Sun 23 Dec 22:23:10 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 2ig6-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ig6-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ig6-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ig6-3.2-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/2ig6-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ig6-3.2-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 22:23:20 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/2ig6-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ig6-3.2-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 260 and 0 Target number of residues in the AU: 260 Target solvent content: 0.6218 Checking the provided sequence file Detected sequence length: 150 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 300 Adjusted target solvent content: 0.56 Input MTZ file: 2ig6-3.2-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: 19 Cell parameters: 52.413 65.299 108.709 90.000 90.000 90.000 Input sequence file: 2ig6-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 2400 target number of atoms Had to go as low as 0.65 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: 55.977 3.200 Wilson plot Bfac: 61.93 6415 reflections ( 97.91 % complete ) and 0 restraints for refining 2648 atoms. Observations/parameters ratio is 0.61 ------------------------------------------------------ Starting model: R = 0.3138 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2492 (Rfree = 0.000) for 2648 atoms. Found 23 (23 requested) and removed 29 (11 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.10 2.86 Search for helices and strands: 0 residues in 0 chains, 2694 seeds are put forward NCS extension: 0 residues added, 2694 seeds are put forward Round 1: 188 peptides, 28 chains. Longest chain 21 peptides. Score 0.509 Round 2: 213 peptides, 21 chains. Longest chain 33 peptides. Score 0.689 Round 3: 223 peptides, 22 chains. Longest chain 28 peptides. Score 0.703 Round 4: 233 peptides, 17 chains. Longest chain 36 peptides. Score 0.779 Round 5: 231 peptides, 17 chains. Longest chain 29 peptides. Score 0.775 Taking the results from Round 4 Chains 17, Residues 216, Estimated correctness of the model 80.1 % 6 chains (138 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 37 B and 40 B Built loop between residues 66 B and 69 B 14 chains (219 residues) following loop building 4 chains (142 residues) in sequence following loop building ------------------------------------------------------ 6415 reflections ( 97.91 % complete ) and 3464 restraints for refining 2371 atoms. 2037 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2646 (Rfree = 0.000) for 2371 atoms. Found 21 (21 requested) and removed 27 (10 requested) atoms. Cycle 2: After refmac, R = 0.2432 (Rfree = 0.000) for 2329 atoms. Found 9 (21 requested) and removed 16 (10 requested) atoms. Cycle 3: After refmac, R = 0.2400 (Rfree = 0.000) for 2306 atoms. Found 8 (19 requested) and removed 12 (10 requested) atoms. Cycle 4: After refmac, R = 0.2254 (Rfree = 0.000) for 2288 atoms. Found 3 (19 requested) and removed 13 (10 requested) atoms. Cycle 5: After refmac, R = 0.2260 (Rfree = 0.000) for 2259 atoms. Found 5 (18 requested) and removed 13 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.15 2.91 Search for helices and strands: 0 residues in 0 chains, 2314 seeds are put forward NCS extension: 57 residues added (58 deleted due to clashes), 2371 seeds are put forward Round 1: 207 peptides, 19 chains. Longest chain 22 peptides. Score 0.698 Round 2: 234 peptides, 18 chains. Longest chain 40 peptides. Score 0.771 Round 3: 240 peptides, 16 chains. Longest chain 51 peptides. Score 0.801 Round 4: 235 peptides, 16 chains. Longest chain 56 peptides. Score 0.792 Round 5: 235 peptides, 16 chains. Longest chain 54 peptides. Score 0.792 Taking the results from Round 3 Chains 16, Residues 224, Estimated correctness of the model 83.6 % 3 chains (83 residues) have been docked in sequence Building loops using Loopy2018 16 chains (224 residues) following loop building 3 chains (83 residues) in sequence following loop building ------------------------------------------------------ 6415 reflections ( 97.91 % complete ) and 3611 restraints for refining 2190 atoms. 2359 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2555 (Rfree = 0.000) for 2190 atoms. Found 17 (17 requested) and removed 13 (9 requested) atoms. Cycle 7: After refmac, R = 0.2339 (Rfree = 0.000) for 2178 atoms. Found 9 (17 requested) and removed 14 (9 requested) atoms. Cycle 8: After refmac, R = 0.2211 (Rfree = 0.000) for 2171 atoms. Found 6 (16 requested) and removed 10 (9 requested) atoms. Cycle 9: After refmac, R = 0.2145 (Rfree = 0.000) for 2163 atoms. Found 5 (16 requested) and removed 9 (9 requested) atoms. Cycle 10: After refmac, R = 0.2112 (Rfree = 0.000) for 2154 atoms. Found 4 (16 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.17 2.93 Search for helices and strands: 0 residues in 0 chains, 2211 seeds are put forward NCS extension: 44 residues added (35 deleted due to clashes), 2255 seeds are put forward Round 1: 213 peptides, 20 chains. Longest chain 33 peptides. Score 0.702 Round 2: 223 peptides, 19 chains. Longest chain 33 peptides. Score 0.737 Round 3: 221 peptides, 18 chains. Longest chain 41 peptides. Score 0.744 Round 4: 222 peptides, 19 chains. Longest chain 35 peptides. Score 0.735 Round 5: 233 peptides, 16 chains. Longest chain 51 peptides. Score 0.789 Taking the results from Round 5 Chains 21, Residues 217, Estimated correctness of the model 81.7 % 5 chains (107 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 85 A and 89 A 19 chains (218 residues) following loop building 4 chains (110 residues) in sequence following loop building ------------------------------------------------------ 6415 reflections ( 97.91 % complete ) and 3548 restraints for refining 2189 atoms. 2246 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2421 (Rfree = 0.000) for 2189 atoms. Found 15 (15 requested) and removed 13 (9 requested) atoms. Cycle 12: After refmac, R = 0.2333 (Rfree = 0.000) for 2181 atoms. Found 15 (15 requested) and removed 11 (9 requested) atoms. Cycle 13: After refmac, R = 0.2135 (Rfree = 0.000) for 2178 atoms. Found 3 (14 requested) and removed 9 (9 requested) atoms. Cycle 14: After refmac, R = 0.2016 (Rfree = 0.000) for 2169 atoms. Found 8 (14 requested) and removed 9 (9 requested) atoms. Cycle 15: After refmac, R = 0.1975 (Rfree = 0.000) for 2165 atoms. Found 4 (14 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.12 2.88 Search for helices and strands: 0 residues in 0 chains, 2221 seeds are put forward NCS extension: 45 residues added (17 deleted due to clashes), 2266 seeds are put forward Round 1: 216 peptides, 19 chains. Longest chain 51 peptides. Score 0.721 Round 2: 232 peptides, 14 chains. Longest chain 58 peptides. Score 0.806 Round 3: 228 peptides, 16 chains. Longest chain 47 peptides. Score 0.779 Round 4: 234 peptides, 18 chains. Longest chain 51 peptides. Score 0.771 Round 5: 231 peptides, 16 chains. Longest chain 35 peptides. Score 0.785 Taking the results from Round 2 Chains 14, Residues 218, Estimated correctness of the model 84.3 % 2 chains (102 residues) have been docked in sequence Building loops using Loopy2018 14 chains (218 residues) following loop building 2 chains (102 residues) in sequence following loop building ------------------------------------------------------ 6415 reflections ( 97.91 % complete ) and 3490 restraints for refining 2191 atoms. 2205 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2548 (Rfree = 0.000) for 2191 atoms. Found 13 (13 requested) and removed 16 (9 requested) atoms. Cycle 17: After refmac, R = 0.2330 (Rfree = 0.000) for 2172 atoms. Found 13 (13 requested) and removed 11 (9 requested) atoms. Cycle 18: After refmac, R = 0.2114 (Rfree = 0.000) for 2168 atoms. Found 9 (13 requested) and removed 10 (9 requested) atoms. Cycle 19: After refmac, R = 0.2041 (Rfree = 0.000) for 2165 atoms. Found 7 (12 requested) and removed 9 (9 requested) atoms. Cycle 20: After refmac, R = 0.1974 (Rfree = 0.000) for 2160 atoms. Found 4 (12 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.15 2.91 Search for helices and strands: 0 residues in 0 chains, 2193 seeds are put forward NCS extension: 35 residues added (6 deleted due to clashes), 2228 seeds are put forward Round 1: 212 peptides, 23 chains. Longest chain 24 peptides. Score 0.661 Round 2: 222 peptides, 20 chains. Longest chain 32 peptides. Score 0.724 Round 3: 231 peptides, 19 chains. Longest chain 63 peptides. Score 0.755 Round 4: 230 peptides, 17 chains. Longest chain 34 peptides. Score 0.773 Round 5: 234 peptides, 19 chains. Longest chain 34 peptides. Score 0.761 Taking the results from Round 4 Chains 18, Residues 213, Estimated correctness of the model 79.1 % 3 chains (64 residues) have been docked in sequence Building loops using Loopy2018 18 chains (213 residues) following loop building 3 chains (64 residues) in sequence following loop building ------------------------------------------------------ 6415 reflections ( 97.91 % complete ) and 4021 restraints for refining 2191 atoms. 2916 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2336 (Rfree = 0.000) for 2191 atoms. Found 11 (11 requested) and removed 11 (9 requested) atoms. Cycle 22: After refmac, R = 0.2132 (Rfree = 0.000) for 2188 atoms. Found 9 (11 requested) and removed 9 (9 requested) atoms. Cycle 23: After refmac, R = 0.2270 (Rfree = 0.000) for 2183 atoms. Found 11 (11 requested) and removed 9 (9 requested) atoms. Cycle 24: After refmac, R = 0.2384 (Rfree = 0.000) for 2183 atoms. Found 10 (10 requested) and removed 11 (9 requested) atoms. Cycle 25: After refmac, R = 0.2358 (Rfree = 0.000) for 2179 atoms. Found 10 (10 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.13 2.89 Search for helices and strands: 0 residues in 0 chains, 2251 seeds are put forward NCS extension: 40 residues added (19 deleted due to clashes), 2291 seeds are put forward Round 1: 214 peptides, 23 chains. Longest chain 26 peptides. Score 0.667 Round 2: 227 peptides, 18 chains. Longest chain 35 peptides. Score 0.757 Round 3: 216 peptides, 23 chains. Longest chain 22 peptides. Score 0.672 Round 4: 225 peptides, 19 chains. Longest chain 28 peptides. Score 0.742 Round 5: 231 peptides, 16 chains. Longest chain 44 peptides. Score 0.785 Taking the results from Round 5 Chains 19, Residues 215, Estimated correctness of the model 81.1 % 5 chains (126 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 65 A and 69 A 18 chains (218 residues) following loop building 4 chains (129 residues) in sequence following loop building ------------------------------------------------------ 6415 reflections ( 97.91 % complete ) and 3375 restraints for refining 2194 atoms. 1976 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2715 (Rfree = 0.000) for 2194 atoms. Found 9 (9 requested) and removed 21 (9 requested) atoms. Cycle 27: After refmac, R = 0.2432 (Rfree = 0.000) for 2173 atoms. Found 9 (9 requested) and removed 12 (9 requested) atoms. Cycle 28: After refmac, R = 0.2273 (Rfree = 0.000) for 2165 atoms. Found 7 (9 requested) and removed 13 (9 requested) atoms. Cycle 29: After refmac, R = 0.2168 (Rfree = 0.000) for 2156 atoms. Found 5 (9 requested) and removed 13 (9 requested) atoms. Cycle 30: After refmac, R = 0.2113 (Rfree = 0.000) for 2145 atoms. Found 9 (9 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.14 2.90 Search for helices and strands: 0 residues in 0 chains, 2211 seeds are put forward NCS extension: 57 residues added (74 deleted due to clashes), 2268 seeds are put forward Round 1: 205 peptides, 21 chains. Longest chain 34 peptides. Score 0.668 Round 2: 215 peptides, 17 chains. Longest chain 38 peptides. Score 0.741 Round 3: 223 peptides, 17 chains. Longest chain 27 peptides. Score 0.759 Round 4: 214 peptides, 20 chains. Longest chain 38 peptides. Score 0.704 Round 5: 220 peptides, 17 chains. Longest chain 81 peptides. Score 0.752 Taking the results from Round 3 Chains 17, Residues 206, Estimated correctness of the model 76.7 % 2 chains (51 residues) have been docked in sequence Building loops using Loopy2018 17 chains (206 residues) following loop building 2 chains (51 residues) in sequence following loop building ------------------------------------------------------ 6415 reflections ( 97.91 % complete ) and 4272 restraints for refining 2191 atoms. 3258 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2443 (Rfree = 0.000) for 2191 atoms. Found 9 (9 requested) and removed 10 (9 requested) atoms. Cycle 32: After refmac, R = 0.2268 (Rfree = 0.000) for 2184 atoms. Found 9 (9 requested) and removed 9 (9 requested) atoms. Cycle 33: After refmac, R = 0.2127 (Rfree = 0.000) for 2181 atoms. Found 4 (9 requested) and removed 9 (9 requested) atoms. Cycle 34: After refmac, R = 0.2067 (Rfree = 0.000) for 2169 atoms. Found 6 (9 requested) and removed 9 (9 requested) atoms. Cycle 35: After refmac, R = 0.1996 (Rfree = 0.000) for 2163 atoms. Found 3 (9 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.15 2.91 Search for helices and strands: 0 residues in 0 chains, 2202 seeds are put forward NCS extension: 46 residues added (18 deleted due to clashes), 2248 seeds are put forward Round 1: 205 peptides, 19 chains. Longest chain 37 peptides. Score 0.693 Round 2: 219 peptides, 17 chains. Longest chain 30 peptides. Score 0.750 Round 3: 223 peptides, 18 chains. Longest chain 48 peptides. Score 0.748 Round 4: 222 peptides, 17 chains. Longest chain 39 peptides. Score 0.757 Round 5: 217 peptides, 19 chains. Longest chain 39 peptides. Score 0.723 Taking the results from Round 4 Chains 17, Residues 205, Estimated correctness of the model 76.3 % 3 chains (83 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 61 A and 65 A 16 chains (208 residues) following loop building 2 chains (86 residues) in sequence following loop building ------------------------------------------------------ 6415 reflections ( 97.91 % complete ) and 3731 restraints for refining 2191 atoms. 2549 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2330 (Rfree = 0.000) for 2191 atoms. Found 9 (9 requested) and removed 21 (9 requested) atoms. Cycle 37: After refmac, R = 0.2207 (Rfree = 0.000) for 2174 atoms. Found 9 (9 requested) and removed 10 (9 requested) atoms. Cycle 38: After refmac, R = 0.2121 (Rfree = 0.000) for 2172 atoms. Found 7 (9 requested) and removed 9 (9 requested) atoms. Cycle 39: After refmac, R = 0.2075 (Rfree = 0.000) for 2166 atoms. Found 4 (9 requested) and removed 9 (9 requested) atoms. Cycle 40: After refmac, R = 0.2060 (Rfree = 0.000) for 2160 atoms. Found 3 (9 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.17 2.93 Search for helices and strands: 0 residues in 0 chains, 2218 seeds are put forward NCS extension: 31 residues added (80 deleted due to clashes), 2249 seeds are put forward Round 1: 203 peptides, 18 chains. Longest chain 39 peptides. Score 0.700 Round 2: 216 peptides, 16 chains. Longest chain 32 peptides. Score 0.754 Round 3: 222 peptides, 18 chains. Longest chain 22 peptides. Score 0.746 Round 4: 218 peptides, 19 chains. Longest chain 19 peptides. Score 0.726 Round 5: 223 peptides, 16 chains. Longest chain 36 peptides. Score 0.769 Taking the results from Round 5 Chains 17, Residues 207, Estimated correctness of the model 78.4 % 2 chains (50 residues) have been docked in sequence Building loops using Loopy2018 17 chains (207 residues) following loop building 2 chains (50 residues) in sequence following loop building ------------------------------------------------------ 6415 reflections ( 97.91 % complete ) and 4010 restraints for refining 2191 atoms. 2975 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2507 (Rfree = 0.000) for 2191 atoms. Found 9 (9 requested) and removed 15 (9 requested) atoms. Cycle 42: After refmac, R = 0.2373 (Rfree = 0.000) for 2179 atoms. Found 6 (9 requested) and removed 10 (9 requested) atoms. Cycle 43: After refmac, R = 0.2277 (Rfree = 0.000) for 2174 atoms. Found 2 (9 requested) and removed 9 (9 requested) atoms. Cycle 44: After refmac, R = 0.2227 (Rfree = 0.000) for 2167 atoms. Found 5 (9 requested) and removed 9 (9 requested) atoms. Cycle 45: After refmac, R = 0.2205 (Rfree = 0.000) for 2162 atoms. Found 5 (9 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.15 2.91 Search for helices and strands: 0 residues in 0 chains, 2227 seeds are put forward NCS extension: 54 residues added (16 deleted due to clashes), 2281 seeds are put forward Round 1: 190 peptides, 18 chains. Longest chain 17 peptides. Score 0.665 Round 2: 200 peptides, 15 chains. Longest chain 32 peptides. Score 0.729 Round 3: 201 peptides, 19 chains. Longest chain 30 peptides. Score 0.683 Round 4: 204 peptides, 17 chains. Longest chain 29 peptides. Score 0.715 Round 5: 200 peptides, 18 chains. Longest chain 27 peptides. Score 0.693 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 17, Residues 185, Estimated correctness of the model 71.1 % 3 chains (49 residues) have been docked in sequence Sequence coverage is 26 % Consider running further cycles of model building using 2ig6-3_warpNtrace.pdb as input Building loops using Loopy2018 17 chains (185 residues) following loop building 3 chains (49 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6415 reflections ( 97.91 % complete ) and 4253 restraints for refining 2191 atoms. 3339 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2376 (Rfree = 0.000) for 2191 atoms. Found 0 (9 requested) and removed 1 (9 requested) atoms. Cycle 47: After refmac, R = 0.2179 (Rfree = 0.000) for 2188 atoms. Found 0 (9 requested) and removed 3 (9 requested) atoms. Cycle 48: After refmac, R = 0.2167 (Rfree = 0.000) for 2183 atoms. Found 0 (9 requested) and removed 2 (9 requested) atoms. Cycle 49: After refmac, R = 0.2163 (Rfree = 0.000) for 2180 atoms. Found 0 (9 requested) and removed 0 (9 requested) atoms. Writing output files ... TimeTaking 49.07