Mon 24 Dec 00:46:45 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 2ich-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2ich-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2ich-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ich-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/2ich-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ich-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 00:46:50 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/2ich-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ich-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 549 and 0 Target number of residues in the AU: 549 Target solvent content: 0.5964 Checking the provided sequence file Detected sequence length: 335 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 670 Adjusted target solvent content: 0.51 Input MTZ file: 2ich-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: 19 Cell parameters: 63.275 95.573 121.745 90.000 90.000 90.000 Input sequence file: 2ich-3.2-parrot-mrncs.fasta_lf Building free atoms model in initial map for 5360 target number of atoms Had to go as low as 0.65 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: 29.160 3.200 Wilson plot Bfac: 51.15 Failed to save intermediate PDB 12684 reflections ( 99.73 % complete ) and 0 restraints for refining 5967 atoms. Observations/parameters ratio is 0.53 ------------------------------------------------------ Starting model: R = 0.3002 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2666 (Rfree = 0.000) for 5967 atoms. Found 48 (53 requested) and removed 59 (26 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.96 2.92 Search for helices and strands: 0 residues in 0 chains, 6021 seeds are put forward NCS extension: 0 residues added, 6021 seeds are put forward Round 1: 397 peptides, 61 chains. Longest chain 13 peptides. Score 0.510 Round 2: 458 peptides, 52 chains. Longest chain 20 peptides. Score 0.673 Round 3: 482 peptides, 48 chains. Longest chain 27 peptides. Score 0.726 Round 4: 502 peptides, 42 chains. Longest chain 51 peptides. Score 0.778 Round 5: 520 peptides, 44 chains. Longest chain 46 peptides. Score 0.786 Taking the results from Round 5 Chains 52, Residues 476, Estimated correctness of the model 81.2 % 11 chains (185 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 109 A and 120 A 50 chains (477 residues) following loop building 10 chains (195 residues) in sequence following loop building ------------------------------------------------------ 12684 reflections ( 99.73 % complete ) and 8125 restraints for refining 4893 atoms. 5534 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2925 (Rfree = 0.000) for 4893 atoms. Found 43 (43 requested) and removed 86 (21 requested) atoms. Cycle 2: After refmac, R = 0.2643 (Rfree = 0.000) for 4812 atoms. Found 31 (42 requested) and removed 40 (21 requested) atoms. Cycle 3: After refmac, R = 0.2494 (Rfree = 0.000) for 4781 atoms. Found 23 (41 requested) and removed 26 (21 requested) atoms. Cycle 4: After refmac, R = 0.2403 (Rfree = 0.000) for 4767 atoms. Found 13 (39 requested) and removed 23 (21 requested) atoms. Cycle 5: After refmac, R = 0.2347 (Rfree = 0.000) for 4747 atoms. Found 13 (39 requested) and removed 22 (21 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.98 2.94 Search for helices and strands: 0 residues in 0 chains, 4835 seeds are put forward NCS extension: 55 residues added (13 deleted due to clashes), 4890 seeds are put forward Round 1: 481 peptides, 46 chains. Longest chain 27 peptides. Score 0.736 Round 2: 514 peptides, 44 chains. Longest chain 38 peptides. Score 0.780 Round 3: 517 peptides, 40 chains. Longest chain 51 peptides. Score 0.801 Round 4: 516 peptides, 44 chains. Longest chain 39 peptides. Score 0.782 Round 5: 517 peptides, 49 chains. Longest chain 38 peptides. Score 0.759 Taking the results from Round 3 Chains 45, Residues 477, Estimated correctness of the model 83.6 % 12 chains (205 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 147 B and 154 B 43 chains (478 residues) following loop building 11 chains (211 residues) in sequence following loop building ------------------------------------------------------ 12684 reflections ( 99.73 % complete ) and 8140 restraints for refining 4893 atoms. 5387 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2667 (Rfree = 0.000) for 4893 atoms. Found 39 (39 requested) and removed 50 (21 requested) atoms. Cycle 7: After refmac, R = 0.2485 (Rfree = 0.000) for 4856 atoms. Found 19 (38 requested) and removed 30 (21 requested) atoms. Cycle 8: After refmac, R = 0.2367 (Rfree = 0.000) for 4837 atoms. Found 5 (37 requested) and removed 25 (21 requested) atoms. Cycle 9: After refmac, R = 0.2341 (Rfree = 0.000) for 4813 atoms. Found 12 (36 requested) and removed 21 (21 requested) atoms. Cycle 10: After refmac, R = 0.2274 (Rfree = 0.000) for 4798 atoms. Found 5 (35 requested) and removed 23 (21 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.97 2.93 Search for helices and strands: 0 residues in 0 chains, 4879 seeds are put forward NCS extension: 40 residues added (23 deleted due to clashes), 4919 seeds are put forward Round 1: 472 peptides, 46 chains. Longest chain 29 peptides. Score 0.726 Round 2: 506 peptides, 40 chains. Longest chain 37 peptides. Score 0.791 Round 3: 506 peptides, 45 chains. Longest chain 25 peptides. Score 0.768 Round 4: 519 peptides, 38 chains. Longest chain 37 peptides. Score 0.811 Round 5: 522 peptides, 40 chains. Longest chain 30 peptides. Score 0.805 Taking the results from Round 4 Chains 47, Residues 481, Estimated correctness of the model 85.1 % 15 chains (268 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 90 A and 97 A Built loop between residues 37 B and 41 B Built loop between residues 81 B and 85 B Built loop between residues 102 B and 113 B Built loop between residues 129 B and 133 B 38 chains (494 residues) following loop building 10 chains (293 residues) in sequence following loop building ------------------------------------------------------ 12684 reflections ( 99.73 % complete ) and 7191 restraints for refining 4893 atoms. 4024 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2748 (Rfree = 0.000) for 4893 atoms. Found 34 (34 requested) and removed 60 (21 requested) atoms. Cycle 12: After refmac, R = 0.2472 (Rfree = 0.000) for 4839 atoms. Found 29 (34 requested) and removed 31 (21 requested) atoms. Failed to save intermediate PDB Cycle 13: After refmac, R = 0.2346 (Rfree = 0.000) for 4827 atoms. Found 9 (33 requested) and removed 28 (21 requested) atoms. Cycle 14: After refmac, R = 0.2282 (Rfree = 0.000) for 4803 atoms. Found 9 (32 requested) and removed 21 (21 requested) atoms. Cycle 15: After refmac, R = 0.2243 (Rfree = 0.000) for 4790 atoms. Found 9 (30 requested) and removed 22 (21 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.96 2.92 Search for helices and strands: 0 residues in 0 chains, 4880 seeds are put forward NCS extension: 23 residues added (26 deleted due to clashes), 4903 seeds are put forward Round 1: 471 peptides, 52 chains. Longest chain 29 peptides. Score 0.690 Round 2: 500 peptides, 44 chains. Longest chain 29 peptides. Score 0.767 Round 3: 506 peptides, 43 chains. Longest chain 39 peptides. Score 0.777 Round 4: 502 peptides, 46 chains. Longest chain 38 peptides. Score 0.759 Round 5: 510 peptides, 45 chains. Longest chain 42 peptides. Score 0.772 Taking the results from Round 3 Chains 48, Residues 463, Estimated correctness of the model 79.8 % 14 chains (249 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 37 A and 41 A Built loop between residues 178 A and 181 A 44 chains (466 residues) following loop building 12 chains (254 residues) in sequence following loop building ------------------------------------------------------ 12684 reflections ( 99.73 % complete ) and 7711 restraints for refining 4894 atoms. 4795 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2653 (Rfree = 0.000) for 4894 atoms. Found 30 (30 requested) and removed 62 (21 requested) atoms. Cycle 17: After refmac, R = 0.2462 (Rfree = 0.000) for 4850 atoms. Found 29 (29 requested) and removed 23 (21 requested) atoms. Cycle 18: After refmac, R = 0.2344 (Rfree = 0.000) for 4851 atoms. Found 15 (28 requested) and removed 26 (21 requested) atoms. Cycle 19: After refmac, R = 0.2291 (Rfree = 0.000) for 4833 atoms. Found 11 (28 requested) and removed 22 (21 requested) atoms. Cycle 20: After refmac, R = 0.2249 (Rfree = 0.000) for 4818 atoms. Found 9 (27 requested) and removed 22 (21 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.01 2.97 Search for helices and strands: 0 residues in 0 chains, 4898 seeds are put forward NCS extension: 57 residues added (12 deleted due to clashes), 4955 seeds are put forward Round 1: 466 peptides, 52 chains. Longest chain 37 peptides. Score 0.684 Round 2: 506 peptides, 43 chains. Longest chain 39 peptides. Score 0.777 Round 3: 498 peptides, 47 chains. Longest chain 39 peptides. Score 0.750 Round 4: 504 peptides, 42 chains. Longest chain 32 peptides. Score 0.780 Round 5: 491 peptides, 44 chains. Longest chain 39 peptides. Score 0.757 Taking the results from Round 4 Chains 44, Residues 462, Estimated correctness of the model 80.3 % 11 chains (192 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 307 B and 317 B 43 chains (466 residues) following loop building 10 chains (201 residues) in sequence following loop building ------------------------------------------------------ 12684 reflections ( 99.73 % complete ) and 8254 restraints for refining 4893 atoms. 5574 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2638 (Rfree = 0.000) for 4893 atoms. Found 26 (26 requested) and removed 55 (21 requested) atoms. Cycle 22: After refmac, R = 0.2372 (Rfree = 0.000) for 4853 atoms. Found 19 (25 requested) and removed 28 (21 requested) atoms. Cycle 23: After refmac, R = 0.2259 (Rfree = 0.000) for 4835 atoms. Found 7 (24 requested) and removed 23 (21 requested) atoms. Cycle 24: After refmac, R = 0.2192 (Rfree = 0.000) for 4810 atoms. Found 7 (23 requested) and removed 23 (21 requested) atoms. Cycle 25: After refmac, R = 0.2138 (Rfree = 0.000) for 4793 atoms. Found 8 (22 requested) and removed 21 (21 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.99 2.95 Search for helices and strands: 0 residues in 0 chains, 4874 seeds are put forward NCS extension: 29 residues added (5 deleted due to clashes), 4903 seeds are put forward Round 1: 438 peptides, 50 chains. Longest chain 39 peptides. Score 0.658 Round 2: 485 peptides, 43 chains. Longest chain 37 peptides. Score 0.756 Round 3: 477 peptides, 44 chains. Longest chain 39 peptides. Score 0.742 Round 4: 474 peptides, 40 chains. Longest chain 39 peptides. Score 0.760 Round 5: 474 peptides, 45 chains. Longest chain 42 peptides. Score 0.734 Taking the results from Round 4 Chains 51, Residues 434, Estimated correctness of the model 76.9 % 15 chains (203 residues) have been docked in sequence Building loops using Loopy2018 51 chains (434 residues) following loop building 15 chains (203 residues) in sequence following loop building ------------------------------------------------------ 12684 reflections ( 99.73 % complete ) and 8310 restraints for refining 4893 atoms. 5751 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2560 (Rfree = 0.000) for 4893 atoms. Found 21 (21 requested) and removed 51 (21 requested) atoms. Cycle 27: After refmac, R = 0.2347 (Rfree = 0.000) for 4850 atoms. Found 19 (21 requested) and removed 25 (21 requested) atoms. Cycle 28: After refmac, R = 0.2297 (Rfree = 0.000) for 4840 atoms. Found 10 (21 requested) and removed 22 (21 requested) atoms. Cycle 29: After refmac, R = 0.2228 (Rfree = 0.000) for 4824 atoms. Found 6 (21 requested) and removed 22 (21 requested) atoms. Cycle 30: After refmac, R = 0.2185 (Rfree = 0.000) for 4801 atoms. Found 7 (21 requested) and removed 21 (21 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.00 2.96 Search for helices and strands: 0 residues in 0 chains, 4870 seeds are put forward NCS extension: 65 residues added (5 deleted due to clashes), 4935 seeds are put forward Round 1: 454 peptides, 50 chains. Longest chain 25 peptides. Score 0.680 Round 2: 486 peptides, 44 chains. Longest chain 39 peptides. Score 0.752 Round 3: 485 peptides, 48 chains. Longest chain 29 peptides. Score 0.730 Round 4: 482 peptides, 41 chains. Longest chain 44 peptides. Score 0.763 Round 5: 473 peptides, 44 chains. Longest chain 38 peptides. Score 0.738 Taking the results from Round 4 Chains 49, Residues 441, Estimated correctness of the model 77.4 % 9 chains (147 residues) have been docked in sequence Building loops using Loopy2018 49 chains (441 residues) following loop building 9 chains (147 residues) in sequence following loop building ------------------------------------------------------ 12684 reflections ( 99.73 % complete ) and 8917 restraints for refining 4894 atoms. 6586 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2607 (Rfree = 0.000) for 4894 atoms. Found 21 (21 requested) and removed 46 (21 requested) atoms. Cycle 32: After refmac, R = 0.2405 (Rfree = 0.000) for 4857 atoms. Found 16 (21 requested) and removed 25 (21 requested) atoms. Cycle 33: After refmac, R = 0.2319 (Rfree = 0.000) for 4839 atoms. Found 9 (21 requested) and removed 23 (21 requested) atoms. Cycle 34: After refmac, R = 0.2362 (Rfree = 0.000) for 4821 atoms. Found 12 (21 requested) and removed 23 (21 requested) atoms. Cycle 35: After refmac, R = 0.2264 (Rfree = 0.000) for 4802 atoms. Found 13 (21 requested) and removed 23 (21 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.01 2.97 Search for helices and strands: 0 residues in 0 chains, 4881 seeds are put forward NCS extension: 11 residues added (6 deleted due to clashes), 4892 seeds are put forward Round 1: 426 peptides, 51 chains. Longest chain 26 peptides. Score 0.634 Round 2: 474 peptides, 45 chains. Longest chain 39 peptides. Score 0.734 Round 3: 468 peptides, 46 chains. Longest chain 32 peptides. Score 0.721 Round 4: 459 peptides, 48 chains. Longest chain 32 peptides. Score 0.699 Round 5: 465 peptides, 44 chains. Longest chain 31 peptides. Score 0.729 Taking the results from Round 2 Chains 53, Residues 429, Estimated correctness of the model 72.1 % 11 chains (161 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 24 A and 32 A 50 chains (427 residues) following loop building 10 chains (168 residues) in sequence following loop building ------------------------------------------------------ 12684 reflections ( 99.73 % complete ) and 8672 restraints for refining 4894 atoms. 6366 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2561 (Rfree = 0.000) for 4894 atoms. Found 21 (21 requested) and removed 47 (21 requested) atoms. Cycle 37: After refmac, R = 0.2363 (Rfree = 0.000) for 4856 atoms. Found 21 (21 requested) and removed 29 (21 requested) atoms. Cycle 38: After refmac, R = 0.2279 (Rfree = 0.000) for 4839 atoms. Found 19 (21 requested) and removed 24 (21 requested) atoms. Cycle 39: After refmac, R = 0.2225 (Rfree = 0.000) for 4830 atoms. Found 14 (21 requested) and removed 23 (21 requested) atoms. Cycle 40: After refmac, R = 0.2178 (Rfree = 0.000) for 4818 atoms. Found 5 (21 requested) and removed 23 (21 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.02 2.98 Search for helices and strands: 0 residues in 0 chains, 4886 seeds are put forward NCS extension: 20 residues added (3 deleted due to clashes), 4906 seeds are put forward Round 1: 405 peptides, 49 chains. Longest chain 26 peptides. Score 0.616 Round 2: 458 peptides, 45 chains. Longest chain 54 peptides. Score 0.715 Round 3: 444 peptides, 53 chains. Longest chain 27 peptides. Score 0.647 Round 4: 455 peptides, 47 chains. Longest chain 43 peptides. Score 0.699 Round 5: 457 peptides, 47 chains. Longest chain 38 peptides. Score 0.702 Taking the results from Round 2 Chains 48, Residues 413, Estimated correctness of the model 68.3 % 10 chains (179 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 37 A and 41 A 47 chains (412 residues) following loop building 9 chains (182 residues) in sequence following loop building ------------------------------------------------------ 12684 reflections ( 99.73 % complete ) and 8647 restraints for refining 4894 atoms. 6317 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2436 (Rfree = 0.000) for 4894 atoms. Found 21 (21 requested) and removed 53 (21 requested) atoms. Cycle 42: After refmac, R = 0.2248 (Rfree = 0.000) for 4854 atoms. Found 21 (21 requested) and removed 23 (21 requested) atoms. Cycle 43: After refmac, R = 0.2164 (Rfree = 0.000) for 4845 atoms. Found 15 (21 requested) and removed 22 (21 requested) atoms. Cycle 44: After refmac, R = 0.2093 (Rfree = 0.000) for 4835 atoms. Found 8 (21 requested) and removed 24 (21 requested) atoms. Cycle 45: After refmac, R = 0.2084 (Rfree = 0.000) for 4817 atoms. Found 17 (21 requested) and removed 21 (21 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.00 2.96 Search for helices and strands: 0 residues in 0 chains, 4893 seeds are put forward NCS extension: 42 residues added (8 deleted due to clashes), 4935 seeds are put forward Round 1: 387 peptides, 52 chains. Longest chain 29 peptides. Score 0.564 Round 2: 425 peptides, 45 chains. Longest chain 27 peptides. Score 0.672 Round 3: 438 peptides, 50 chains. Longest chain 27 peptides. Score 0.658 Round 4: 426 peptides, 44 chains. Longest chain 30 peptides. Score 0.680 Round 5: 415 peptides, 48 chains. Longest chain 26 peptides. Score 0.638 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 50, Residues 382, Estimated correctness of the model 60.8 % 11 chains (162 residues) have been docked in sequence Sequence coverage is 42 % Consider running further cycles of model building using 2ich-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 9 A and 20 A Built loop between residues 137 A and 151 A Built loop between residues 298 B and 312 B 45 chains (404 residues) following loop building 8 chains (198 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 12684 reflections ( 99.73 % complete ) and 8477 restraints for refining 4893 atoms. 6193 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2629 (Rfree = 0.000) for 4893 atoms. Found 0 (21 requested) and removed 20 (21 requested) atoms. Cycle 47: After refmac, R = 0.2522 (Rfree = 0.000) for 4858 atoms. Found 0 (21 requested) and removed 7 (21 requested) atoms. Failed to save intermediate PDB Cycle 48: After refmac, R = 0.2468 (Rfree = 0.000) for 4847 atoms. Found 0 (21 requested) and removed 6 (21 requested) atoms. Cycle 49: After refmac, R = 0.2440 (Rfree = 0.000) for 4837 atoms. TimeTaking 65.4