Sun 23 Dec 22:22:52 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 2ooj-1.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ooj-1.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ooj-1.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ooj-1.8-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/2ooj-1.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ooj-1.8-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 22:23:02 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/2ooj-1.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ooj-1.8-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 250 and 0 Target number of residues in the AU: 250 Target solvent content: 0.5111 Checking the provided sequence file Detected sequence length: 141 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 282 Adjusted target solvent content: 0.45 Input MTZ file: 2ooj-1.8-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: 19 Cell parameters: 47.211 55.254 106.086 90.000 90.000 90.000 Input sequence file: 2ooj-1.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 2256 target number of atoms Had to go as low as 0.45 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 1 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: 53.043 1.840 Wilson plot Bfac: 25.62 24751 reflections ( 99.86 % complete ) and 0 restraints for refining 2506 atoms. Observations/parameters ratio is 2.47 ------------------------------------------------------ Starting model: R = 0.3695 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3244 (Rfree = 0.000) for 2506 atoms. Found 46 (108 requested) and removed 82 (54 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.26 2.42 NCS extension: 0 residues added, 2470 seeds are put forward Round 1: 201 peptides, 21 chains. Longest chain 24 peptides. Score 0.745 Round 2: 229 peptides, 18 chains. Longest chain 28 peptides. Score 0.841 Round 3: 249 peptides, 9 chains. Longest chain 77 peptides. Score 0.929 Round 4: 248 peptides, 10 chains. Longest chain 73 peptides. Score 0.923 Round 5: 247 peptides, 10 chains. Longest chain 51 peptides. Score 0.922 Taking the results from Round 3 Chains 9, Residues 240, Estimated correctness of the model 99.6 % 7 chains (220 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 24 A and 27 A Built loop between residues 88 A and 95 A Built loop between residues 120 A and 123 A Built loop between residues 43 B and 46 B 5 chains (252 residues) following loop building 3 chains (232 residues) in sequence following loop building ------------------------------------------------------ 24751 reflections ( 99.86 % complete ) and 2531 restraints for refining 2285 atoms. 684 conditional restraints added. Observations/parameters ratio is 2.71 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3337 (Rfree = 0.000) for 2285 atoms. Found 80 (99 requested) and removed 54 (49 requested) atoms. Cycle 2: After refmac, R = 0.3058 (Rfree = 0.000) for 2303 atoms. Found 64 (98 requested) and removed 50 (50 requested) atoms. Cycle 3: After refmac, R = 0.2857 (Rfree = 0.000) for 2295 atoms. Found 52 (96 requested) and removed 44 (50 requested) atoms. Cycle 4: After refmac, R = 0.2715 (Rfree = 0.000) for 2285 atoms. Found 53 (94 requested) and removed 35 (50 requested) atoms. Cycle 5: After refmac, R = 0.2577 (Rfree = 0.000) for 2291 atoms. Found 48 (92 requested) and removed 22 (50 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.05 2.19 NCS extension: 35 residues added (114 deleted due to clashes), 2356 seeds are put forward Round 1: 249 peptides, 8 chains. Longest chain 110 peptides. Score 0.935 Round 2: 251 peptides, 6 chains. Longest chain 76 peptides. Score 0.946 Round 3: 253 peptides, 8 chains. Longest chain 111 peptides. Score 0.937 Round 4: 252 peptides, 7 chains. Longest chain 89 peptides. Score 0.942 Round 5: 254 peptides, 6 chains. Longest chain 131 peptides. Score 0.948 Taking the results from Round 5 Chains 6, Residues 248, Estimated correctness of the model 99.8 % 6 chains (248 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 44 A and 47 A Built loop between residues 58 A and 62 A Built loop between residues 89 A and 95 A Built loop between residues 113 A and 116 A 2 chains (260 residues) following loop building 2 chains (260 residues) in sequence following loop building ------------------------------------------------------ 24751 reflections ( 99.86 % complete ) and 2188 restraints for refining 2256 atoms. 194 conditional restraints added. Observations/parameters ratio is 2.74 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2496 (Rfree = 0.000) for 2256 atoms. Found 73 (90 requested) and removed 51 (49 requested) atoms. Cycle 7: After refmac, R = 0.2369 (Rfree = 0.000) for 2275 atoms. Found 61 (88 requested) and removed 49 (49 requested) atoms. Cycle 8: After refmac, R = 0.2257 (Rfree = 0.000) for 2280 atoms. Found 56 (87 requested) and removed 40 (49 requested) atoms. Cycle 9: After refmac, R = 0.2183 (Rfree = 0.000) for 2289 atoms. Found 62 (85 requested) and removed 42 (49 requested) atoms. Cycle 10: After refmac, R = 0.2130 (Rfree = 0.000) for 2302 atoms. Found 59 (84 requested) and removed 30 (50 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.03 2.17 NCS extension: 18 residues added (56 deleted due to clashes), 2352 seeds are put forward Round 1: 253 peptides, 5 chains. Longest chain 130 peptides. Score 0.952 Round 2: 253 peptides, 6 chains. Longest chain 69 peptides. Score 0.947 Round 3: 250 peptides, 7 chains. Longest chain 131 peptides. Score 0.941 Round 4: 253 peptides, 7 chains. Longest chain 91 peptides. Score 0.943 Round 5: 254 peptides, 8 chains. Longest chain 95 peptides. Score 0.938 Taking the results from Round 1 Chains 5, Residues 248, Estimated correctness of the model 99.8 % 5 chains (248 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 57 B and 62 B Built loop between residues 89 B and 95 B Built loop between residues 113 B and 116 B 2 chains (259 residues) following loop building 2 chains (259 residues) in sequence following loop building ------------------------------------------------------ 24751 reflections ( 99.86 % complete ) and 2217 restraints for refining 2248 atoms. 229 conditional restraints added. Observations/parameters ratio is 2.75 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2230 (Rfree = 0.000) for 2248 atoms. Found 80 (80 requested) and removed 49 (48 requested) atoms. Cycle 12: After refmac, R = 0.2122 (Rfree = 0.000) for 2276 atoms. Found 67 (79 requested) and removed 33 (49 requested) atoms. Cycle 13: After refmac, R = 0.2045 (Rfree = 0.000) for 2310 atoms. Found 55 (80 requested) and removed 34 (50 requested) atoms. Cycle 14: After refmac, R = 0.2000 (Rfree = 0.000) for 2327 atoms. Found 57 (79 requested) and removed 35 (50 requested) atoms. Cycle 15: After refmac, R = 0.1983 (Rfree = 0.000) for 2344 atoms. Found 52 (78 requested) and removed 52 (51 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.02 2.16 NCS extension: 0 residues added, 2344 seeds are put forward Round 1: 256 peptides, 6 chains. Longest chain 87 peptides. Score 0.949 Round 2: 257 peptides, 6 chains. Longest chain 95 peptides. Score 0.950 Round 3: 258 peptides, 4 chains. Longest chain 131 peptides. Score 0.960 Round 4: 254 peptides, 6 chains. Longest chain 91 peptides. Score 0.948 Round 5: 260 peptides, 4 chains. Longest chain 133 peptides. Score 0.960 Taking the results from Round 5 Chains 4, Residues 256, Estimated correctness of the model 99.9 % 4 chains (256 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 89 B and 95 B Built loop between residues 112 B and 115 B 2 chains (263 residues) following loop building 2 chains (263 residues) in sequence following loop building ------------------------------------------------------ 24751 reflections ( 99.86 % complete ) and 2161 restraints for refining 2245 atoms. 141 conditional restraints added. Observations/parameters ratio is 2.76 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2133 (Rfree = 0.000) for 2245 atoms. Found 72 (72 requested) and removed 50 (48 requested) atoms. Cycle 17: After refmac, R = 0.2044 (Rfree = 0.000) for 2264 atoms. Found 66 (71 requested) and removed 46 (49 requested) atoms. Cycle 18: After refmac, R = 0.1968 (Rfree = 0.000) for 2281 atoms. Found 69 (69 requested) and removed 43 (49 requested) atoms. Cycle 19: After refmac, R = 0.1937 (Rfree = 0.000) for 2304 atoms. Found 59 (68 requested) and removed 42 (50 requested) atoms. Cycle 20: After refmac, R = 0.1920 (Rfree = 0.000) for 2318 atoms. Found 57 (66 requested) and removed 33 (50 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.02 2.16 NCS extension: 17 residues added (59 deleted due to clashes), 2363 seeds are put forward Round 1: 259 peptides, 4 chains. Longest chain 133 peptides. Score 0.960 Round 2: 259 peptides, 4 chains. Longest chain 91 peptides. Score 0.960 Round 3: 255 peptides, 6 chains. Longest chain 109 peptides. Score 0.949 Round 4: 256 peptides, 4 chains. Longest chain 87 peptides. Score 0.959 Round 5: 255 peptides, 6 chains. Longest chain 109 peptides. Score 0.949 Taking the results from Round 2 Chains 4, Residues 255, Estimated correctness of the model 99.9 % 4 chains (255 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 43 A and 46 A Built loop between residues 89 B and 95 B 2 chains (262 residues) following loop building 2 chains (262 residues) in sequence following loop building ------------------------------------------------------ 24751 reflections ( 99.86 % complete ) and 2151 restraints for refining 2236 atoms. 140 conditional restraints added. Observations/parameters ratio is 2.77 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2106 (Rfree = 0.000) for 2236 atoms. Found 62 (62 requested) and removed 46 (48 requested) atoms. Cycle 22: After refmac, R = 0.2013 (Rfree = 0.000) for 2249 atoms. Found 60 (60 requested) and removed 30 (48 requested) atoms. Cycle 23: After refmac, R = 0.1954 (Rfree = 0.000) for 2276 atoms. Found 61 (61 requested) and removed 27 (49 requested) atoms. Cycle 24: After refmac, R = 0.1957 (Rfree = 0.000) for 2309 atoms. Found 54 (62 requested) and removed 40 (50 requested) atoms. Cycle 25: After refmac, R = 0.1918 (Rfree = 0.000) for 2321 atoms. Found 60 (60 requested) and removed 48 (50 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.03 2.17 NCS extension: 19 residues added (57 deleted due to clashes), 2355 seeds are put forward Round 1: 258 peptides, 6 chains. Longest chain 70 peptides. Score 0.950 Round 2: 259 peptides, 4 chains. Longest chain 91 peptides. Score 0.960 Round 3: 256 peptides, 5 chains. Longest chain 131 peptides. Score 0.954 Round 4: 252 peptides, 8 chains. Longest chain 69 peptides. Score 0.937 Round 5: 260 peptides, 4 chains. Longest chain 133 peptides. Score 0.960 Taking the results from Round 5 Chains 4, Residues 256, Estimated correctness of the model 99.9 % 4 chains (256 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 89 B and 95 B Built loop between residues 112 B and 115 B 2 chains (263 residues) following loop building 2 chains (263 residues) in sequence following loop building ------------------------------------------------------ 24751 reflections ( 99.86 % complete ) and 2147 restraints for refining 2243 atoms. 127 conditional restraints added. Observations/parameters ratio is 2.76 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2067 (Rfree = 0.000) for 2243 atoms. Found 56 (56 requested) and removed 50 (48 requested) atoms. Cycle 27: After refmac, R = 0.1987 (Rfree = 0.000) for 2247 atoms. Found 54 (54 requested) and removed 20 (48 requested) atoms. Cycle 28: After refmac, R = 0.1942 (Rfree = 0.000) for 2280 atoms. Found 54 (55 requested) and removed 23 (49 requested) atoms. Cycle 29: After refmac, R = 0.1918 (Rfree = 0.000) for 2309 atoms. Found 56 (56 requested) and removed 39 (50 requested) atoms. Cycle 30: After refmac, R = 0.1904 (Rfree = 0.000) for 2323 atoms. Found 55 (55 requested) and removed 45 (50 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.03 2.17 NCS extension: 23 residues added (110 deleted due to clashes), 2358 seeds are put forward Round 1: 257 peptides, 5 chains. Longest chain 109 peptides. Score 0.955 Round 2: 255 peptides, 5 chains. Longest chain 91 peptides. Score 0.953 Round 3: 256 peptides, 7 chains. Longest chain 87 peptides. Score 0.945 Round 4: 256 peptides, 7 chains. Longest chain 69 peptides. Score 0.945 Round 5: 257 peptides, 4 chains. Longest chain 131 peptides. Score 0.959 Taking the results from Round 5 Chains 4, Residues 253, Estimated correctness of the model 99.8 % 4 chains (253 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 89 B and 95 B Built loop between residues 113 B and 116 B 2 chains (260 residues) following loop building 2 chains (260 residues) in sequence following loop building ------------------------------------------------------ 24751 reflections ( 99.86 % complete ) and 2159 restraints for refining 2228 atoms. 163 conditional restraints added. Observations/parameters ratio is 2.78 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2072 (Rfree = 0.000) for 2228 atoms. Found 50 (50 requested) and removed 42 (48 requested) atoms. Cycle 32: After refmac, R = 0.1969 (Rfree = 0.000) for 2229 atoms. Found 48 (48 requested) and removed 15 (48 requested) atoms. Cycle 33: After refmac, R = 0.1938 (Rfree = 0.000) for 2261 atoms. Found 49 (49 requested) and removed 31 (49 requested) atoms. Cycle 34: After refmac, R = 0.1903 (Rfree = 0.000) for 2278 atoms. Found 49 (49 requested) and removed 33 (49 requested) atoms. Cycle 35: After refmac, R = 0.1911 (Rfree = 0.000) for 2292 atoms. Found 49 (49 requested) and removed 37 (49 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.02 2.16 NCS extension: 0 residues added, 2305 seeds are put forward Round 1: 259 peptides, 4 chains. Longest chain 132 peptides. Score 0.960 Round 2: 258 peptides, 5 chains. Longest chain 91 peptides. Score 0.955 Round 3: 257 peptides, 7 chains. Longest chain 81 peptides. Score 0.945 Round 4: 252 peptides, 5 chains. Longest chain 88 peptides. Score 0.952 Round 5: 256 peptides, 5 chains. Longest chain 130 peptides. Score 0.954 Taking the results from Round 1 Chains 4, Residues 255, Estimated correctness of the model 99.9 % 4 chains (255 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 89 B and 95 B Built loop between residues 112 B and 115 B 2 chains (262 residues) following loop building 2 chains (262 residues) in sequence following loop building ------------------------------------------------------ 24751 reflections ( 99.86 % complete ) and 2138 restraints for refining 2245 atoms. 126 conditional restraints added. Observations/parameters ratio is 2.76 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2063 (Rfree = 0.000) for 2245 atoms. Found 48 (48 requested) and removed 42 (48 requested) atoms. Cycle 37: After refmac, R = 0.1980 (Rfree = 0.000) for 2250 atoms. Found 48 (48 requested) and removed 25 (48 requested) atoms. Cycle 38: After refmac, R = 0.1937 (Rfree = 0.000) for 2273 atoms. Found 49 (49 requested) and removed 42 (49 requested) atoms. Cycle 39: After refmac, R = 0.1927 (Rfree = 0.000) for 2279 atoms. Found 49 (49 requested) and removed 35 (49 requested) atoms. Cycle 40: After refmac, R = 0.1899 (Rfree = 0.000) for 2292 atoms. Found 49 (49 requested) and removed 37 (49 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.02 2.16 NCS extension: 0 residues added, 2306 seeds are put forward Round 1: 258 peptides, 4 chains. Longest chain 131 peptides. Score 0.960 Round 2: 252 peptides, 7 chains. Longest chain 69 peptides. Score 0.942 Round 3: 257 peptides, 5 chains. Longest chain 131 peptides. Score 0.955 Round 4: 257 peptides, 5 chains. Longest chain 91 peptides. Score 0.955 Round 5: 254 peptides, 6 chains. Longest chain 94 peptides. Score 0.948 Taking the results from Round 1 Chains 4, Residues 254, Estimated correctness of the model 99.9 % 4 chains (254 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 39 B and 42 B Built loop between residues 89 B and 95 B 2 chains (261 residues) following loop building 2 chains (261 residues) in sequence following loop building ------------------------------------------------------ 24751 reflections ( 99.86 % complete ) and 2154 restraints for refining 2243 atoms. 149 conditional restraints added. Observations/parameters ratio is 2.76 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2061 (Rfree = 0.000) for 2243 atoms. Found 48 (48 requested) and removed 46 (48 requested) atoms. Cycle 42: After refmac, R = 0.1961 (Rfree = 0.000) for 2245 atoms. Found 48 (48 requested) and removed 20 (48 requested) atoms. Cycle 43: After refmac, R = 0.1939 (Rfree = 0.000) for 2273 atoms. Found 49 (49 requested) and removed 32 (49 requested) atoms. Cycle 44: After refmac, R = 0.1915 (Rfree = 0.000) for 2288 atoms. Found 49 (49 requested) and removed 31 (49 requested) atoms. Cycle 45: After refmac, R = 0.1917 (Rfree = 0.000) for 2305 atoms. Found 50 (50 requested) and removed 38 (50 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.01 2.15 NCS extension: 48 residues added (83 deleted due to clashes), 2367 seeds are put forward Round 1: 256 peptides, 5 chains. Longest chain 87 peptides. Score 0.954 Round 2: 257 peptides, 5 chains. Longest chain 95 peptides. Score 0.955 Round 3: 256 peptides, 6 chains. Longest chain 69 peptides. Score 0.949 Round 4: 256 peptides, 5 chains. Longest chain 131 peptides. Score 0.954 Round 5: 253 peptides, 6 chains. Longest chain 87 peptides. Score 0.947 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 5, Residues 252, Estimated correctness of the model 99.8 % 5 chains (252 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 39 A and 42 A Built loop between residues 43 B and 46 B Built loop between residues 89 B and 95 B 2 chains (261 residues) following loop building 2 chains (261 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 24751 reflections ( 99.86 % complete ) and 2003 restraints for refining 1966 atoms. Observations/parameters ratio is 3.15 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2526 (Rfree = 0.000) for 1966 atoms. Found 37 (42 requested) and removed 0 (42 requested) atoms. Cycle 47: After refmac, R = 0.2313 (Rfree = 0.000) for 1966 atoms. Found 21 (43 requested) and removed 0 (43 requested) atoms. Cycle 48: After refmac, R = 0.2175 (Rfree = 0.000) for 1966 atoms. Found 16 (43 requested) and removed 1 (43 requested) atoms. Cycle 49: After refmac, R = 0.2109 (Rfree = 0.000) for 1966 atoms. Found 7 (44 requested) and removed 3 (44 requested) atoms. Writing output files ... TimeTaking 52.07