Sun 23 Dec 22:22:41 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 2ozj-1.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ozj-1.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ozj-1.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ozj-1.6-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/2ozj-1.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ozj-1.6-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 22:22:50 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/2ozj-1.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ozj-1.6-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 206 and 0 Target number of residues in the AU: 206 Target solvent content: 0.4818 Checking the provided sequence file Detected sequence length: 114 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 228 Adjusted target solvent content: 0.43 Input MTZ file: 2ozj-1.6-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: 20 Cell parameters: 40.940 69.810 150.550 90.000 90.000 90.000 Input sequence file: 2ozj-1.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 1824 target number of atoms Had to go as low as 0.40 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: 75.275 1.600 Wilson plot Bfac: 19.88 28908 reflections ( 99.72 % complete ) and 0 restraints for refining 2014 atoms. Observations/parameters ratio is 3.59 ------------------------------------------------------ Starting model: R = 0.3255 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2677 (Rfree = 0.000) for 2014 atoms. Found 73 (130 requested) and removed 67 (65 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.84 2.02 NCS extension: 0 residues added, 2020 seeds are put forward Round 1: 165 peptides, 13 chains. Longest chain 31 peptides. Score 0.821 Round 2: 177 peptides, 11 chains. Longest chain 37 peptides. Score 0.871 Round 3: 190 peptides, 8 chains. Longest chain 43 peptides. Score 0.918 Round 4: 194 peptides, 10 chains. Longest chain 43 peptides. Score 0.907 Round 5: 195 peptides, 9 chains. Longest chain 42 peptides. Score 0.916 Taking the results from Round 3 Chains 12, Residues 182, Estimated correctness of the model 99.6 % 6 chains (157 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 45 B and 54 B Built loop between residues 72 B and 76 B 8 chains (190 residues) following loop building 4 chains (168 residues) in sequence following loop building ------------------------------------------------------ 28908 reflections ( 99.72 % complete ) and 2106 restraints for refining 1838 atoms. 684 conditional restraints added. Observations/parameters ratio is 3.93 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3123 (Rfree = 0.000) for 1838 atoms. Found 50 (118 requested) and removed 59 (59 requested) atoms. Cycle 2: After refmac, R = 0.2734 (Rfree = 0.000) for 1828 atoms. Found 47 (116 requested) and removed 25 (59 requested) atoms. Cycle 3: After refmac, R = 0.2558 (Rfree = 0.000) for 1845 atoms. Found 52 (114 requested) and removed 11 (59 requested) atoms. Cycle 4: After refmac, R = 0.2468 (Rfree = 0.000) for 1882 atoms. Found 48 (116 requested) and removed 10 (60 requested) atoms. Cycle 5: After refmac, R = 0.2391 (Rfree = 0.000) for 1913 atoms. Found 38 (119 requested) and removed 16 (62 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.79 1.97 NCS extension: 16 residues added (68 deleted due to clashes), 1957 seeds are put forward Round 1: 190 peptides, 7 chains. Longest chain 56 peptides. Score 0.925 Round 2: 194 peptides, 7 chains. Longest chain 55 peptides. Score 0.929 Round 3: 194 peptides, 6 chains. Longest chain 55 peptides. Score 0.936 Round 4: 195 peptides, 6 chains. Longest chain 55 peptides. Score 0.937 Round 5: 194 peptides, 8 chains. Longest chain 46 peptides. Score 0.922 Taking the results from Round 4 Chains 7, Residues 189, Estimated correctness of the model 99.8 % 5 chains (180 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 47 A and 55 A Built loop between residues 72 B and 78 B 5 chains (201 residues) following loop building 3 chains (192 residues) in sequence following loop building ------------------------------------------------------ 28908 reflections ( 99.72 % complete ) and 2016 restraints for refining 1950 atoms. 446 conditional restraints added. Observations/parameters ratio is 3.71 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2655 (Rfree = 0.000) for 1950 atoms. Found 63 (121 requested) and removed 64 (63 requested) atoms. Cycle 7: After refmac, R = 0.2490 (Rfree = 0.000) for 1944 atoms. Found 49 (118 requested) and removed 20 (63 requested) atoms. Cycle 8: After refmac, R = 0.2412 (Rfree = 0.000) for 1970 atoms. Found 41 (119 requested) and removed 12 (63 requested) atoms. Cycle 9: After refmac, R = 0.2348 (Rfree = 0.000) for 1995 atoms. Found 35 (121 requested) and removed 7 (64 requested) atoms. Cycle 10: After refmac, R = 0.2291 (Rfree = 0.000) for 2015 atoms. Found 41 (122 requested) and removed 10 (65 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.79 1.97 NCS extension: 3 residues added (22 deleted due to clashes), 2057 seeds are put forward Round 1: 196 peptides, 7 chains. Longest chain 47 peptides. Score 0.931 Round 2: 195 peptides, 7 chains. Longest chain 47 peptides. Score 0.930 Round 3: 194 peptides, 6 chains. Longest chain 56 peptides. Score 0.936 Round 4: 191 peptides, 6 chains. Longest chain 56 peptides. Score 0.933 Round 5: 192 peptides, 6 chains. Longest chain 56 peptides. Score 0.934 Taking the results from Round 3 Chains 7, Residues 188, Estimated correctness of the model 99.8 % 5 chains (179 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 47 A and 56 A Built loop between residues 72 A and 79 A 4 chains (201 residues) following loop building 3 chains (193 residues) in sequence following loop building ------------------------------------------------------ 28908 reflections ( 99.72 % complete ) and 2059 restraints for refining 1984 atoms. 483 conditional restraints added. Observations/parameters ratio is 3.64 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2595 (Rfree = 0.000) for 1984 atoms. Found 70 (120 requested) and removed 67 (64 requested) atoms. Cycle 12: After refmac, R = 0.2446 (Rfree = 0.000) for 1983 atoms. Found 52 (118 requested) and removed 4 (64 requested) atoms. Cycle 13: After refmac, R = 0.2362 (Rfree = 0.000) for 2028 atoms. Found 47 (121 requested) and removed 9 (65 requested) atoms. Cycle 14: After refmac, R = 0.2318 (Rfree = 0.000) for 2063 atoms. Found 38 (122 requested) and removed 11 (66 requested) atoms. Cycle 15: After refmac, R = 0.2285 (Rfree = 0.000) for 2089 atoms. Found 38 (124 requested) and removed 15 (67 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.79 1.97 NCS extension: 11 residues added (7 deleted due to clashes), 2129 seeds are put forward Round 1: 194 peptides, 8 chains. Longest chain 45 peptides. Score 0.922 Round 2: 196 peptides, 6 chains. Longest chain 56 peptides. Score 0.938 Round 3: 198 peptides, 6 chains. Longest chain 56 peptides. Score 0.940 Round 4: 197 peptides, 7 chains. Longest chain 56 peptides. Score 0.932 Round 5: 197 peptides, 7 chains. Longest chain 45 peptides. Score 0.932 Taking the results from Round 3 Chains 9, Residues 192, Estimated correctness of the model 99.8 % 6 chains (177 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 46 B and 54 B Built loop between residues 72 B and 78 B Built loop between residues 92 B and 97 B 4 chains (201 residues) following loop building 3 chains (193 residues) in sequence following loop building ------------------------------------------------------ 28908 reflections ( 99.72 % complete ) and 2105 restraints for refining 2045 atoms. 529 conditional restraints added. Observations/parameters ratio is 3.53 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2582 (Rfree = 0.000) for 2045 atoms. Found 68 (121 requested) and removed 62 (66 requested) atoms. Cycle 17: After refmac, R = 0.2439 (Rfree = 0.000) for 2043 atoms. Found 48 (119 requested) and removed 9 (66 requested) atoms. Cycle 18: After refmac, R = 0.2369 (Rfree = 0.000) for 2078 atoms. Found 32 (121 requested) and removed 8 (67 requested) atoms. Cycle 19: After refmac, R = 0.2315 (Rfree = 0.000) for 2095 atoms. Found 40 (121 requested) and removed 13 (67 requested) atoms. Failed to save intermediate PDB Cycle 20: After refmac, R = 0.2276 (Rfree = 0.000) for 2119 atoms. Found 32 (123 requested) and removed 6 (68 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.79 1.97 NCS extension: 3 residues added (19 deleted due to clashes), 2155 seeds are put forward Round 1: 193 peptides, 8 chains. Longest chain 44 peptides. Score 0.921 Round 2: 196 peptides, 6 chains. Longest chain 56 peptides. Score 0.938 Round 3: 196 peptides, 6 chains. Longest chain 56 peptides. Score 0.938 Round 4: 196 peptides, 6 chains. Longest chain 56 peptides. Score 0.938 Round 5: 196 peptides, 6 chains. Longest chain 56 peptides. Score 0.938 Taking the results from Round 5 Chains 7, Residues 190, Estimated correctness of the model 99.8 % 5 chains (181 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 45 A and 54 A Built loop between residues 72 B and 78 B 4 chains (202 residues) following loop building 3 chains (194 residues) in sequence following loop building ------------------------------------------------------ 28908 reflections ( 99.72 % complete ) and 2127 restraints for refining 2044 atoms. 542 conditional restraints added. Observations/parameters ratio is 3.54 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2586 (Rfree = 0.000) for 2044 atoms. Found 81 (119 requested) and removed 69 (66 requested) atoms. Cycle 22: After refmac, R = 0.2453 (Rfree = 0.000) for 2053 atoms. Found 48 (116 requested) and removed 19 (66 requested) atoms. Cycle 23: After refmac, R = 0.2364 (Rfree = 0.000) for 2079 atoms. Found 37 (118 requested) and removed 12 (67 requested) atoms. Cycle 24: After refmac, R = 0.2286 (Rfree = 0.000) for 2102 atoms. Found 30 (119 requested) and removed 9 (67 requested) atoms. Cycle 25: After refmac, R = 0.2230 (Rfree = 0.000) for 2116 atoms. Found 30 (121 requested) and removed 11 (68 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.79 1.97 NCS extension: 11 residues added (6 deleted due to clashes), 2149 seeds are put forward Round 1: 193 peptides, 8 chains. Longest chain 43 peptides. Score 0.921 Round 2: 198 peptides, 6 chains. Longest chain 57 peptides. Score 0.940 Round 3: 199 peptides, 7 chains. Longest chain 57 peptides. Score 0.934 Round 4: 201 peptides, 8 chains. Longest chain 47 peptides. Score 0.930 Round 5: 199 peptides, 6 chains. Longest chain 57 peptides. Score 0.941 Taking the results from Round 5 Chains 6, Residues 193, Estimated correctness of the model 99.8 % 5 chains (185 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 46 A and 53 A Built loop between residues 73 A and 78 A 4 chains (203 residues) following loop building 3 chains (195 residues) in sequence following loop building ------------------------------------------------------ 28908 reflections ( 99.72 % complete ) and 2096 restraints for refining 2036 atoms. 506 conditional restraints added. Observations/parameters ratio is 3.55 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2506 (Rfree = 0.000) for 2036 atoms. Found 86 (115 requested) and removed 67 (65 requested) atoms. Cycle 27: After refmac, R = 0.2386 (Rfree = 0.000) for 2051 atoms. Found 44 (114 requested) and removed 8 (66 requested) atoms. Cycle 28: After refmac, R = 0.2313 (Rfree = 0.000) for 2082 atoms. Found 41 (115 requested) and removed 9 (67 requested) atoms. Cycle 29: After refmac, R = 0.2261 (Rfree = 0.000) for 2108 atoms. Found 41 (117 requested) and removed 10 (68 requested) atoms. Cycle 30: After refmac, R = 0.2184 (Rfree = 0.000) for 2135 atoms. Found 33 (119 requested) and removed 6 (69 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.79 1.97 NCS extension: 6 residues added (7 deleted due to clashes), 2174 seeds are put forward Round 1: 193 peptides, 9 chains. Longest chain 43 peptides. Score 0.914 Round 2: 199 peptides, 7 chains. Longest chain 44 peptides. Score 0.934 Round 3: 198 peptides, 7 chains. Longest chain 57 peptides. Score 0.933 Round 4: 199 peptides, 6 chains. Longest chain 57 peptides. Score 0.941 Round 5: 193 peptides, 7 chains. Longest chain 57 peptides. Score 0.928 Taking the results from Round 4 Chains 7, Residues 193, Estimated correctness of the model 99.8 % 5 chains (182 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 44 A and 53 A Built loop between residues 73 B and 78 B 4 chains (204 residues) following loop building 3 chains (194 residues) in sequence following loop building ------------------------------------------------------ 28908 reflections ( 99.72 % complete ) and 2135 restraints for refining 2075 atoms. 542 conditional restraints added. Observations/parameters ratio is 3.48 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2516 (Rfree = 0.000) for 2075 atoms. Found 79 (115 requested) and removed 70 (67 requested) atoms. Cycle 32: After refmac, R = 0.2373 (Rfree = 0.000) for 2079 atoms. Found 57 (113 requested) and removed 17 (67 requested) atoms. Cycle 33: After refmac, R = 0.2291 (Rfree = 0.000) for 2118 atoms. Found 51 (114 requested) and removed 6 (68 requested) atoms. Cycle 34: After refmac, R = 0.2229 (Rfree = 0.000) for 2159 atoms. Found 38 (117 requested) and removed 15 (69 requested) atoms. Cycle 35: After refmac, R = 0.2181 (Rfree = 0.000) for 2179 atoms. Found 39 (118 requested) and removed 14 (70 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.79 1.97 NCS extension: 5 residues added (21 deleted due to clashes), 2212 seeds are put forward Round 1: 193 peptides, 10 chains. Longest chain 36 peptides. Score 0.906 Round 2: 199 peptides, 6 chains. Longest chain 56 peptides. Score 0.941 Round 3: 199 peptides, 6 chains. Longest chain 56 peptides. Score 0.941 Round 4: 196 peptides, 7 chains. Longest chain 44 peptides. Score 0.931 Round 5: 199 peptides, 6 chains. Longest chain 56 peptides. Score 0.941 Taking the results from Round 5 Chains 8, Residues 193, Estimated correctness of the model 99.8 % 5 chains (180 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 45 A and 54 A Built loop between residues 72 B and 78 B 5 chains (205 residues) following loop building 3 chains (193 residues) in sequence following loop building ------------------------------------------------------ 28908 reflections ( 99.72 % complete ) and 2156 restraints for refining 2078 atoms. 568 conditional restraints added. Observations/parameters ratio is 3.48 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2517 (Rfree = 0.000) for 2078 atoms. Found 93 (113 requested) and removed 71 (67 requested) atoms. Cycle 37: After refmac, R = 0.2415 (Rfree = 0.000) for 2094 atoms. Found 51 (111 requested) and removed 21 (67 requested) atoms. Cycle 38: After refmac, R = 0.2311 (Rfree = 0.000) for 2122 atoms. Found 37 (112 requested) and removed 11 (68 requested) atoms. Cycle 39: After refmac, R = 0.2256 (Rfree = 0.000) for 2144 atoms. Found 30 (113 requested) and removed 12 (69 requested) atoms. Cycle 40: After refmac, R = 0.2194 (Rfree = 0.000) for 2160 atoms. Found 26 (114 requested) and removed 16 (69 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.79 1.97 NCS extension: 10 residues added (8 deleted due to clashes), 2186 seeds are put forward Round 1: 193 peptides, 8 chains. Longest chain 43 peptides. Score 0.921 Round 2: 195 peptides, 7 chains. Longest chain 43 peptides. Score 0.930 Round 3: 197 peptides, 7 chains. Longest chain 44 peptides. Score 0.932 Round 4: 198 peptides, 7 chains. Longest chain 44 peptides. Score 0.933 Round 5: 196 peptides, 8 chains. Longest chain 44 peptides. Score 0.924 Taking the results from Round 4 Chains 9, Residues 191, Estimated correctness of the model 99.8 % 6 chains (178 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 72 A and 78 A Built loop between residues 45 B and 54 B Built loop between residues 72 B and 75 B 5 chains (205 residues) following loop building 3 chains (193 residues) in sequence following loop building ------------------------------------------------------ 28908 reflections ( 99.72 % complete ) and 2145 restraints for refining 2096 atoms. 557 conditional restraints added. Observations/parameters ratio is 3.45 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2508 (Rfree = 0.000) for 2096 atoms. Found 83 (108 requested) and removed 60 (67 requested) atoms. Cycle 42: After refmac, R = 0.2397 (Rfree = 0.000) for 2116 atoms. Found 55 (106 requested) and removed 16 (68 requested) atoms. Cycle 43: After refmac, R = 0.2327 (Rfree = 0.000) for 2151 atoms. Found 53 (108 requested) and removed 24 (69 requested) atoms. Cycle 44: After refmac, R = 0.2274 (Rfree = 0.000) for 2179 atoms. Found 46 (109 requested) and removed 21 (70 requested) atoms. Cycle 45: After refmac, R = 0.2234 (Rfree = 0.000) for 2196 atoms. Found 37 (111 requested) and removed 20 (71 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.80 1.98 NCS extension: 8 residues added (7 deleted due to clashes), 2227 seeds are put forward Round 1: 192 peptides, 7 chains. Longest chain 43 peptides. Score 0.927 Round 2: 196 peptides, 6 chains. Longest chain 56 peptides. Score 0.938 Round 3: 196 peptides, 7 chains. Longest chain 43 peptides. Score 0.931 Round 4: 195 peptides, 7 chains. Longest chain 43 peptides. Score 0.930 Round 5: 188 peptides, 7 chains. Longest chain 43 peptides. Score 0.923 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 7, Residues 190, Estimated correctness of the model 99.8 % 5 chains (178 residues) have been docked in sequence Sequence coverage is 93 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 45 A and 54 A Built loop between residues 72 B and 78 B 5 chains (203 residues) following loop building 3 chains (191 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 28908 reflections ( 99.72 % complete ) and 1577 restraints for refining 1556 atoms. Observations/parameters ratio is 4.64 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3161 (Rfree = 0.000) for 1556 atoms. Found 23 (76 requested) and removed 0 (76 requested) atoms. Cycle 47: After refmac, R = 0.3010 (Rfree = 0.000) for 1556 atoms. Found 8 (78 requested) and removed 0 (51 requested) atoms. Cycle 48: After refmac, R = 0.2878 (Rfree = 0.000) for 1556 atoms. Found 6 (78 requested) and removed 1 (51 requested) atoms. Cycle 49: After refmac, R = 0.2788 (Rfree = 0.000) for 1556 atoms. TimeTaking 52.18