Mon 24 Dec 08:02:28 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2i8d-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2i8d-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2i8d-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2i8d-3.2-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2i8d-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2i8d-3.2-parrot-noncs ############### 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 08:02:33 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/noncs/ArpWArp/wArpResults/WorkingDir/2i8d-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2i8d-3.2-parrot-noncs/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 218 and 0 Target number of residues in the AU: 218 Target solvent content: 0.6100 Checking the provided sequence file Detected sequence length: 123 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 246 Adjusted target solvent content: 0.56 Input MTZ file: 2i8d-3.2-parrot-noncs.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: 19 Cell parameters: 47.981 69.366 90.889 90.000 90.000 90.000 Input sequence file: 2i8d-3.2-parrot-noncs.fasta_lf Building free atoms model in initial map for 1968 target number of atoms Had to go as low as 0.80 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: 55.142 3.200 Wilson plot Bfac: 56.63 5298 reflections ( 99.07 % complete ) and 0 restraints for refining 2175 atoms. Observations/parameters ratio is 0.61 ------------------------------------------------------ Starting model: R = 0.3290 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3194 (Rfree = 0.000) for 2175 atoms. Found 19 (19 requested) and removed 41 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.00 2.77 Search for helices and strands: 0 residues in 0 chains, 2203 seeds are put forward NCS extension: 0 residues added, 2203 seeds are put forward Round 1: 133 peptides, 22 chains. Longest chain 12 peptides. Score 0.430 Round 2: 170 peptides, 26 chains. Longest chain 18 peptides. Score 0.523 Round 3: 180 peptides, 23 chains. Longest chain 32 peptides. Score 0.618 Round 4: 189 peptides, 19 chains. Longest chain 23 peptides. Score 0.711 Round 5: 184 peptides, 17 chains. Longest chain 32 peptides. Score 0.724 Taking the results from Round 5 Chains 17, Residues 167, Estimated correctness of the model 70.1 % 2 chains (48 residues) have been docked in sequence Building loops using Loopy2018 17 chains (167 residues) following loop building 2 chains (48 residues) in sequence following loop building ------------------------------------------------------ 5298 reflections ( 99.07 % complete ) and 3080 restraints for refining 1795 atoms. 2234 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2694 (Rfree = 0.000) for 1795 atoms. Found 12 (16 requested) and removed 14 (8 requested) atoms. Cycle 2: After refmac, R = 0.2542 (Rfree = 0.000) for 1779 atoms. Found 7 (16 requested) and removed 12 (8 requested) atoms. Cycle 3: After refmac, R = 0.2353 (Rfree = 0.000) for 1769 atoms. Found 7 (14 requested) and removed 8 (7 requested) atoms. Cycle 4: After refmac, R = 0.2315 (Rfree = 0.000) for 1765 atoms. Found 5 (14 requested) and removed 7 (7 requested) atoms. Cycle 5: After refmac, R = 0.2299 (Rfree = 0.000) for 1760 atoms. Found 7 (14 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.11 2.87 Search for helices and strands: 0 residues in 0 chains, 1836 seeds are put forward NCS extension: 33 residues added (9 deleted due to clashes), 1869 seeds are put forward Round 1: 166 peptides, 19 chains. Longest chain 23 peptides. Score 0.634 Round 2: 168 peptides, 17 chains. Longest chain 22 peptides. Score 0.674 Round 3: 170 peptides, 18 chains. Longest chain 24 peptides. Score 0.665 Round 4: 163 peptides, 19 chains. Longest chain 22 peptides. Score 0.623 Round 5: 173 peptides, 20 chains. Longest chain 16 peptides. Score 0.643 Taking the results from Round 2 Chains 17, Residues 151, Estimated correctness of the model 59.5 % 1 chains (21 residues) have been docked in sequence ------------------------------------------------------ 5298 reflections ( 99.07 % complete ) and 3544 restraints for refining 1797 atoms. 2860 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2520 (Rfree = 0.000) for 1797 atoms. Found 13 (14 requested) and removed 13 (8 requested) atoms. Cycle 7: After refmac, R = 0.2422 (Rfree = 0.000) for 1792 atoms. Found 8 (14 requested) and removed 9 (8 requested) atoms. Cycle 8: After refmac, R = 0.2365 (Rfree = 0.000) for 1788 atoms. Found 7 (14 requested) and removed 9 (8 requested) atoms. Cycle 9: After refmac, R = 0.2273 (Rfree = 0.000) for 1784 atoms. Found 5 (14 requested) and removed 8 (8 requested) atoms. Cycle 10: After refmac, R = 0.2193 (Rfree = 0.000) for 1780 atoms. Found 8 (13 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.12 2.88 Search for helices and strands: 0 residues in 0 chains, 1851 seeds are put forward NCS extension: 29 residues added (7 deleted due to clashes), 1880 seeds are put forward Round 1: 168 peptides, 18 chains. Longest chain 22 peptides. Score 0.658 Round 2: 177 peptides, 18 chains. Longest chain 22 peptides. Score 0.688 Round 3: 188 peptides, 19 chains. Longest chain 35 peptides. Score 0.708 Round 4: 187 peptides, 19 chains. Longest chain 22 peptides. Score 0.705 Round 5: 186 peptides, 17 chains. Longest chain 22 peptides. Score 0.730 Taking the results from Round 5 Chains 18, Residues 169, Estimated correctness of the model 71.3 % 2 chains (38 residues) have been docked in sequence Building loops using Loopy2018 18 chains (169 residues) following loop building 2 chains (38 residues) in sequence following loop building ------------------------------------------------------ 5298 reflections ( 99.07 % complete ) and 3291 restraints for refining 1796 atoms. 2456 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2656 (Rfree = 0.000) for 1796 atoms. Found 14 (14 requested) and removed 16 (8 requested) atoms. Cycle 12: After refmac, R = 0.2422 (Rfree = 0.000) for 1790 atoms. Found 8 (14 requested) and removed 8 (8 requested) atoms. Cycle 13: After refmac, R = 0.2302 (Rfree = 0.000) for 1784 atoms. Found 6 (14 requested) and removed 8 (8 requested) atoms. Cycle 14: After refmac, R = 0.2239 (Rfree = 0.000) for 1779 atoms. Found 7 (13 requested) and removed 8 (7 requested) atoms. Cycle 15: After refmac, R = 0.2121 (Rfree = 0.000) for 1773 atoms. Found 3 (12 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.07 2.83 Search for helices and strands: 0 residues in 0 chains, 1836 seeds are put forward NCS extension: 20 residues added (5 deleted due to clashes), 1856 seeds are put forward Round 1: 175 peptides, 18 chains. Longest chain 31 peptides. Score 0.681 Round 2: 183 peptides, 15 chains. Longest chain 31 peptides. Score 0.748 Round 3: 188 peptides, 17 chains. Longest chain 39 peptides. Score 0.735 Round 4: 181 peptides, 16 chains. Longest chain 25 peptides. Score 0.729 Round 5: 181 peptides, 19 chains. Longest chain 29 peptides. Score 0.686 Taking the results from Round 2 Chains 16, Residues 168, Estimated correctness of the model 74.7 % 3 chains (66 residues) have been docked in sequence Building loops using Loopy2018 16 chains (168 residues) following loop building 3 chains (66 residues) in sequence following loop building ------------------------------------------------------ 5298 reflections ( 99.07 % complete ) and 3064 restraints for refining 1797 atoms. 2113 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2536 (Rfree = 0.000) for 1797 atoms. Found 11 (13 requested) and removed 19 (8 requested) atoms. Cycle 17: After refmac, R = 0.2380 (Rfree = 0.000) for 1787 atoms. Found 10 (12 requested) and removed 10 (8 requested) atoms. Cycle 18: After refmac, R = 0.2206 (Rfree = 0.000) for 1786 atoms. Found 5 (12 requested) and removed 8 (8 requested) atoms. Cycle 19: After refmac, R = 0.2183 (Rfree = 0.000) for 1783 atoms. Found 6 (12 requested) and removed 8 (8 requested) atoms. Cycle 20: After refmac, R = 0.2167 (Rfree = 0.000) for 1781 atoms. Found 5 (11 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.06 2.82 Search for helices and strands: 0 residues in 0 chains, 1836 seeds are put forward NCS extension: 15 residues added (13 deleted due to clashes), 1851 seeds are put forward Round 1: 158 peptides, 17 chains. Longest chain 21 peptides. Score 0.638 Round 2: 174 peptides, 17 chains. Longest chain 32 peptides. Score 0.693 Round 3: 173 peptides, 18 chains. Longest chain 25 peptides. Score 0.675 Round 4: 174 peptides, 15 chains. Longest chain 35 peptides. Score 0.723 Round 5: 165 peptides, 17 chains. Longest chain 29 peptides. Score 0.663 Taking the results from Round 4 Chains 15, Residues 159, Estimated correctness of the model 69.9 % 3 chains (79 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 68 A and 75 A 14 chains (165 residues) following loop building 2 chains (85 residues) in sequence following loop building ------------------------------------------------------ 5298 reflections ( 99.07 % complete ) and 2938 restraints for refining 1797 atoms. 1914 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2647 (Rfree = 0.000) for 1797 atoms. Found 11 (11 requested) and removed 18 (8 requested) atoms. Cycle 22: After refmac, R = 0.2409 (Rfree = 0.000) for 1789 atoms. Found 6 (11 requested) and removed 10 (8 requested) atoms. Cycle 23: After refmac, R = 0.2327 (Rfree = 0.000) for 1783 atoms. Found 4 (11 requested) and removed 9 (8 requested) atoms. Cycle 24: After refmac, R = 0.2309 (Rfree = 0.000) for 1776 atoms. Found 5 (10 requested) and removed 7 (7 requested) atoms. Cycle 25: After refmac, R = 0.2489 (Rfree = 0.000) for 1771 atoms. Found 9 (9 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.04 2.81 Search for helices and strands: 0 residues in 0 chains, 1837 seeds are put forward NCS extension: 53 residues added (13 deleted due to clashes), 1890 seeds are put forward Round 1: 159 peptides, 17 chains. Longest chain 21 peptides. Score 0.642 Round 2: 173 peptides, 17 chains. Longest chain 28 peptides. Score 0.690 Round 3: 167 peptides, 14 chains. Longest chain 32 peptides. Score 0.716 Round 4: 171 peptides, 16 chains. Longest chain 22 peptides. Score 0.699 Round 5: 174 peptides, 16 chains. Longest chain 24 peptides. Score 0.708 Taking the results from Round 3 Chains 14, Residues 153, Estimated correctness of the model 68.5 % 2 chains (38 residues) have been docked in sequence Building loops using Loopy2018 14 chains (153 residues) following loop building 2 chains (38 residues) in sequence following loop building ------------------------------------------------------ 5298 reflections ( 99.07 % complete ) and 3424 restraints for refining 1797 atoms. 2644 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2580 (Rfree = 0.000) for 1797 atoms. Found 10 (10 requested) and removed 11 (8 requested) atoms. Cycle 27: After refmac, R = 0.2433 (Rfree = 0.000) for 1794 atoms. Found 5 (9 requested) and removed 9 (8 requested) atoms. Cycle 28: After refmac, R = 0.2624 (Rfree = 0.000) for 1790 atoms. Found 9 (9 requested) and removed 10 (8 requested) atoms. Cycle 29: After refmac, R = 0.2611 (Rfree = 0.000) for 1787 atoms. Found 9 (9 requested) and removed 11 (8 requested) atoms. Cycle 30: After refmac, R = 0.2560 (Rfree = 0.000) for 1782 atoms. Found 8 (8 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.06 2.82 Search for helices and strands: 0 residues in 0 chains, 1839 seeds are put forward NCS extension: 33 residues added (2 deleted due to clashes), 1872 seeds are put forward Round 1: 171 peptides, 18 chains. Longest chain 24 peptides. Score 0.668 Round 2: 177 peptides, 13 chains. Longest chain 31 peptides. Score 0.759 Round 3: 179 peptides, 15 chains. Longest chain 28 peptides. Score 0.737 Round 4: 173 peptides, 16 chains. Longest chain 30 peptides. Score 0.705 Round 5: 177 peptides, 17 chains. Longest chain 30 peptides. Score 0.703 Taking the results from Round 2 Chains 14, Residues 164, Estimated correctness of the model 76.7 % 3 chains (70 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 71 A and 82 A 12 chains (170 residues) following loop building 2 chains (80 residues) in sequence following loop building ------------------------------------------------------ 5298 reflections ( 99.07 % complete ) and 2916 restraints for refining 1797 atoms. 1892 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2460 (Rfree = 0.000) for 1797 atoms. Found 8 (8 requested) and removed 19 (8 requested) atoms. Cycle 32: After refmac, R = 0.2368 (Rfree = 0.000) for 1782 atoms. Found 8 (8 requested) and removed 12 (8 requested) atoms. Cycle 33: After refmac, R = 0.2497 (Rfree = 0.000) for 1776 atoms. Found 7 (7 requested) and removed 11 (7 requested) atoms. Cycle 34: After refmac, R = 0.2531 (Rfree = 0.000) for 1772 atoms. Found 7 (7 requested) and removed 11 (7 requested) atoms. Cycle 35: After refmac, R = 0.2371 (Rfree = 0.000) for 1768 atoms. Found 7 (7 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.11 2.87 Search for helices and strands: 0 residues in 0 chains, 1825 seeds are put forward NCS extension: 37 residues added (18 deleted due to clashes), 1862 seeds are put forward Round 1: 166 peptides, 19 chains. Longest chain 15 peptides. Score 0.634 Round 2: 176 peptides, 13 chains. Longest chain 36 peptides. Score 0.756 Round 3: 176 peptides, 16 chains. Longest chain 28 peptides. Score 0.714 Round 4: 173 peptides, 16 chains. Longest chain 21 peptides. Score 0.705 Round 5: 184 peptides, 15 chains. Longest chain 39 peptides. Score 0.751 Taking the results from Round 2 Chains 14, Residues 163, Estimated correctness of the model 76.1 % 3 chains (67 residues) have been docked in sequence Building loops using Loopy2018 14 chains (163 residues) following loop building 3 chains (67 residues) in sequence following loop building ------------------------------------------------------ 5298 reflections ( 99.07 % complete ) and 3031 restraints for refining 1796 atoms. 2095 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2553 (Rfree = 0.000) for 1796 atoms. Found 8 (8 requested) and removed 20 (8 requested) atoms. Cycle 37: After refmac, R = 0.2592 (Rfree = 0.000) for 1777 atoms. Found 8 (8 requested) and removed 12 (8 requested) atoms. Cycle 38: After refmac, R = 0.2665 (Rfree = 0.000) for 1771 atoms. Found 7 (7 requested) and removed 10 (7 requested) atoms. Cycle 39: After refmac, R = 0.2244 (Rfree = 0.000) for 1768 atoms. Found 6 (7 requested) and removed 10 (7 requested) atoms. Cycle 40: After refmac, R = 0.2510 (Rfree = 0.000) for 1762 atoms. Found 7 (7 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.08 2.84 Search for helices and strands: 0 residues in 0 chains, 1817 seeds are put forward NCS extension: 23 residues added (11 deleted due to clashes), 1840 seeds are put forward Round 1: 170 peptides, 16 chains. Longest chain 27 peptides. Score 0.696 Round 2: 178 peptides, 13 chains. Longest chain 29 peptides. Score 0.761 Round 3: 179 peptides, 15 chains. Longest chain 30 peptides. Score 0.737 Round 4: 179 peptides, 14 chains. Longest chain 30 peptides. Score 0.751 Round 5: 172 peptides, 13 chains. Longest chain 28 peptides. Score 0.745 Taking the results from Round 2 Chains 14, Residues 165, Estimated correctness of the model 77.0 % 4 chains (75 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 72 A and 77 A 13 chains (169 residues) following loop building 3 chains (79 residues) in sequence following loop building ------------------------------------------------------ 5298 reflections ( 99.07 % complete ) and 2804 restraints for refining 1797 atoms. 1786 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2546 (Rfree = 0.000) for 1797 atoms. Found 8 (8 requested) and removed 22 (8 requested) atoms. Cycle 42: After refmac, R = 0.2456 (Rfree = 0.000) for 1780 atoms. Found 8 (8 requested) and removed 14 (8 requested) atoms. Cycle 43: After refmac, R = 0.2270 (Rfree = 0.000) for 1770 atoms. Found 4 (7 requested) and removed 10 (7 requested) atoms. Cycle 44: After refmac, R = 0.2225 (Rfree = 0.000) for 1763 atoms. Found 3 (7 requested) and removed 7 (7 requested) atoms. Cycle 45: After refmac, R = 0.2193 (Rfree = 0.000) for 1759 atoms. Found 3 (7 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.09 2.85 Search for helices and strands: 0 residues in 0 chains, 1804 seeds are put forward NCS extension: 54 residues added (17 deleted due to clashes), 1858 seeds are put forward Round 1: 159 peptides, 16 chains. Longest chain 25 peptides. Score 0.659 Round 2: 177 peptides, 14 chains. Longest chain 29 peptides. Score 0.745 Round 3: 180 peptides, 15 chains. Longest chain 24 peptides. Score 0.740 Round 4: 168 peptides, 16 chains. Longest chain 23 peptides. Score 0.689 Round 5: 171 peptides, 16 chains. Longest chain 22 peptides. Score 0.699 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 15, Residues 163, Estimated correctness of the model 74.1 % 3 chains (63 residues) have been docked in sequence Sequence coverage is 38 % Consider running further cycles of model building using 2i8d-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 72 A and 78 A 14 chains (168 residues) following loop building 2 chains (68 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5298 reflections ( 99.07 % complete ) and 2919 restraints for refining 1797 atoms. 1952 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2568 (Rfree = 0.000) for 1797 atoms. Found 0 (8 requested) and removed 3 (8 requested) atoms. Cycle 47: After refmac, R = 0.2474 (Rfree = 0.000) for 1790 atoms. Found 0 (8 requested) and removed 1 (8 requested) atoms. Cycle 48: After refmac, R = 0.2438 (Rfree = 0.000) for 1788 atoms. Found 0 (8 requested) and removed 0 (8 requested) atoms. Cycle 49: After refmac, R = 0.2467 (Rfree = 0.000) for 1788 atoms. TimeTaking 29.35