Sun 23 Dec 23:59:11 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 2fno-1.9-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2fno-1.9-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2fno-1.9-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fno-1.9-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/2fno-1.9-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fno-1.9-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 ============================================================ Sun 23 Dec 23:59:15 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/2fno-1.9-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fno-1.9-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 529 and 0 Target number of residues in the AU: 529 Target solvent content: 0.5124 Checking the provided sequence file Detected sequence length: 248 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 496 Adjusted target solvent content: 0.54 Input MTZ file: 2fno-1.9-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: 5 Cell parameters: 110.204 50.261 117.660 90.000 115.716 90.000 Input sequence file: 2fno-1.9-parrot-mrncs.fasta_lf Building free atoms model in initial map for 3968 target number of atoms Had to go as low as 0.50 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: 106.006 1.904 Wilson plot Bfac: 26.04 38894 reflections ( 85.02 % complete ) and 0 restraints for refining 4450 atoms. Observations/parameters ratio is 2.19 ------------------------------------------------------ Starting model: R = 0.3396 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2827 (Rfree = 0.000) for 4450 atoms. Found 175 (175 requested) and removed 110 (87 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.07 1.96 NCS extension: 0 residues added, 4515 seeds are put forward Round 1: 366 peptides, 45 chains. Longest chain 31 peptides. Score 0.646 Round 2: 403 peptides, 24 chains. Longest chain 94 peptides. Score 0.833 Round 3: 422 peptides, 21 chains. Longest chain 73 peptides. Score 0.863 Round 4: 438 peptides, 20 chains. Longest chain 62 peptides. Score 0.879 Round 5: 439 peptides, 14 chains. Longest chain 113 peptides. Score 0.903 Taking the results from Round 5 Chains 17, Residues 425, Estimated correctness of the model 99.2 % 9 chains (382 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 100 A and 107 A Built loop between residues 127 A and 137 A Built loop between residues 70 B and 73 B Built loop between residues 153 B and 156 B Built loop between residues 203 B and 206 B 11 chains (444 residues) following loop building 4 chains (403 residues) in sequence following loop building ------------------------------------------------------ 38894 reflections ( 85.02 % complete ) and 4566 restraints for refining 4132 atoms. 1235 conditional restraints added. Observations/parameters ratio is 2.35 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3155 (Rfree = 0.000) for 4132 atoms. Found 162 (162 requested) and removed 92 (81 requested) atoms. Cycle 2: After refmac, R = 0.2815 (Rfree = 0.000) for 4187 atoms. Found 127 (162 requested) and removed 72 (82 requested) atoms. Cycle 3: After refmac, R = 0.2653 (Rfree = 0.000) for 4221 atoms. Found 115 (159 requested) and removed 46 (83 requested) atoms. Cycle 4: After refmac, R = 0.2529 (Rfree = 0.000) for 4271 atoms. Found 103 (161 requested) and removed 37 (84 requested) atoms. Cycle 5: After refmac, R = 0.2414 (Rfree = 0.000) for 4319 atoms. Found 103 (163 requested) and removed 45 (85 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.04 1.93 NCS extension: 14 residues added (20 deleted due to clashes), 4406 seeds are put forward Round 1: 454 peptides, 13 chains. Longest chain 91 peptides. Score 0.914 Round 2: 456 peptides, 7 chains. Longest chain 177 peptides. Score 0.934 Round 3: 445 peptides, 15 chains. Longest chain 123 peptides. Score 0.903 Round 4: 459 peptides, 10 chains. Longest chain 167 peptides. Score 0.926 Round 5: 458 peptides, 9 chains. Longest chain 95 peptides. Score 0.929 Taking the results from Round 2 Chains 10, Residues 449, Estimated correctness of the model 99.6 % 7 chains (440 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 36 A and 41 A Built loop between residues 71 A and 74 A Built loop between residues 100 A and 108 A Built loop between residues 126 A and 131 A Built loop between residues 69 B and 73 B 4 chains (466 residues) following loop building 2 chains (460 residues) in sequence following loop building ------------------------------------------------------ 38894 reflections ( 85.02 % complete ) and 4032 restraints for refining 4261 atoms. 351 conditional restraints added. Observations/parameters ratio is 2.28 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2543 (Rfree = 0.000) for 4261 atoms. Found 160 (160 requested) and removed 91 (83 requested) atoms. Cycle 7: After refmac, R = 0.2328 (Rfree = 0.000) for 4323 atoms. Found 132 (160 requested) and removed 62 (85 requested) atoms. Cycle 8: After refmac, R = 0.2222 (Rfree = 0.000) for 4385 atoms. Found 119 (162 requested) and removed 58 (86 requested) atoms. Cycle 9: After refmac, R = 0.2150 (Rfree = 0.000) for 4441 atoms. Found 112 (164 requested) and removed 58 (87 requested) atoms. Cycle 10: After refmac, R = 0.2105 (Rfree = 0.000) for 4489 atoms. Found 101 (162 requested) and removed 74 (88 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.04 1.93 NCS extension: 5 residues added (1 deleted due to clashes), 4529 seeds are put forward Round 1: 458 peptides, 10 chains. Longest chain 119 peptides. Score 0.926 Round 2: 466 peptides, 6 chains. Longest chain 177 peptides. Score 0.941 Round 3: 462 peptides, 9 chains. Longest chain 177 peptides. Score 0.931 Round 4: 461 peptides, 7 chains. Longest chain 119 peptides. Score 0.936 Round 5: 456 peptides, 12 chains. Longest chain 177 peptides. Score 0.919 Taking the results from Round 2 Chains 8, Residues 460, Estimated correctness of the model 99.7 % 6 chains (454 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 70 A and 73 A Built loop between residues 27 B and 30 B Built loop between residues 70 B and 73 B Built loop between residues 127 B and 131 B 4 chains (469 residues) following loop building 2 chains (463 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 38894 reflections ( 85.02 % complete ) and 4080 restraints for refining 4320 atoms. 369 conditional restraints added. Observations/parameters ratio is 2.25 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2336 (Rfree = 0.000) for 4320 atoms. Found 153 (153 requested) and removed 81 (85 requested) atoms. Cycle 12: After refmac, R = 0.2224 (Rfree = 0.000) for 4387 atoms. Found 116 (151 requested) and removed 76 (86 requested) atoms. Cycle 13: After refmac, R = 0.2173 (Rfree = 0.000) for 4423 atoms. Found 115 (150 requested) and removed 66 (87 requested) atoms. Cycle 14: After refmac, R = 0.2121 (Rfree = 0.000) for 4466 atoms. Found 105 (147 requested) and removed 81 (87 requested) atoms. Cycle 15: After refmac, R = 0.2097 (Rfree = 0.000) for 4487 atoms. Found 107 (144 requested) and removed 68 (88 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.03 1.92 NCS extension: 9 residues added (226 deleted due to clashes), 4540 seeds are put forward Round 1: 464 peptides, 7 chains. Longest chain 119 peptides. Score 0.937 Round 2: 464 peptides, 7 chains. Longest chain 167 peptides. Score 0.937 Round 3: 461 peptides, 10 chains. Longest chain 141 peptides. Score 0.927 Round 4: 465 peptides, 7 chains. Longest chain 95 peptides. Score 0.938 Round 5: 460 peptides, 9 chains. Longest chain 119 peptides. Score 0.930 Taking the results from Round 4 Chains 8, Residues 458, Estimated correctness of the model 99.6 % 7 chains (457 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 103 A and 106 A Built loop between residues 199 A and 201 A Built loop between residues 84 B and 87 B Built loop between residues 203 B and 206 B 4 chains (465 residues) following loop building 3 chains (464 residues) in sequence following loop building ------------------------------------------------------ 38894 reflections ( 85.02 % complete ) and 4114 restraints for refining 4305 atoms. 423 conditional restraints added. Observations/parameters ratio is 2.26 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2284 (Rfree = 0.000) for 4305 atoms. Found 135 (135 requested) and removed 82 (84 requested) atoms. Cycle 17: After refmac, R = 0.2203 (Rfree = 0.000) for 4352 atoms. Found 111 (133 requested) and removed 55 (85 requested) atoms. Cycle 18: After refmac, R = 0.2123 (Rfree = 0.000) for 4406 atoms. Found 129 (135 requested) and removed 61 (86 requested) atoms. Cycle 19: After refmac, R = 0.2091 (Rfree = 0.000) for 4471 atoms. Found 99 (137 requested) and removed 90 (88 requested) atoms. Cycle 20: After refmac, R = 0.2059 (Rfree = 0.000) for 4473 atoms. Found 122 (134 requested) and removed 87 (88 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.05 1.94 NCS extension: 0 residues added, 4514 seeds are put forward Round 1: 464 peptides, 7 chains. Longest chain 176 peptides. Score 0.937 Round 2: 464 peptides, 8 chains. Longest chain 142 peptides. Score 0.934 Round 3: 464 peptides, 9 chains. Longest chain 142 peptides. Score 0.932 Round 4: 462 peptides, 9 chains. Longest chain 142 peptides. Score 0.931 Round 5: 462 peptides, 8 chains. Longest chain 119 peptides. Score 0.934 Taking the results from Round 1 Chains 8, Residues 457, Estimated correctness of the model 99.6 % 7 chains (456 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 70 A and 73 A Built loop between residues 27 B and 30 B Built loop between residues 68 B and 72 B Built loop between residues 203 B and 206 B 4 chains (466 residues) following loop building 3 chains (465 residues) in sequence following loop building ------------------------------------------------------ 38894 reflections ( 85.02 % complete ) and 4094 restraints for refining 4314 atoms. 392 conditional restraints added. Observations/parameters ratio is 2.25 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2285 (Rfree = 0.000) for 4314 atoms. Found 126 (126 requested) and removed 63 (85 requested) atoms. Cycle 22: After refmac, R = 0.2218 (Rfree = 0.000) for 4373 atoms. Found 127 (127 requested) and removed 54 (86 requested) atoms. Cycle 23: After refmac, R = 0.2153 (Rfree = 0.000) for 4445 atoms. Found 118 (129 requested) and removed 76 (87 requested) atoms. Cycle 24: After refmac, R = 0.2109 (Rfree = 0.000) for 4483 atoms. Found 127 (127 requested) and removed 78 (88 requested) atoms. Cycle 25: After refmac, R = 0.2088 (Rfree = 0.000) for 4526 atoms. Found 110 (125 requested) and removed 84 (89 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.04 1.93 NCS extension: 0 residues added, 4559 seeds are put forward Round 1: 463 peptides, 5 chains. Longest chain 177 peptides. Score 0.943 Round 2: 461 peptides, 8 chains. Longest chain 170 peptides. Score 0.933 Round 3: 458 peptides, 7 chains. Longest chain 177 peptides. Score 0.935 Round 4: 459 peptides, 8 chains. Longest chain 164 peptides. Score 0.932 Round 5: 455 peptides, 10 chains. Longest chain 130 peptides. Score 0.924 Taking the results from Round 1 Chains 6, Residues 458, Estimated correctness of the model 99.7 % 4 chains (451 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 70 A and 73 A Built loop between residues 71 B and 82 B 3 chains (465 residues) following loop building 2 chains (463 residues) in sequence following loop building ------------------------------------------------------ 38894 reflections ( 85.02 % complete ) and 4084 restraints for refining 4327 atoms. 397 conditional restraints added. Observations/parameters ratio is 2.25 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2271 (Rfree = 0.000) for 4327 atoms. Found 116 (116 requested) and removed 86 (85 requested) atoms. Cycle 27: After refmac, R = 0.2199 (Rfree = 0.000) for 4351 atoms. Found 113 (113 requested) and removed 43 (85 requested) atoms. Cycle 28: After refmac, R = 0.2119 (Rfree = 0.000) for 4418 atoms. Found 114 (114 requested) and removed 60 (86 requested) atoms. Cycle 29: After refmac, R = 0.2070 (Rfree = 0.000) for 4468 atoms. Found 112 (112 requested) and removed 70 (87 requested) atoms. Cycle 30: After refmac, R = 0.2035 (Rfree = 0.000) for 4506 atoms. Found 110 (110 requested) and removed 73 (88 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.04 1.93 NCS extension: 0 residues added, 4548 seeds are put forward Round 1: 458 peptides, 9 chains. Longest chain 147 peptides. Score 0.929 Round 2: 462 peptides, 6 chains. Longest chain 141 peptides. Score 0.940 Round 3: 459 peptides, 8 chains. Longest chain 118 peptides. Score 0.932 Round 4: 458 peptides, 9 chains. Longest chain 72 peptides. Score 0.929 Round 5: 452 peptides, 12 chains. Longest chain 73 peptides. Score 0.917 Taking the results from Round 2 Chains 8, Residues 456, Estimated correctness of the model 99.6 % 6 chains (451 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 71 A and 76 A Built loop between residues 105 A and 108 A Built loop between residues 71 B and 74 B 4 chains (462 residues) following loop building 3 chains (459 residues) in sequence following loop building ------------------------------------------------------ 38894 reflections ( 85.02 % complete ) and 4117 restraints for refining 4312 atoms. 458 conditional restraints added. Observations/parameters ratio is 2.25 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2246 (Rfree = 0.000) for 4312 atoms. Found 101 (101 requested) and removed 55 (84 requested) atoms. Cycle 32: After refmac, R = 0.2175 (Rfree = 0.000) for 4351 atoms. Found 99 (99 requested) and removed 39 (85 requested) atoms. Cycle 33: After refmac, R = 0.2097 (Rfree = 0.000) for 4409 atoms. Found 100 (100 requested) and removed 46 (86 requested) atoms. Cycle 34: After refmac, R = 0.2071 (Rfree = 0.000) for 4462 atoms. Found 101 (101 requested) and removed 78 (87 requested) atoms. Cycle 35: After refmac, R = 0.2038 (Rfree = 0.000) for 4481 atoms. Found 99 (99 requested) and removed 75 (88 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.04 1.93 NCS extension: 0 residues added, 4508 seeds are put forward Round 1: 461 peptides, 8 chains. Longest chain 142 peptides. Score 0.933 Round 2: 461 peptides, 6 chains. Longest chain 142 peptides. Score 0.939 Round 3: 459 peptides, 8 chains. Longest chain 142 peptides. Score 0.932 Round 4: 460 peptides, 7 chains. Longest chain 137 peptides. Score 0.936 Round 5: 459 peptides, 11 chains. Longest chain 69 peptides. Score 0.923 Taking the results from Round 2 Chains 10, Residues 455, Estimated correctness of the model 99.6 % 6 chains (438 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 71 A and 74 A Built loop between residues 71 B and 74 B 8 chains (459 residues) following loop building 4 chains (442 residues) in sequence following loop building ------------------------------------------------------ 38894 reflections ( 85.02 % complete ) and 4283 restraints for refining 4310 atoms. 695 conditional restraints added. Observations/parameters ratio is 2.26 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2231 (Rfree = 0.000) for 4310 atoms. Found 91 (91 requested) and removed 53 (84 requested) atoms. Cycle 37: After refmac, R = 0.2125 (Rfree = 0.000) for 4343 atoms. Found 89 (89 requested) and removed 28 (85 requested) atoms. Cycle 38: After refmac, R = 0.2061 (Rfree = 0.000) for 4399 atoms. Found 90 (90 requested) and removed 49 (86 requested) atoms. Cycle 39: After refmac, R = 0.2009 (Rfree = 0.000) for 4439 atoms. Found 87 (87 requested) and removed 49 (87 requested) atoms. Cycle 40: After refmac, R = 0.1993 (Rfree = 0.000) for 4474 atoms. Found 88 (88 requested) and removed 80 (88 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.04 1.93 NCS extension: 5 residues added (33 deleted due to clashes), 4493 seeds are put forward Round 1: 460 peptides, 9 chains. Longest chain 125 peptides. Score 0.930 Round 2: 462 peptides, 6 chains. Longest chain 142 peptides. Score 0.940 Round 3: 464 peptides, 7 chains. Longest chain 146 peptides. Score 0.937 Round 4: 455 peptides, 10 chains. Longest chain 137 peptides. Score 0.924 Round 5: 459 peptides, 9 chains. Longest chain 100 peptides. Score 0.929 Taking the results from Round 2 Chains 9, Residues 456, Estimated correctness of the model 99.6 % 6 chains (437 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 70 A and 73 A Built loop between residues 71 B and 74 B Built loop between residues 103 B and 112 B 5 chains (464 residues) following loop building 3 chains (449 residues) in sequence following loop building ------------------------------------------------------ 38894 reflections ( 85.02 % complete ) and 4205 restraints for refining 4319 atoms. 576 conditional restraints added. Observations/parameters ratio is 2.25 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2202 (Rfree = 0.000) for 4319 atoms. Found 85 (85 requested) and removed 50 (85 requested) atoms. Cycle 42: After refmac, R = 0.2115 (Rfree = 0.000) for 4353 atoms. Found 85 (85 requested) and removed 26 (85 requested) atoms. Cycle 43: After refmac, R = 0.2053 (Rfree = 0.000) for 4405 atoms. Found 86 (86 requested) and removed 44 (86 requested) atoms. Cycle 44: After refmac, R = 0.2006 (Rfree = 0.000) for 4442 atoms. Found 87 (87 requested) and removed 54 (87 requested) atoms. Cycle 45: After refmac, R = 0.1993 (Rfree = 0.000) for 4471 atoms. Found 88 (88 requested) and removed 58 (88 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.04 1.93 NCS extension: 6 residues added (221 deleted due to clashes), 4511 seeds are put forward Round 1: 460 peptides, 8 chains. Longest chain 177 peptides. Score 0.933 Round 2: 461 peptides, 6 chains. Longest chain 142 peptides. Score 0.939 Round 3: 460 peptides, 10 chains. Longest chain 142 peptides. Score 0.927 Round 4: 463 peptides, 6 chains. Longest chain 145 peptides. Score 0.940 Round 5: 454 peptides, 9 chains. Longest chain 118 peptides. Score 0.927 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 7, Residues 457, Estimated correctness of the model 99.6 % 6 chains (454 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 102 A and 105 A Built loop between residues 51 B and 54 B Built loop between residues 71 B and 75 B 4 chains (464 residues) following loop building 3 chains (461 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 38894 reflections ( 85.02 % complete ) and 3673 restraints for refining 3593 atoms. Observations/parameters ratio is 2.71 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2816 (Rfree = 0.000) for 3593 atoms. Found 69 (70 requested) and removed 0 (70 requested) atoms. Cycle 47: After refmac, R = 0.2628 (Rfree = 0.000) for 3593 atoms. Found 17 (72 requested) and removed 2 (72 requested) atoms. Cycle 48: After refmac, R = 0.2510 (Rfree = 0.000) for 3593 atoms. Found 14 (72 requested) and removed 4 (72 requested) atoms. Cycle 49: After refmac, R = 0.2445 (Rfree = 0.000) for 3593 atoms. TimeTaking 54.8