Sun 23 Dec 23:59:48 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 2afb-2.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2afb-2.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2afb-2.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2afb-2.0-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/2afb-2.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2afb-2.0-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 23:59:52 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/2afb-2.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2afb-2.0-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 656 and 0 Target number of residues in the AU: 656 Target solvent content: 0.5159 Checking the provided sequence file Detected sequence length: 351 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 702 Adjusted target solvent content: 0.48 Input MTZ file: 2afb-2.0-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: 155 Cell parameters: 120.993 120.993 260.300 90.000 90.000 120.000 Input sequence file: 2afb-2.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 5616 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: 97.203 2.050 Wilson plot Bfac: 26.83 45456 reflections ( 98.19 % complete ) and 0 restraints for refining 6295 atoms. Observations/parameters ratio is 1.81 ------------------------------------------------------ Starting model: R = 0.3357 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2848 (Rfree = 0.000) for 6295 atoms. Found 155 (200 requested) and removed 110 (100 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.14 2.20 NCS extension: 0 residues added, 6340 seeds are put forward Round 1: 492 peptides, 48 chains. Longest chain 31 peptides. Score 0.739 Round 2: 558 peptides, 29 chains. Longest chain 114 peptides. Score 0.873 Round 3: 583 peptides, 16 chains. Longest chain 150 peptides. Score 0.921 Round 4: 591 peptides, 14 chains. Longest chain 147 peptides. Score 0.929 Round 5: 597 peptides, 12 chains. Longest chain 149 peptides. Score 0.935 Taking the results from Round 5 Chains 14, Residues 585, Estimated correctness of the model 99.5 % 11 chains (572 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 161 A and 167 A Built loop between residues 255 A and 259 A Built loop between residues 289 A and 294 A Built loop between residues 78 B and 81 B Built loop between residues 160 B and 167 B Built loop between residues 301 B and 310 B 7 chains (608 residues) following loop building 5 chains (600 residues) in sequence following loop building ------------------------------------------------------ 45456 reflections ( 98.19 % complete ) and 5802 restraints for refining 5613 atoms. 953 conditional restraints added. Observations/parameters ratio is 2.02 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3059 (Rfree = 0.000) for 5613 atoms. Found 160 (179 requested) and removed 111 (89 requested) atoms. Cycle 2: After refmac, R = 0.2699 (Rfree = 0.000) for 5637 atoms. Found 146 (176 requested) and removed 90 (90 requested) atoms. Cycle 3: After refmac, R = 0.2511 (Rfree = 0.000) for 5641 atoms. Found 116 (174 requested) and removed 60 (90 requested) atoms. Cycle 4: After refmac, R = 0.2372 (Rfree = 0.000) for 5671 atoms. Found 106 (170 requested) and removed 52 (90 requested) atoms. Cycle 5: After refmac, R = 0.2289 (Rfree = 0.000) for 5693 atoms. Found 109 (171 requested) and removed 42 (91 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.10 2.16 NCS extension: 10 residues added (30 deleted due to clashes), 5776 seeds are put forward Round 1: 613 peptides, 8 chains. Longest chain 171 peptides. Score 0.949 Round 2: 618 peptides, 6 chains. Longest chain 172 peptides. Score 0.954 Round 3: 611 peptides, 9 chains. Longest chain 206 peptides. Score 0.946 Round 4: 616 peptides, 12 chains. Longest chain 170 peptides. Score 0.941 Round 5: 615 peptides, 9 chains. Longest chain 183 peptides. Score 0.947 Taking the results from Round 2 Chains 6, Residues 612, Estimated correctness of the model 99.7 % 5 chains (595 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 43 A and 46 A 5 chains (614 residues) following loop building 4 chains (597 residues) in sequence following loop building ------------------------------------------------------ 45456 reflections ( 98.19 % complete ) and 5690 restraints for refining 5626 atoms. 831 conditional restraints added. Observations/parameters ratio is 2.02 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2482 (Rfree = 0.000) for 5626 atoms. Found 166 (168 requested) and removed 97 (89 requested) atoms. Cycle 7: After refmac, R = 0.2255 (Rfree = 0.000) for 5692 atoms. Found 127 (167 requested) and removed 76 (90 requested) atoms. Cycle 8: After refmac, R = 0.2174 (Rfree = 0.000) for 5736 atoms. Found 133 (165 requested) and removed 39 (91 requested) atoms. Cycle 9: After refmac, R = 0.2114 (Rfree = 0.000) for 5815 atoms. Found 99 (166 requested) and removed 66 (92 requested) atoms. Cycle 10: After refmac, R = 0.2083 (Rfree = 0.000) for 5833 atoms. Found 121 (164 requested) and removed 64 (93 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.10 2.16 NCS extension: 16 residues added (19 deleted due to clashes), 5906 seeds are put forward Round 1: 622 peptides, 6 chains. Longest chain 205 peptides. Score 0.955 Round 2: 622 peptides, 7 chains. Longest chain 173 peptides. Score 0.953 Round 3: 624 peptides, 9 chains. Longest chain 207 peptides. Score 0.949 Round 4: 620 peptides, 10 chains. Longest chain 171 peptides. Score 0.946 Round 5: 615 peptides, 12 chains. Longest chain 186 peptides. Score 0.941 Taking the results from Round 1 Chains 6, Residues 616, Estimated correctness of the model 99.7 % 5 chains (597 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 256 A and 259 A 5 chains (618 residues) following loop building 4 chains (599 residues) in sequence following loop building ------------------------------------------------------ 45456 reflections ( 98.19 % complete ) and 5658 restraints for refining 5667 atoms. 766 conditional restraints added. Observations/parameters ratio is 2.01 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2239 (Rfree = 0.000) for 5667 atoms. Found 155 (155 requested) and removed 100 (90 requested) atoms. Cycle 12: After refmac, R = 0.2140 (Rfree = 0.000) for 5707 atoms. Found 150 (153 requested) and removed 65 (91 requested) atoms. Cycle 13: After refmac, R = 0.2067 (Rfree = 0.000) for 5788 atoms. Found 119 (155 requested) and removed 79 (92 requested) atoms. Cycle 14: After refmac, R = 0.2028 (Rfree = 0.000) for 5822 atoms. Found 132 (152 requested) and removed 75 (92 requested) atoms. Cycle 15: After refmac, R = 0.2018 (Rfree = 0.000) for 5874 atoms. Found 99 (150 requested) and removed 86 (93 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.11 2.17 NCS extension: 11 residues added (20 deleted due to clashes), 5899 seeds are put forward Round 1: 617 peptides, 9 chains. Longest chain 170 peptides. Score 0.948 Round 2: 621 peptides, 6 chains. Longest chain 208 peptides. Score 0.955 Round 3: 619 peptides, 10 chains. Longest chain 137 peptides. Score 0.946 Round 4: 615 peptides, 12 chains. Longest chain 185 peptides. Score 0.941 Round 5: 624 peptides, 11 chains. Longest chain 146 peptides. Score 0.945 Taking the results from Round 2 Chains 6, Residues 615, Estimated correctness of the model 99.7 % 5 chains (610 residues) have been docked in sequence Building loops using Loopy2018 6 chains (615 residues) following loop building 5 chains (610 residues) in sequence following loop building ------------------------------------------------------ 45456 reflections ( 98.19 % complete ) and 5745 restraints for refining 5718 atoms. 838 conditional restraints added. Observations/parameters ratio is 1.99 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2180 (Rfree = 0.000) for 5718 atoms. Found 142 (142 requested) and removed 95 (91 requested) atoms. Cycle 17: After refmac, R = 0.2095 (Rfree = 0.000) for 5753 atoms. Found 136 (139 requested) and removed 73 (91 requested) atoms. Cycle 18: After refmac, R = 0.2041 (Rfree = 0.000) for 5809 atoms. Found 119 (137 requested) and removed 80 (92 requested) atoms. Cycle 19: After refmac, R = 0.2012 (Rfree = 0.000) for 5845 atoms. Found 131 (134 requested) and removed 78 (93 requested) atoms. Cycle 20: After refmac, R = 0.2000 (Rfree = 0.000) for 5892 atoms. Found 112 (132 requested) and removed 97 (94 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.10 2.16 NCS extension: 14 residues added (20 deleted due to clashes), 5921 seeds are put forward Round 1: 622 peptides, 9 chains. Longest chain 171 peptides. Score 0.949 Round 2: 626 peptides, 6 chains. Longest chain 208 peptides. Score 0.956 Round 3: 621 peptides, 10 chains. Longest chain 171 peptides. Score 0.947 Round 4: 618 peptides, 17 chains. Longest chain 144 peptides. Score 0.931 Round 5: 623 peptides, 11 chains. Longest chain 186 peptides. Score 0.945 Taking the results from Round 2 Chains 6, Residues 620, Estimated correctness of the model 99.7 % 6 chains (620 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 218 A and 229 A Built loop between residues 255 A and 259 A 4 chains (633 residues) following loop building 4 chains (633 residues) in sequence following loop building ------------------------------------------------------ 45456 reflections ( 98.19 % complete ) and 5705 restraints for refining 5800 atoms. 629 conditional restraints added. Observations/parameters ratio is 1.96 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2193 (Rfree = 0.000) for 5800 atoms. Found 126 (126 requested) and removed 96 (92 requested) atoms. Cycle 22: After refmac, R = 0.2079 (Rfree = 0.000) for 5820 atoms. Found 123 (123 requested) and removed 91 (93 requested) atoms. Cycle 23: After refmac, R = 0.2030 (Rfree = 0.000) for 5850 atoms. Found 119 (119 requested) and removed 82 (93 requested) atoms. Cycle 24: After refmac, R = 0.2005 (Rfree = 0.000) for 5883 atoms. Found 116 (116 requested) and removed 91 (93 requested) atoms. Cycle 25: After refmac, R = 0.2001 (Rfree = 0.000) for 5903 atoms. Found 113 (113 requested) and removed 88 (94 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.10 2.16 NCS extension: 14 residues added (24 deleted due to clashes), 5948 seeds are put forward Round 1: 622 peptides, 8 chains. Longest chain 171 peptides. Score 0.951 Round 2: 632 peptides, 6 chains. Longest chain 208 peptides. Score 0.957 Round 3: 627 peptides, 9 chains. Longest chain 171 peptides. Score 0.950 Round 4: 629 peptides, 10 chains. Longest chain 112 peptides. Score 0.949 Round 5: 627 peptides, 12 chains. Longest chain 130 peptides. Score 0.944 Taking the results from Round 2 Chains 7, Residues 626, Estimated correctness of the model 99.8 % 6 chains (625 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 31 A and 34 A Built loop between residues 220 A and 228 A 4 chains (634 residues) following loop building 4 chains (634 residues) in sequence following loop building ------------------------------------------------------ 45456 reflections ( 98.19 % complete ) and 5723 restraints for refining 5815 atoms. 638 conditional restraints added. Observations/parameters ratio is 1.95 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2187 (Rfree = 0.000) for 5815 atoms. Found 107 (107 requested) and removed 95 (92 requested) atoms. Cycle 27: After refmac, R = 0.2099 (Rfree = 0.000) for 5817 atoms. Found 104 (104 requested) and removed 79 (92 requested) atoms. Cycle 28: After refmac, R = 0.2045 (Rfree = 0.000) for 5839 atoms. Found 100 (100 requested) and removed 59 (93 requested) atoms. Cycle 29: After refmac, R = 0.2005 (Rfree = 0.000) for 5875 atoms. Found 97 (97 requested) and removed 61 (93 requested) atoms. Cycle 30: After refmac, R = 0.1989 (Rfree = 0.000) for 5907 atoms. Found 94 (94 requested) and removed 73 (94 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.10 2.16 NCS extension: 14 residues added (28 deleted due to clashes), 5948 seeds are put forward Round 1: 623 peptides, 9 chains. Longest chain 171 peptides. Score 0.949 Round 2: 628 peptides, 6 chains. Longest chain 208 peptides. Score 0.956 Round 3: 625 peptides, 8 chains. Longest chain 208 peptides. Score 0.952 Round 4: 623 peptides, 12 chains. Longest chain 167 peptides. Score 0.943 Round 5: 623 peptides, 12 chains. Longest chain 185 peptides. Score 0.943 Taking the results from Round 2 Chains 6, Residues 622, Estimated correctness of the model 99.7 % 6 chains (622 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 221 A and 228 A Built loop between residues 254 A and 257 A 4 chains (630 residues) following loop building 4 chains (630 residues) in sequence following loop building ------------------------------------------------------ 45456 reflections ( 98.19 % complete ) and 5723 restraints for refining 5772 atoms. 673 conditional restraints added. Observations/parameters ratio is 1.97 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2189 (Rfree = 0.000) for 5772 atoms. Found 92 (92 requested) and removed 95 (92 requested) atoms. Cycle 32: After refmac, R = 0.2087 (Rfree = 0.000) for 5761 atoms. Found 92 (92 requested) and removed 52 (92 requested) atoms. Cycle 33: After refmac, R = 0.2026 (Rfree = 0.000) for 5799 atoms. Found 92 (92 requested) and removed 57 (92 requested) atoms. Cycle 34: After refmac, R = 0.2011 (Rfree = 0.000) for 5832 atoms. Found 93 (93 requested) and removed 67 (93 requested) atoms. Cycle 35: After refmac, R = 0.1986 (Rfree = 0.000) for 5853 atoms. Found 93 (93 requested) and removed 54 (93 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.10 2.16 NCS extension: 15 residues added (28 deleted due to clashes), 5909 seeds are put forward Round 1: 622 peptides, 10 chains. Longest chain 171 peptides. Score 0.947 Round 2: 628 peptides, 6 chains. Longest chain 208 peptides. Score 0.956 Round 3: 629 peptides, 6 chains. Longest chain 208 peptides. Score 0.956 Round 4: 630 peptides, 9 chains. Longest chain 167 peptides. Score 0.951 Round 5: 624 peptides, 9 chains. Longest chain 167 peptides. Score 0.949 Taking the results from Round 3 Chains 6, Residues 623, Estimated correctness of the model 99.7 % 6 chains (623 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 82 A and 85 A Built loop between residues 222 A and 227 A 4 chains (629 residues) following loop building 4 chains (629 residues) in sequence following loop building ------------------------------------------------------ 45456 reflections ( 98.19 % complete ) and 5736 restraints for refining 5771 atoms. 695 conditional restraints added. Observations/parameters ratio is 1.97 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2165 (Rfree = 0.000) for 5771 atoms. Found 92 (92 requested) and removed 97 (92 requested) atoms. Cycle 37: After refmac, R = 0.2064 (Rfree = 0.000) for 5759 atoms. Found 91 (91 requested) and removed 41 (91 requested) atoms. Cycle 38: After refmac, R = 0.2021 (Rfree = 0.000) for 5807 atoms. Found 92 (92 requested) and removed 51 (92 requested) atoms. Cycle 39: After refmac, R = 0.1986 (Rfree = 0.000) for 5843 atoms. Found 93 (93 requested) and removed 39 (93 requested) atoms. Cycle 40: After refmac, R = 0.1972 (Rfree = 0.000) for 5888 atoms. Found 94 (94 requested) and removed 54 (94 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.11 2.17 NCS extension: 19 residues added (25 deleted due to clashes), 5952 seeds are put forward Round 1: 628 peptides, 7 chains. Longest chain 171 peptides. Score 0.954 Round 2: 629 peptides, 6 chains. Longest chain 208 peptides. Score 0.956 Round 3: 630 peptides, 6 chains. Longest chain 208 peptides. Score 0.957 Round 4: 626 peptides, 10 chains. Longest chain 171 peptides. Score 0.948 Round 5: 626 peptides, 7 chains. Longest chain 186 peptides. Score 0.954 Taking the results from Round 3 Chains 6, Residues 624, Estimated correctness of the model 99.8 % 6 chains (624 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 222 A and 227 A Built loop between residues 243 A and 246 A 4 chains (630 residues) following loop building 4 chains (630 residues) in sequence following loop building ------------------------------------------------------ 45456 reflections ( 98.19 % complete ) and 5766 restraints for refining 5802 atoms. 717 conditional restraints added. Observations/parameters ratio is 1.96 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2159 (Rfree = 0.000) for 5802 atoms. Found 92 (92 requested) and removed 97 (92 requested) atoms. Cycle 42: After refmac, R = 0.2052 (Rfree = 0.000) for 5789 atoms. Found 92 (92 requested) and removed 36 (92 requested) atoms. Cycle 43: After refmac, R = 0.2003 (Rfree = 0.000) for 5840 atoms. Found 93 (93 requested) and removed 51 (93 requested) atoms. Cycle 44: After refmac, R = 0.1982 (Rfree = 0.000) for 5878 atoms. Found 93 (93 requested) and removed 48 (93 requested) atoms. Cycle 45: After refmac, R = 0.1954 (Rfree = 0.000) for 5921 atoms. Found 94 (94 requested) and removed 64 (94 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.10 2.16 NCS extension: 21 residues added (25 deleted due to clashes), 5975 seeds are put forward Round 1: 626 peptides, 9 chains. Longest chain 171 peptides. Score 0.950 Round 2: 629 peptides, 6 chains. Longest chain 208 peptides. Score 0.956 Round 3: 626 peptides, 8 chains. Longest chain 208 peptides. Score 0.952 Round 4: 626 peptides, 11 chains. Longest chain 144 peptides. Score 0.946 Round 5: 621 peptides, 11 chains. Longest chain 186 peptides. Score 0.944 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 6, Residues 623, Estimated correctness of the model 99.7 % 6 chains (623 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 222 A and 227 A Built loop between residues 255 A and 259 A Built loop between residues 217 B and 231 B 3 chains (643 residues) following loop building 3 chains (643 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 45456 reflections ( 98.19 % complete ) and 5151 restraints for refining 5043 atoms. Observations/parameters ratio is 2.25 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2799 (Rfree = 0.000) for 5043 atoms. Found 58 (80 requested) and removed 0 (80 requested) atoms. Cycle 47: After refmac, R = 0.2580 (Rfree = 0.000) for 5043 atoms. Found 36 (81 requested) and removed 2 (81 requested) atoms. Cycle 48: After refmac, R = 0.2501 (Rfree = 0.000) for 5043 atoms. Found 22 (81 requested) and removed 6 (81 requested) atoms. Cycle 49: After refmac, R = 0.2457 (Rfree = 0.000) for 5043 atoms. TimeTaking 88.18