Mon 24 Dec 07:27:53 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2o8q-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2o8q-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2o8q-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2o8q-3.2-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2o8q-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2o8q-3.2-parrot-noncs ############### 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 07:27:58 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/noncs/ArpWArp/wArpResults/WorkingDir/2o8q-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2o8q-3.2-parrot-noncs/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 287 and 0 Target number of residues in the AU: 287 Target solvent content: 0.6092 Checking the provided sequence file Detected sequence length: 134 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 268 Adjusted target solvent content: 0.64 Input MTZ file: 2o8q-3.2-parrot-noncs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 94 Cell parameters: 103.170 103.170 74.680 90.000 90.000 90.000 Input sequence file: 2o8q-3.2-parrot-noncs.fasta_lf Building free atoms model in initial map for 2144 target number of atoms Had to go as low as 0.85 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 3 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 29.026 3.200 Wilson plot Bfac: 56.34 6965 reflections ( 98.78 % complete ) and 0 restraints for refining 2365 atoms. Observations/parameters ratio is 0.74 ------------------------------------------------------ Starting model: R = 0.3080 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2778 (Rfree = 0.000) for 2365 atoms. Found 21 (21 requested) and removed 16 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.15 2.60 Search for helices and strands: 0 residues in 0 chains, 2387 seeds are put forward NCS extension: 0 residues added, 2387 seeds are put forward Round 1: 182 peptides, 23 chains. Longest chain 38 peptides. Score 0.550 Round 2: 197 peptides, 20 chains. Longest chain 27 peptides. Score 0.639 Round 3: 207 peptides, 16 chains. Longest chain 40 peptides. Score 0.714 Round 4: 210 peptides, 18 chains. Longest chain 44 peptides. Score 0.698 Round 5: 209 peptides, 15 chains. Longest chain 41 peptides. Score 0.730 Taking the results from Round 5 Chains 18, Residues 194, Estimated correctness of the model 71.3 % 3 chains (65 residues) have been docked in sequence Building loops using Loopy2018 18 chains (194 residues) following loop building 3 chains (65 residues) in sequence following loop building ------------------------------------------------------ 6965 reflections ( 98.78 % complete ) and 3256 restraints for refining 1955 atoms. 2216 conditional restraints added. Observations/parameters ratio is 0.89 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2706 (Rfree = 0.000) for 1955 atoms. Found 17 (17 requested) and removed 15 (8 requested) atoms. Cycle 2: After refmac, R = 0.2483 (Rfree = 0.000) for 1936 atoms. Found 17 (17 requested) and removed 13 (8 requested) atoms. Cycle 3: After refmac, R = 0.2344 (Rfree = 0.000) for 1915 atoms. Found 16 (16 requested) and removed 10 (8 requested) atoms. Cycle 4: After refmac, R = 0.2246 (Rfree = 0.000) for 1913 atoms. Found 8 (16 requested) and removed 9 (8 requested) atoms. Cycle 5: After refmac, R = 0.2304 (Rfree = 0.000) for 1904 atoms. Found 13 (16 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.07 2.53 Search for helices and strands: 0 residues in 0 chains, 1945 seeds are put forward NCS extension: 27 residues added (10 deleted due to clashes), 1972 seeds are put forward Round 1: 197 peptides, 16 chains. Longest chain 52 peptides. Score 0.690 Round 2: 199 peptides, 13 chains. Longest chain 29 peptides. Score 0.730 Round 3: 202 peptides, 17 chains. Longest chain 35 peptides. Score 0.690 Round 4: 203 peptides, 15 chains. Longest chain 36 peptides. Score 0.717 Round 5: 199 peptides, 15 chains. Longest chain 38 peptides. Score 0.707 Taking the results from Round 2 Chains 17, Residues 186, Estimated correctness of the model 71.3 % 5 chains (97 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 83 A and 86 A 16 chains (188 residues) following loop building 4 chains (99 residues) in sequence following loop building ------------------------------------------------------ 6965 reflections ( 98.78 % complete ) and 3008 restraints for refining 1957 atoms. 1805 conditional restraints added. Observations/parameters ratio is 0.89 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2452 (Rfree = 0.000) for 1957 atoms. Found 15 (15 requested) and removed 15 (8 requested) atoms. Cycle 7: After refmac, R = 0.2379 (Rfree = 0.000) for 1945 atoms. Found 15 (15 requested) and removed 13 (8 requested) atoms. Cycle 8: After refmac, R = 0.2264 (Rfree = 0.000) for 1936 atoms. Found 15 (15 requested) and removed 13 (8 requested) atoms. Cycle 9: After refmac, R = 0.2084 (Rfree = 0.000) for 1935 atoms. Found 12 (14 requested) and removed 9 (8 requested) atoms. Cycle 10: After refmac, R = 0.2067 (Rfree = 0.000) for 1932 atoms. Found 12 (14 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.05 2.52 Search for helices and strands: 0 residues in 0 chains, 1962 seeds are put forward NCS extension: 45 residues added (23 deleted due to clashes), 2007 seeds are put forward Round 1: 194 peptides, 16 chains. Longest chain 44 peptides. Score 0.682 Round 2: 208 peptides, 15 chains. Longest chain 52 peptides. Score 0.728 Round 3: 207 peptides, 14 chains. Longest chain 51 peptides. Score 0.737 Round 4: 200 peptides, 18 chains. Longest chain 31 peptides. Score 0.673 Round 5: 213 peptides, 18 chains. Longest chain 43 peptides. Score 0.705 Taking the results from Round 3 Chains 15, Residues 193, Estimated correctness of the model 72.6 % 4 chains (84 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 86 B and 90 B 14 chains (196 residues) following loop building 3 chains (87 residues) in sequence following loop building ------------------------------------------------------ 6965 reflections ( 98.78 % complete ) and 3171 restraints for refining 1957 atoms. 2017 conditional restraints added. Observations/parameters ratio is 0.89 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2586 (Rfree = 0.000) for 1957 atoms. Found 14 (14 requested) and removed 18 (8 requested) atoms. Cycle 12: After refmac, R = 0.2224 (Rfree = 0.000) for 1938 atoms. Found 13 (13 requested) and removed 13 (8 requested) atoms. Cycle 13: After refmac, R = 0.2221 (Rfree = 0.000) for 1925 atoms. Found 13 (13 requested) and removed 11 (8 requested) atoms. Cycle 14: After refmac, R = 0.2042 (Rfree = 0.000) for 1924 atoms. Found 12 (13 requested) and removed 12 (8 requested) atoms. Cycle 15: After refmac, R = 0.1965 (Rfree = 0.000) for 1920 atoms. Found 11 (12 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.06 2.53 Search for helices and strands: 0 residues in 0 chains, 1971 seeds are put forward NCS extension: 23 residues added (46 deleted due to clashes), 1994 seeds are put forward Round 1: 205 peptides, 17 chains. Longest chain 41 peptides. Score 0.698 Round 2: 217 peptides, 16 chains. Longest chain 58 peptides. Score 0.737 Round 3: 207 peptides, 13 chains. Longest chain 54 peptides. Score 0.748 Round 4: 220 peptides, 15 chains. Longest chain 47 peptides. Score 0.754 Round 5: 221 peptides, 13 chains. Longest chain 41 peptides. Score 0.776 Taking the results from Round 5 Chains 15, Residues 208, Estimated correctness of the model 79.6 % 4 chains (117 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 82 A and 85 A 14 chains (210 residues) following loop building 3 chains (119 residues) in sequence following loop building ------------------------------------------------------ 6965 reflections ( 98.78 % complete ) and 2827 restraints for refining 1957 atoms. 1480 conditional restraints added. Observations/parameters ratio is 0.89 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2613 (Rfree = 0.000) for 1957 atoms. Found 12 (12 requested) and removed 23 (8 requested) atoms. Cycle 17: After refmac, R = 0.2431 (Rfree = 0.000) for 1941 atoms. Found 12 (12 requested) and removed 13 (8 requested) atoms. Cycle 18: After refmac, R = 0.2349 (Rfree = 0.000) for 1936 atoms. Found 11 (11 requested) and removed 11 (8 requested) atoms. Cycle 19: After refmac, R = 0.2410 (Rfree = 0.000) for 1933 atoms. Found 11 (11 requested) and removed 11 (8 requested) atoms. Cycle 20: After refmac, R = 0.2384 (Rfree = 0.000) for 1927 atoms. Found 11 (11 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.08 2.54 Search for helices and strands: 0 residues in 0 chains, 1963 seeds are put forward NCS extension: 23 residues added (13 deleted due to clashes), 1986 seeds are put forward Round 1: 203 peptides, 19 chains. Longest chain 33 peptides. Score 0.668 Round 2: 212 peptides, 18 chains. Longest chain 32 peptides. Score 0.703 Round 3: 194 peptides, 18 chains. Longest chain 42 peptides. Score 0.657 Round 4: 205 peptides, 13 chains. Longest chain 54 peptides. Score 0.744 Round 5: 202 peptides, 14 chains. Longest chain 40 peptides. Score 0.726 Taking the results from Round 4 Chains 14, Residues 192, Estimated correctness of the model 74.0 % 3 chains (107 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 48 A and 56 A 12 chains (198 residues) following loop building 2 chains (114 residues) in sequence following loop building ------------------------------------------------------ 6965 reflections ( 98.78 % complete ) and 2820 restraints for refining 1956 atoms. 1520 conditional restraints added. Observations/parameters ratio is 0.89 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2618 (Rfree = 0.000) for 1956 atoms. Found 10 (10 requested) and removed 24 (8 requested) atoms. Cycle 22: After refmac, R = 0.2347 (Rfree = 0.000) for 1925 atoms. Found 10 (10 requested) and removed 16 (8 requested) atoms. Cycle 23: After refmac, R = 0.2220 (Rfree = 0.000) for 1909 atoms. Found 10 (10 requested) and removed 11 (8 requested) atoms. Cycle 24: After refmac, R = 0.2171 (Rfree = 0.000) for 1904 atoms. Found 9 (9 requested) and removed 10 (8 requested) atoms. Cycle 25: After refmac, R = 0.2186 (Rfree = 0.000) for 1901 atoms. Found 9 (9 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.06 2.53 Search for helices and strands: 0 residues in 0 chains, 1950 seeds are put forward NCS extension: 133 residues added (77 deleted due to clashes), 2083 seeds are put forward Round 1: 199 peptides, 17 chains. Longest chain 43 peptides. Score 0.683 Round 2: 213 peptides, 16 chains. Longest chain 45 peptides. Score 0.728 Round 3: 211 peptides, 17 chains. Longest chain 47 peptides. Score 0.712 Round 4: 207 peptides, 17 chains. Longest chain 43 peptides. Score 0.703 Round 5: 198 peptides, 16 chains. Longest chain 36 peptides. Score 0.693 Taking the results from Round 2 Chains 17, Residues 197, Estimated correctness of the model 70.9 % 4 chains (92 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 81 B and 91 B 15 chains (202 residues) following loop building 3 chains (101 residues) in sequence following loop building ------------------------------------------------------ 6965 reflections ( 98.78 % complete ) and 3058 restraints for refining 1955 atoms. 1824 conditional restraints added. Observations/parameters ratio is 0.89 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2489 (Rfree = 0.000) for 1955 atoms. Found 8 (8 requested) and removed 20 (8 requested) atoms. Cycle 27: After refmac, R = 0.2545 (Rfree = 0.000) for 1937 atoms. Found 8 (8 requested) and removed 13 (8 requested) atoms. Cycle 28: After refmac, R = 0.2292 (Rfree = 0.000) for 1925 atoms. Found 8 (8 requested) and removed 11 (8 requested) atoms. Cycle 29: After refmac, R = 0.2178 (Rfree = 0.000) for 1917 atoms. Found 8 (8 requested) and removed 8 (8 requested) atoms. Cycle 30: After refmac, R = 0.2265 (Rfree = 0.000) for 1915 atoms. Found 8 (8 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.09 2.55 Search for helices and strands: 0 residues in 0 chains, 1944 seeds are put forward NCS extension: 78 residues added (27 deleted due to clashes), 2022 seeds are put forward Round 1: 196 peptides, 17 chains. Longest chain 31 peptides. Score 0.675 Round 2: 207 peptides, 16 chains. Longest chain 30 peptides. Score 0.714 Round 3: 207 peptides, 18 chains. Longest chain 33 peptides. Score 0.691 Round 4: 207 peptides, 16 chains. Longest chain 35 peptides. Score 0.714 Round 5: 195 peptides, 17 chains. Longest chain 30 peptides. Score 0.672 Taking the results from Round 4 Chains 17, Residues 191, Estimated correctness of the model 68.1 % 4 chains (91 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 49 B and 55 B 16 chains (196 residues) following loop building 3 chains (96 residues) in sequence following loop building ------------------------------------------------------ 6965 reflections ( 98.78 % complete ) and 3184 restraints for refining 1956 atoms. 1991 conditional restraints added. Observations/parameters ratio is 0.89 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2649 (Rfree = 0.000) for 1956 atoms. Found 8 (8 requested) and removed 27 (8 requested) atoms. Cycle 32: After refmac, R = 0.2500 (Rfree = 0.000) for 1935 atoms. Found 8 (8 requested) and removed 18 (8 requested) atoms. Cycle 33: After refmac, R = 0.2284 (Rfree = 0.000) for 1922 atoms. Found 8 (8 requested) and removed 17 (8 requested) atoms. Cycle 34: After refmac, R = 0.2221 (Rfree = 0.000) for 1913 atoms. Found 8 (8 requested) and removed 17 (8 requested) atoms. Cycle 35: After refmac, R = 0.2125 (Rfree = 0.000) for 1899 atoms. Found 8 (8 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.03 2.50 Search for helices and strands: 0 residues in 0 chains, 1938 seeds are put forward NCS extension: 47 residues added (25 deleted due to clashes), 1985 seeds are put forward Round 1: 196 peptides, 17 chains. Longest chain 43 peptides. Score 0.675 Round 2: 212 peptides, 15 chains. Longest chain 44 peptides. Score 0.737 Round 3: 213 peptides, 15 chains. Longest chain 39 peptides. Score 0.739 Round 4: 205 peptides, 13 chains. Longest chain 40 peptides. Score 0.744 Round 5: 210 peptides, 15 chains. Longest chain 40 peptides. Score 0.732 Taking the results from Round 4 Chains 13, Residues 192, Estimated correctness of the model 74.0 % 3 chains (108 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 51 A and 55 A 12 chains (195 residues) following loop building 2 chains (111 residues) in sequence following loop building ------------------------------------------------------ 6965 reflections ( 98.78 % complete ) and 3035 restraints for refining 1957 atoms. 1800 conditional restraints added. Observations/parameters ratio is 0.89 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2568 (Rfree = 0.000) for 1957 atoms. Found 8 (8 requested) and removed 18 (8 requested) atoms. Cycle 37: After refmac, R = 0.2326 (Rfree = 0.000) for 1944 atoms. Found 8 (8 requested) and removed 19 (8 requested) atoms. Cycle 38: After refmac, R = 0.2306 (Rfree = 0.000) for 1925 atoms. Found 8 (8 requested) and removed 11 (8 requested) atoms. Cycle 39: After refmac, R = 0.2317 (Rfree = 0.000) for 1917 atoms. Found 8 (8 requested) and removed 15 (8 requested) atoms. Cycle 40: After refmac, R = 0.2097 (Rfree = 0.000) for 1906 atoms. Found 8 (8 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.04 2.51 Search for helices and strands: 0 residues in 0 chains, 1948 seeds are put forward NCS extension: 123 residues added (25 deleted due to clashes), 2071 seeds are put forward Round 1: 187 peptides, 18 chains. Longest chain 27 peptides. Score 0.637 Round 2: 203 peptides, 13 chains. Longest chain 40 peptides. Score 0.739 Round 3: 213 peptides, 15 chains. Longest chain 44 peptides. Score 0.739 Round 4: 217 peptides, 12 chains. Longest chain 54 peptides. Score 0.778 Round 5: 204 peptides, 16 chains. Longest chain 40 peptides. Score 0.707 Taking the results from Round 4 Chains 14, Residues 205, Estimated correctness of the model 79.9 % 5 chains (139 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 50 A and 54 A Built loop between residues 33 B and 40 B Built loop between residues 48 B and 56 B 10 chains (217 residues) following loop building 2 chains (155 residues) in sequence following loop building ------------------------------------------------------ 6965 reflections ( 98.78 % complete ) and 2452 restraints for refining 1957 atoms. 923 conditional restraints added. Observations/parameters ratio is 0.89 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2405 (Rfree = 0.000) for 1957 atoms. Found 8 (8 requested) and removed 23 (8 requested) atoms. Cycle 42: After refmac, R = 0.2177 (Rfree = 0.000) for 1927 atoms. Found 8 (8 requested) and removed 13 (8 requested) atoms. Cycle 43: After refmac, R = 0.2075 (Rfree = 0.000) for 1919 atoms. Found 8 (8 requested) and removed 9 (8 requested) atoms. Cycle 44: After refmac, R = 0.2014 (Rfree = 0.000) for 1915 atoms. Found 8 (8 requested) and removed 9 (8 requested) atoms. Cycle 45: After refmac, R = 0.1949 (Rfree = 0.000) for 1910 atoms. Found 8 (8 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.05 2.52 Search for helices and strands: 0 residues in 0 chains, 1952 seeds are put forward NCS extension: 86 residues added (22 deleted due to clashes), 2038 seeds are put forward Round 1: 208 peptides, 15 chains. Longest chain 44 peptides. Score 0.728 Round 2: 215 peptides, 16 chains. Longest chain 61 peptides. Score 0.732 Round 3: 212 peptides, 15 chains. Longest chain 55 peptides. Score 0.737 Round 4: 219 peptides, 15 chains. Longest chain 40 peptides. Score 0.752 Round 5: 222 peptides, 13 chains. Longest chain 86 peptides. Score 0.778 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 15, Residues 209, Estimated correctness of the model 79.9 % 2 chains (108 residues) have been docked in sequence Sequence coverage is 51 % Consider running further cycles of model building using 2o8q-3_warpNtrace.pdb as input Building loops using Loopy2018 15 chains (209 residues) following loop building 2 chains (108 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6965 reflections ( 98.78 % complete ) and 3015 restraints for refining 1957 atoms. 1715 conditional restraints added. Observations/parameters ratio is 0.89 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2311 (Rfree = 0.000) for 1957 atoms. Found 0 (8 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2251 (Rfree = 0.000) for 1939 atoms. Found 0 (8 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.2319 (Rfree = 0.000) for 1927 atoms. Found 0 (8 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.2177 (Rfree = 0.000) for 1915 atoms. TimeTaking 32.28