Sun 23 Dec 22:22:40 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 1vqy-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vqy-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vqy-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vqy-3.2-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/1vqy-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vqy-3.2-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 22:22:49 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/hancs/ArpWArp/wArpResults/WorkingDir/1vqy-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vqy-3.2-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 829 and 0 Target number of residues in the AU: 829 Target solvent content: 0.5420 Checking the provided sequence file Detected sequence length: 116 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 8 Adjusted target number of residues: 928 Adjusted target solvent content: 0.49 Input MTZ file: 1vqy-3.2-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: 19 Cell parameters: 68.026 110.931 129.804 90.000 90.000 90.000 Input sequence file: 1vqy-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 7424 target number of atoms Had to go as low as 0.60 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: 29.074 3.200 Wilson plot Bfac: 33.34 16523 reflections ( 98.25 % complete ) and 0 restraints for refining 8230 atoms. Observations/parameters ratio is 0.50 ------------------------------------------------------ Starting model: R = 0.2784 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2212 (Rfree = 0.000) for 8230 atoms. Found 55 (73 requested) and removed 65 (36 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.68 2.72 Search for helices and strands: 0 residues in 0 chains, 8374 seeds are put forward NCS extension: 0 residues added, 8374 seeds are put forward Round 1: 532 peptides, 79 chains. Longest chain 19 peptides. Score 0.529 Round 2: 625 peptides, 69 chains. Longest chain 22 peptides. Score 0.690 Round 3: 686 peptides, 56 chains. Longest chain 38 peptides. Score 0.791 Round 4: 694 peptides, 59 chains. Longest chain 31 peptides. Score 0.786 Round 5: 703 peptides, 51 chains. Longest chain 39 peptides. Score 0.818 Taking the results from Round 5 Chains 58, Residues 652, Estimated correctness of the model 86.0 % 15 chains (364 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 90 B and 93 B 57 chains (653 residues) following loop building 14 chains (366 residues) in sequence following loop building ------------------------------------------------------ 16523 reflections ( 98.25 % complete ) and 10349 restraints for refining 6779 atoms. 6316 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2652 (Rfree = 0.000) for 6779 atoms. Found 60 (60 requested) and removed 71 (30 requested) atoms. Failed to save intermediate PDB Cycle 2: After refmac, R = 0.2442 (Rfree = 0.000) for 6679 atoms. Found 52 (59 requested) and removed 45 (30 requested) atoms. Cycle 3: After refmac, R = 0.2361 (Rfree = 0.000) for 6649 atoms. Found 28 (58 requested) and removed 36 (30 requested) atoms. Cycle 4: After refmac, R = 0.2188 (Rfree = 0.000) for 6609 atoms. Found 23 (55 requested) and removed 34 (29 requested) atoms. Cycle 5: After refmac, R = 0.2104 (Rfree = 0.000) for 6582 atoms. Found 20 (54 requested) and removed 36 (29 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.67 2.71 Search for helices and strands: 0 residues in 0 chains, 6788 seeds are put forward NCS extension: 19 residues added (21 deleted due to clashes), 6807 seeds are put forward Round 1: 684 peptides, 57 chains. Longest chain 42 peptides. Score 0.786 Round 2: 726 peptides, 50 chains. Longest chain 38 peptides. Score 0.834 Round 3: 722 peptides, 54 chains. Longest chain 51 peptides. Score 0.820 Round 4: 704 peptides, 52 chains. Longest chain 44 peptides. Score 0.815 Round 5: 700 peptides, 65 chains. Longest chain 32 peptides. Score 0.769 Taking the results from Round 2 Chains 63, Residues 676, Estimated correctness of the model 88.2 % 18 chains (410 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 72 A and 81 A Built loop between residues 56 C and 61 C Built loop between residues 46 B and 51 B Built loop between residues 26 H and 29 H Built loop between residues 46 H and 52 H 57 chains (695 residues) following loop building 13 chains (433 residues) in sequence following loop building ------------------------------------------------------ 16523 reflections ( 98.25 % complete ) and 9707 restraints for refining 6777 atoms. 5189 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2477 (Rfree = 0.000) for 6777 atoms. Found 54 (54 requested) and removed 71 (30 requested) atoms. Cycle 7: After refmac, R = 0.2268 (Rfree = 0.000) for 6730 atoms. Found 42 (53 requested) and removed 38 (30 requested) atoms. Cycle 8: After refmac, R = 0.2168 (Rfree = 0.000) for 6720 atoms. Found 21 (52 requested) and removed 31 (30 requested) atoms. Cycle 9: After refmac, R = 0.2112 (Rfree = 0.000) for 6703 atoms. Found 18 (50 requested) and removed 34 (30 requested) atoms. Cycle 10: After refmac, R = 0.2066 (Rfree = 0.000) for 6671 atoms. Found 19 (49 requested) and removed 30 (30 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.73 2.77 Search for helices and strands: 0 residues in 0 chains, 6835 seeds are put forward NCS extension: 14 residues added (29 deleted due to clashes), 6849 seeds are put forward Round 1: 662 peptides, 68 chains. Longest chain 30 peptides. Score 0.728 Round 2: 711 peptides, 57 chains. Longest chain 46 peptides. Score 0.804 Round 3: 704 peptides, 57 chains. Longest chain 33 peptides. Score 0.799 Round 4: 691 peptides, 58 chains. Longest chain 37 peptides. Score 0.787 Round 5: 691 peptides, 56 chains. Longest chain 39 peptides. Score 0.794 Taking the results from Round 2 Chains 64, Residues 654, Estimated correctness of the model 84.0 % 13 chains (258 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 57 C and 61 C 63 chains (657 residues) following loop building 12 chains (261 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 16523 reflections ( 98.25 % complete ) and 11639 restraints for refining 6777 atoms. 8013 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2361 (Rfree = 0.000) for 6777 atoms. Found 48 (48 requested) and removed 54 (30 requested) atoms. Failed to save intermediate PDB Cycle 12: After refmac, R = 0.2126 (Rfree = 0.000) for 6746 atoms. Found 23 (47 requested) and removed 33 (30 requested) atoms. Cycle 13: After refmac, R = 0.2040 (Rfree = 0.000) for 6723 atoms. Found 11 (46 requested) and removed 34 (30 requested) atoms. Cycle 14: After refmac, R = 0.2015 (Rfree = 0.000) for 6692 atoms. Found 8 (44 requested) and removed 31 (30 requested) atoms. Cycle 15: After refmac, R = 0.1988 (Rfree = 0.000) for 6663 atoms. Found 12 (42 requested) and removed 29 (29 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.75 2.79 Search for helices and strands: 0 residues in 0 chains, 6830 seeds are put forward NCS extension: 22 residues added (24 deleted due to clashes), 6852 seeds are put forward Round 1: 659 peptides, 70 chains. Longest chain 31 peptides. Score 0.717 Round 2: 679 peptides, 63 chains. Longest chain 34 peptides. Score 0.761 Round 3: 671 peptides, 56 chains. Longest chain 54 peptides. Score 0.780 Round 4: 670 peptides, 60 chains. Longest chain 36 peptides. Score 0.765 Round 5: 686 peptides, 59 chains. Longest chain 30 peptides. Score 0.780 Taking the results from Round 5 Chains 70, Residues 627, Estimated correctness of the model 80.3 % 14 chains (233 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 25 A and 34 A Built loop between residues 52 C and 60 C Built loop between residues 24 B and 33 B Built loop between residues 45 B and 50 B Built loop between residues 39 D and 48 D 62 chains (649 residues) following loop building 9 chains (268 residues) in sequence following loop building ------------------------------------------------------ 16523 reflections ( 98.25 % complete ) and 11395 restraints for refining 6776 atoms. 7843 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2573 (Rfree = 0.000) for 6776 atoms. Found 42 (42 requested) and removed 61 (30 requested) atoms. Cycle 17: After refmac, R = 0.2341 (Rfree = 0.000) for 6713 atoms. Found 41 (41 requested) and removed 35 (30 requested) atoms. Cycle 18: After refmac, R = 0.2170 (Rfree = 0.000) for 6708 atoms. Found 20 (40 requested) and removed 36 (30 requested) atoms. Cycle 19: After refmac, R = 0.2076 (Rfree = 0.000) for 6678 atoms. Found 22 (38 requested) and removed 31 (30 requested) atoms. Cycle 20: After refmac, R = 0.2032 (Rfree = 0.000) for 6660 atoms. Found 16 (37 requested) and removed 29 (29 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.72 2.76 Search for helices and strands: 0 residues in 0 chains, 6842 seeds are put forward NCS extension: 70 residues added (12 deleted due to clashes), 6912 seeds are put forward Round 1: 603 peptides, 69 chains. Longest chain 25 peptides. Score 0.667 Round 2: 684 peptides, 65 chains. Longest chain 51 peptides. Score 0.757 Round 3: 675 peptides, 67 chains. Longest chain 32 peptides. Score 0.743 Round 4: 671 peptides, 64 chains. Longest chain 38 peptides. Score 0.751 Round 5: 647 peptides, 70 chains. Longest chain 33 peptides. Score 0.706 Taking the results from Round 2 Chains 73, Residues 619, Estimated correctness of the model 76.3 % 14 chains (229 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 76 C and 84 C 72 chains (622 residues) following loop building 13 chains (236 residues) in sequence following loop building ------------------------------------------------------ 16523 reflections ( 98.25 % complete ) and 11625 restraints for refining 6776 atoms. 8244 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2510 (Rfree = 0.000) for 6776 atoms. Found 36 (36 requested) and removed 57 (30 requested) atoms. Cycle 22: After refmac, R = 0.2282 (Rfree = 0.000) for 6727 atoms. Found 31 (35 requested) and removed 33 (30 requested) atoms. Cycle 23: After refmac, R = 0.2179 (Rfree = 0.000) for 6712 atoms. Found 11 (34 requested) and removed 30 (30 requested) atoms. Cycle 24: After refmac, R = 0.2082 (Rfree = 0.000) for 6686 atoms. Found 14 (32 requested) and removed 31 (30 requested) atoms. Cycle 25: After refmac, R = 0.2015 (Rfree = 0.000) for 6661 atoms. Found 11 (31 requested) and removed 29 (29 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.71 2.75 Search for helices and strands: 0 residues in 0 chains, 6807 seeds are put forward NCS extension: 57 residues added (25 deleted due to clashes), 6864 seeds are put forward Round 1: 623 peptides, 73 chains. Longest chain 25 peptides. Score 0.669 Round 2: 652 peptides, 67 chains. Longest chain 28 peptides. Score 0.723 Round 3: 644 peptides, 68 chains. Longest chain 27 peptides. Score 0.712 Round 4: 662 peptides, 59 chains. Longest chain 31 peptides. Score 0.763 Round 5: 664 peptides, 71 chains. Longest chain 21 peptides. Score 0.717 Taking the results from Round 4 Chains 66, Residues 603, Estimated correctness of the model 77.4 % 10 chains (167 residues) have been docked in sequence Building loops using Loopy2018 66 chains (603 residues) following loop building 10 chains (167 residues) in sequence following loop building ------------------------------------------------------ 16523 reflections ( 98.25 % complete ) and 12732 restraints for refining 6777 atoms. 9673 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2441 (Rfree = 0.000) for 6777 atoms. Found 30 (30 requested) and removed 49 (30 requested) atoms. Cycle 27: After refmac, R = 0.2279 (Rfree = 0.000) for 6735 atoms. Found 30 (30 requested) and removed 39 (30 requested) atoms. Cycle 28: After refmac, R = 0.2179 (Rfree = 0.000) for 6717 atoms. Found 22 (30 requested) and removed 31 (30 requested) atoms. Cycle 29: After refmac, R = 0.2099 (Rfree = 0.000) for 6703 atoms. Found 20 (30 requested) and removed 30 (30 requested) atoms. Cycle 30: After refmac, R = 0.2044 (Rfree = 0.000) for 6690 atoms. Found 18 (30 requested) and removed 30 (30 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.69 2.73 Search for helices and strands: 0 residues in 0 chains, 6838 seeds are put forward NCS extension: 17 residues added (10 deleted due to clashes), 6855 seeds are put forward Round 1: 600 peptides, 77 chains. Longest chain 19 peptides. Score 0.625 Round 2: 629 peptides, 62 chains. Longest chain 26 peptides. Score 0.724 Round 3: 645 peptides, 65 chains. Longest chain 32 peptides. Score 0.725 Round 4: 658 peptides, 59 chains. Longest chain 26 peptides. Score 0.760 Round 5: 647 peptides, 65 chains. Longest chain 24 peptides. Score 0.727 Taking the results from Round 4 Chains 71, Residues 599, Estimated correctness of the model 76.9 % 14 chains (214 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 56 B and 62 B 67 chains (600 residues) following loop building 13 chains (219 residues) in sequence following loop building ------------------------------------------------------ 16523 reflections ( 98.25 % complete ) and 11887 restraints for refining 6774 atoms. 8616 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2446 (Rfree = 0.000) for 6774 atoms. Found 30 (30 requested) and removed 57 (30 requested) atoms. Cycle 32: After refmac, R = 0.2322 (Rfree = 0.000) for 6713 atoms. Found 30 (30 requested) and removed 33 (30 requested) atoms. Cycle 33: After refmac, R = 0.2223 (Rfree = 0.000) for 6702 atoms. Found 27 (30 requested) and removed 31 (30 requested) atoms. Cycle 34: After refmac, R = 0.2132 (Rfree = 0.000) for 6688 atoms. Found 28 (30 requested) and removed 31 (30 requested) atoms. Cycle 35: After refmac, R = 0.2060 (Rfree = 0.000) for 6674 atoms. Found 11 (29 requested) and removed 29 (29 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.70 2.74 Search for helices and strands: 0 residues in 0 chains, 6821 seeds are put forward NCS extension: 14 residues added (12 deleted due to clashes), 6835 seeds are put forward Round 1: 566 peptides, 68 chains. Longest chain 22 peptides. Score 0.632 Round 2: 597 peptides, 58 chains. Longest chain 39 peptides. Score 0.712 Round 3: 597 peptides, 64 chains. Longest chain 24 peptides. Score 0.685 Round 4: 621 peptides, 61 chains. Longest chain 39 peptides. Score 0.721 Round 5: 618 peptides, 67 chains. Longest chain 28 peptides. Score 0.692 Taking the results from Round 4 Chains 63, Residues 560, Estimated correctness of the model 69.5 % 7 chains (143 residues) have been docked in sequence Building loops using Loopy2018 63 chains (560 residues) following loop building 7 chains (143 residues) in sequence following loop building ------------------------------------------------------ 16523 reflections ( 98.25 % complete ) and 12996 restraints for refining 6776 atoms. 10225 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2343 (Rfree = 0.000) for 6776 atoms. Found 30 (30 requested) and removed 53 (30 requested) atoms. Cycle 37: After refmac, R = 0.2141 (Rfree = 0.000) for 6738 atoms. Found 30 (30 requested) and removed 35 (30 requested) atoms. Cycle 38: After refmac, R = 0.2048 (Rfree = 0.000) for 6725 atoms. Found 14 (30 requested) and removed 32 (30 requested) atoms. Cycle 39: After refmac, R = 0.2003 (Rfree = 0.000) for 6702 atoms. Found 24 (30 requested) and removed 30 (30 requested) atoms. Cycle 40: After refmac, R = 0.1975 (Rfree = 0.000) for 6689 atoms. Found 19 (30 requested) and removed 32 (30 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.69 2.73 Search for helices and strands: 0 residues in 0 chains, 6847 seeds are put forward NCS extension: 20 residues added (17 deleted due to clashes), 6867 seeds are put forward Round 1: 541 peptides, 72 chains. Longest chain 21 peptides. Score 0.581 Round 2: 589 peptides, 65 chains. Longest chain 34 peptides. Score 0.672 Round 3: 605 peptides, 65 chains. Longest chain 29 peptides. Score 0.688 Round 4: 582 peptides, 69 chains. Longest chain 24 peptides. Score 0.645 Round 5: 586 peptides, 75 chains. Longest chain 30 peptides. Score 0.619 Taking the results from Round 3 Chains 68, Residues 540, Estimated correctness of the model 62.6 % 7 chains (117 residues) have been docked in sequence ------------------------------------------------------ 16523 reflections ( 98.25 % complete ) and 13302 restraints for refining 6777 atoms. 10706 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2485 (Rfree = 0.000) for 6777 atoms. Found 30 (30 requested) and removed 53 (30 requested) atoms. Failed to save intermediate PDB Cycle 42: After refmac, R = 0.2066 (Rfree = 0.000) for 6728 atoms. Found 30 (30 requested) and removed 37 (30 requested) atoms. Cycle 43: After refmac, R = 0.1948 (Rfree = 0.000) for 6716 atoms. Found 28 (30 requested) and removed 36 (30 requested) atoms. Cycle 44: After refmac, R = 0.1888 (Rfree = 0.000) for 6703 atoms. Found 18 (30 requested) and removed 33 (30 requested) atoms. Cycle 45: After refmac, R = 0.1838 (Rfree = 0.000) for 6685 atoms. Found 16 (30 requested) and removed 30 (30 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.69 2.73 Search for helices and strands: 0 residues in 0 chains, 6804 seeds are put forward NCS extension: 14 residues added (9 deleted due to clashes), 6818 seeds are put forward Round 1: 536 peptides, 76 chains. Longest chain 29 peptides. Score 0.552 Round 2: 585 peptides, 66 chains. Longest chain 39 peptides. Score 0.663 Round 3: 597 peptides, 72 chains. Longest chain 29 peptides. Score 0.647 Round 4: 581 peptides, 63 chains. Longest chain 35 peptides. Score 0.673 Round 5: 581 peptides, 66 chains. Longest chain 26 peptides. Score 0.659 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 65, Residues 518, Estimated correctness of the model 59.2 % 2 chains (42 residues) have been docked in sequence Sequence coverage is 8 % Consider running further cycles of model building using 1vqy-3_warpNtrace.pdb as input Building loops using Loopy2018 65 chains (518 residues) following loop building 2 chains (42 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 16523 reflections ( 98.25 % complete ) and 14258 restraints for refining 6776 atoms. 12085 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2091 (Rfree = 0.000) for 6776 atoms. Found 0 (30 requested) and removed 23 (30 requested) atoms. Cycle 47: After refmac, R = 0.1992 (Rfree = 0.000) for 6741 atoms. Found 0 (30 requested) and removed 15 (30 requested) atoms. Cycle 48: After refmac, R = 0.1943 (Rfree = 0.000) for 6723 atoms. Found 0 (30 requested) and removed 3 (30 requested) atoms. Cycle 49: After refmac, R = 0.1909 (Rfree = 0.000) for 6718 atoms. TimeTaking 95