms. Cycle 12: After refmac, R = 0.1963 (Rfree = 0.000) for 2162 atoms. Found 30 (30 requested) and removed 19 (19 requested) atoms. Cycle 13: After refmac, R = 0.1869 (Rfree = 0.000) for 2169 atoms. Found 30 (30 requested) and removed 20 (19 requested) atoms. Cycle 14: After refmac, R = 0.1816 (Rfree = 0.000) for 2172 atoms. Found 29 (29 requested) and removed 21 (19 requested) atoms. Cycle 15: After refmac, R = 0.1797 (Rfree = 0.000) for 2176 atoms. Found 25 (28 requested) and removed 23 (19 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.45 2.02 NCS extension: 127 residues added (129 deleted due to clashes), 2308 seeds are put forward Round 1: 236 peptides, 10 chains. Longest chain 87 peptides. Score 0.829 Round 2: 238 peptides, 9 chains. Longest chain 55 peptides. Score 0.840 Round 3: 239 peptides, 11 chains. Longest chain 55 peptides. Score 0.825 Round 4: 235 peptides, 11 chains. Longest chain 76 peptides. Score 0.819 Round 5: 238 peptides, 7 chains. Longest chain 95 peptides. Score 0.856 Taking the results from Round 5 Chains 7, Residues 231, Estimated correctness of the model 95.8 % 4 chains (202 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 54 A and 57 A Built loop between residues 116 B and 119 B 5 chains (235 residues) following loop building 2 chains (206 residues) in sequence following loop building ------------------------------------------------------ 14305 reflections ( 98.97 % complete ) and 2365 restraints for refining 2095 atoms. 580 conditional restraints added. Observations/parameters ratio is 1.71 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1986 (Rfree = 0.000) for 2095 atoms. Found 26 (26 requested) and removed 18 (18 requested) atoms. Cycle 17: After refmac, R = 0.1882 (Rfree = 0.000) for 2099 atoms. Found 26 (26 requested) and removed 19 (19 requested) atoms. Cycle 18: After refmac, R = 0.1825 (Rfree = 0.000) for 2102 atoms. Found 25 (25 requested) and removed 20 (19 requested) atoms. Cycle 19: After refmac, R = 0.1799 (Rfree = 0.000) for 2101 atoms. Found 24 (24 requested) and removed 20 (19 requested) atoms. Cycle 20: After refmac, R = 0.1833 (Rfree = 0.000) for 2102 atoms. Found 23 (24 requested) and removed 19 (19 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.49 2.06 NCS extension: 11 residues added (92 deleted due to clashes), 2120 seeds are put forward Round 1: 240 peptides, 6 chains. Longest chain 93 peptides. Score 0.866 Round 2: 240 peptides, 9 chains. Longest chain 74 peptides. Score 0.843 Round 3: 237 peptides, 6 chains. Longest chain 102 peptides. Score 0.862 Round 4: 238 peptides, 10 chains. Longest chain 47 peptides. Score 0.832 Round 5: 240 peptides, 8 chains. Longest chain 94 peptides. Score 0.850 Taking the results from Round 1 Chains 6, Residues 234, Estimated correctness of the model 96.3 % 4 chains (206 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 88 A and 91 A Built loop between residues 116 B and 119 B 4 chains (238 residues) following loop building 2 chains (210 residues) in sequence following loop building ------------------------------------------------------ 14305 reflections ( 98.97 % complete ) and 2315 restraints for refining 2083 atoms. 499 conditional restraints added. Observations/parameters ratio is 1.72 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1948 (Rfree = 0.000) for 2083 atoms. Found 22 (22 requested) and removed 21 (18 requested) atoms. Cycle 22: After refmac, R = 0.1821 (Rfree = 0.000) for 2081 atoms. Found 21 (21 requested) and removed 20 (18 requested) atoms. Cycle 23: After refmac, R = 0.1806 (Rfree = 0.000) for 2081 atoms. Found 20 (21 requested) and removed 19 (18 requested) atoms. Cycle 24: After refmac, R = 0.1759 (Rfree = 0.000) for 2081 atoms. Found 20 (20 requested) and removed 10 (18 requested) atoms. Cycle 25: After refmac, R = 0.1746 (Rfree = 0.000) for 2088 atoms. Found 16 (20 requested) and removed 14 (18 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.44 2.01 NCS extension: 14 residues added (95 deleted due to clashes), 2106 seeds are put forward Round 1: 236 peptides, 7 chains. Longest chain 101 peptides. Score 0.853 Round 2: 230 peptides, 12 chains. Longest chain 41 peptides. Score 0.802 Round 3: 238 peptides, 6 chains. Longest chain 102 peptides. Score 0.863 Round 4: 239 peptides, 7 chains. Longest chain 95 peptides. Score 0.857 Round 5: 238 peptides, 8 chains. Longest chain 64 peptides. Score 0.848 Taking the results from Round 3 Chains 6, Residues 232, Estimated correctness of the model 96.2 % 3 chains (203 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 53 B and 56 B 5 chains (234 residues) following loop building 2 chains (205 residues) in sequence following loop building ------------------------------------------------------ 14305 reflections ( 98.97 % complete ) and 2368 restraints for refining 2075 atoms. 587 conditional restraints added. Observations/parameters ratio is 1.72 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1969 (Rfree = 0.000) for 2075 atoms. Found 19 (19 requested) and removed 21 (18 requested) atoms. Cycle 27: After refmac, R = 0.1897 (Rfree = 0.000) for 2071 atoms. Found 18 (18 requested) and removed 18 (18 requested) atoms. Cycle 28: After refmac, R = 0.1841 (Rfree = 0.000) for 2068 atoms. Found 18 (18 requested) and removed 17 (18 requested) atoms. Cycle 29: After refmac, R = 0.1819 (Rfree = 0.000) for 2068 atoms. Found 18 (18 requested) and removed 15 (18 requested) atoms. Cycle 30: After refmac, R = 0.1830 (Rfree = 0.000) for 2070 atoms. Found 18 (18 requested) and removed 15 (18 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.45 2.02 NCS extension: 20 residues added (97 deleted due to clashes), 2096 seeds are put forward Round 1: 239 peptides, 7 chains. Longest chain 113 peptides. Score 0.857 Round 2: 228 peptides, 10 chains. Longest chain 66 peptides. Score 0.816 Round 3: 235 peptides, 8 chains. Longest chain 96 peptides. Score 0.844 Round 4: 236 peptides, 10 chains. Longest chain 98 peptides. Score 0.829 Round 5: 235 peptides, 9 chains. Longest chain 86 peptides. Score 0.836 Taking the results from Round 1 Chains 9, Residues 232, Estimated correctness of the model 95.9 % 5 chains (206 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 47 B and 50 B Built loop between residues 116 B and 119 B 7 chains (236 residues) following loop building 3 chains (210 residues) in sequence following loop building ------------------------------------------------------ 14305 reflections ( 98.97 % complete ) and 2317 restraints for refining 2065 atoms. 519 conditional restraints added. Observations/parameters ratio is 1.73 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1931 (Rfree = 0.000) for 2065 atoms. Found 18 (18 requested) and removed 19 (18 requested) atoms. Cycle 32: After refmac, R = 0.1824 (Rfree = 0.000) for 2063 atoms. Found 18 (18 requested) and removed 18 (18 requested) atoms. Cycle 33: After refmac, R = 0.1794 (Rfree = 0.000) for 2060 atoms. Found 18 (18 requested) and removed 16 (18 requested) atoms. Cycle 34: After refmac, R = 0.1771 (Rfree = 0.000) for 2060 atoms. Found 18 (18 requested) and removed 14 (18 requested) atoms. Cycle 35: After refmac, R = 0.1769 (Rfree = 0.000) for 2064 atoms. Found 18 (18 requested) and removed 9 (18 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.46 2.03 NCS extension: 19 residues added (95 deleted due to clashes), 2097 seeds are put forward Round 1: 233 peptides, 9 chains. Longest chain 66 peptides. Score 0.833 Round 2: 239 peptides, 5 chains. Longest chain 114 peptides. Score 0.872 Round 3: 231 peptides, 10 chains. Longest chain 71 peptides. Score 0.821 Round 4: 233 peptides, 7 chains. Longest chain 74 peptides. Score 0.849 Round 5: 233 peptides, 10 chains. Longest chain 74 peptides. Score 0.824 Taking the results from Round 2 Chains 6, Residues 234, Estimated correctness of the model 96.6 % 4 chains (212 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 51 A and 53 A Built loop between residues 116 B and 119 B 4 chains (237 residues) following loop building 2 chains (215 residues) in sequence following loop building ------------------------------------------------------ 14305 reflections ( 98.97 % complete ) and 2306 restraints for refining 2079 atoms. 483 conditional restraints added. Observations/parameters ratio is 1.72 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1972 (Rfree = 0.000) for 2079 atoms. Found 18 (18 requested) and removed 19 (18 requested) atoms. Cycle 37: After refmac, R = 0.1914 (Rfree = 0.000) for 2078 atoms. Found 18 (18 requested) and removed 18 (18 requested) atoms. Cycle 38: After refmac, R = 0.1873 (Rfree = 0.000) for 2078 atoms. Found 18 (18 requested) and removed 17 (18 requested) atoms. Cycle 39: After refmac, R = 0.1854 (Rfree = 0.000) for 2077 atoms. Found 18 (18 requested) and removed 16 (18 requested) atoms. Cycle 40: After refmac, R = 0.1793 (Rfree = 0.000) for 2079 atoms. Found 18 (18 requested) and removed 17 (18 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.43 2.01 NCS extension: 32 residues added (82 deleted due to clashes), 2117 seeds are put forward Round 1: 233 peptides, 8 chains. Longest chain 75 peptides. Score 0.841 Round 2: 236 peptides, 7 chains. Longest chain 101 peptides. Score 0.853 Round 3: 235 peptides, 9 chains. Longest chain 74 peptides. Score 0.836 Round 4: 234 peptides, 7 chains. Longest chain 117 peptides. Score 0.850 Round 5: 231 peptides, 10 chains. Longest chain 68 peptides. Score 0.821 Taking the results from Round 2 Chains 10, Residues 229, Estimated correctness of the model 95.7 % 5 chains (200 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 49 A and 56 A Built loop between residues 115 A and 119 A Built loop between residues 94 B and 98 B 5 chains (235 residues) following loop building 2 chains (212 residues) in sequence following loop building ------------------------------------------------------ 14305 reflections ( 98.97 % complete ) and 2322 restraints for refining 2073 atoms. 517 conditional restraints added. Observations/parameters ratio is 1.73 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1933 (Rfree = 0.000) for 2073 atoms. Found 18 (18 requested) and removed 18 (18 requested) atoms. Cycle 42: After refmac, R = 0.1830 (Rfree = 0.000) for 2072 atoms. Found 18 (18 requested) and removed 18 (18 requested) atoms. Cycle 43: After refmac, R = 0.1800 (Rfree = 0.000) for 2069 atoms. Found 18 (18 requested) and removed 18 (18 requested) atoms. Cycle 44: After refmac, R = 0.1790 (Rfree = 0.000) for 2069 atoms. Found 18 (18 requested) and removed 17 (18 requested) atoms. Cycle 45: After refmac, R = 0.1783 (Rfree = 0.000) for 2070 atoms. Found 18 (18 requested) and removed 15 (18 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.43 2.01 NCS extension: 30 residues added (91 deleted due to clashes), 2107 seeds are put forward Round 1: 234 peptides, 9 chains. Longest chain 68 peptides. Score 0.834 Round 2: 240 peptides, 6 chains. Longest chain 112 peptides. Score 0.866 Round 3: 234 peptides, 9 chains. Longest chain 93 peptides. Score 0.834 Round 4: 236 peptides, 10 chains. Longest chain 102 peptides. Score 0.829 Round 5: 237 peptides, 7 chains. Longest chain 104 peptides. Score 0.854 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 6, Residues 234, Estimated correctness of the model 96.3 % 3 chains (210 residues) have been docked in sequence Sequence coverage is 89 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 116 B and 119 B 5 chains (236 residues) following loop building 2 chains (212 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 14305 reflections ( 98.97 % complete ) and 1809 restraints for refining 1763 atoms. Observations/parameters ratio is 2.03 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2750 (Rfree = 0.000) for 1763 atoms. Found 15 (15 requested) and removed 0 (15 requested) atoms. Cycle 47: After refmac, R = 0.2559 (Rfree = 0.000) for 1763 atoms. Found 13 (16 requested) and removed 5 (16 requested) atoms. Cycle 48: After refmac, R = 0.2515 (Rfree = 0.000) for 1763 atoms. Found 13 (16 requested) and removed 3 (16 requested) atoms. Cycle 49: After refmac, R = 0.2437 (Rfree = 0.000) for 1763 atoms. Found 5 (16 requested) and removed 7 (16 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 00:23:18 GMT 2018 Job finished. TimeTaking 40.48 Used memory is bytes: 1573176