Mon 24 Dec 01:01:39 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 2ozj-1.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2ozj-1.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2ozj-1.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ozj-1.6-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/2ozj-1.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ozj-1.6-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 01:01:44 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/2ozj-1.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ozj-1.6-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 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-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: 20 Cell parameters: 40.940 69.810 150.550 90.000 90.000 90.000 Input sequence file: 2ozj-1.6-parrot-mrncs.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 2017 atoms. Observations/parameters ratio is 3.58 ------------------------------------------------------ Starting model: R = 0.3243 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2634 (Rfree = 0.000) for 2017 atoms. Found 79 (130 requested) and removed 70 (65 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.84 2.02 NCS extension: 0 residues added, 2026 seeds are put forward Round 1: 173 peptides, 15 chains. Longest chain 23 peptides. Score 0.816 Round 2: 188 peptides, 8 chains. Longest chain 55 peptides. Score 0.915 Round 3: 197 peptides, 10 chains. Longest chain 36 peptides. Score 0.911 Round 4: 202 peptides, 6 chains. Longest chain 72 peptides. Score 0.943 Round 5: 202 peptides, 8 chains. Longest chain 56 peptides. Score 0.931 Taking the results from Round 4 Chains 7, Residues 196, Estimated correctness of the model 99.8 % 6 chains (189 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 34 A and 38 A Built loop between residues 49 A and 54 A Built loop between residues 71 A and 80 A Built loop between residues 34 B and 38 B 3 chains (213 residues) following loop building 2 chains (207 residues) in sequence following loop building ------------------------------------------------------ 28908 reflections ( 99.72 % complete ) and 1861 restraints for refining 1869 atoms. 186 conditional restraints added. Observations/parameters ratio is 3.87 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3212 (Rfree = 0.000) for 1869 atoms. Found 52 (121 requested) and removed 62 (60 requested) atoms. Cycle 2: After refmac, R = 0.2959 (Rfree = 0.000) for 1853 atoms. Found 37 (118 requested) and removed 28 (60 requested) atoms. Cycle 3: After refmac, R = 0.2685 (Rfree = 0.000) for 1858 atoms. Found 46 (115 requested) and removed 18 (60 requested) atoms. Cycle 4: After refmac, R = 0.2525 (Rfree = 0.000) for 1879 atoms. Found 40 (117 requested) and removed 13 (61 requested) atoms. Cycle 5: After refmac, R = 0.2457 (Rfree = 0.000) for 1899 atoms. Found 36 (118 requested) and removed 16 (61 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.80 1.98 NCS extension: 37 residues added (69 deleted due to clashes), 1959 seeds are put forward Round 1: 199 peptides, 6 chains. Longest chain 56 peptides. Score 0.941 Round 2: 205 peptides, 5 chains. Longest chain 70 peptides. Score 0.952 Round 3: 204 peptides, 6 chains. Longest chain 56 peptides. Score 0.945 Round 4: 204 peptides, 6 chains. Longest chain 70 peptides. Score 0.945 Round 5: 205 peptides, 5 chains. Longest chain 71 peptides. Score 0.952 Taking the results from Round 5 Chains 5, Residues 200, Estimated correctness of the model 99.9 % 5 chains (200 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 34 A and 39 A Built loop between residues 49 B and 52 B Built loop between residues 72 B and 78 B 2 chains (211 residues) following loop building 2 chains (211 residues) in sequence following loop building ------------------------------------------------------ 28908 reflections ( 99.72 % complete ) and 1846 restraints for refining 1949 atoms. 158 conditional restraints added. Observations/parameters ratio is 3.71 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2712 (Rfree = 0.000) for 1949 atoms. Found 54 (121 requested) and removed 59 (63 requested) atoms. Cycle 7: After refmac, R = 0.2536 (Rfree = 0.000) for 1942 atoms. Found 60 (117 requested) and removed 15 (62 requested) atoms. Cycle 8: After refmac, R = 0.2415 (Rfree = 0.000) for 1986 atoms. Found 38 (120 requested) and removed 16 (64 requested) atoms. Cycle 9: After refmac, R = 0.2356 (Rfree = 0.000) for 2003 atoms. Found 45 (121 requested) and removed 13 (64 requested) atoms. Cycle 10: After refmac, R = 0.2298 (Rfree = 0.000) for 2031 atoms. Found 45 (123 requested) and removed 18 (65 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.80 1.98 NCS extension: 0 residues added, 2058 seeds are put forward Round 1: 206 peptides, 5 chains. Longest chain 71 peptides. Score 0.952 Round 2: 206 peptides, 5 chains. Longest chain 71 peptides. Score 0.952 Round 3: 206 peptides, 5 chains. Longest chain 71 peptides. Score 0.952 Round 4: 208 peptides, 4 chains. Longest chain 71 peptides. Score 0.959 Round 5: 202 peptides, 6 chains. Longest chain 58 peptides. Score 0.943 Taking the results from Round 4 Chains 4, Residues 204, Estimated correctness of the model 99.9 % 4 chains (204 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 34 A and 39 A Built loop between residues 72 B and 77 B 2 chains (212 residues) following loop building 2 chains (212 residues) in sequence following loop building ------------------------------------------------------ 28908 reflections ( 99.72 % complete ) and 1877 restraints for refining 2005 atoms. 184 conditional restraints added. Observations/parameters ratio is 3.60 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2573 (Rfree = 0.000) for 2005 atoms. Found 67 (121 requested) and removed 62 (64 requested) atoms. Cycle 12: After refmac, R = 0.2441 (Rfree = 0.000) for 2008 atoms. Found 44 (120 requested) and removed 17 (65 requested) atoms. Cycle 13: After refmac, R = 0.2359 (Rfree = 0.000) for 2031 atoms. Found 38 (121 requested) and removed 9 (65 requested) atoms. Cycle 14: After refmac, R = 0.2289 (Rfree = 0.000) for 2056 atoms. Found 34 (122 requested) and removed 5 (66 requested) atoms. Cycle 15: After refmac, R = 0.2250 (Rfree = 0.000) for 2077 atoms. Found 40 (123 requested) and removed 11 (67 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.79 1.97 NCS extension: 69 residues added (37 deleted due to clashes), 2178 seeds are put forward Round 1: 205 peptides, 6 chains. Longest chain 71 peptides. Score 0.946 Round 2: 208 peptides, 3 chains. Longest chain 105 peptides. Score 0.964 Round 3: 206 peptides, 5 chains. Longest chain 105 peptides. Score 0.952 Round 4: 208 peptides, 3 chains. Longest chain 105 peptides. Score 0.964 Round 5: 208 peptides, 3 chains. Longest chain 105 peptides. Score 0.964 Taking the results from Round 5 Chains 3, Residues 205, Estimated correctness of the model 99.9 % 3 chains (205 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 72 B and 78 B 2 chains (210 residues) following loop building 2 chains (210 residues) in sequence following loop building ------------------------------------------------------ 28908 reflections ( 99.72 % complete ) and 1921 restraints for refining 2014 atoms. 244 conditional restraints added. Observations/parameters ratio is 3.59 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2518 (Rfree = 0.000) for 2014 atoms. Found 73 (120 requested) and removed 55 (65 requested) atoms. Cycle 17: After refmac, R = 0.2376 (Rfree = 0.000) for 2028 atoms. Found 46 (118 requested) and removed 17 (65 requested) atoms. Cycle 18: After refmac, R = 0.2295 (Rfree = 0.000) for 2054 atoms. Found 32 (119 requested) and removed 8 (66 requested) atoms. Cycle 19: After refmac, R = 0.2236 (Rfree = 0.000) for 2074 atoms. Found 30 (121 requested) and removed 11 (67 requested) atoms. Cycle 20: After refmac, R = 0.2198 (Rfree = 0.000) for 2088 atoms. Found 34 (121 requested) and removed 22 (67 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.78 1.96 NCS extension: 70 residues added (35 deleted due to clashes), 2171 seeds are put forward Round 1: 204 peptides, 6 chains. Longest chain 70 peptides. Score 0.945 Round 2: 207 peptides, 4 chains. Longest chain 105 peptides. Score 0.959 Round 3: 206 peptides, 5 chains. Longest chain 105 peptides. Score 0.952 Round 4: 206 peptides, 5 chains. Longest chain 105 peptides. Score 0.952 Round 5: 208 peptides, 4 chains. Longest chain 72 peptides. Score 0.959 Taking the results from Round 5 Chains 5, Residues 204, Estimated correctness of the model 99.9 % 4 chains (203 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 34 A and 38 A Built loop between residues 72 B and 78 B 2 chains (211 residues) following loop building 2 chains (211 residues) in sequence following loop building ------------------------------------------------------ 28908 reflections ( 99.72 % complete ) and 1920 restraints for refining 2027 atoms. 232 conditional restraints added. Observations/parameters ratio is 3.57 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2493 (Rfree = 0.000) for 2027 atoms. Found 73 (115 requested) and removed 66 (65 requested) atoms. Cycle 22: After refmac, R = 0.2401 (Rfree = 0.000) for 2031 atoms. Found 49 (113 requested) and removed 18 (65 requested) atoms. Cycle 23: After refmac, R = 0.2321 (Rfree = 0.000) for 2060 atoms. Found 33 (114 requested) and removed 21 (66 requested) atoms. Cycle 24: After refmac, R = 0.2275 (Rfree = 0.000) for 2069 atoms. Found 33 (112 requested) and removed 8 (66 requested) atoms. Cycle 25: After refmac, R = 0.2249 (Rfree = 0.000) for 2088 atoms. Found 25 (113 requested) and removed 13 (67 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.79 1.97 NCS extension: 63 residues added (47 deleted due to clashes), 2168 seeds are put forward Round 1: 207 peptides, 5 chains. Longest chain 70 peptides. Score 0.953 Round 2: 206 peptides, 5 chains. Longest chain 105 peptides. Score 0.952 Round 3: 204 peptides, 5 chains. Longest chain 105 peptides. Score 0.951 Round 4: 207 peptides, 5 chains. Longest chain 105 peptides. Score 0.953 Round 5: 209 peptides, 4 chains. Longest chain 105 peptides. Score 0.960 Taking the results from Round 5 Chains 4, Residues 205, Estimated correctness of the model 99.9 % 3 chains (195 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 76 B and 80 B 3 chains (208 residues) following loop building 2 chains (198 residues) in sequence following loop building ------------------------------------------------------ 28908 reflections ( 99.72 % complete ) and 2135 restraints for refining 2043 atoms. 524 conditional restraints added. Observations/parameters ratio is 3.54 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2580 (Rfree = 0.000) for 2043 atoms. Found 65 (108 requested) and removed 69 (66 requested) atoms. Cycle 27: After refmac, R = 0.2448 (Rfree = 0.000) for 2032 atoms. Found 59 (105 requested) and removed 24 (65 requested) atoms. Cycle 28: After refmac, R = 0.2370 (Rfree = 0.000) for 2066 atoms. Found 40 (106 requested) and removed 19 (66 requested) atoms. Cycle 29: After refmac, R = 0.2323 (Rfree = 0.000) for 2084 atoms. Found 37 (107 requested) and removed 11 (67 requested) atoms. Cycle 30: After refmac, R = 0.2297 (Rfree = 0.000) for 2106 atoms. Found 33 (109 requested) and removed 21 (68 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.79 1.97 NCS extension: 75 residues added (72 deleted due to clashes), 2198 seeds are put forward Round 1: 203 peptides, 5 chains. Longest chain 71 peptides. Score 0.950 Round 2: 204 peptides, 4 chains. Longest chain 105 peptides. Score 0.957 Round 3: 202 peptides, 6 chains. Longest chain 72 peptides. Score 0.943 Round 4: 204 peptides, 4 chains. Longest chain 105 peptides. Score 0.957 Round 5: 201 peptides, 7 chains. Longest chain 56 peptides. Score 0.936 Taking the results from Round 4 Chains 4, Residues 200, Estimated correctness of the model 99.9 % 4 chains (200 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 46 B and 53 B Built loop between residues 72 B and 78 B 2 chains (211 residues) following loop building 2 chains (211 residues) in sequence following loop building ------------------------------------------------------ 28908 reflections ( 99.72 % complete ) and 1959 restraints for refining 2060 atoms. 277 conditional restraints added. Observations/parameters ratio is 3.51 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2573 (Rfree = 0.000) for 2060 atoms. Found 68 (104 requested) and removed 67 (66 requested) atoms. Cycle 32: After refmac, R = 0.2501 (Rfree = 0.000) for 2052 atoms. Found 57 (101 requested) and removed 17 (66 requested) atoms. Cycle 33: After refmac, R = 0.2396 (Rfree = 0.000) for 2090 atoms. Found 36 (103 requested) and removed 11 (67 requested) atoms. Cycle 34: After refmac, R = 0.2332 (Rfree = 0.000) for 2114 atoms. Found 31 (103 requested) and removed 13 (68 requested) atoms. Cycle 35: After refmac, R = 0.2266 (Rfree = 0.000) for 2127 atoms. Found 36 (104 requested) and removed 11 (68 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.79 1.97 NCS extension: 75 residues added (30 deleted due to clashes), 2229 seeds are put forward Round 1: 198 peptides, 6 chains. Longest chain 56 peptides. Score 0.940 Round 2: 204 peptides, 4 chains. Longest chain 105 peptides. Score 0.957 Round 3: 207 peptides, 4 chains. Longest chain 105 peptides. Score 0.959 Round 4: 204 peptides, 4 chains. Longest chain 105 peptides. Score 0.957 Round 5: 202 peptides, 5 chains. Longest chain 105 peptides. Score 0.949 Taking the results from Round 3 Chains 4, Residues 203, Estimated correctness of the model 99.9 % 4 chains (203 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 46 B and 52 B Built loop between residues 72 B and 76 B 2 chains (211 residues) following loop building 2 chains (211 residues) in sequence following loop building ------------------------------------------------------ 28908 reflections ( 99.72 % complete ) and 1947 restraints for refining 2066 atoms. 265 conditional restraints added. Observations/parameters ratio is 3.50 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2588 (Rfree = 0.000) for 2066 atoms. Found 74 (101 requested) and removed 66 (66 requested) atoms. Cycle 37: After refmac, R = 0.2446 (Rfree = 0.000) for 2069 atoms. Found 48 (99 requested) and removed 14 (67 requested) atoms. Cycle 38: After refmac, R = 0.2343 (Rfree = 0.000) for 2093 atoms. Found 31 (100 requested) and removed 10 (67 requested) atoms. Cycle 39: After refmac, R = 0.2258 (Rfree = 0.000) for 2110 atoms. Found 35 (101 requested) and removed 9 (68 requested) atoms. Cycle 40: After refmac, R = 0.2220 (Rfree = 0.000) for 2132 atoms. Found 36 (102 requested) and removed 14 (69 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.79 1.97 NCS extension: 189 residues added (44 deleted due to clashes), 2344 seeds are put forward Round 1: 192 peptides, 8 chains. Longest chain 72 peptides. Score 0.920 Round 2: 201 peptides, 6 chains. Longest chain 59 peptides. Score 0.943 Round 3: 202 peptides, 6 chains. Longest chain 72 peptides. Score 0.943 Round 4: 203 peptides, 6 chains. Longest chain 72 peptides. Score 0.944 Round 5: 205 peptides, 6 chains. Longest chain 72 peptides. Score 0.946 Taking the results from Round 5 Chains 8, Residues 199, Estimated correctness of the model 99.8 % 5 chains (187 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 33 A and 38 A Built loop between residues 47 B and 53 B Built loop between residues 72 B and 78 B 3 chains (210 residues) following loop building 2 chains (201 residues) in sequence following loop building ------------------------------------------------------ 28908 reflections ( 99.72 % complete ) and 2016 restraints for refining 2047 atoms. 381 conditional restraints added. Observations/parameters ratio is 3.53 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2603 (Rfree = 0.000) for 2047 atoms. Found 73 (98 requested) and removed 70 (66 requested) atoms. Cycle 42: After refmac, R = 0.2428 (Rfree = 0.000) for 2042 atoms. Found 47 (95 requested) and removed 10 (66 requested) atoms. Cycle 43: After refmac, R = 0.2345 (Rfree = 0.000) for 2071 atoms. Found 33 (96 requested) and removed 12 (67 requested) atoms. Cycle 44: After refmac, R = 0.2278 (Rfree = 0.000) for 2088 atoms. Found 39 (97 requested) and removed 12 (67 requested) atoms. Cycle 45: After refmac, R = 0.2235 (Rfree = 0.000) for 2106 atoms. Found 47 (98 requested) and removed 14 (68 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.79 1.97 NCS extension: 1 residues added (9 deleted due to clashes), 2141 seeds are put forward Round 1: 196 peptides, 9 chains. Longest chain 45 peptides. Score 0.917 Round 2: 197 peptides, 6 chains. Longest chain 66 peptides. Score 0.939 Round 3: 203 peptides, 6 chains. Longest chain 72 peptides. Score 0.944 Round 4: 205 peptides, 5 chains. Longest chain 72 peptides. Score 0.952 Round 5: 201 peptides, 9 chains. Longest chain 72 peptides. Score 0.923 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 6, Residues 200, Estimated correctness of the model 99.9 % 5 chains (199 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 71 A and 78 A Built loop between residues 96 A and 99 A Built loop between residues 33 B and 38 B 2 chains (211 residues) following loop building 2 chains (211 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 28908 reflections ( 99.72 % complete ) and 1688 restraints for refining 1662 atoms. Observations/parameters ratio is 4.35 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2907 (Rfree = 0.000) for 1662 atoms. Found 25 (77 requested) and removed 0 (77 requested) atoms. Cycle 47: After refmac, R = 0.2731 (Rfree = 0.000) for 1662 atoms. Found 10 (78 requested) and removed 0 (54 requested) atoms. Cycle 48: After refmac, R = 0.2588 (Rfree = 0.000) for 1662 atoms. Found 7 (78 requested) and removed 1 (54 requested) atoms. Cycle 49: After refmac, R = 0.2505 (Rfree = 0.000) for 1662 atoms. TimeTaking 42.33