Mon 24 Dec 00:01:49 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 2anu-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2anu-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2anu-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2anu-3.2-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/2anu-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2anu-3.2-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 ============================================================ Mon 24 Dec 00:01:54 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/2anu-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2anu-3.2-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 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-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: 146 Cell parameters: 111.273 111.273 383.188 90.000 90.000 120.000 Input sequence file: 2anu-3.2-parrot-mrncs.fasta_lf Building free atoms model in initial map for 12240 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: 127.729 3.200 Wilson plot Bfac: 52.43 29175 reflections ( 99.85 % complete ) and 0 restraints for refining 13485 atoms. Observations/parameters ratio is 0.54 ------------------------------------------------------ Starting model: R = 0.2767 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2348 (Rfree = 0.000) for 13485 atoms. Found 121 (121 requested) and removed 87 (60 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.02 2.82 Search for helices and strands: 0 residues in 0 chains, 13754 seeds are put forward NCS extension: 0 residues added, 13754 seeds are put forward Round 1: 897 peptides, 134 chains. Longest chain 21 peptides. Score 0.501 Round 2: 1008 peptides, 103 chains. Longest chain 38 peptides. Score 0.669 Round 3: 1089 peptides, 100 chains. Longest chain 43 peptides. Score 0.719 Round 4: 1090 peptides, 88 chains. Longest chain 35 peptides. Score 0.747 Round 5: 1121 peptides, 92 chains. Longest chain 48 peptides. Score 0.752 Taking the results from Round 5 Chains 96, Residues 1029, Estimated correctness of the model 75.4 % 23 chains (495 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 154 B and 164 B Built loop between residues 223 B and 229 B 92 chains (1036 residues) following loop building 21 chains (509 residues) in sequence following loop building ------------------------------------------------------ 29175 reflections ( 99.85 % complete ) and 18439 restraints for refining 11220 atoms. 12203 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2519 (Rfree = 0.000) for 11220 atoms. Found 100 (100 requested) and removed 85 (50 requested) atoms. Cycle 2: After refmac, R = 0.2259 (Rfree = 0.000) for 11107 atoms. Found 67 (98 requested) and removed 64 (50 requested) atoms. Cycle 3: After refmac, R = 0.2103 (Rfree = 0.000) for 11053 atoms. Found 40 (95 requested) and removed 52 (49 requested) atoms. Cycle 4: After refmac, R = 0.2015 (Rfree = 0.000) for 10997 atoms. Found 30 (93 requested) and removed 49 (49 requested) atoms. Cycle 5: After refmac, R = 0.1963 (Rfree = 0.000) for 10946 atoms. Found 24 (90 requested) and removed 50 (49 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.00 2.81 Search for helices and strands: 0 residues in 0 chains, 11215 seeds are put forward NCS extension: 17 residues added (39 deleted due to clashes), 11232 seeds are put forward Round 1: 1067 peptides, 95 chains. Longest chain 38 peptides. Score 0.720 Round 2: 1091 peptides, 87 chains. Longest chain 36 peptides. Score 0.749 Round 3: 1085 peptides, 85 chains. Longest chain 39 peptides. Score 0.751 Round 4: 1093 peptides, 84 chains. Longest chain 61 peptides. Score 0.757 Round 5: 1088 peptides, 89 chains. Longest chain 43 peptides. Score 0.744 Taking the results from Round 4 Chains 88, Residues 1009, Estimated correctness of the model 76.3 % 20 chains (426 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 77 A and 88 A Built loop between residues 107 A and 112 A Built loop between residues 157 A and 162 A Built loop between residues 179 A and 182 A 83 chains (1024 residues) following loop building 16 chains (446 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 29175 reflections ( 99.85 % complete ) and 19411 restraints for refining 11174 atoms. 13390 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2387 (Rfree = 0.000) for 11174 atoms. Found 90 (90 requested) and removed 83 (50 requested) atoms. Cycle 7: After refmac, R = 0.2124 (Rfree = 0.000) for 11133 atoms. Found 46 (88 requested) and removed 52 (50 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.2017 (Rfree = 0.000) for 11095 atoms. Found 27 (85 requested) and removed 51 (49 requested) atoms. Cycle 9: After refmac, R = 0.1936 (Rfree = 0.000) for 11052 atoms. Found 28 (83 requested) and removed 51 (49 requested) atoms. Cycle 10: After refmac, R = 0.1872 (Rfree = 0.000) for 11016 atoms. Found 14 (80 requested) and removed 51 (49 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.00 2.81 Search for helices and strands: 0 residues in 0 chains, 11245 seeds are put forward NCS extension: 63 residues added (57 deleted due to clashes), 11308 seeds are put forward Round 1: 1051 peptides, 94 chains. Longest chain 44 peptides. Score 0.715 Round 2: 1085 peptides, 88 chains. Longest chain 44 peptides. Score 0.745 Round 3: 1073 peptides, 91 chains. Longest chain 48 peptides. Score 0.732 Round 4: 1067 peptides, 88 chains. Longest chain 43 peptides. Score 0.736 Round 5: 1054 peptides, 96 chains. Longest chain 45 peptides. Score 0.711 Taking the results from Round 2 Chains 94, Residues 997, Estimated correctness of the model 74.1 % 19 chains (410 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 77 A and 86 A Built loop between residues 224 A and 233 A Built loop between residues 109 B and 117 B 88 chains (1015 residues) following loop building 16 chains (433 residues) in sequence following loop building ------------------------------------------------------ 29175 reflections ( 99.85 % complete ) and 19720 restraints for refining 11174 atoms. 13814 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2318 (Rfree = 0.000) for 11174 atoms. Found 80 (80 requested) and removed 88 (50 requested) atoms. Cycle 12: After refmac, R = 0.2096 (Rfree = 0.000) for 11118 atoms. Found 50 (78 requested) and removed 54 (50 requested) atoms. Cycle 13: After refmac, R = 0.2009 (Rfree = 0.000) for 11082 atoms. Found 28 (75 requested) and removed 51 (49 requested) atoms. Cycle 14: After refmac, R = 0.1961 (Rfree = 0.000) for 11047 atoms. Found 21 (73 requested) and removed 51 (49 requested) atoms. Cycle 15: After refmac, R = 0.1916 (Rfree = 0.000) for 11007 atoms. Found 11 (71 requested) and removed 50 (49 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.98 2.79 Search for helices and strands: 0 residues in 0 chains, 11249 seeds are put forward NCS extension: 42 residues added (13 deleted due to clashes), 11291 seeds are put forward Round 1: 1031 peptides, 95 chains. Longest chain 68 peptides. Score 0.702 Round 2: 1101 peptides, 91 chains. Longest chain 51 peptides. Score 0.745 Round 3: 1086 peptides, 92 chains. Longest chain 49 peptides. Score 0.736 Round 4: 1081 peptides, 88 chains. Longest chain 44 peptides. Score 0.743 Round 5: 1079 peptides, 93 chains. Longest chain 47 peptides. Score 0.730 Taking the results from Round 2 Chains 99, Residues 1010, Estimated correctness of the model 74.1 % 17 chains (402 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 222 A and 233 A 98 chains (1015 residues) following loop building 16 chains (412 residues) in sequence following loop building ------------------------------------------------------ 29175 reflections ( 99.85 % complete ) and 19799 restraints for refining 11174 atoms. 14119 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2295 (Rfree = 0.000) for 11174 atoms. Found 70 (70 requested) and removed 72 (50 requested) atoms. Cycle 17: After refmac, R = 0.2101 (Rfree = 0.000) for 11133 atoms. Found 68 (68 requested) and removed 51 (50 requested) atoms. Cycle 18: After refmac, R = 0.1980 (Rfree = 0.000) for 11136 atoms. Found 25 (66 requested) and removed 52 (50 requested) atoms. Cycle 19: After refmac, R = 0.1912 (Rfree = 0.000) for 11098 atoms. Found 21 (63 requested) and removed 49 (49 requested) atoms. Cycle 20: After refmac, R = 0.1868 (Rfree = 0.000) for 11062 atoms. Found 17 (61 requested) and removed 49 (49 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.99 2.80 Search for helices and strands: 0 residues in 0 chains, 11320 seeds are put forward NCS extension: 10 residues added (21 deleted due to clashes), 11330 seeds are put forward Round 1: 1017 peptides, 103 chains. Longest chain 42 peptides. Score 0.674 Round 2: 1029 peptides, 93 chains. Longest chain 47 peptides. Score 0.706 Round 3: 1036 peptides, 91 chains. Longest chain 47 peptides. Score 0.714 Round 4: 1034 peptides, 104 chains. Longest chain 37 peptides. Score 0.681 Round 5: 1040 peptides, 101 chains. Longest chain 39 peptides. Score 0.692 Taking the results from Round 3 Chains 98, Residues 945, Estimated correctness of the model 68.1 % 11 chains (267 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 108 A and 111 A Built loop between residues 137 A and 146 A 94 chains (951 residues) following loop building 9 chains (277 residues) in sequence following loop building ------------------------------------------------------ 29175 reflections ( 99.85 % complete ) and 21668 restraints for refining 11173 atoms. 16765 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2223 (Rfree = 0.000) for 11173 atoms. Found 60 (60 requested) and removed 64 (50 requested) atoms. Cycle 22: After refmac, R = 0.2028 (Rfree = 0.000) for 11149 atoms. Found 40 (58 requested) and removed 51 (50 requested) atoms. Cycle 23: After refmac, R = 0.1938 (Rfree = 0.000) for 11122 atoms. Found 30 (55 requested) and removed 49 (49 requested) atoms. Cycle 24: After refmac, R = 0.1878 (Rfree = 0.000) for 11096 atoms. Found 14 (53 requested) and removed 50 (49 requested) atoms. Cycle 25: After refmac, R = 0.1852 (Rfree = 0.000) for 11052 atoms. Found 26 (51 requested) and removed 49 (49 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.99 2.80 Search for helices and strands: 0 residues in 0 chains, 11335 seeds are put forward NCS extension: 22 residues added (28 deleted due to clashes), 11357 seeds are put forward Round 1: 999 peptides, 116 chains. Longest chain 38 peptides. Score 0.628 Round 2: 1047 peptides, 105 chains. Longest chain 39 peptides. Score 0.685 Round 3: 1062 peptides, 91 chains. Longest chain 39 peptides. Score 0.727 Round 4: 1062 peptides, 98 chains. Longest chain 39 peptides. Score 0.710 Round 5: 1032 peptides, 100 chains. Longest chain 42 peptides. Score 0.690 Taking the results from Round 3 Chains 100, Residues 971, Estimated correctness of the model 70.7 % 16 chains (289 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 222 B and 230 B 97 chains (971 residues) following loop building 15 chains (296 residues) in sequence following loop building ------------------------------------------------------ 29175 reflections ( 99.85 % complete ) and 21280 restraints for refining 11173 atoms. 16198 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2299 (Rfree = 0.000) for 11173 atoms. Found 50 (50 requested) and removed 66 (50 requested) atoms. Cycle 27: After refmac, R = 0.2123 (Rfree = 0.000) for 11131 atoms. Found 46 (50 requested) and removed 51 (50 requested) atoms. Cycle 28: After refmac, R = 0.2031 (Rfree = 0.000) for 11115 atoms. Found 12 (49 requested) and removed 49 (49 requested) atoms. Cycle 29: After refmac, R = 0.1976 (Rfree = 0.000) for 11071 atoms. Found 19 (49 requested) and removed 49 (49 requested) atoms. Cycle 30: After refmac, R = 0.1935 (Rfree = 0.000) for 11036 atoms. Found 7 (49 requested) and removed 50 (49 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.99 2.80 Search for helices and strands: 0 residues in 0 chains, 11299 seeds are put forward NCS extension: 7 residues added (17 deleted due to clashes), 11306 seeds are put forward Round 1: 956 peptides, 105 chains. Longest chain 36 peptides. Score 0.633 Round 2: 1018 peptides, 101 chains. Longest chain 39 peptides. Score 0.680 Round 3: 1041 peptides, 103 chains. Longest chain 39 peptides. Score 0.687 Round 4: 1053 peptides, 102 chains. Longest chain 47 peptides. Score 0.696 Round 5: 1011 peptides, 105 chains. Longest chain 32 peptides. Score 0.665 Taking the results from Round 4 Chains 109, Residues 951, Estimated correctness of the model 64.3 % 16 chains (358 residues) have been docked in sequence ------------------------------------------------------ 29175 reflections ( 99.85 % complete ) and 20417 restraints for refining 11175 atoms. 15033 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2336 (Rfree = 0.000) for 11175 atoms. Found 50 (50 requested) and removed 81 (50 requested) atoms. Cycle 32: After refmac, R = 0.2157 (Rfree = 0.000) for 11110 atoms. Found 45 (50 requested) and removed 56 (50 requested) atoms. Cycle 33: After refmac, R = 0.2064 (Rfree = 0.000) for 11080 atoms. Found 19 (49 requested) and removed 50 (49 requested) atoms. Cycle 34: After refmac, R = 0.2014 (Rfree = 0.000) for 11035 atoms. Found 14 (49 requested) and removed 49 (49 requested) atoms. Cycle 35: After refmac, R = 0.1979 (Rfree = 0.000) for 10994 atoms. Found 7 (49 requested) and removed 49 (49 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.96 2.77 Search for helices and strands: 0 residues in 0 chains, 11203 seeds are put forward NCS extension: 12 residues added (24 deleted due to clashes), 11215 seeds are put forward Round 1: 944 peptides, 115 chains. Longest chain 21 peptides. Score 0.596 Round 2: 1009 peptides, 103 chains. Longest chain 29 peptides. Score 0.670 Round 3: 978 peptides, 102 chains. Longest chain 44 peptides. Score 0.654 Round 4: 994 peptides, 94 chains. Longest chain 40 peptides. Score 0.685 Round 5: 984 peptides, 101 chains. Longest chain 45 peptides. Score 0.661 Taking the results from Round 4 Chains 97, Residues 900, Estimated correctness of the model 61.9 % 10 chains (218 residues) have been docked in sequence ------------------------------------------------------ 29175 reflections ( 99.85 % complete ) and 22377 restraints for refining 11175 atoms. 17804 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2224 (Rfree = 0.000) for 11175 atoms. Found 50 (50 requested) and removed 67 (50 requested) atoms. Cycle 37: After refmac, R = 0.2070 (Rfree = 0.000) for 11139 atoms. Found 38 (50 requested) and removed 51 (50 requested) atoms. Cycle 38: After refmac, R = 0.1989 (Rfree = 0.000) for 11116 atoms. Found 16 (49 requested) and removed 50 (49 requested) atoms. Cycle 39: After refmac, R = 0.1952 (Rfree = 0.000) for 11071 atoms. Found 20 (49 requested) and removed 49 (49 requested) atoms. Cycle 40: After refmac, R = 0.1931 (Rfree = 0.000) for 11035 atoms. Found 19 (49 requested) and removed 49 (49 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.98 2.79 Search for helices and strands: 0 residues in 0 chains, 11262 seeds are put forward NCS extension: 18 residues added (17 deleted due to clashes), 11280 seeds are put forward Round 1: 902 peptides, 123 chains. Longest chain 25 peptides. Score 0.541 Round 2: 963 peptides, 103 chains. Longest chain 28 peptides. Score 0.643 Round 3: 1004 peptides, 106 chains. Longest chain 28 peptides. Score 0.659 Round 4: 991 peptides, 103 chains. Longest chain 27 peptides. Score 0.659 Round 5: 967 peptides, 109 chains. Longest chain 32 peptides. Score 0.628 Taking the results from Round 4 Chains 106, Residues 888, Estimated correctness of the model 56.0 % 7 chains (126 residues) have been docked in sequence ------------------------------------------------------ 29175 reflections ( 99.85 % complete ) and 23760 restraints for refining 11175 atoms. 19722 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2186 (Rfree = 0.000) for 11175 atoms. Found 50 (50 requested) and removed 57 (50 requested) atoms. Cycle 42: After refmac, R = 0.2043 (Rfree = 0.000) for 11149 atoms. Found 50 (50 requested) and removed 50 (50 requested) atoms. Cycle 43: After refmac, R = 0.1975 (Rfree = 0.000) for 11139 atoms. Found 30 (50 requested) and removed 50 (50 requested) atoms. Cycle 44: After refmac, R = 0.1943 (Rfree = 0.000) for 11108 atoms. Found 37 (49 requested) and removed 49 (49 requested) atoms. Cycle 45: After refmac, R = 0.1906 (Rfree = 0.000) for 11085 atoms. Found 31 (49 requested) and removed 50 (49 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.98 2.79 Search for helices and strands: 0 residues in 0 chains, 11322 seeds are put forward NCS extension: 16 residues added (8 deleted due to clashes), 11338 seeds are put forward Round 1: 882 peptides, 115 chains. Longest chain 23 peptides. Score 0.553 Round 2: 930 peptides, 97 chains. Longest chain 32 peptides. Score 0.640 Round 3: 937 peptides, 101 chains. Longest chain 27 peptides. Score 0.632 Round 4: 938 peptides, 102 chains. Longest chain 30 peptides. Score 0.630 Round 5: 908 peptides, 109 chains. Longest chain 28 peptides. Score 0.590 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 101, Residues 833, Estimated correctness of the model 51.4 % 10 chains (158 residues) have been docked in sequence Sequence coverage is 18 % Consider running further cycles of model building using 2anu-3_warpNtrace.pdb as input Building loops using Loopy2018 101 chains (833 residues) following loop building 10 chains (158 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 29175 reflections ( 99.85 % complete ) and 23633 restraints for refining 11174 atoms. 19604 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2082 (Rfree = 0.000) for 11174 atoms. Found 0 (50 requested) and removed 29 (50 requested) atoms. Cycle 47: After refmac, R = 0.2019 (Rfree = 0.000) for 11123 atoms. Found 0 (50 requested) and removed 13 (50 requested) atoms. Cycle 48: After refmac, R = 0.1958 (Rfree = 0.000) for 11101 atoms. Found 0 (49 requested) and removed 15 (49 requested) atoms. Cycle 49: After refmac, R = 0.1933 (Rfree = 0.000) for 11078 atoms. TimeTaking 146