Sun 23 Dec 22:22:49 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 2anu-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2anu-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2anu-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2anu-3.2-parrot-hancs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2anu-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2anu-3.2-parrot-hancs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Sun 23 Dec 22:22:59 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/2anu-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2anu-3.2-parrot-hancs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 1351 and 0 Target number of residues in the AU: 1351 Target solvent content: 0.5996 Checking the provided sequence file Detected sequence length: 255 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 6 Adjusted target number of residues: 1530 Adjusted target solvent content: 0.55 Input MTZ file: 2anu-3.2-parrot-hancs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 146 Cell parameters: 111.273 111.273 383.188 90.000 90.000 120.000 Input sequence file: 2anu-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 12240 target number of atoms Had to go as low as 0.80 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 3 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 127.729 3.200 Wilson plot Bfac: 52.43 29175 reflections ( 99.85 % complete ) and 0 restraints for refining 13545 atoms. Observations/parameters ratio is 0.54 ------------------------------------------------------ Starting model: R = 0.2752 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2398 (Rfree = 0.000) for 13545 atoms. Found 121 (121 requested) and removed 107 (60 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.00 2.81 Search for helices and strands: 0 residues in 0 chains, 13812 seeds are put forward NCS extension: 0 residues added, 13812 seeds are put forward Round 1: 882 peptides, 132 chains. Longest chain 24 peptides. Score 0.496 Round 2: 1034 peptides, 114 chains. Longest chain 39 peptides. Score 0.654 Round 3: 1071 peptides, 109 chains. Longest chain 40 peptides. Score 0.688 Round 4: 1113 peptides, 98 chains. Longest chain 37 peptides. Score 0.735 Round 5: 1122 peptides, 92 chains. Longest chain 49 peptides. Score 0.752 Taking the results from Round 5 Chains 102, Residues 1030, Estimated correctness of the model 75.4 % 23 chains (446 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 194 A and 198 A Built loop between residues 206 A and 210 A Built loop between residues 133 B and 140 B Built loop between residues 202 B and 207 B 95 chains (1039 residues) following loop building 19 chains (462 residues) in sequence following loop building ------------------------------------------------------ 29175 reflections ( 99.85 % complete ) and 18723 restraints for refining 11208 atoms. 12627 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2530 (Rfree = 0.000) for 11208 atoms. Found 100 (100 requested) and removed 86 (50 requested) atoms. Cycle 2: After refmac, R = 0.2256 (Rfree = 0.000) for 11063 atoms. Found 71 (98 requested) and removed 59 (50 requested) atoms. Failed to save intermediate PDB Cycle 3: After refmac, R = 0.2128 (Rfree = 0.000) for 11003 atoms. Found 48 (95 requested) and removed 51 (49 requested) atoms. Cycle 4: After refmac, R = 0.2026 (Rfree = 0.000) for 10979 atoms. Found 28 (92 requested) and removed 53 (49 requested) atoms. Cycle 5: After refmac, R = 0.1966 (Rfree = 0.000) for 10918 atoms. Found 32 (90 requested) and removed 51 (49 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.00 2.81 Search for helices and strands: 0 residues in 0 chains, 11192 seeds are put forward NCS extension: 48 residues added (55 deleted due to clashes), 11240 seeds are put forward Round 1: 1058 peptides, 108 chains. Longest chain 29 peptides. Score 0.684 Round 2: 1134 peptides, 94 chains. Longest chain 37 peptides. Score 0.753 Round 3: 1112 peptides, 94 chains. Longest chain 40 peptides. Score 0.744 Round 4: 1068 peptides, 93 chains. Longest chain 39 peptides. Score 0.725 Round 5: 1087 peptides, 88 chains. Longest chain 49 peptides. Score 0.745 Taking the results from Round 2 Chains 100, Residues 1040, Estimated correctness of the model 75.6 % 19 chains (416 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 114 B and 118 B 98 chains (1042 residues) following loop building 18 chains (419 residues) in sequence following loop building ------------------------------------------------------ 29175 reflections ( 99.85 % complete ) and 19420 restraints for refining 11173 atoms. 13428 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2330 (Rfree = 0.000) for 11173 atoms. Found 90 (90 requested) and removed 92 (50 requested) atoms. Failed to save intermediate PDB Cycle 7: After refmac, R = 0.2112 (Rfree = 0.000) for 11120 atoms. Found 50 (88 requested) and removed 59 (50 requested) atoms. Cycle 8: After refmac, R = 0.2027 (Rfree = 0.000) for 11080 atoms. Found 34 (85 requested) and removed 49 (49 requested) atoms. Cycle 9: After refmac, R = 0.1974 (Rfree = 0.000) for 11038 atoms. Found 33 (83 requested) and removed 50 (49 requested) atoms. Cycle 10: After refmac, R = 0.1930 (Rfree = 0.000) for 10997 atoms. Found 29 (80 requested) and removed 49 (49 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.99 2.80 Search for helices and strands: 0 residues in 0 chains, 11247 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 11270 seeds are put forward Round 1: 1047 peptides, 110 chains. Longest chain 35 peptides. Score 0.672 Round 2: 1101 peptides, 94 chains. Longest chain 43 peptides. Score 0.738 Round 3: 1090 peptides, 94 chains. Longest chain 44 peptides. Score 0.733 Round 4: 1075 peptides, 99 chains. Longest chain 44 peptides. Score 0.715 Round 5: 1097 peptides, 91 chains. Longest chain 50 peptides. Score 0.743 Taking the results from Round 5 Chains 100, Residues 1006, Estimated correctness of the model 73.8 % 21 chains (413 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 190 A and 196 A Built loop between residues 224 A and 231 A Built loop between residues 134 C and 140 C Built loop between residues 227 B and 232 B Built loop between residues 227 E and 232 E 93 chains (1027 residues) following loop building 16 chains (437 residues) in sequence following loop building ------------------------------------------------------ 29175 reflections ( 99.85 % complete ) and 19419 restraints for refining 11169 atoms. 13522 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2399 (Rfree = 0.000) for 11169 atoms. Found 80 (80 requested) and removed 76 (50 requested) atoms. Cycle 12: After refmac, R = 0.2182 (Rfree = 0.000) for 11123 atoms. Found 52 (78 requested) and removed 58 (50 requested) atoms. Cycle 13: After refmac, R = 0.2059 (Rfree = 0.000) for 11076 atoms. Found 41 (75 requested) and removed 49 (49 requested) atoms. Cycle 14: After refmac, R = 0.2009 (Rfree = 0.000) for 11048 atoms. Found 37 (73 requested) and removed 49 (49 requested) atoms. Cycle 15: After refmac, R = 0.1972 (Rfree = 0.000) for 11018 atoms. Found 28 (71 requested) and removed 49 (49 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.98 2.79 Search for helices and strands: 0 residues in 0 chains, 11250 seeds are put forward NCS extension: 34 residues added (99 deleted due to clashes), 11284 seeds are put forward Round 1: 1011 peptides, 105 chains. Longest chain 37 peptides. Score 0.665 Round 2: 1042 peptides, 85 chains. Longest chain 40 peptides. Score 0.731 Round 3: 1056 peptides, 96 chains. Longest chain 47 peptides. Score 0.712 Round 4: 1035 peptides, 97 chains. Longest chain 36 peptides. Score 0.699 Round 5: 1055 peptides, 103 chains. Longest chain 33 peptides. Score 0.695 Taking the results from Round 2 Chains 99, Residues 957, Estimated correctness of the model 71.5 % 22 chains (417 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 222 B and 228 B 98 chains (959 residues) following loop building 21 chains (422 residues) in sequence following loop building ------------------------------------------------------ 29175 reflections ( 99.85 % complete ) and 19872 restraints for refining 11173 atoms. 14292 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2315 (Rfree = 0.000) for 11173 atoms. Found 70 (70 requested) and removed 75 (50 requested) atoms. Cycle 17: After refmac, R = 0.2097 (Rfree = 0.000) for 11133 atoms. Found 54 (68 requested) and removed 53 (50 requested) atoms. Cycle 18: After refmac, R = 0.1995 (Rfree = 0.000) for 11117 atoms. Found 22 (65 requested) and removed 50 (49 requested) atoms. Cycle 19: After refmac, R = 0.1963 (Rfree = 0.000) for 11080 atoms. Found 21 (63 requested) and removed 49 (49 requested) atoms. Cycle 20: After refmac, R = 0.1915 (Rfree = 0.000) for 11045 atoms. Found 21 (61 requested) and removed 51 (49 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.97 2.78 Search for helices and strands: 0 residues in 0 chains, 11287 seeds are put forward NCS extension: 7 residues added (14 deleted due to clashes), 11294 seeds are put forward Round 1: 979 peptides, 105 chains. Longest chain 38 peptides. Score 0.647 Round 2: 1047 peptides, 98 chains. Longest chain 29 peptides. Score 0.703 Round 3: 1042 peptides, 100 chains. Longest chain 44 peptides. Score 0.695 Round 4: 1058 peptides, 95 chains. Longest chain 46 peptides. Score 0.716 Round 5: 1075 peptides, 86 chains. Longest chain 48 peptides. Score 0.745 Taking the results from Round 5 Chains 91, Residues 989, Estimated correctness of the model 74.1 % 16 chains (387 residues) have been docked in sequence Building loops using Loopy2018 91 chains (989 residues) following loop building 16 chains (387 residues) in sequence following loop building ------------------------------------------------------ 29175 reflections ( 99.85 % complete ) and 19999 restraints for refining 11175 atoms. 14302 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2369 (Rfree = 0.000) for 11175 atoms. Found 60 (60 requested) and removed 84 (50 requested) atoms. Cycle 22: After refmac, R = 0.2148 (Rfree = 0.000) for 11127 atoms. Found 55 (58 requested) and removed 52 (50 requested) atoms. Cycle 23: After refmac, R = 0.2043 (Rfree = 0.000) for 11107 atoms. Found 33 (55 requested) and removed 49 (49 requested) atoms. Cycle 24: After refmac, R = 0.1985 (Rfree = 0.000) for 11076 atoms. Found 22 (53 requested) and removed 49 (49 requested) atoms. Cycle 25: After refmac, R = 0.1961 (Rfree = 0.000) for 11041 atoms. Found 22 (51 requested) and removed 49 (49 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.96 2.77 Search for helices and strands: 0 residues in 0 chains, 11290 seeds are put forward NCS extension: 14 residues added (5 deleted due to clashes), 11304 seeds are put forward Round 1: 986 peptides, 106 chains. Longest chain 24 peptides. Score 0.648 Round 2: 1053 peptides, 95 chains. Longest chain 55 peptides. Score 0.713 Round 3: 1038 peptides, 93 chains. Longest chain 49 peptides. Score 0.710 Round 4: 1050 peptides, 90 chains. Longest chain 50 peptides. Score 0.724 Round 5: 1043 peptides, 97 chains. Longest chain 42 peptides. Score 0.703 Taking the results from Round 4 Chains 98, Residues 960, Estimated correctness of the model 70.1 % 13 chains (319 residues) have been docked in sequence Building loops using Loopy2018 98 chains (960 residues) following loop building 13 chains (319 residues) in sequence following loop building ------------------------------------------------------ 29175 reflections ( 99.85 % complete ) and 20862 restraints for refining 11174 atoms. 15626 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2289 (Rfree = 0.000) for 11174 atoms. Found 50 (50 requested) and removed 77 (50 requested) atoms. Cycle 27: After refmac, R = 0.2116 (Rfree = 0.000) for 11105 atoms. Found 50 (50 requested) and removed 53 (50 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.2027 (Rfree = 0.000) for 11087 atoms. Found 32 (49 requested) and removed 50 (49 requested) atoms. Cycle 29: After refmac, R = 0.1951 (Rfree = 0.000) for 11052 atoms. Found 32 (49 requested) and removed 50 (49 requested) atoms. Cycle 30: After refmac, R = 0.1909 (Rfree = 0.000) for 11022 atoms. Found 27 (49 requested) and removed 50 (49 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.98 2.79 Search for helices and strands: 0 residues in 0 chains, 11265 seeds are put forward NCS extension: 34 residues added (17 deleted due to clashes), 11299 seeds are put forward Round 1: 919 peptides, 96 chains. Longest chain 31 peptides. Score 0.636 Round 2: 1013 peptides, 94 chains. Longest chain 50 peptides. Score 0.695 Round 3: 1024 peptides, 94 chains. Longest chain 30 peptides. Score 0.701 Round 4: 1012 peptides, 89 chains. Longest chain 51 peptides. Score 0.707 Round 5: 1041 peptides, 96 chains. Longest chain 44 peptides. Score 0.705 Taking the results from Round 4 Chains 95, Residues 923, Estimated correctness of the model 66.7 % 11 chains (293 residues) have been docked in sequence Building loops using Loopy2018 95 chains (923 residues) following loop building 11 chains (293 residues) in sequence following loop building ------------------------------------------------------ 29175 reflections ( 99.85 % complete ) and 21583 restraints for refining 11174 atoms. 16646 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2205 (Rfree = 0.000) for 11174 atoms. Found 50 (50 requested) and removed 65 (50 requested) atoms. Cycle 32: After refmac, R = 0.2067 (Rfree = 0.000) for 11130 atoms. Found 50 (50 requested) and removed 50 (50 requested) atoms. Cycle 33: After refmac, R = 0.2001 (Rfree = 0.000) for 11120 atoms. Found 41 (49 requested) and removed 49 (49 requested) atoms. Cycle 34: After refmac, R = 0.1932 (Rfree = 0.000) for 11097 atoms. Found 27 (49 requested) and removed 50 (49 requested) atoms. Cycle 35: After refmac, R = 0.1881 (Rfree = 0.000) for 11063 atoms. Found 35 (49 requested) and removed 49 (49 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.98 2.79 Search for helices and strands: 0 residues in 0 chains, 11331 seeds are put forward NCS extension: 49 residues added (14 deleted due to clashes), 11380 seeds are put forward Round 1: 924 peptides, 109 chains. Longest chain 24 peptides. Score 0.601 Round 2: 989 peptides, 91 chains. Longest chain 36 peptides. Score 0.690 Round 3: 994 peptides, 100 chains. Longest chain 34 peptides. Score 0.669 Round 4: 984 peptides, 105 chains. Longest chain 33 peptides. Score 0.650 Round 5: 976 peptides, 102 chains. Longest chain 34 peptides. Score 0.653 Taking the results from Round 2 Chains 99, Residues 898, Estimated correctness of the model 63.0 % 14 chains (244 residues) have been docked in sequence ------------------------------------------------------ 29175 reflections ( 99.85 % complete ) and 22215 restraints for refining 11175 atoms. 17565 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2116 (Rfree = 0.000) for 11175 atoms. Found 50 (50 requested) and removed 62 (50 requested) atoms. Cycle 37: After refmac, R = 0.1984 (Rfree = 0.000) for 11129 atoms. Found 46 (50 requested) and removed 52 (50 requested) atoms. Cycle 38: After refmac, R = 0.1929 (Rfree = 0.000) for 11115 atoms. Found 27 (49 requested) and removed 49 (49 requested) atoms. Cycle 39: After refmac, R = 0.1893 (Rfree = 0.000) for 11081 atoms. Found 18 (49 requested) and removed 50 (49 requested) atoms. Cycle 40: After refmac, R = 0.1885 (Rfree = 0.000) for 11042 atoms. Found 19 (49 requested) and removed 49 (49 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.99 2.80 Search for helices and strands: 0 residues in 0 chains, 11275 seeds are put forward NCS extension: 12 residues added (6 deleted due to clashes), 11287 seeds are put forward Round 1: 942 peptides, 106 chains. Longest chain 30 peptides. Score 0.621 Round 2: 991 peptides, 90 chains. Longest chain 51 peptides. Score 0.694 Round 3: 982 peptides, 94 chains. Longest chain 27 peptides. Score 0.678 Round 4: 938 peptides, 105 chains. Longest chain 27 peptides. Score 0.622 Round 5: 952 peptides, 99 chains. Longest chain 35 peptides. Score 0.647 Taking the results from Round 2 Chains 99, Residues 901, Estimated correctness of the model 63.9 % 11 chains (243 residues) have been docked in sequence ------------------------------------------------------ 29175 reflections ( 99.85 % complete ) and 22307 restraints for refining 11173 atoms. 17715 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2089 (Rfree = 0.000) for 11173 atoms. Found 50 (50 requested) and removed 64 (50 requested) atoms. Cycle 42: After refmac, R = 0.1968 (Rfree = 0.000) for 11144 atoms. Found 45 (50 requested) and removed 51 (50 requested) atoms. Cycle 43: After refmac, R = 0.1917 (Rfree = 0.000) for 11125 atoms. Found 30 (49 requested) and removed 49 (49 requested) atoms. Cycle 44: After refmac, R = 0.1878 (Rfree = 0.000) for 11091 atoms. Found 28 (49 requested) and removed 49 (49 requested) atoms. Cycle 45: After refmac, R = 0.1859 (Rfree = 0.000) for 11056 atoms. Found 39 (49 requested) and removed 49 (49 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.99 2.80 Search for helices and strands: 0 residues in 0 chains, 11305 seeds are put forward NCS extension: 14 residues added (10 deleted due to clashes), 11319 seeds are put forward Round 1: 894 peptides, 113 chains. Longest chain 23 peptides. Score 0.568 Round 2: 956 peptides, 97 chains. Longest chain 28 peptides. Score 0.655 Round 3: 972 peptides, 100 chains. Longest chain 31 peptides. Score 0.656 Round 4: 954 peptides, 102 chains. Longest chain 25 peptides. Score 0.640 Round 5: 981 peptides, 100 chains. Longest chain 40 peptides. Score 0.662 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 105, Residues 881, Estimated correctness of the model 56.7 % 9 chains (197 residues) have been docked in sequence Sequence coverage is 22 % Consider running further cycles of model building using 2anu-3_warpNtrace.pdb as input Building loops using Loopy2018 105 chains (881 residues) following loop building 9 chains (197 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 29175 reflections ( 99.85 % complete ) and 22959 restraints for refining 11174 atoms. 18611 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2185 (Rfree = 0.000) for 11174 atoms. Found 0 (50 requested) and removed 50 (50 requested) atoms. Cycle 47: After refmac, R = 0.2086 (Rfree = 0.000) for 11087 atoms. Found 0 (49 requested) and removed 26 (49 requested) atoms. Cycle 48: After refmac, R = 0.2027 (Rfree = 0.000) for 11053 atoms. Found 0 (49 requested) and removed 5 (49 requested) atoms. Cycle 49: After refmac, R = 0.1971 (Rfree = 0.000) for 11039 atoms. TimeTaking 178.43