Mon 24 Dec 07:40:38 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 1vkz-2.9-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vkz-2.9-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vkz-2.9-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkz-2.9-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/1vkz-2.9-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkz-2.9-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 07:40:42 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/1vkz-2.9-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkz-2.9-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 777 and 0 Target number of residues in the AU: 777 Target solvent content: 0.5035 Checking the provided sequence file Detected sequence length: 412 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 824 Adjusted target solvent content: 0.47 Input MTZ file: 1vkz-2.9-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: 4 Cell parameters: 63.745 78.443 85.018 90.000 95.062 90.000 Input sequence file: 1vkz-2.9-parrot-noncs.fasta_lf Building free atoms model in initial map for 6592 target number of atoms Had to go as low as 0.50 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: 19.959 2.900 Wilson plot Bfac: 24.19 17874 reflections ( 95.70 % complete ) and 0 restraints for refining 7279 atoms. Observations/parameters ratio is 0.61 ------------------------------------------------------ Starting model: R = 0.3005 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2292 (Rfree = 0.000) for 7279 atoms. Found 44 (86 requested) and removed 105 (43 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.39 2.49 Search for helices and strands: 0 residues in 0 chains, 7352 seeds are put forward NCS extension: 0 residues added, 7352 seeds are put forward Round 1: 421 peptides, 75 chains. Longest chain 13 peptides. Score 0.413 Round 2: 502 peptides, 75 chains. Longest chain 18 peptides. Score 0.548 Round 3: 551 peptides, 64 chains. Longest chain 23 peptides. Score 0.679 Round 4: 561 peptides, 65 chains. Longest chain 36 peptides. Score 0.685 Round 5: 590 peptides, 64 chains. Longest chain 41 peptides. Score 0.721 Taking the results from Round 5 Chains 70, Residues 526, Estimated correctness of the model 77.6 % 13 chains (164 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 365 A and 371 A 69 chains (531 residues) following loop building 12 chains (169 residues) in sequence following loop building ------------------------------------------------------ 17874 reflections ( 95.70 % complete ) and 10950 restraints for refining 6070 atoms. 8240 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2697 (Rfree = 0.000) for 6070 atoms. Found 72 (72 requested) and removed 63 (36 requested) atoms. Cycle 2: After refmac, R = 0.2518 (Rfree = 0.000) for 6008 atoms. Found 48 (71 requested) and removed 46 (36 requested) atoms. Cycle 3: After refmac, R = 0.2413 (Rfree = 0.000) for 5970 atoms. Found 35 (68 requested) and removed 40 (35 requested) atoms. Cycle 4: After refmac, R = 0.2332 (Rfree = 0.000) for 5939 atoms. Found 42 (66 requested) and removed 39 (35 requested) atoms. Cycle 5: After refmac, R = 0.2265 (Rfree = 0.000) for 5927 atoms. Found 21 (64 requested) and removed 35 (35 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.40 2.50 Search for helices and strands: 0 residues in 0 chains, 6086 seeds are put forward NCS extension: 51 residues added (1 deleted due to clashes), 6137 seeds are put forward Round 1: 558 peptides, 58 chains. Longest chain 31 peptides. Score 0.717 Round 2: 610 peptides, 56 chains. Longest chain 45 peptides. Score 0.774 Round 3: 617 peptides, 52 chains. Longest chain 38 peptides. Score 0.795 Round 4: 626 peptides, 56 chains. Longest chain 36 peptides. Score 0.787 Round 5: 624 peptides, 52 chains. Longest chain 42 peptides. Score 0.800 Taking the results from Round 5 Chains 62, Residues 572, Estimated correctness of the model 87.8 % 17 chains (280 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 366 A and 371 A 61 chains (575 residues) following loop building 16 chains (284 residues) in sequence following loop building ------------------------------------------------------ 17874 reflections ( 95.70 % complete ) and 9839 restraints for refining 6070 atoms. 6494 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2704 (Rfree = 0.000) for 6070 atoms. Found 65 (65 requested) and removed 74 (36 requested) atoms. Cycle 7: After refmac, R = 0.2488 (Rfree = 0.000) for 6016 atoms. Found 35 (63 requested) and removed 41 (36 requested) atoms. Cycle 8: After refmac, R = 0.2371 (Rfree = 0.000) for 5974 atoms. Found 27 (61 requested) and removed 38 (35 requested) atoms. Cycle 9: After refmac, R = 0.2276 (Rfree = 0.000) for 5944 atoms. Found 33 (59 requested) and removed 37 (35 requested) atoms. Cycle 10: After refmac, R = 0.2215 (Rfree = 0.000) for 5922 atoms. Found 21 (57 requested) and removed 37 (35 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.42 2.52 Search for helices and strands: 0 residues in 0 chains, 6050 seeds are put forward NCS extension: 32 residues added (29 deleted due to clashes), 6082 seeds are put forward Round 1: 599 peptides, 55 chains. Longest chain 47 peptides. Score 0.769 Round 2: 631 peptides, 43 chains. Longest chain 51 peptides. Score 0.836 Round 3: 629 peptides, 52 chains. Longest chain 51 peptides. Score 0.804 Round 4: 624 peptides, 44 chains. Longest chain 51 peptides. Score 0.829 Round 5: 634 peptides, 44 chains. Longest chain 48 peptides. Score 0.835 Taking the results from Round 2 Chains 58, Residues 588, Estimated correctness of the model 91.5 % 20 chains (384 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 277 A and 280 A 57 chains (590 residues) following loop building 19 chains (386 residues) in sequence following loop building ------------------------------------------------------ 17874 reflections ( 95.70 % complete ) and 8813 restraints for refining 6070 atoms. 4939 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2614 (Rfree = 0.000) for 6070 atoms. Found 58 (58 requested) and removed 84 (36 requested) atoms. Cycle 12: After refmac, R = 0.2395 (Rfree = 0.000) for 6015 atoms. Found 42 (55 requested) and removed 36 (35 requested) atoms. Cycle 13: After refmac, R = 0.2286 (Rfree = 0.000) for 6003 atoms. Found 33 (54 requested) and removed 38 (35 requested) atoms. Cycle 14: After refmac, R = 0.2187 (Rfree = 0.000) for 5980 atoms. Found 25 (53 requested) and removed 35 (35 requested) atoms. Cycle 15: After refmac, R = 0.2142 (Rfree = 0.000) for 5955 atoms. Found 25 (50 requested) and removed 36 (35 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.39 2.49 Search for helices and strands: 0 residues in 0 chains, 6090 seeds are put forward NCS extension: 23 residues added (23 deleted due to clashes), 6113 seeds are put forward Round 1: 608 peptides, 52 chains. Longest chain 46 peptides. Score 0.788 Round 2: 632 peptides, 43 chains. Longest chain 64 peptides. Score 0.837 Round 3: 640 peptides, 49 chains. Longest chain 50 peptides. Score 0.822 Round 4: 630 peptides, 45 chains. Longest chain 51 peptides. Score 0.829 Round 5: 639 peptides, 50 chains. Longest chain 51 peptides. Score 0.818 Taking the results from Round 2 Chains 48, Residues 589, Estimated correctness of the model 91.6 % 15 chains (362 residues) have been docked in sequence Building loops using Loopy2018 48 chains (589 residues) following loop building 15 chains (362 residues) in sequence following loop building ------------------------------------------------------ 17874 reflections ( 95.70 % complete ) and 8994 restraints for refining 6069 atoms. 5195 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2480 (Rfree = 0.000) for 6069 atoms. Found 50 (50 requested) and removed 75 (36 requested) atoms. Cycle 17: After refmac, R = 0.2282 (Rfree = 0.000) for 6020 atoms. Found 31 (48 requested) and removed 41 (35 requested) atoms. Cycle 18: After refmac, R = 0.2170 (Rfree = 0.000) for 5995 atoms. Found 28 (47 requested) and removed 37 (35 requested) atoms. Cycle 19: After refmac, R = 0.2113 (Rfree = 0.000) for 5975 atoms. Found 29 (45 requested) and removed 35 (35 requested) atoms. Cycle 20: After refmac, R = 0.2057 (Rfree = 0.000) for 5962 atoms. Found 19 (43 requested) and removed 35 (35 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.41 2.51 Search for helices and strands: 0 residues in 0 chains, 6101 seeds are put forward NCS extension: 51 residues added (15 deleted due to clashes), 6152 seeds are put forward Round 1: 589 peptides, 54 chains. Longest chain 39 peptides. Score 0.764 Round 2: 621 peptides, 43 chains. Longest chain 72 peptides. Score 0.830 Round 3: 619 peptides, 50 chains. Longest chain 50 peptides. Score 0.804 Round 4: 638 peptides, 45 chains. Longest chain 45 peptides. Score 0.834 Round 5: 627 peptides, 51 chains. Longest chain 51 peptides. Score 0.806 Taking the results from Round 4 Chains 50, Residues 593, Estimated correctness of the model 91.4 % 14 chains (335 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 336 A and 343 A Built loop between residues 105 B and 108 B 47 chains (600 residues) following loop building 12 chains (343 residues) in sequence following loop building ------------------------------------------------------ 17874 reflections ( 95.70 % complete ) and 9113 restraints for refining 6070 atoms. 5382 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2535 (Rfree = 0.000) for 6070 atoms. Found 43 (43 requested) and removed 65 (36 requested) atoms. Cycle 22: After refmac, R = 0.2363 (Rfree = 0.000) for 6026 atoms. Found 41 (41 requested) and removed 37 (35 requested) atoms. Cycle 23: After refmac, R = 0.2256 (Rfree = 0.000) for 6014 atoms. Found 37 (40 requested) and removed 36 (35 requested) atoms. Cycle 24: After refmac, R = 0.2175 (Rfree = 0.000) for 6004 atoms. Found 30 (38 requested) and removed 35 (35 requested) atoms. Cycle 25: After refmac, R = 0.2136 (Rfree = 0.000) for 5987 atoms. Found 21 (37 requested) and removed 35 (35 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.42 2.52 Search for helices and strands: 0 residues in 0 chains, 6124 seeds are put forward NCS extension: 40 residues added (3 deleted due to clashes), 6164 seeds are put forward Round 1: 610 peptides, 46 chains. Longest chain 49 peptides. Score 0.812 Round 2: 626 peptides, 40 chains. Longest chain 50 peptides. Score 0.843 Round 3: 626 peptides, 50 chains. Longest chain 51 peptides. Score 0.809 Round 4: 624 peptides, 48 chains. Longest chain 51 peptides. Score 0.815 Round 5: 619 peptides, 44 chains. Longest chain 49 peptides. Score 0.825 Taking the results from Round 2 Chains 41, Residues 586, Estimated correctness of the model 92.2 % 15 chains (369 residues) have been docked in sequence Building loops using Loopy2018 41 chains (586 residues) following loop building 15 chains (369 residues) in sequence following loop building ------------------------------------------------------ 17874 reflections ( 95.70 % complete ) and 9074 restraints for refining 6070 atoms. 5259 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2392 (Rfree = 0.000) for 6070 atoms. Found 36 (36 requested) and removed 59 (36 requested) atoms. Cycle 27: After refmac, R = 0.2264 (Rfree = 0.000) for 6028 atoms. Found 35 (35 requested) and removed 35 (35 requested) atoms. Cycle 28: After refmac, R = 0.2182 (Rfree = 0.000) for 6019 atoms. Found 33 (35 requested) and removed 35 (35 requested) atoms. Cycle 29: After refmac, R = 0.2106 (Rfree = 0.000) for 6004 atoms. Found 26 (35 requested) and removed 35 (35 requested) atoms. Cycle 30: After refmac, R = 0.2053 (Rfree = 0.000) for 5987 atoms. Found 26 (35 requested) and removed 36 (35 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.43 2.53 Search for helices and strands: 0 residues in 0 chains, 6114 seeds are put forward NCS extension: 16 residues added (18 deleted due to clashes), 6130 seeds are put forward Round 1: 606 peptides, 56 chains. Longest chain 51 peptides. Score 0.771 Round 2: 623 peptides, 46 chains. Longest chain 51 peptides. Score 0.821 Round 3: 642 peptides, 48 chains. Longest chain 48 peptides. Score 0.827 Round 4: 618 peptides, 49 chains. Longest chain 48 peptides. Score 0.807 Round 5: 618 peptides, 46 chains. Longest chain 45 peptides. Score 0.818 Taking the results from Round 3 Chains 51, Residues 594, Estimated correctness of the model 90.7 % 17 chains (336 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 229 B and 238 B Built loop between residues 261 B and 269 B Built loop between residues 287 B and 290 B Built loop between residues 364 B and 367 B 45 chains (607 residues) following loop building 13 chains (355 residues) in sequence following loop building ------------------------------------------------------ 17874 reflections ( 95.70 % complete ) and 9023 restraints for refining 6069 atoms. 5262 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2510 (Rfree = 0.000) for 6069 atoms. Found 36 (36 requested) and removed 70 (36 requested) atoms. Cycle 32: After refmac, R = 0.2313 (Rfree = 0.000) for 6016 atoms. Found 35 (35 requested) and removed 36 (35 requested) atoms. Cycle 33: After refmac, R = 0.2241 (Rfree = 0.000) for 6002 atoms. Found 28 (35 requested) and removed 36 (35 requested) atoms. Cycle 34: After refmac, R = 0.2197 (Rfree = 0.000) for 5988 atoms. Found 28 (35 requested) and removed 36 (35 requested) atoms. Cycle 35: After refmac, R = 0.2165 (Rfree = 0.000) for 5967 atoms. Found 31 (35 requested) and removed 35 (35 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.44 2.54 Search for helices and strands: 0 residues in 0 chains, 6097 seeds are put forward NCS extension: 64 residues added (97 deleted due to clashes), 6161 seeds are put forward Round 1: 617 peptides, 50 chains. Longest chain 48 peptides. Score 0.803 Round 2: 625 peptides, 43 chains. Longest chain 69 peptides. Score 0.833 Round 3: 624 peptides, 49 chains. Longest chain 59 peptides. Score 0.811 Round 4: 630 peptides, 43 chains. Longest chain 67 peptides. Score 0.836 Round 5: 612 peptides, 44 chains. Longest chain 75 peptides. Score 0.821 Taking the results from Round 4 Chains 45, Residues 587, Estimated correctness of the model 91.5 % 16 chains (390 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 156 A and 164 A Built loop between residues 382 A and 385 A 43 chains (593 residues) following loop building 14 chains (399 residues) in sequence following loop building ------------------------------------------------------ 17874 reflections ( 95.70 % complete ) and 8706 restraints for refining 6069 atoms. 4792 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2619 (Rfree = 0.000) for 6069 atoms. Found 36 (36 requested) and removed 87 (36 requested) atoms. Cycle 37: After refmac, R = 0.2441 (Rfree = 0.000) for 5988 atoms. Found 35 (35 requested) and removed 35 (35 requested) atoms. Cycle 38: After refmac, R = 0.2319 (Rfree = 0.000) for 5967 atoms. Found 35 (35 requested) and removed 35 (35 requested) atoms. Cycle 39: After refmac, R = 0.2215 (Rfree = 0.000) for 5956 atoms. Found 29 (35 requested) and removed 35 (35 requested) atoms. Cycle 40: After refmac, R = 0.2140 (Rfree = 0.000) for 5937 atoms. Found 21 (35 requested) and removed 35 (35 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.42 2.52 Search for helices and strands: 0 residues in 0 chains, 6069 seeds are put forward NCS extension: 24 residues added (52 deleted due to clashes), 6093 seeds are put forward Round 1: 574 peptides, 49 chains. Longest chain 51 peptides. Score 0.772 Round 2: 644 peptides, 38 chains. Longest chain 68 peptides. Score 0.859 Round 3: 630 peptides, 46 chains. Longest chain 46 peptides. Score 0.826 Round 4: 645 peptides, 48 chains. Longest chain 54 peptides. Score 0.829 Round 5: 640 peptides, 46 chains. Longest chain 49 peptides. Score 0.832 Taking the results from Round 2 Chains 42, Residues 606, Estimated correctness of the model 93.6 % 16 chains (441 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 227 A and 238 A Built loop between residues 284 A and 294 A 38 chains (620 residues) following loop building 14 chains (460 residues) in sequence following loop building ------------------------------------------------------ 17874 reflections ( 95.70 % complete ) and 8111 restraints for refining 6069 atoms. 3808 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2498 (Rfree = 0.000) for 6069 atoms. Found 36 (36 requested) and removed 76 (36 requested) atoms. Cycle 42: After refmac, R = 0.2334 (Rfree = 0.000) for 6005 atoms. Found 35 (35 requested) and removed 38 (35 requested) atoms. Cycle 43: After refmac, R = 0.2254 (Rfree = 0.000) for 5991 atoms. Found 35 (35 requested) and removed 36 (35 requested) atoms. Cycle 44: After refmac, R = 0.2175 (Rfree = 0.000) for 5984 atoms. Found 24 (35 requested) and removed 35 (35 requested) atoms. Cycle 45: After refmac, R = 0.2122 (Rfree = 0.000) for 5966 atoms. Found 20 (35 requested) and removed 35 (35 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.43 2.53 Search for helices and strands: 0 residues in 0 chains, 6077 seeds are put forward NCS extension: 19 residues added (43 deleted due to clashes), 6096 seeds are put forward Round 1: 599 peptides, 44 chains. Longest chain 49 peptides. Score 0.812 Round 2: 628 peptides, 44 chains. Longest chain 51 peptides. Score 0.831 Round 3: 620 peptides, 44 chains. Longest chain 45 peptides. Score 0.826 Round 4: 614 peptides, 53 chains. Longest chain 43 peptides. Score 0.789 Round 5: 618 peptides, 46 chains. Longest chain 51 peptides. Score 0.818 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 49, Residues 584, Estimated correctness of the model 91.1 % 16 chains (363 residues) have been docked in sequence Sequence coverage is 62 % Consider running further cycles of model building using 1vkz-2_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 34 A and 46 A Built loop between residues 139 A and 151 A Built loop between residues 383 A and 386 A 44 chains (600 residues) following loop building 13 chains (387 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 17874 reflections ( 95.70 % complete ) and 8906 restraints for refining 6070 atoms. 5062 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2479 (Rfree = 0.000) for 6070 atoms. Found 0 (36 requested) and removed 9 (36 requested) atoms. Cycle 47: After refmac, R = 0.2368 (Rfree = 0.000) for 6051 atoms. Found 0 (36 requested) and removed 11 (36 requested) atoms. Cycle 48: After refmac, R = 0.2295 (Rfree = 0.000) for 6034 atoms. Found 0 (35 requested) and removed 9 (35 requested) atoms. Cycle 49: After refmac, R = 0.2252 (Rfree = 0.000) for 6020 atoms. TimeTaking 68.98