Mon 24 Dec 01:12:31 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 2fg0-1.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2fg0-1.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2fg0-1.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fg0-1.8-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/2fg0-1.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fg0-1.8-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 01:12:36 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/2fg0-1.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fg0-1.8-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 730 and 0 Target number of residues in the AU: 730 Target solvent content: 0.4806 Checking the provided sequence file Detected sequence length: 246 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 492 Adjusted target solvent content: 0.65 Input MTZ file: 2fg0-1.8-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: 92 Cell parameters: 124.890 124.890 97.540 90.000 90.000 90.000 Input sequence file: 2fg0-1.8-parrot-mrncs.fasta_lf Building free atoms model in initial map for 3936 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 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: 88.311 1.791 Wilson plot Bfac: 19.73 72462 reflections ( 99.59 % complete ) and 0 restraints for refining 4373 atoms. Observations/parameters ratio is 4.14 ------------------------------------------------------ Starting model: R = 0.3305 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2822 (Rfree = 0.000) for 4373 atoms. Found 205 (205 requested) and removed 106 (102 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.90 1.55 NCS extension: 0 residues added, 4472 seeds are put forward Round 1: 396 peptides, 26 chains. Longest chain 38 peptides. Score 0.742 Round 2: 407 peptides, 17 chains. Longest chain 56 peptides. Score 0.801 Round 3: 421 peptides, 9 chains. Longest chain 136 peptides. Score 0.850 Round 4: 420 peptides, 10 chains. Longest chain 95 peptides. Score 0.845 Round 5: 432 peptides, 9 chains. Longest chain 104 peptides. Score 0.858 Taking the results from Round 5 Chains 11, Residues 423, Estimated correctness of the model 98.6 % 7 chains (403 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 85 A and 88 A Built loop between residues 132 A and 143 A Built loop between residues 62 B and 65 B Built loop between residues 132 B and 143 B 5 chains (436 residues) following loop building 3 chains (427 residues) in sequence following loop building ------------------------------------------------------ 72462 reflections ( 99.59 % complete ) and 4056 restraints for refining 4176 atoms. 607 conditional restraints added. Observations/parameters ratio is 4.34 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2371 (Rfree = 0.000) for 4176 atoms. Found 196 (196 requested) and removed 108 (98 requested) atoms. Failed to save intermediate PDB Cycle 2: After refmac, R = 0.2119 (Rfree = 0.000) for 4244 atoms. Found 196 (196 requested) and removed 60 (100 requested) atoms. Cycle 3: After refmac, R = 0.1994 (Rfree = 0.000) for 4355 atoms. Found 180 (201 requested) and removed 32 (102 requested) atoms. Cycle 4: After refmac, R = 0.1944 (Rfree = 0.000) for 4474 atoms. Found 172 (207 requested) and removed 75 (105 requested) atoms. Cycle 5: After refmac, R = 0.1921 (Rfree = 0.000) for 4544 atoms. Found 176 (210 requested) and removed 81 (107 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.85 1.51 NCS extension: 20 residues added (214 deleted due to clashes), 4661 seeds are put forward Round 1: 437 peptides, 6 chains. Longest chain 112 peptides. Score 0.873 Round 2: 434 peptides, 7 chains. Longest chain 112 peptides. Score 0.867 Round 3: 438 peptides, 6 chains. Longest chain 112 peptides. Score 0.874 Round 4: 433 peptides, 7 chains. Longest chain 111 peptides. Score 0.867 Round 5: 433 peptides, 8 chains. Longest chain 104 peptides. Score 0.863 Taking the results from Round 3 Chains 7, Residues 432, Estimated correctness of the model 98.9 % 6 chains (429 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 80 A and 83 A Built loop between residues 132 A and 135 A Built loop between residues 167 A and 170 A Built loop between residues 129 B and 134 B 2 chains (439 residues) following loop building 2 chains (439 residues) in sequence following loop building ------------------------------------------------------ 72462 reflections ( 99.59 % complete ) and 4007 restraints for refining 4244 atoms. 508 conditional restraints added. Observations/parameters ratio is 4.27 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1954 (Rfree = 0.000) for 4244 atoms. Found 195 (195 requested) and removed 30 (99 requested) atoms. Cycle 7: After refmac, R = 0.1910 (Rfree = 0.000) for 4400 atoms. Found 175 (202 requested) and removed 72 (103 requested) atoms. Cycle 8: After refmac, R = 0.1868 (Rfree = 0.000) for 4495 atoms. Found 174 (207 requested) and removed 72 (105 requested) atoms. Cycle 9: After refmac, R = 0.1862 (Rfree = 0.000) for 4584 atoms. Found 147 (211 requested) and removed 86 (107 requested) atoms. Cycle 10: After refmac, R = 0.1830 (Rfree = 0.000) for 4622 atoms. Found 174 (208 requested) and removed 63 (108 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.85 1.51 NCS extension: 0 residues added, 4736 seeds are put forward Round 1: 436 peptides, 5 chains. Longest chain 111 peptides. Score 0.877 Round 2: 435 peptides, 6 chains. Longest chain 112 peptides. Score 0.872 Round 3: 438 peptides, 5 chains. Longest chain 111 peptides. Score 0.878 Round 4: 435 peptides, 6 chains. Longest chain 112 peptides. Score 0.872 Round 5: 436 peptides, 6 chains. Longest chain 111 peptides. Score 0.873 Taking the results from Round 3 Chains 8, Residues 433, Estimated correctness of the model 98.9 % 5 chains (429 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 132 A and 135 A Built loop between residues 79 B and 84 B Built loop between residues 132 B and 136 B 3 chains (439 residues) following loop building 2 chains (438 residues) in sequence following loop building ------------------------------------------------------ 72462 reflections ( 99.59 % complete ) and 4012 restraints for refining 4279 atoms. 519 conditional restraints added. Observations/parameters ratio is 4.23 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1905 (Rfree = 0.000) for 4279 atoms. Found 192 (192 requested) and removed 27 (100 requested) atoms. Cycle 12: After refmac, R = 0.1849 (Rfree = 0.000) for 4434 atoms. Found 164 (200 requested) and removed 60 (104 requested) atoms. Cycle 13: After refmac, R = 0.1823 (Rfree = 0.000) for 4526 atoms. Found 142 (204 requested) and removed 74 (106 requested) atoms. Cycle 14: After refmac, R = 0.1809 (Rfree = 0.000) for 4585 atoms. Found 174 (202 requested) and removed 89 (107 requested) atoms. Cycle 15: After refmac, R = 0.1816 (Rfree = 0.000) for 4651 atoms. Found 146 (201 requested) and removed 109 (109 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.85 1.51 NCS extension: 0 residues added, 4689 seeds are put forward Round 1: 436 peptides, 6 chains. Longest chain 111 peptides. Score 0.873 Round 2: 436 peptides, 6 chains. Longest chain 116 peptides. Score 0.873 Round 3: 437 peptides, 5 chains. Longest chain 112 peptides. Score 0.877 Round 4: 433 peptides, 6 chains. Longest chain 112 peptides. Score 0.871 Round 5: 434 peptides, 6 chains. Longest chain 112 peptides. Score 0.871 Taking the results from Round 3 Chains 5, Residues 432, Estimated correctness of the model 98.9 % 5 chains (432 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 131 A and 135 A Built loop between residues 83 B and 86 B Built loop between residues 132 B and 135 B 2 chains (439 residues) following loop building 2 chains (439 residues) in sequence following loop building ------------------------------------------------------ 72462 reflections ( 99.59 % complete ) and 4118 restraints for refining 4315 atoms. 617 conditional restraints added. Observations/parameters ratio is 4.20 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1912 (Rfree = 0.000) for 4315 atoms. Found 182 (182 requested) and removed 36 (101 requested) atoms. Cycle 17: After refmac, R = 0.1864 (Rfree = 0.000) for 4452 atoms. Found 173 (188 requested) and removed 62 (104 requested) atoms. Cycle 18: After refmac, R = 0.1837 (Rfree = 0.000) for 4551 atoms. Found 155 (193 requested) and removed 74 (107 requested) atoms. Cycle 19: After refmac, R = 0.1823 (Rfree = 0.000) for 4619 atoms. Found 145 (195 requested) and removed 71 (108 requested) atoms. Cycle 20: After refmac, R = 0.1812 (Rfree = 0.000) for 4665 atoms. Found 158 (198 requested) and removed 86 (110 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.85 1.51 NCS extension: 0 residues added, 4739 seeds are put forward Round 1: 434 peptides, 6 chains. Longest chain 112 peptides. Score 0.871 Round 2: 436 peptides, 6 chains. Longest chain 117 peptides. Score 0.873 Round 3: 438 peptides, 7 chains. Longest chain 112 peptides. Score 0.870 Round 4: 436 peptides, 6 chains. Longest chain 112 peptides. Score 0.873 Round 5: 436 peptides, 7 chains. Longest chain 117 peptides. Score 0.869 Taking the results from Round 4 Chains 6, Residues 430, Estimated correctness of the model 98.9 % 6 chains (430 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 81 A and 85 A Built loop between residues 131 A and 135 A Built loop between residues 83 B and 86 B Built loop between residues 132 B and 135 B 2 chains (440 residues) following loop building 2 chains (440 residues) in sequence following loop building ------------------------------------------------------ 72462 reflections ( 99.59 % complete ) and 4076 restraints for refining 4304 atoms. 566 conditional restraints added. Observations/parameters ratio is 4.21 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2073 (Rfree = 0.000) for 4304 atoms. Found 177 (177 requested) and removed 27 (100 requested) atoms. Cycle 22: After refmac, R = 0.1917 (Rfree = 0.000) for 4446 atoms. Found 155 (183 requested) and removed 32 (104 requested) atoms. Cycle 23: After refmac, R = 0.1847 (Rfree = 0.000) for 4548 atoms. Found 139 (188 requested) and removed 63 (107 requested) atoms. Cycle 24: After refmac, R = 0.1821 (Rfree = 0.000) for 4605 atoms. Found 176 (190 requested) and removed 58 (108 requested) atoms. Cycle 25: After refmac, R = 0.1838 (Rfree = 0.000) for 4711 atoms. Found 151 (194 requested) and removed 115 (110 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.85 1.51 NCS extension: 0 residues added, 4750 seeds are put forward Round 1: 435 peptides, 6 chains. Longest chain 112 peptides. Score 0.872 Round 2: 434 peptides, 7 chains. Longest chain 112 peptides. Score 0.867 Round 3: 434 peptides, 6 chains. Longest chain 111 peptides. Score 0.871 Round 4: 439 peptides, 4 chains. Longest chain 168 peptides. Score 0.882 Round 5: 431 peptides, 9 chains. Longest chain 115 peptides. Score 0.857 Taking the results from Round 4 Chains 4, Residues 435, Estimated correctness of the model 99.0 % 4 chains (435 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 75 A and 78 A Built loop between residues 131 B and 134 B 2 chains (439 residues) following loop building 2 chains (439 residues) in sequence following loop building ------------------------------------------------------ 72462 reflections ( 99.59 % complete ) and 4126 restraints for refining 4322 atoms. 624 conditional restraints added. Observations/parameters ratio is 4.19 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1904 (Rfree = 0.000) for 4322 atoms. Found 174 (174 requested) and removed 29 (101 requested) atoms. Cycle 27: After refmac, R = 0.1845 (Rfree = 0.000) for 4457 atoms. Found 180 (180 requested) and removed 47 (104 requested) atoms. Cycle 28: After refmac, R = 0.1835 (Rfree = 0.000) for 4582 atoms. Found 152 (185 requested) and removed 84 (107 requested) atoms. Cycle 29: After refmac, R = 0.1830 (Rfree = 0.000) for 4640 atoms. Found 181 (183 requested) and removed 76 (109 requested) atoms. Cycle 30: After refmac, R = 0.1831 (Rfree = 0.000) for 4723 atoms. Found 157 (186 requested) and removed 115 (111 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.84 1.50 NCS extension: 0 residues added, 4767 seeds are put forward Round 1: 436 peptides, 6 chains. Longest chain 111 peptides. Score 0.873 Round 2: 433 peptides, 7 chains. Longest chain 112 peptides. Score 0.867 Round 3: 436 peptides, 5 chains. Longest chain 111 peptides. Score 0.877 Round 4: 438 peptides, 6 chains. Longest chain 167 peptides. Score 0.874 Round 5: 435 peptides, 8 chains. Longest chain 112 peptides. Score 0.864 Taking the results from Round 3 Chains 5, Residues 431, Estimated correctness of the model 98.9 % 5 chains (431 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 132 A and 135 A Built loop between residues 80 B and 85 B Built loop between residues 132 B and 135 B 2 chains (439 residues) following loop building 2 chains (439 residues) in sequence following loop building ------------------------------------------------------ 72462 reflections ( 99.59 % complete ) and 4118 restraints for refining 4342 atoms. 619 conditional restraints added. Observations/parameters ratio is 4.17 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1892 (Rfree = 0.000) for 4342 atoms. Found 166 (166 requested) and removed 37 (101 requested) atoms. Cycle 32: After refmac, R = 0.1843 (Rfree = 0.000) for 4458 atoms. Found 168 (171 requested) and removed 42 (104 requested) atoms. Cycle 33: After refmac, R = 0.1828 (Rfree = 0.000) for 4577 atoms. Found 141 (176 requested) and removed 71 (107 requested) atoms. Cycle 34: After refmac, R = 0.1792 (Rfree = 0.000) for 4635 atoms. Found 161 (174 requested) and removed 68 (108 requested) atoms. Cycle 35: After refmac, R = 0.1796 (Rfree = 0.000) for 4712 atoms. Found 134 (177 requested) and removed 115 (110 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.84 1.50 NCS extension: 0 residues added, 4731 seeds are put forward Round 1: 438 peptides, 5 chains. Longest chain 111 peptides. Score 0.878 Round 2: 436 peptides, 6 chains. Longest chain 117 peptides. Score 0.873 Round 3: 436 peptides, 6 chains. Longest chain 111 peptides. Score 0.873 Round 4: 436 peptides, 6 chains. Longest chain 111 peptides. Score 0.873 Round 5: 435 peptides, 8 chains. Longest chain 111 peptides. Score 0.864 Taking the results from Round 1 Chains 5, Residues 433, Estimated correctness of the model 98.9 % 5 chains (433 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 81 A and 84 A Built loop between residues 132 A and 135 A Built loop between residues 131 B and 135 B 2 chains (440 residues) following loop building 2 chains (440 residues) in sequence following loop building ------------------------------------------------------ 72462 reflections ( 99.59 % complete ) and 4116 restraints for refining 4356 atoms. 608 conditional restraints added. Observations/parameters ratio is 4.16 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2031 (Rfree = 0.000) for 4356 atoms. Found 159 (159 requested) and removed 26 (102 requested) atoms. Cycle 37: After refmac, R = 0.1889 (Rfree = 0.000) for 4481 atoms. Found 137 (164 requested) and removed 33 (105 requested) atoms. Cycle 38: After refmac, R = 0.1826 (Rfree = 0.000) for 4570 atoms. Found 125 (168 requested) and removed 54 (107 requested) atoms. Cycle 39: After refmac, R = 0.1792 (Rfree = 0.000) for 4616 atoms. Found 139 (169 requested) and removed 59 (108 requested) atoms. Cycle 40: After refmac, R = 0.1790 (Rfree = 0.000) for 4679 atoms. Found 172 (172 requested) and removed 89 (110 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.85 1.51 NCS extension: 0 residues added, 4762 seeds are put forward Round 1: 434 peptides, 7 chains. Longest chain 111 peptides. Score 0.867 Round 2: 436 peptides, 5 chains. Longest chain 111 peptides. Score 0.877 Round 3: 436 peptides, 6 chains. Longest chain 118 peptides. Score 0.873 Round 4: 434 peptides, 6 chains. Longest chain 111 peptides. Score 0.871 Round 5: 437 peptides, 6 chains. Longest chain 167 peptides. Score 0.873 Taking the results from Round 2 Chains 5, Residues 431, Estimated correctness of the model 98.9 % 5 chains (431 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 81 A and 85 A Built loop between residues 132 A and 135 A Built loop between residues 131 B and 135 B 2 chains (439 residues) following loop building 2 chains (439 residues) in sequence following loop building ------------------------------------------------------ 72462 reflections ( 99.59 % complete ) and 4171 restraints for refining 4359 atoms. 672 conditional restraints added. Observations/parameters ratio is 4.16 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2026 (Rfree = 0.000) for 4359 atoms. Found 155 (155 requested) and removed 19 (102 requested) atoms. Cycle 42: After refmac, R = 0.1889 (Rfree = 0.000) for 4486 atoms. Found 160 (160 requested) and removed 28 (105 requested) atoms. Cycle 43: After refmac, R = 0.1861 (Rfree = 0.000) for 4608 atoms. Found 126 (164 requested) and removed 63 (108 requested) atoms. Cycle 44: After refmac, R = 0.1811 (Rfree = 0.000) for 4653 atoms. Found 161 (166 requested) and removed 81 (109 requested) atoms. Cycle 45: After refmac, R = 0.1827 (Rfree = 0.000) for 4713 atoms. Found 160 (164 requested) and removed 102 (110 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.84 1.50 NCS extension: 0 residues added, 4771 seeds are put forward Round 1: 433 peptides, 6 chains. Longest chain 111 peptides. Score 0.871 Round 2: 436 peptides, 5 chains. Longest chain 111 peptides. Score 0.877 Round 3: 440 peptides, 4 chains. Longest chain 118 peptides. Score 0.883 Round 4: 437 peptides, 5 chains. Longest chain 111 peptides. Score 0.877 Round 5: 438 peptides, 6 chains. Longest chain 150 peptides. Score 0.874 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 4, Residues 436, Estimated correctness of the model 99.0 % 4 chains (436 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 141 A and 144 A Built loop between residues 131 B and 135 B 2 chains (441 residues) following loop building 2 chains (441 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 72462 reflections ( 99.59 % complete ) and 3519 restraints for refining 3435 atoms. Observations/parameters ratio is 5.27 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2510 (Rfree = 0.000) for 3435 atoms. Found 116 (116 requested) and removed 0 (116 requested) atoms. Cycle 47: After refmac, R = 0.2169 (Rfree = 0.000) for 3435 atoms. Found 120 (120 requested) and removed 0 (83 requested) atoms. Cycle 48: After refmac, R = 0.1974 (Rfree = 0.000) for 3435 atoms. Found 64 (124 requested) and removed 1 (86 requested) atoms. Cycle 49: After refmac, R = 0.1870 (Rfree = 0.000) for 3435 atoms. Found 30 (126 requested) and removed 1 (87 requested) atoms. Writing output files ... TimeTaking 79.43