Sun 23 Dec 22:23:05 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 2pke-1.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2pke-1.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2pke-1.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pke-1.8-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/2pke-1.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pke-1.8-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 22:23:13 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/2pke-1.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pke-1.8-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 424 and 0 Target number of residues in the AU: 424 Target solvent content: 0.4894 Checking the provided sequence file Detected sequence length: 251 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 502 Adjusted target solvent content: 0.40 Input MTZ file: 2pke-1.8-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: 4 Cell parameters: 34.220 107.280 62.650 90.000 102.296 90.000 Input sequence file: 2pke-1.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 4016 target number of atoms Had to go as low as 0.35 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: 61.213 1.810 Wilson plot Bfac: 21.23 33222 reflections ( 85.82 % complete ) and 0 restraints for refining 4447 atoms. Observations/parameters ratio is 1.87 ------------------------------------------------------ Starting model: R = 0.3143 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2631 (Rfree = 0.000) for 4447 atoms. Found 140 (202 requested) and removed 105 (101 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.99 2.28 NCS extension: 0 residues added, 4482 seeds are put forward Round 1: 330 peptides, 41 chains. Longest chain 18 peptides. Score 0.691 Round 2: 380 peptides, 23 chains. Longest chain 50 peptides. Score 0.880 Round 3: 400 peptides, 16 chains. Longest chain 101 peptides. Score 0.922 Round 4: 409 peptides, 11 chains. Longest chain 137 peptides. Score 0.943 Round 5: 412 peptides, 11 chains. Longest chain 137 peptides. Score 0.944 Taking the results from Round 5 Chains 13, Residues 401, Estimated correctness of the model 99.7 % 11 chains (391 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 208 A and 218 A Built loop between residues 103 B and 106 B Built loop between residues 123 B and 126 B Built loop between residues 153 B and 158 B Built loop between residues 185 B and 188 B 8 chains (420 residues) following loop building 6 chains (410 residues) in sequence following loop building ------------------------------------------------------ 33222 reflections ( 85.82 % complete ) and 4227 restraints for refining 3964 atoms. 943 conditional restraints added. Observations/parameters ratio is 2.10 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2953 (Rfree = 0.000) for 3964 atoms. Found 128 (180 requested) and removed 93 (90 requested) atoms. Cycle 2: After refmac, R = 0.2600 (Rfree = 0.000) for 3991 atoms. Found 101 (178 requested) and removed 81 (91 requested) atoms. Cycle 3: After refmac, R = 0.2422 (Rfree = 0.000) for 3990 atoms. Found 87 (175 requested) and removed 29 (91 requested) atoms. Cycle 4: After refmac, R = 0.2317 (Rfree = 0.000) for 4036 atoms. Found 70 (177 requested) and removed 16 (92 requested) atoms. Cycle 5: After refmac, R = 0.2221 (Rfree = 0.000) for 4076 atoms. Found 77 (179 requested) and removed 22 (93 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.92 2.20 NCS extension: 17 residues added (2 deleted due to clashes), 4159 seeds are put forward Round 1: 426 peptides, 8 chains. Longest chain 137 peptides. Score 0.957 Round 2: 427 peptides, 10 chains. Longest chain 137 peptides. Score 0.952 Round 3: 428 peptides, 9 chains. Longest chain 103 peptides. Score 0.955 Round 4: 432 peptides, 6 chains. Longest chain 157 peptides. Score 0.964 Round 5: 430 peptides, 9 chains. Longest chain 137 peptides. Score 0.956 Taking the results from Round 4 Chains 6, Residues 426, Estimated correctness of the model 99.9 % 6 chains (426 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 207 A and 218 A Built loop between residues 42 B and 52 B 4 chains (445 residues) following loop building 4 chains (445 residues) in sequence following loop building ------------------------------------------------------ 33222 reflections ( 85.82 % complete ) and 4140 restraints for refining 4111 atoms. 610 conditional restraints added. Observations/parameters ratio is 2.02 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2409 (Rfree = 0.000) for 4111 atoms. Found 122 (180 requested) and removed 97 (93 requested) atoms. Cycle 7: After refmac, R = 0.2254 (Rfree = 0.000) for 4126 atoms. Found 85 (177 requested) and removed 45 (94 requested) atoms. Cycle 8: After refmac, R = 0.2165 (Rfree = 0.000) for 4157 atoms. Found 72 (174 requested) and removed 33 (94 requested) atoms. Cycle 9: After refmac, R = 0.2081 (Rfree = 0.000) for 4194 atoms. Found 79 (176 requested) and removed 27 (95 requested) atoms. Cycle 10: After refmac, R = 0.2017 (Rfree = 0.000) for 4238 atoms. Found 78 (178 requested) and removed 40 (96 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.91 2.19 NCS extension: 30 residues added (6 deleted due to clashes), 4310 seeds are put forward Round 1: 428 peptides, 8 chains. Longest chain 148 peptides. Score 0.958 Round 2: 431 peptides, 7 chains. Longest chain 137 peptides. Score 0.962 Round 3: 431 peptides, 9 chains. Longest chain 137 peptides. Score 0.956 Round 4: 433 peptides, 8 chains. Longest chain 120 peptides. Score 0.960 Round 5: 426 peptides, 11 chains. Longest chain 102 peptides. Score 0.949 Taking the results from Round 2 Chains 7, Residues 424, Estimated correctness of the model 99.9 % 7 chains (424 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 207 A and 217 A Built loop between residues 185 B and 188 B 5 chains (435 residues) following loop building 5 chains (435 residues) in sequence following loop building ------------------------------------------------------ 33222 reflections ( 85.82 % complete ) and 4290 restraints for refining 4154 atoms. 842 conditional restraints added. Observations/parameters ratio is 2.00 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2198 (Rfree = 0.000) for 4154 atoms. Found 121 (170 requested) and removed 94 (94 requested) atoms. Cycle 12: After refmac, R = 0.2086 (Rfree = 0.000) for 4177 atoms. Found 91 (167 requested) and removed 42 (95 requested) atoms. Cycle 13: After refmac, R = 0.2022 (Rfree = 0.000) for 4218 atoms. Found 87 (169 requested) and removed 30 (96 requested) atoms. Cycle 14: After refmac, R = 0.1960 (Rfree = 0.000) for 4273 atoms. Found 64 (171 requested) and removed 33 (97 requested) atoms. Cycle 15: After refmac, R = 0.1925 (Rfree = 0.000) for 4297 atoms. Found 82 (168 requested) and removed 37 (97 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.90 2.17 NCS extension: 40 residues added (25 deleted due to clashes), 4382 seeds are put forward Round 1: 433 peptides, 8 chains. Longest chain 132 peptides. Score 0.960 Round 2: 431 peptides, 9 chains. Longest chain 120 peptides. Score 0.956 Round 3: 430 peptides, 10 chains. Longest chain 120 peptides. Score 0.953 Round 4: 436 peptides, 7 chains. Longest chain 155 peptides. Score 0.963 Round 5: 435 peptides, 9 chains. Longest chain 138 peptides. Score 0.958 Taking the results from Round 4 Chains 8, Residues 429, Estimated correctness of the model 99.9 % 7 chains (427 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 102 A and 105 A Built loop between residues 208 A and 217 A 6 chains (439 residues) following loop building 5 chains (437 residues) in sequence following loop building ------------------------------------------------------ 33222 reflections ( 85.82 % complete ) and 4231 restraints for refining 4177 atoms. 754 conditional restraints added. Observations/parameters ratio is 1.99 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2112 (Rfree = 0.000) for 4177 atoms. Found 142 (163 requested) and removed 98 (95 requested) atoms. Cycle 17: After refmac, R = 0.2021 (Rfree = 0.000) for 4218 atoms. Found 84 (161 requested) and removed 47 (96 requested) atoms. Cycle 18: After refmac, R = 0.1967 (Rfree = 0.000) for 4249 atoms. Found 82 (158 requested) and removed 36 (96 requested) atoms. Cycle 19: After refmac, R = 0.1920 (Rfree = 0.000) for 4292 atoms. Found 74 (160 requested) and removed 36 (97 requested) atoms. Cycle 20: After refmac, R = 0.1878 (Rfree = 0.000) for 4327 atoms. Found 72 (162 requested) and removed 45 (98 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.91 2.19 NCS extension: 28 residues added (4 deleted due to clashes), 4384 seeds are put forward Round 1: 425 peptides, 12 chains. Longest chain 119 peptides. Score 0.946 Round 2: 430 peptides, 9 chains. Longest chain 120 peptides. Score 0.956 Round 3: 432 peptides, 8 chains. Longest chain 154 peptides. Score 0.959 Round 4: 433 peptides, 6 chains. Longest chain 154 peptides. Score 0.965 Round 5: 430 peptides, 12 chains. Longest chain 85 peptides. Score 0.948 Taking the results from Round 4 Chains 6, Residues 427, Estimated correctness of the model 99.9 % 6 chains (427 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 206 A and 217 A 5 chains (437 residues) following loop building 5 chains (437 residues) in sequence following loop building ------------------------------------------------------ 33222 reflections ( 85.82 % complete ) and 4242 restraints for refining 4189 atoms. 775 conditional restraints added. Observations/parameters ratio is 1.98 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2105 (Rfree = 0.000) for 4189 atoms. Found 144 (152 requested) and removed 96 (95 requested) atoms. Cycle 22: After refmac, R = 0.1988 (Rfree = 0.000) for 4236 atoms. Found 106 (150 requested) and removed 36 (96 requested) atoms. Cycle 23: After refmac, R = 0.1914 (Rfree = 0.000) for 4304 atoms. Found 83 (153 requested) and removed 44 (98 requested) atoms. Cycle 24: After refmac, R = 0.1866 (Rfree = 0.000) for 4338 atoms. Found 91 (150 requested) and removed 39 (98 requested) atoms. Failed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDB Cycle 25: After refmac, R = 0.1844 (Rfree = 0.000) for 4387 atoms. Found 80 (151 requested) and removed 58 (99 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.89 2.16 NCS extension: 43 residues added (24 deleted due to clashes), 4455 seeds are put forward Round 1: 426 peptides, 9 chains. Longest chain 100 peptides. Score 0.955 Round 2: 428 peptides, 11 chains. Longest chain 89 peptides. Score 0.950 Round 3: 430 peptides, 10 chains. Longest chain 119 peptides. Score 0.953 Round 4: 427 peptides, 11 chains. Longest chain 87 peptides. Score 0.950 Round 5: 432 peptides, 9 chains. Longest chain 105 peptides. Score 0.957 Taking the results from Round 5 Chains 10, Residues 423, Estimated correctness of the model 99.8 % 8 chains (393 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 107 A and 110 A Built loop between residues 102 B and 105 B Built loop between residues 208 B and 218 B 7 chains (436 residues) following loop building 5 chains (406 residues) in sequence following loop building ------------------------------------------------------ 33222 reflections ( 85.82 % complete ) and 4398 restraints for refining 4159 atoms. 1059 conditional restraints added. Observations/parameters ratio is 2.00 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2081 (Rfree = 0.000) for 4159 atoms. Found 140 (140 requested) and removed 73 (94 requested) atoms. Cycle 27: After refmac, R = 0.1991 (Rfree = 0.000) for 4222 atoms. Found 97 (138 requested) and removed 35 (96 requested) atoms. Cycle 28: After refmac, R = 0.1917 (Rfree = 0.000) for 4281 atoms. Found 73 (140 requested) and removed 37 (97 requested) atoms. Cycle 29: After refmac, R = 0.1850 (Rfree = 0.000) for 4315 atoms. Found 77 (137 requested) and removed 33 (98 requested) atoms. Cycle 30: After refmac, R = 0.1820 (Rfree = 0.000) for 4352 atoms. Found 81 (139 requested) and removed 46 (99 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.90 2.17 NCS extension: 37 residues added (43 deleted due to clashes), 4427 seeds are put forward Round 1: 429 peptides, 8 chains. Longest chain 120 peptides. Score 0.958 Round 2: 431 peptides, 9 chains. Longest chain 120 peptides. Score 0.956 Round 3: 429 peptides, 10 chains. Longest chain 101 peptides. Score 0.953 Round 4: 428 peptides, 12 chains. Longest chain 102 peptides. Score 0.947 Round 5: 431 peptides, 8 chains. Longest chain 120 peptides. Score 0.959 Taking the results from Round 5 Chains 10, Residues 423, Estimated correctness of the model 99.9 % 8 chains (408 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 153 A and 158 A Built loop between residues 86 B and 89 B Built loop between residues 207 B and 217 B 6 chains (437 residues) following loop building 5 chains (423 residues) in sequence following loop building ------------------------------------------------------ 33222 reflections ( 85.82 % complete ) and 4238 restraints for refining 4177 atoms. 838 conditional restraints added. Observations/parameters ratio is 1.99 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2022 (Rfree = 0.000) for 4177 atoms. Found 129 (129 requested) and removed 63 (95 requested) atoms. Cycle 32: After refmac, R = 0.1920 (Rfree = 0.000) for 4238 atoms. Found 122 (131 requested) and removed 35 (96 requested) atoms. Cycle 33: After refmac, R = 0.1862 (Rfree = 0.000) for 4322 atoms. Found 90 (133 requested) and removed 35 (98 requested) atoms. Cycle 34: After refmac, R = 0.1830 (Rfree = 0.000) for 4372 atoms. Found 75 (135 requested) and removed 54 (99 requested) atoms. Cycle 35: After refmac, R = 0.1789 (Rfree = 0.000) for 4387 atoms. Found 93 (132 requested) and removed 37 (100 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.90 2.17 NCS extension: 13 residues added (0 deleted due to clashes), 4458 seeds are put forward Round 1: 429 peptides, 9 chains. Longest chain 120 peptides. Score 0.956 Round 2: 435 peptides, 8 chains. Longest chain 132 peptides. Score 0.960 Round 3: 433 peptides, 8 chains. Longest chain 154 peptides. Score 0.960 Round 4: 433 peptides, 8 chains. Longest chain 120 peptides. Score 0.960 Round 5: 432 peptides, 9 chains. Longest chain 154 peptides. Score 0.957 Taking the results from Round 4 Chains 10, Residues 425, Estimated correctness of the model 99.9 % 8 chains (415 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 153 A and 158 A Built loop between residues 86 B and 89 B Built loop between residues 207 B and 217 B 6 chains (439 residues) following loop building 5 chains (430 residues) in sequence following loop building ------------------------------------------------------ 33222 reflections ( 85.82 % complete ) and 4191 restraints for refining 4223 atoms. 748 conditional restraints added. Observations/parameters ratio is 1.97 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1985 (Rfree = 0.000) for 4223 atoms. Found 127 (127 requested) and removed 73 (96 requested) atoms. Cycle 37: After refmac, R = 0.1887 (Rfree = 0.000) for 4275 atoms. Found 98 (124 requested) and removed 31 (97 requested) atoms. Cycle 38: After refmac, R = 0.1834 (Rfree = 0.000) for 4340 atoms. Found 79 (126 requested) and removed 40 (98 requested) atoms. Cycle 39: After refmac, R = 0.1786 (Rfree = 0.000) for 4374 atoms. Found 74 (123 requested) and removed 42 (99 requested) atoms. Cycle 40: After refmac, R = 0.1763 (Rfree = 0.000) for 4403 atoms. Found 70 (120 requested) and removed 48 (100 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.90 2.17 NCS extension: 37 residues added (21 deleted due to clashes), 4466 seeds are put forward Round 1: 426 peptides, 8 chains. Longest chain 137 peptides. Score 0.957 Round 2: 430 peptides, 7 chains. Longest chain 154 peptides. Score 0.961 Round 3: 431 peptides, 10 chains. Longest chain 132 peptides. Score 0.954 Round 4: 432 peptides, 9 chains. Longest chain 121 peptides. Score 0.957 Round 5: 427 peptides, 12 chains. Longest chain 114 peptides. Score 0.947 Taking the results from Round 2 Chains 7, Residues 423, Estimated correctness of the model 99.9 % 7 chains (423 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 86 A and 89 A Built loop between residues 208 A and 217 A 5 chains (433 residues) following loop building 5 chains (433 residues) in sequence following loop building ------------------------------------------------------ 33222 reflections ( 85.82 % complete ) and 4295 restraints for refining 4237 atoms. 857 conditional restraints added. Observations/parameters ratio is 1.96 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1985 (Rfree = 0.000) for 4237 atoms. Found 111 (111 requested) and removed 89 (96 requested) atoms. Cycle 42: After refmac, R = 0.1888 (Rfree = 0.000) for 4257 atoms. Found 104 (108 requested) and removed 33 (96 requested) atoms. Cycle 43: After refmac, R = 0.1821 (Rfree = 0.000) for 4324 atoms. Found 83 (110 requested) and removed 40 (98 requested) atoms. Cycle 44: After refmac, R = 0.1774 (Rfree = 0.000) for 4366 atoms. Found 73 (111 requested) and removed 47 (99 requested) atoms. Cycle 45: After refmac, R = 0.1750 (Rfree = 0.000) for 4385 atoms. Found 89 (107 requested) and removed 57 (99 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.90 2.17 NCS extension: 44 residues added (21 deleted due to clashes), 4462 seeds are put forward Round 1: 420 peptides, 11 chains. Longest chain 120 peptides. Score 0.947 Round 2: 427 peptides, 7 chains. Longest chain 154 peptides. Score 0.960 Round 3: 425 peptides, 11 chains. Longest chain 132 peptides. Score 0.949 Round 4: 421 peptides, 9 chains. Longest chain 102 peptides. Score 0.953 Round 5: 423 peptides, 11 chains. Longest chain 104 peptides. Score 0.948 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 7, Residues 420, Estimated correctness of the model 99.9 % 7 chains (420 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 86 A and 89 A Built loop between residues 207 A and 218 A 5 chains (432 residues) following loop building 5 chains (432 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 33222 reflections ( 85.82 % complete ) and 3429 restraints for refining 3366 atoms. Observations/parameters ratio is 2.47 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2552 (Rfree = 0.000) for 3366 atoms. Found 50 (80 requested) and removed 0 (80 requested) atoms. Cycle 47: After refmac, R = 0.2367 (Rfree = 0.000) for 3366 atoms. Found 12 (81 requested) and removed 0 (77 requested) atoms. Cycle 48: After refmac, R = 0.2278 (Rfree = 0.000) for 3366 atoms. Found 7 (81 requested) and removed 0 (78 requested) atoms. Cycle 49: After refmac, R = 0.2227 (Rfree = 0.000) for 3366 atoms. TimeTaking 72.5