Mon 24 Dec 00:39:44 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 1vkn-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vkn-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vkn-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkn-3.2-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/1vkn-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkn-3.2-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 00:39:49 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/1vkn-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkn-3.2-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 1034 and 0 Target number of residues in the AU: 1034 Target solvent content: 0.6187 Checking the provided sequence file Detected sequence length: 351 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1404 Adjusted target solvent content: 0.48 Input MTZ file: 1vkn-3.2-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: 4 Cell parameters: 85.135 92.128 101.299 90.000 112.538 90.000 Input sequence file: 1vkn-3.2-parrot-mrncs.fasta_lf Building free atoms model in initial map for 11232 target number of atoms Had to go as low as 0.70 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: 93.562 3.200 Wilson plot Bfac: 60.76 23822 reflections ( 98.91 % complete ) and 0 restraints for refining 12541 atoms. Observations/parameters ratio is 0.47 ------------------------------------------------------ Starting model: R = 0.2964 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2260 (Rfree = 0.000) for 12541 atoms. Found 112 (112 requested) and removed 104 (56 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.14 3.22 Search for helices and strands: 0 residues in 0 chains, 12772 seeds are put forward NCS extension: 0 residues added, 12772 seeds are put forward Round 1: 747 peptides, 117 chains. Longest chain 16 peptides. Score 0.487 Round 2: 845 peptides, 107 chains. Longest chain 27 peptides. Score 0.612 Round 3: 923 peptides, 102 chains. Longest chain 33 peptides. Score 0.685 Round 4: 968 peptides, 88 chains. Longest chain 47 peptides. Score 0.751 Round 5: 978 peptides, 92 chains. Longest chain 31 peptides. Score 0.746 Taking the results from Round 4 Chains 93, Residues 880, Estimated correctness of the model 75.2 % 17 chains (303 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 154 B and 159 B 92 chains (884 residues) following loop building 16 chains (307 residues) in sequence following loop building ------------------------------------------------------ 23822 reflections ( 98.91 % complete ) and 18608 restraints for refining 10244 atoms. 13972 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2406 (Rfree = 0.000) for 10244 atoms. Found 92 (92 requested) and removed 104 (46 requested) atoms. Cycle 2: After refmac, R = 0.2204 (Rfree = 0.000) for 10053 atoms. Found 56 (89 requested) and removed 66 (45 requested) atoms. Cycle 3: After refmac, R = 0.2093 (Rfree = 0.000) for 9961 atoms. Found 53 (86 requested) and removed 52 (45 requested) atoms. Cycle 4: After refmac, R = 0.1980 (Rfree = 0.000) for 9920 atoms. Found 26 (84 requested) and removed 48 (44 requested) atoms. Cycle 5: After refmac, R = 0.1962 (Rfree = 0.000) for 9867 atoms. Found 22 (81 requested) and removed 46 (44 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.12 3.20 Search for helices and strands: 0 residues in 0 chains, 10164 seeds are put forward NCS extension: 29 residues added (10 deleted due to clashes), 10193 seeds are put forward Round 1: 867 peptides, 109 chains. Longest chain 24 peptides. Score 0.622 Round 2: 958 peptides, 90 chains. Longest chain 40 peptides. Score 0.740 Round 3: 955 peptides, 87 chains. Longest chain 51 peptides. Score 0.747 Round 4: 964 peptides, 82 chains. Longest chain 42 peptides. Score 0.764 Round 5: 965 peptides, 82 chains. Longest chain 51 peptides. Score 0.765 Taking the results from Round 5 Chains 92, Residues 883, Estimated correctness of the model 77.7 % 17 chains (314 residues) have been docked in sequence Building loops using Loopy2018 92 chains (883 residues) following loop building 17 chains (314 residues) in sequence following loop building ------------------------------------------------------ 23822 reflections ( 98.91 % complete ) and 19053 restraints for refining 10252 atoms. 14372 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2366 (Rfree = 0.000) for 10252 atoms. Found 76 (83 requested) and removed 97 (46 requested) atoms. Cycle 7: After refmac, R = 0.2095 (Rfree = 0.000) for 10164 atoms. Found 50 (80 requested) and removed 59 (45 requested) atoms. Cycle 8: After refmac, R = 0.1966 (Rfree = 0.000) for 10125 atoms. Found 24 (78 requested) and removed 47 (45 requested) atoms. Cycle 9: After refmac, R = 0.1932 (Rfree = 0.000) for 10089 atoms. Found 34 (76 requested) and removed 46 (45 requested) atoms. Cycle 10: After refmac, R = 0.1880 (Rfree = 0.000) for 10058 atoms. Found 29 (74 requested) and removed 45 (45 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.14 3.22 Search for helices and strands: 0 residues in 0 chains, 10336 seeds are put forward NCS extension: 19 residues added (6 deleted due to clashes), 10355 seeds are put forward Round 1: 893 peptides, 101 chains. Longest chain 35 peptides. Score 0.668 Round 2: 950 peptides, 86 chains. Longest chain 47 peptides. Score 0.747 Round 3: 941 peptides, 89 chains. Longest chain 35 peptides. Score 0.733 Round 4: 935 peptides, 85 chains. Longest chain 36 peptides. Score 0.741 Round 5: 948 peptides, 91 chains. Longest chain 49 peptides. Score 0.732 Taking the results from Round 2 Chains 90, Residues 864, Estimated correctness of the model 74.5 % 14 chains (319 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 262 C and 271 C 89 chains (871 residues) following loop building 13 chains (327 residues) in sequence following loop building ------------------------------------------------------ 23822 reflections ( 98.91 % complete ) and 19070 restraints for refining 10252 atoms. 14381 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2206 (Rfree = 0.000) for 10252 atoms. Found 74 (74 requested) and removed 85 (46 requested) atoms. Cycle 12: After refmac, R = 0.1997 (Rfree = 0.000) for 10203 atoms. Found 32 (71 requested) and removed 48 (45 requested) atoms. Cycle 13: After refmac, R = 0.1927 (Rfree = 0.000) for 10165 atoms. Found 21 (69 requested) and removed 45 (45 requested) atoms. Cycle 14: After refmac, R = 0.1896 (Rfree = 0.000) for 10122 atoms. Found 27 (67 requested) and removed 46 (45 requested) atoms. Cycle 15: After refmac, R = 0.1878 (Rfree = 0.000) for 10091 atoms. Found 21 (65 requested) and removed 45 (45 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.16 3.25 Search for helices and strands: 0 residues in 0 chains, 10355 seeds are put forward NCS extension: 45 residues added (43 deleted due to clashes), 10400 seeds are put forward Round 1: 898 peptides, 102 chains. Longest chain 32 peptides. Score 0.668 Round 2: 955 peptides, 87 chains. Longest chain 56 peptides. Score 0.747 Round 3: 921 peptides, 87 chains. Longest chain 40 peptides. Score 0.727 Round 4: 926 peptides, 84 chains. Longest chain 47 peptides. Score 0.739 Round 5: 912 peptides, 88 chains. Longest chain 38 peptides. Score 0.719 Taking the results from Round 2 Chains 99, Residues 868, Estimated correctness of the model 74.5 % 14 chains (270 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 260 B and 271 B 98 chains (873 residues) following loop building 13 chains (280 residues) in sequence following loop building ------------------------------------------------------ 23822 reflections ( 98.91 % complete ) and 19336 restraints for refining 10251 atoms. 14887 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2234 (Rfree = 0.000) for 10251 atoms. Found 64 (64 requested) and removed 91 (46 requested) atoms. Cycle 17: After refmac, R = 0.2045 (Rfree = 0.000) for 10192 atoms. Found 34 (62 requested) and removed 48 (45 requested) atoms. Cycle 18: After refmac, R = 0.1987 (Rfree = 0.000) for 10161 atoms. Found 19 (60 requested) and removed 47 (45 requested) atoms. Cycle 19: After refmac, R = 0.1942 (Rfree = 0.000) for 10115 atoms. Found 19 (58 requested) and removed 45 (45 requested) atoms. Cycle 20: After refmac, R = 0.1909 (Rfree = 0.000) for 10079 atoms. Found 18 (56 requested) and removed 45 (45 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.17 3.26 Search for helices and strands: 0 residues in 0 chains, 10379 seeds are put forward NCS extension: 33 residues added (10 deleted due to clashes), 10412 seeds are put forward Round 1: 807 peptides, 101 chains. Longest chain 29 peptides. Score 0.603 Round 2: 886 peptides, 85 chains. Longest chain 37 peptides. Score 0.712 Round 3: 909 peptides, 83 chains. Longest chain 49 peptides. Score 0.732 Round 4: 898 peptides, 96 chains. Longest chain 38 peptides. Score 0.687 Round 5: 905 peptides, 91 chains. Longest chain 43 peptides. Score 0.706 Taking the results from Round 3 Chains 87, Residues 826, Estimated correctness of the model 71.7 % 12 chains (258 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 26 B and 29 B 85 chains (826 residues) following loop building 11 chains (260 residues) in sequence following loop building ------------------------------------------------------ 23822 reflections ( 98.91 % complete ) and 19858 restraints for refining 10252 atoms. 15569 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2213 (Rfree = 0.000) for 10252 atoms. Found 55 (55 requested) and removed 77 (46 requested) atoms. Cycle 22: After refmac, R = 0.2054 (Rfree = 0.000) for 10203 atoms. Found 33 (53 requested) and removed 49 (45 requested) atoms. Cycle 23: After refmac, R = 0.2003 (Rfree = 0.000) for 10170 atoms. Found 26 (51 requested) and removed 45 (45 requested) atoms. Cycle 24: After refmac, R = 0.1944 (Rfree = 0.000) for 10139 atoms. Found 23 (49 requested) and removed 46 (45 requested) atoms. Cycle 25: After refmac, R = 0.1830 (Rfree = 0.000) for 10101 atoms. Found 27 (47 requested) and removed 46 (45 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.16 3.25 Search for helices and strands: 0 residues in 0 chains, 10355 seeds are put forward NCS extension: 29 residues added (34 deleted due to clashes), 10384 seeds are put forward Round 1: 797 peptides, 103 chains. Longest chain 25 peptides. Score 0.588 Round 2: 867 peptides, 93 chains. Longest chain 24 peptides. Score 0.675 Round 3: 890 peptides, 88 chains. Longest chain 36 peptides. Score 0.706 Round 4: 890 peptides, 90 chains. Longest chain 29 peptides. Score 0.700 Round 5: 841 peptides, 88 chains. Longest chain 38 peptides. Score 0.673 Taking the results from Round 3 Chains 93, Residues 802, Estimated correctness of the model 66.4 % 13 chains (174 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 291 B and 297 B 93 chains (806 residues) following loop building 12 chains (179 residues) in sequence following loop building ------------------------------------------------------ 23822 reflections ( 98.91 % complete ) and 20627 restraints for refining 10253 atoms. 16839 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2076 (Rfree = 0.000) for 10253 atoms. Found 46 (46 requested) and removed 68 (46 requested) atoms. Cycle 27: After refmac, R = 0.1928 (Rfree = 0.000) for 10204 atoms. Found 35 (45 requested) and removed 48 (45 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.1896 (Rfree = 0.000) for 10179 atoms. Found 26 (45 requested) and removed 45 (45 requested) atoms. Cycle 29: After refmac, R = 0.1840 (Rfree = 0.000) for 10154 atoms. Found 19 (45 requested) and removed 45 (45 requested) atoms. Cycle 30: After refmac, R = 0.1845 (Rfree = 0.000) for 10117 atoms. Found 34 (45 requested) and removed 45 (45 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.17 3.26 Search for helices and strands: 0 residues in 0 chains, 10423 seeds are put forward NCS extension: 16 residues added (12 deleted due to clashes), 10439 seeds are put forward Round 1: 784 peptides, 98 chains. Longest chain 31 peptides. Score 0.596 Round 2: 838 peptides, 84 chains. Longest chain 32 peptides. Score 0.684 Round 3: 855 peptides, 85 chains. Longest chain 36 peptides. Score 0.692 Round 4: 870 peptides, 87 chains. Longest chain 43 peptides. Score 0.696 Round 5: 844 peptides, 78 chains. Longest chain 47 peptides. Score 0.707 Taking the results from Round 5 Chains 86, Residues 766, Estimated correctness of the model 66.7 % 13 chains (226 residues) have been docked in sequence Building loops using Loopy2018 86 chains (766 residues) following loop building 13 chains (226 residues) in sequence following loop building ------------------------------------------------------ 23822 reflections ( 98.91 % complete ) and 20481 restraints for refining 10254 atoms. 16594 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2119 (Rfree = 0.000) for 10254 atoms. Found 46 (46 requested) and removed 81 (46 requested) atoms. Failed to save intermediate PDB Cycle 32: After refmac, R = 0.2012 (Rfree = 0.000) for 10190 atoms. Found 34 (45 requested) and removed 50 (45 requested) atoms. Cycle 33: After refmac, R = 0.1958 (Rfree = 0.000) for 10165 atoms. Found 27 (45 requested) and removed 46 (45 requested) atoms. Cycle 34: After refmac, R = 0.1901 (Rfree = 0.000) for 10133 atoms. Found 26 (45 requested) and removed 46 (45 requested) atoms. Cycle 35: After refmac, R = 0.1867 (Rfree = 0.000) for 10109 atoms. Found 22 (45 requested) and removed 45 (45 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.16 3.25 Search for helices and strands: 0 residues in 0 chains, 10382 seeds are put forward NCS extension: 31 residues added (20 deleted due to clashes), 10413 seeds are put forward Round 1: 768 peptides, 104 chains. Longest chain 20 peptides. Score 0.559 Round 2: 819 peptides, 89 chains. Longest chain 27 peptides. Score 0.655 Round 3: 831 peptides, 90 chains. Longest chain 41 peptides. Score 0.660 Round 4: 829 peptides, 92 chains. Longest chain 32 peptides. Score 0.652 Round 5: 841 peptides, 91 chains. Longest chain 32 peptides. Score 0.664 Taking the results from Round 5 Chains 101, Residues 750, Estimated correctness of the model 57.2 % 16 chains (242 residues) have been docked in sequence ------------------------------------------------------ 23822 reflections ( 98.91 % complete ) and 20237 restraints for refining 10254 atoms. 16418 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2148 (Rfree = 0.000) for 10254 atoms. Found 46 (46 requested) and removed 94 (46 requested) atoms. Cycle 37: After refmac, R = 0.2013 (Rfree = 0.000) for 10185 atoms. Found 38 (45 requested) and removed 50 (45 requested) atoms. Failed to save intermediate PDB Cycle 38: After refmac, R = 0.1953 (Rfree = 0.000) for 10165 atoms. Found 42 (45 requested) and removed 48 (45 requested) atoms. Cycle 39: After refmac, R = 0.1899 (Rfree = 0.000) for 10154 atoms. Found 31 (45 requested) and removed 47 (45 requested) atoms. Cycle 40: After refmac, R = 0.1860 (Rfree = 0.000) for 10123 atoms. Found 38 (45 requested) and removed 46 (45 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.16 3.25 Search for helices and strands: 0 residues in 0 chains, 10387 seeds are put forward NCS extension: 20 residues added (5 deleted due to clashes), 10407 seeds are put forward Round 1: 740 peptides, 100 chains. Longest chain 24 peptides. Score 0.550 Round 2: 804 peptides, 89 chains. Longest chain 42 peptides. Score 0.644 Round 3: 789 peptides, 95 chains. Longest chain 30 peptides. Score 0.611 Round 4: 783 peptides, 94 chains. Longest chain 28 peptides. Score 0.610 Round 5: 781 peptides, 93 chains. Longest chain 36 peptides. Score 0.612 Taking the results from Round 2 Chains 96, Residues 715, Estimated correctness of the model 52.4 % 11 chains (195 residues) have been docked in sequence ------------------------------------------------------ 23822 reflections ( 98.91 % complete ) and 20878 restraints for refining 10253 atoms. 17309 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2060 (Rfree = 0.000) for 10253 atoms. Found 46 (46 requested) and removed 71 (46 requested) atoms. Cycle 42: After refmac, R = 0.1951 (Rfree = 0.000) for 10211 atoms. Found 45 (45 requested) and removed 46 (45 requested) atoms. Cycle 43: After refmac, R = 0.1889 (Rfree = 0.000) for 10189 atoms. Found 37 (45 requested) and removed 47 (45 requested) atoms. Cycle 44: After refmac, R = 0.1829 (Rfree = 0.000) for 10173 atoms. Found 36 (45 requested) and removed 48 (45 requested) atoms. Cycle 45: After refmac, R = 0.1805 (Rfree = 0.000) for 10155 atoms. Found 31 (45 requested) and removed 49 (45 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.15 3.24 Search for helices and strands: 0 residues in 0 chains, 10446 seeds are put forward NCS extension: 10 residues added (7 deleted due to clashes), 10456 seeds are put forward Round 1: 703 peptides, 99 chains. Longest chain 39 peptides. Score 0.521 Round 2: 766 peptides, 97 chains. Longest chain 40 peptides. Score 0.584 Round 3: 788 peptides, 93 chains. Longest chain 31 peptides. Score 0.617 Round 4: 757 peptides, 91 chains. Longest chain 39 peptides. Score 0.600 Round 5: 735 peptides, 95 chains. Longest chain 37 peptides. Score 0.566 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 101, Residues 695, Estimated correctness of the model 45.6 % 13 chains (199 residues) have been docked in sequence Sequence coverage is 28 % Consider running further cycles of model building using 1vkn-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 291 A and 295 A Built loop between residues 305 A and 316 A Built loop between residues 26 B and 30 B 95 chains (705 residues) following loop building 10 chains (215 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 23822 reflections ( 98.91 % complete ) and 20621 restraints for refining 10254 atoms. 17024 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2001 (Rfree = 0.000) for 10254 atoms. Found 0 (46 requested) and removed 25 (46 requested) atoms. Cycle 47: After refmac, R = 0.1940 (Rfree = 0.000) for 10206 atoms. Found 0 (45 requested) and removed 12 (45 requested) atoms. Cycle 48: After refmac, R = 0.1908 (Rfree = 0.000) for 10187 atoms. Found 0 (45 requested) and removed 14 (45 requested) atoms. Cycle 49: After refmac, R = 0.1868 (Rfree = 0.000) for 10165 atoms. TimeTaking 108.2