Sun 23 Dec 22:22:50 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 1vk9-2.7-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vk9-2.7-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vk9-2.7-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk9-2.7-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/1vk9-2.7-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk9-2.7-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 22:23:00 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/1vk9-2.7-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk9-2.7-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 242 and 0 Target number of residues in the AU: 242 Target solvent content: 0.6132 Checking the provided sequence file Detected sequence length: 151 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 302 Adjusted target solvent content: 0.52 Input MTZ file: 1vk9-2.7-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: 180 Cell parameters: 132.922 132.922 66.385 90.000 90.000 120.000 Input sequence file: 1vk9-2.7-parrot-hancs.fasta_lf Building free atoms model in initial map for 2416 target number of atoms Had to go as low as 0.40 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 3 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 115.114 2.701 Wilson plot Bfac: 58.15 9660 reflections ( 97.23 % complete ) and 0 restraints for refining 2677 atoms. Observations/parameters ratio is 0.90 ------------------------------------------------------ Starting model: R = 0.3180 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2344 (Rfree = 0.000) for 2677 atoms. Found 32 (38 requested) and removed 36 (19 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.96 2.88 Search for helices and strands: 0 residues in 0 chains, 2684 seeds are put forward NCS extension: 0 residues added, 2684 seeds are put forward Round 1: 125 peptides, 9 chains. Longest chain 58 peptides. Score 0.626 Round 2: 138 peptides, 8 chains. Longest chain 42 peptides. Score 0.686 Round 3: 141 peptides, 4 chains. Longest chain 91 peptides. Score 0.755 Round 4: 146 peptides, 6 chains. Longest chain 75 peptides. Score 0.739 Round 5: 141 peptides, 10 chains. Longest chain 37 peptides. Score 0.663 Taking the results from Round 3 Chains 4, Residues 137, Estimated correctness of the model 85.9 % 2 chains (119 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 49 A and 55 A 3 chains (142 residues) following loop building 1 chains (124 residues) in sequence following loop building ------------------------------------------------------ 9660 reflections ( 97.23 % complete ) and 3346 restraints for refining 2110 atoms. 2276 conditional restraints added. Observations/parameters ratio is 1.14 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3347 (Rfree = 0.000) for 2110 atoms. Found 31 (31 requested) and removed 65 (15 requested) atoms. Cycle 2: After refmac, R = 0.2891 (Rfree = 0.000) for 1986 atoms. Found 29 (29 requested) and removed 33 (15 requested) atoms. Cycle 3: After refmac, R = 0.2721 (Rfree = 0.000) for 1936 atoms. Found 27 (27 requested) and removed 29 (14 requested) atoms. Cycle 4: After refmac, R = 0.2885 (Rfree = 0.000) for 1895 atoms. Found 26 (26 requested) and removed 31 (14 requested) atoms. Cycle 5: After refmac, R = 0.2390 (Rfree = 0.000) for 1866 atoms. Found 25 (25 requested) and removed 23 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.90 2.82 Search for helices and strands: 0 residues in 0 chains, 1885 seeds are put forward NCS extension: 0 residues added, 1885 seeds are put forward Round 1: 138 peptides, 6 chains. Longest chain 67 peptides. Score 0.717 Round 2: 138 peptides, 5 chains. Longest chain 70 peptides. Score 0.732 Round 3: 139 peptides, 8 chains. Longest chain 59 peptides. Score 0.689 Round 4: 141 peptides, 9 chains. Longest chain 43 peptides. Score 0.679 Round 5: 132 peptides, 6 chains. Longest chain 51 peptides. Score 0.700 Taking the results from Round 2 Chains 5, Residues 133, Estimated correctness of the model 83.4 % 2 chains (111 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 61 A and 64 A 4 chains (135 residues) following loop building 1 chains (113 residues) in sequence following loop building ------------------------------------------------------ 9660 reflections ( 97.23 % complete ) and 2641 restraints for refining 1808 atoms. 1651 conditional restraints added. Observations/parameters ratio is 1.34 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2636 (Rfree = 0.000) for 1808 atoms. Found 23 (23 requested) and removed 35 (13 requested) atoms. Cycle 7: After refmac, R = 0.2484 (Rfree = 0.000) for 1777 atoms. Found 23 (23 requested) and removed 24 (13 requested) atoms. Cycle 8: After refmac, R = 0.2074 (Rfree = 0.000) for 1757 atoms. Found 21 (21 requested) and removed 18 (12 requested) atoms. Cycle 9: After refmac, R = 0.1957 (Rfree = 0.000) for 1749 atoms. Found 12 (21 requested) and removed 14 (12 requested) atoms. Cycle 10: After refmac, R = 0.1890 (Rfree = 0.000) for 1743 atoms. Found 17 (20 requested) and removed 14 (12 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.92 2.84 Search for helices and strands: 0 residues in 0 chains, 1752 seeds are put forward NCS extension: 192 residues added (16 deleted due to clashes), 1944 seeds are put forward Round 1: 142 peptides, 7 chains. Longest chain 82 peptides. Score 0.713 Round 2: 147 peptides, 4 chains. Longest chain 92 peptides. Score 0.769 Round 3: 135 peptides, 7 chains. Longest chain 72 peptides. Score 0.693 Round 4: 139 peptides, 10 chains. Longest chain 57 peptides. Score 0.657 Round 5: 139 peptides, 7 chains. Longest chain 41 peptides. Score 0.705 Taking the results from Round 2 Chains 4, Residues 143, Estimated correctness of the model 87.4 % 2 chains (136 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 47 A and 55 A 3 chains (150 residues) following loop building 1 chains (143 residues) in sequence following loop building ------------------------------------------------------ 9660 reflections ( 97.23 % complete ) and 2009 restraints for refining 1781 atoms. 812 conditional restraints added. Observations/parameters ratio is 1.36 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2475 (Rfree = 0.000) for 1781 atoms. Found 21 (21 requested) and removed 41 (13 requested) atoms. Cycle 12: After refmac, R = 0.2139 (Rfree = 0.000) for 1749 atoms. Found 19 (19 requested) and removed 22 (12 requested) atoms. Cycle 13: After refmac, R = 0.1997 (Rfree = 0.000) for 1740 atoms. Found 19 (19 requested) and removed 17 (12 requested) atoms. Cycle 14: After refmac, R = 0.1941 (Rfree = 0.000) for 1736 atoms. Found 14 (18 requested) and removed 17 (12 requested) atoms. Cycle 15: After refmac, R = 0.2126 (Rfree = 0.000) for 1727 atoms. Found 18 (18 requested) and removed 18 (12 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.88 2.80 Search for helices and strands: 0 residues in 0 chains, 1748 seeds are put forward NCS extension: 0 residues added, 1748 seeds are put forward Round 1: 143 peptides, 2 chains. Longest chain 129 peptides. Score 0.787 Round 2: 135 peptides, 6 chains. Longest chain 62 peptides. Score 0.709 Round 3: 130 peptides, 5 chains. Longest chain 68 peptides. Score 0.710 Round 4: 133 peptides, 9 chains. Longest chain 45 peptides. Score 0.654 Round 5: 137 peptides, 5 chains. Longest chain 85 peptides. Score 0.730 Taking the results from Round 1 Chains 3, Residues 141, Estimated correctness of the model 89.1 % 2 chains (128 residues) have been docked in sequence Building loops using Loopy2018 3 chains (141 residues) following loop building 2 chains (128 residues) in sequence following loop building ------------------------------------------------------ 9660 reflections ( 97.23 % complete ) and 2149 restraints for refining 1751 atoms. 1049 conditional restraints added. Observations/parameters ratio is 1.38 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2357 (Rfree = 0.000) for 1751 atoms. Found 17 (17 requested) and removed 33 (12 requested) atoms. Cycle 17: After refmac, R = 0.2219 (Rfree = 0.000) for 1725 atoms. Found 17 (17 requested) and removed 20 (12 requested) atoms. Cycle 18: After refmac, R = 0.2113 (Rfree = 0.000) for 1714 atoms. Found 16 (16 requested) and removed 23 (12 requested) atoms. Cycle 19: After refmac, R = 0.2074 (Rfree = 0.000) for 1693 atoms. Found 15 (15 requested) and removed 18 (12 requested) atoms. Cycle 20: After refmac, R = 0.2167 (Rfree = 0.000) for 1681 atoms. Found 15 (15 requested) and removed 15 (12 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.91 2.83 Search for helices and strands: 0 residues in 0 chains, 1693 seeds are put forward NCS extension: 99 residues added (3 deleted due to clashes), 1792 seeds are put forward Round 1: 136 peptides, 6 chains. Longest chain 76 peptides. Score 0.712 Round 2: 139 peptides, 5 chains. Longest chain 67 peptides. Score 0.735 Round 3: 130 peptides, 5 chains. Longest chain 65 peptides. Score 0.710 Round 4: 135 peptides, 4 chains. Longest chain 77 peptides. Score 0.739 Round 5: 138 peptides, 6 chains. Longest chain 46 peptides. Score 0.717 Taking the results from Round 4 Chains 5, Residues 131, Estimated correctness of the model 84.2 % 2 chains (102 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 46 A and 55 A 4 chains (139 residues) following loop building 1 chains (110 residues) in sequence following loop building ------------------------------------------------------ 9660 reflections ( 97.23 % complete ) and 2345 restraints for refining 1723 atoms. 1348 conditional restraints added. Observations/parameters ratio is 1.40 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2463 (Rfree = 0.000) for 1723 atoms. Found 15 (15 requested) and removed 35 (12 requested) atoms. Cycle 22: After refmac, R = 0.2041 (Rfree = 0.000) for 1695 atoms. Found 14 (14 requested) and removed 19 (12 requested) atoms. Cycle 23: After refmac, R = 0.1914 (Rfree = 0.000) for 1686 atoms. Found 9 (13 requested) and removed 15 (12 requested) atoms. Cycle 24: After refmac, R = 0.1846 (Rfree = 0.000) for 1677 atoms. Found 11 (13 requested) and removed 12 (12 requested) atoms. Cycle 25: After refmac, R = 0.1805 (Rfree = 0.000) for 1675 atoms. Found 12 (12 requested) and removed 14 (12 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.88 2.80 Search for helices and strands: 0 residues in 0 chains, 1690 seeds are put forward NCS extension: 0 residues added, 1690 seeds are put forward Round 1: 145 peptides, 6 chains. Longest chain 78 peptides. Score 0.736 Round 2: 144 peptides, 7 chains. Longest chain 77 peptides. Score 0.719 Round 3: 139 peptides, 6 chains. Longest chain 55 peptides. Score 0.720 Round 4: 140 peptides, 7 chains. Longest chain 49 peptides. Score 0.708 Round 5: 137 peptides, 7 chains. Longest chain 36 peptides. Score 0.699 Taking the results from Round 1 Chains 8, Residues 139, Estimated correctness of the model 83.9 % 3 chains (120 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 127 A and 134 A 6 chains (142 residues) following loop building 2 chains (126 residues) in sequence following loop building ------------------------------------------------------ 9660 reflections ( 97.23 % complete ) and 2028 restraints for refining 1716 atoms. 935 conditional restraints added. Observations/parameters ratio is 1.41 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2052 (Rfree = 0.000) for 1716 atoms. Found 12 (12 requested) and removed 30 (12 requested) atoms. Cycle 27: After refmac, R = 0.2161 (Rfree = 0.000) for 1694 atoms. Found 12 (12 requested) and removed 19 (12 requested) atoms. Cycle 28: After refmac, R = 0.2231 (Rfree = 0.000) for 1685 atoms. Found 12 (12 requested) and removed 17 (12 requested) atoms. Cycle 29: After refmac, R = 0.1848 (Rfree = 0.000) for 1672 atoms. Found 12 (12 requested) and removed 12 (12 requested) atoms. Cycle 30: After refmac, R = 0.1783 (Rfree = 0.000) for 1668 atoms. Found 12 (12 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.87 2.79 Search for helices and strands: 0 residues in 0 chains, 1682 seeds are put forward NCS extension: 0 residues added, 1682 seeds are put forward Round 1: 138 peptides, 4 chains. Longest chain 68 peptides. Score 0.747 Round 2: 140 peptides, 8 chains. Longest chain 65 peptides. Score 0.692 Round 3: 145 peptides, 3 chains. Longest chain 105 peptides. Score 0.778 Round 4: 141 peptides, 7 chains. Longest chain 72 peptides. Score 0.710 Round 5: 141 peptides, 7 chains. Longest chain 52 peptides. Score 0.710 Taking the results from Round 3 Chains 3, Residues 142, Estimated correctness of the model 88.3 % 2 chains (129 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 42 A and 45 A 2 chains (144 residues) following loop building 1 chains (131 residues) in sequence following loop building ------------------------------------------------------ 9660 reflections ( 97.23 % complete ) and 2013 restraints for refining 1701 atoms. 902 conditional restraints added. Observations/parameters ratio is 1.42 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2263 (Rfree = 0.000) for 1701 atoms. Found 12 (12 requested) and removed 22 (12 requested) atoms. Cycle 32: After refmac, R = 0.2218 (Rfree = 0.000) for 1680 atoms. Found 12 (12 requested) and removed 20 (12 requested) atoms. Cycle 33: After refmac, R = 0.1882 (Rfree = 0.000) for 1670 atoms. Found 12 (12 requested) and removed 13 (12 requested) atoms. Cycle 34: After refmac, R = 0.1792 (Rfree = 0.000) for 1666 atoms. Found 12 (12 requested) and removed 12 (12 requested) atoms. Cycle 35: After refmac, R = 0.1751 (Rfree = 0.000) for 1661 atoms. Found 12 (12 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.89 2.81 Search for helices and strands: 0 residues in 0 chains, 1668 seeds are put forward NCS extension: 0 residues added, 1668 seeds are put forward Round 1: 144 peptides, 5 chains. Longest chain 70 peptides. Score 0.748 Round 2: 138 peptides, 5 chains. Longest chain 61 peptides. Score 0.732 Round 3: 145 peptides, 4 chains. Longest chain 96 peptides. Score 0.765 Round 4: 137 peptides, 10 chains. Longest chain 54 peptides. Score 0.650 Round 5: 139 peptides, 8 chains. Longest chain 34 peptides. Score 0.689 Taking the results from Round 3 Chains 4, Residues 141, Estimated correctness of the model 87.0 % 2 chains (116 residues) have been docked in sequence Building loops using Loopy2018 4 chains (141 residues) following loop building 2 chains (116 residues) in sequence following loop building ------------------------------------------------------ 9660 reflections ( 97.23 % complete ) and 2115 restraints for refining 1685 atoms. 1074 conditional restraints added. Observations/parameters ratio is 1.43 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2379 (Rfree = 0.000) for 1685 atoms. Found 12 (12 requested) and removed 28 (12 requested) atoms. Cycle 37: After refmac, R = 0.2138 (Rfree = 0.000) for 1666 atoms. Found 12 (12 requested) and removed 18 (12 requested) atoms. Cycle 38: After refmac, R = 0.1810 (Rfree = 0.000) for 1653 atoms. Found 12 (12 requested) and removed 14 (12 requested) atoms. Cycle 39: After refmac, R = 0.1712 (Rfree = 0.000) for 1650 atoms. Found 11 (11 requested) and removed 13 (11 requested) atoms. Cycle 40: After refmac, R = 0.1971 (Rfree = 0.000) for 1647 atoms. Found 11 (11 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.90 2.82 Search for helices and strands: 0 residues in 0 chains, 1656 seeds are put forward NCS extension: 0 residues added, 1656 seeds are put forward Round 1: 141 peptides, 5 chains. Longest chain 88 peptides. Score 0.740 Round 2: 140 peptides, 7 chains. Longest chain 67 peptides. Score 0.708 Round 3: 146 peptides, 5 chains. Longest chain 51 peptides. Score 0.753 Round 4: 143 peptides, 5 chains. Longest chain 80 peptides. Score 0.746 Round 5: 138 peptides, 6 chains. Longest chain 70 peptides. Score 0.717 Taking the results from Round 3 Chains 5, Residues 141, Estimated correctness of the model 85.7 % 4 chains (137 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 49 A and 52 A Built loop between residues 101 A and 104 A Built loop between residues 120 A and 127 A 2 chains (148 residues) following loop building 1 chains (147 residues) in sequence following loop building ------------------------------------------------------ 9660 reflections ( 97.23 % complete ) and 1845 restraints for refining 1718 atoms. 637 conditional restraints added. Observations/parameters ratio is 1.41 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2279 (Rfree = 0.000) for 1718 atoms. Found 12 (12 requested) and removed 25 (12 requested) atoms. Cycle 42: After refmac, R = 0.2078 (Rfree = 0.000) for 1698 atoms. Found 12 (12 requested) and removed 14 (12 requested) atoms. Cycle 43: After refmac, R = 0.1928 (Rfree = 0.000) for 1689 atoms. Found 12 (12 requested) and removed 14 (12 requested) atoms. Cycle 44: After refmac, R = 0.1927 (Rfree = 0.000) for 1683 atoms. Found 12 (12 requested) and removed 14 (12 requested) atoms. Cycle 45: After refmac, R = 0.1917 (Rfree = 0.000) for 1676 atoms. Found 12 (12 requested) and removed 14 (12 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.89 2.81 Search for helices and strands: 0 residues in 0 chains, 1689 seeds are put forward NCS extension: 0 residues added, 1689 seeds are put forward Round 1: 140 peptides, 6 chains. Longest chain 81 peptides. Score 0.723 Round 2: 141 peptides, 6 chains. Longest chain 57 peptides. Score 0.726 Round 3: 144 peptides, 4 chains. Longest chain 65 peptides. Score 0.762 Round 4: 135 peptides, 8 chains. Longest chain 44 peptides. Score 0.677 Round 5: 136 peptides, 6 chains. Longest chain 49 peptides. Score 0.712 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 5, Residues 140, Estimated correctness of the model 86.7 % 3 chains (126 residues) have been docked in sequence Sequence coverage is 89 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 119 A and 128 A 3 chains (143 residues) following loop building 2 chains (134 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 9660 reflections ( 97.23 % complete ) and 1124 restraints for refining 1104 atoms. Observations/parameters ratio is 2.19 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3349 (Rfree = 0.000) for 1104 atoms. Found 8 (8 requested) and removed 0 (8 requested) atoms. Cycle 47: After refmac, R = 0.3137 (Rfree = 0.000) for 1104 atoms. Found 8 (8 requested) and removed 1 (8 requested) atoms. Cycle 48: After refmac, R = 0.3002 (Rfree = 0.000) for 1104 atoms. Found 8 (8 requested) and removed 5 (8 requested) atoms. Cycle 49: After refmac, R = 0.2945 (Rfree = 0.000) for 1104 atoms. TimeTaking 54.95