Mon 24 Dec 00:53:00 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 1vky-3.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vky-3.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vky-3.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vky-3.0-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/1vky-3.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vky-3.0-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 00:53:05 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/1vky-3.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vky-3.0-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 806 and 0 Target number of residues in the AU: 806 Target solvent content: 0.5479 Checking the provided sequence file Detected sequence length: 347 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 694 Adjusted target solvent content: 0.61 Input MTZ file: 1vky-3.0-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: 23 Cell parameters: 119.363 122.591 131.880 90.000 90.000 90.000 Input sequence file: 1vky-3.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 5552 target number of atoms Had to go as low as 0.75 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: 41.380 3.000 Wilson plot Bfac: 34.93 19666 reflections ( 99.68 % complete ) and 0 restraints for refining 6148 atoms. Observations/parameters ratio is 0.80 ------------------------------------------------------ Starting model: R = 0.3173 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2283 (Rfree = 0.000) for 6148 atoms. Found 55 (66 requested) and removed 90 (33 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.67 2.30 Search for helices and strands: 0 residues in 0 chains, 6218 seeds are put forward NCS extension: 0 residues added, 6218 seeds are put forward Round 1: 385 peptides, 56 chains. Longest chain 16 peptides. Score 0.466 Round 2: 382 peptides, 48 chains. Longest chain 26 peptides. Score 0.516 Round 3: 417 peptides, 44 chains. Longest chain 29 peptides. Score 0.590 Round 4: 420 peptides, 42 chains. Longest chain 24 peptides. Score 0.606 Round 5: 423 peptides, 47 chains. Longest chain 25 peptides. Score 0.580 Taking the results from Round 4 Chains 45, Residues 378, Estimated correctness of the model 53.2 % 9 chains (131 residues) have been docked in sequence ------------------------------------------------------ 19666 reflections ( 99.68 % complete ) and 9402 restraints for refining 5093 atoms. 7378 conditional restraints added. Observations/parameters ratio is 0.97 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2699 (Rfree = 0.000) for 5093 atoms. Found 54 (54 requested) and removed 33 (27 requested) atoms. Cycle 2: After refmac, R = 0.2448 (Rfree = 0.000) for 5080 atoms. Found 55 (55 requested) and removed 34 (27 requested) atoms. Cycle 3: After refmac, R = 0.2330 (Rfree = 0.000) for 5081 atoms. Found 40 (55 requested) and removed 33 (27 requested) atoms. Cycle 4: After refmac, R = 0.2272 (Rfree = 0.000) for 5063 atoms. Found 35 (54 requested) and removed 29 (27 requested) atoms. Cycle 5: After refmac, R = 0.2204 (Rfree = 0.000) for 5058 atoms. Found 24 (54 requested) and removed 30 (27 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.68 2.31 Search for helices and strands: 0 residues in 0 chains, 5174 seeds are put forward NCS extension: 22 residues added (5 deleted due to clashes), 5196 seeds are put forward Round 1: 408 peptides, 50 chains. Longest chain 21 peptides. Score 0.540 Round 2: 445 peptides, 38 chains. Longest chain 31 peptides. Score 0.659 Round 3: 452 peptides, 42 chains. Longest chain 33 peptides. Score 0.645 Round 4: 458 peptides, 40 chains. Longest chain 41 peptides. Score 0.663 Round 5: 458 peptides, 39 chains. Longest chain 45 peptides. Score 0.668 Taking the results from Round 5 Chains 46, Residues 419, Estimated correctness of the model 65.8 % 10 chains (199 residues) have been docked in sequence ------------------------------------------------------ 19666 reflections ( 99.68 % complete ) and 8467 restraints for refining 5094 atoms. 5980 conditional restraints added. Observations/parameters ratio is 0.97 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2704 (Rfree = 0.000) for 5094 atoms. Found 54 (54 requested) and removed 45 (27 requested) atoms. Cycle 7: After refmac, R = 0.2427 (Rfree = 0.000) for 5078 atoms. Found 55 (55 requested) and removed 35 (27 requested) atoms. Cycle 8: After refmac, R = 0.2281 (Rfree = 0.000) for 5072 atoms. Found 32 (54 requested) and removed 29 (27 requested) atoms. Cycle 9: After refmac, R = 0.2196 (Rfree = 0.000) for 5066 atoms. Found 29 (54 requested) and removed 30 (27 requested) atoms. Cycle 10: After refmac, R = 0.2137 (Rfree = 0.000) for 5056 atoms. Found 31 (54 requested) and removed 30 (27 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.68 2.31 Search for helices and strands: 0 residues in 0 chains, 5162 seeds are put forward NCS extension: 23 residues added (39 deleted due to clashes), 5185 seeds are put forward Round 1: 431 peptides, 41 chains. Longest chain 44 peptides. Score 0.626 Round 2: 446 peptides, 39 chains. Longest chain 51 peptides. Score 0.655 Round 3: 461 peptides, 36 chains. Longest chain 40 peptides. Score 0.687 Round 4: 461 peptides, 37 chains. Longest chain 51 peptides. Score 0.682 Round 5: 460 peptides, 40 chains. Longest chain 41 peptides. Score 0.665 Taking the results from Round 3 Chains 43, Residues 425, Estimated correctness of the model 69.3 % 10 chains (253 residues) have been docked in sequence ------------------------------------------------------ 19666 reflections ( 99.68 % complete ) and 7878 restraints for refining 5095 atoms. 5121 conditional restraints added. Observations/parameters ratio is 0.96 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2540 (Rfree = 0.000) for 5095 atoms. Found 54 (54 requested) and removed 47 (27 requested) atoms. Cycle 12: After refmac, R = 0.2290 (Rfree = 0.000) for 5086 atoms. Found 36 (55 requested) and removed 33 (27 requested) atoms. Cycle 13: After refmac, R = 0.2196 (Rfree = 0.000) for 5074 atoms. Found 29 (54 requested) and removed 30 (27 requested) atoms. Cycle 14: After refmac, R = 0.2132 (Rfree = 0.000) for 5056 atoms. Found 35 (54 requested) and removed 28 (27 requested) atoms. Cycle 15: After refmac, R = 0.2094 (Rfree = 0.000) for 5051 atoms. Found 32 (54 requested) and removed 32 (27 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.67 2.30 Search for helices and strands: 0 residues in 0 chains, 5158 seeds are put forward NCS extension: 30 residues added (42 deleted due to clashes), 5188 seeds are put forward Round 1: 448 peptides, 36 chains. Longest chain 39 peptides. Score 0.673 Round 2: 463 peptides, 37 chains. Longest chain 48 peptides. Score 0.684 Round 3: 460 peptides, 37 chains. Longest chain 59 peptides. Score 0.681 Round 4: 452 peptides, 34 chains. Longest chain 51 peptides. Score 0.688 Round 5: 452 peptides, 37 chains. Longest chain 36 peptides. Score 0.672 Taking the results from Round 4 Chains 36, Residues 418, Estimated correctness of the model 69.5 % 9 chains (221 residues) have been docked in sequence ------------------------------------------------------ 19666 reflections ( 99.68 % complete ) and 8252 restraints for refining 5094 atoms. 5650 conditional restraints added. Observations/parameters ratio is 0.97 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2528 (Rfree = 0.000) for 5094 atoms. Found 54 (54 requested) and removed 57 (27 requested) atoms. Cycle 17: After refmac, R = 0.2309 (Rfree = 0.000) for 5075 atoms. Found 45 (54 requested) and removed 29 (27 requested) atoms. Cycle 18: After refmac, R = 0.2200 (Rfree = 0.000) for 5077 atoms. Found 34 (54 requested) and removed 28 (27 requested) atoms. Cycle 19: After refmac, R = 0.2131 (Rfree = 0.000) for 5074 atoms. Found 22 (54 requested) and removed 30 (27 requested) atoms. Cycle 20: After refmac, R = 0.2097 (Rfree = 0.000) for 5058 atoms. Found 26 (54 requested) and removed 27 (27 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.68 2.31 Search for helices and strands: 0 residues in 0 chains, 5167 seeds are put forward NCS extension: 43 residues added (36 deleted due to clashes), 5210 seeds are put forward Round 1: 446 peptides, 36 chains. Longest chain 49 peptides. Score 0.671 Round 2: 467 peptides, 31 chains. Longest chain 72 peptides. Score 0.718 Round 3: 469 peptides, 27 chains. Longest chain 74 peptides. Score 0.739 Round 4: 468 peptides, 35 chains. Longest chain 51 peptides. Score 0.699 Round 5: 467 peptides, 38 chains. Longest chain 36 peptides. Score 0.683 Taking the results from Round 3 Chains 32, Residues 442, Estimated correctness of the model 78.0 % 12 chains (307 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 243 A and 246 A Built loop between residues 269 A and 272 A Built loop between residues 288 A and 292 A Built loop between residues 306 A and 310 A Built loop between residues 323 A and 327 A Built loop between residues 288 B and 295 B 23 chains (453 residues) following loop building 6 chains (326 residues) in sequence following loop building ------------------------------------------------------ 19666 reflections ( 99.68 % complete ) and 6880 restraints for refining 5095 atoms. 3648 conditional restraints added. Observations/parameters ratio is 0.96 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2520 (Rfree = 0.000) for 5095 atoms. Found 54 (54 requested) and removed 63 (27 requested) atoms. Cycle 22: After refmac, R = 0.2330 (Rfree = 0.000) for 5075 atoms. Found 48 (53 requested) and removed 36 (27 requested) atoms. Cycle 23: After refmac, R = 0.2243 (Rfree = 0.000) for 5071 atoms. Found 34 (52 requested) and removed 30 (27 requested) atoms. Cycle 24: After refmac, R = 0.2215 (Rfree = 0.000) for 5065 atoms. Found 29 (51 requested) and removed 33 (27 requested) atoms. Cycle 25: After refmac, R = 0.2171 (Rfree = 0.000) for 5056 atoms. Found 23 (50 requested) and removed 34 (27 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.66 2.29 Search for helices and strands: 0 residues in 0 chains, 5173 seeds are put forward NCS extension: 27 residues added (47 deleted due to clashes), 5200 seeds are put forward Round 1: 444 peptides, 35 chains. Longest chain 42 peptides. Score 0.674 Round 2: 473 peptides, 29 chains. Longest chain 75 peptides. Score 0.734 Round 3: 458 peptides, 36 chains. Longest chain 45 peptides. Score 0.684 Round 4: 473 peptides, 31 chains. Longest chain 49 peptides. Score 0.724 Round 5: 463 peptides, 32 chains. Longest chain 47 peptides. Score 0.709 Taking the results from Round 2 Chains 34, Residues 444, Estimated correctness of the model 77.2 % 13 chains (307 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 52 A and 55 A Built loop between residues 248 A and 254 A Built loop between residues 271 B and 274 B Built loop between residues 284 B and 291 B Built loop between residues 306 B and 309 B 26 chains (455 residues) following loop building 8 chains (324 residues) in sequence following loop building ------------------------------------------------------ 19666 reflections ( 99.68 % complete ) and 7015 restraints for refining 5095 atoms. 3821 conditional restraints added. Observations/parameters ratio is 0.96 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2482 (Rfree = 0.000) for 5095 atoms. Found 49 (49 requested) and removed 53 (27 requested) atoms. Cycle 27: After refmac, R = 0.2302 (Rfree = 0.000) for 5078 atoms. Found 48 (48 requested) and removed 28 (27 requested) atoms. Cycle 28: After refmac, R = 0.2208 (Rfree = 0.000) for 5088 atoms. Found 34 (46 requested) and removed 37 (27 requested) atoms. Cycle 29: After refmac, R = 0.2149 (Rfree = 0.000) for 5078 atoms. Found 26 (45 requested) and removed 33 (27 requested) atoms. Cycle 30: After refmac, R = 0.2119 (Rfree = 0.000) for 5068 atoms. Found 31 (44 requested) and removed 37 (27 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.64 2.27 Search for helices and strands: 0 residues in 0 chains, 5163 seeds are put forward NCS extension: 87 residues added (22 deleted due to clashes), 5250 seeds are put forward Round 1: 459 peptides, 32 chains. Longest chain 95 peptides. Score 0.705 Round 2: 471 peptides, 37 chains. Longest chain 40 peptides. Score 0.692 Round 3: 488 peptides, 31 chains. Longest chain 44 peptides. Score 0.738 Round 4: 464 peptides, 36 chains. Longest chain 48 peptides. Score 0.690 Round 5: 462 peptides, 36 chains. Longest chain 34 peptides. Score 0.688 Taking the results from Round 3 Chains 36, Residues 457, Estimated correctness of the model 77.8 % 12 chains (304 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 61 A and 64 A Built loop between residues 265 A and 268 A Built loop between residues 282 A and 286 A Built loop between residues 279 B and 283 B 31 chains (466 residues) following loop building 8 chains (314 residues) in sequence following loop building ------------------------------------------------------ 19666 reflections ( 99.68 % complete ) and 6985 restraints for refining 5095 atoms. 3788 conditional restraints added. Observations/parameters ratio is 0.96 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2488 (Rfree = 0.000) for 5095 atoms. Found 43 (43 requested) and removed 62 (27 requested) atoms. Cycle 32: After refmac, R = 0.2245 (Rfree = 0.000) for 5061 atoms. Found 42 (42 requested) and removed 34 (27 requested) atoms. Cycle 33: After refmac, R = 0.2126 (Rfree = 0.000) for 5063 atoms. Found 31 (41 requested) and removed 34 (27 requested) atoms. Cycle 34: After refmac, R = 0.2047 (Rfree = 0.000) for 5051 atoms. Found 26 (40 requested) and removed 30 (27 requested) atoms. Cycle 35: After refmac, R = 0.1999 (Rfree = 0.000) for 5037 atoms. Found 25 (39 requested) and removed 32 (27 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.66 2.29 Search for helices and strands: 0 residues in 0 chains, 5144 seeds are put forward NCS extension: 44 residues added (51 deleted due to clashes), 5188 seeds are put forward Round 1: 453 peptides, 37 chains. Longest chain 42 peptides. Score 0.673 Round 2: 475 peptides, 29 chains. Longest chain 77 peptides. Score 0.736 Round 3: 473 peptides, 32 chains. Longest chain 36 peptides. Score 0.719 Round 4: 467 peptides, 29 chains. Longest chain 76 peptides. Score 0.728 Round 5: 471 peptides, 29 chains. Longest chain 61 peptides. Score 0.732 Taking the results from Round 2 Chains 36, Residues 446, Estimated correctness of the model 77.5 % 14 chains (330 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 52 A and 57 A Built loop between residues 259 B and 262 B Built loop between residues 282 B and 291 B Built loop between residues 327 B and 330 B 30 chains (457 residues) following loop building 10 chains (346 residues) in sequence following loop building ------------------------------------------------------ 19666 reflections ( 99.68 % complete ) and 6622 restraints for refining 5095 atoms. 3305 conditional restraints added. Observations/parameters ratio is 0.96 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2326 (Rfree = 0.000) for 5095 atoms. Found 38 (38 requested) and removed 47 (27 requested) atoms. Cycle 37: After refmac, R = 0.2152 (Rfree = 0.000) for 5064 atoms. Found 37 (37 requested) and removed 32 (27 requested) atoms. Cycle 38: After refmac, R = 0.2064 (Rfree = 0.000) for 5057 atoms. Found 25 (36 requested) and removed 29 (27 requested) atoms. Cycle 39: After refmac, R = 0.1992 (Rfree = 0.000) for 5046 atoms. Found 27 (35 requested) and removed 30 (27 requested) atoms. Cycle 40: After refmac, R = 0.1964 (Rfree = 0.000) for 5029 atoms. Found 27 (33 requested) and removed 31 (27 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.65 2.28 Search for helices and strands: 0 residues in 0 chains, 5142 seeds are put forward NCS extension: 74 residues added (32 deleted due to clashes), 5216 seeds are put forward Round 1: 443 peptides, 33 chains. Longest chain 73 peptides. Score 0.684 Round 2: 467 peptides, 28 chains. Longest chain 77 peptides. Score 0.733 Round 3: 473 peptides, 31 chains. Longest chain 51 peptides. Score 0.724 Round 4: 461 peptides, 32 chains. Longest chain 60 peptides. Score 0.707 Round 5: 461 peptides, 31 chains. Longest chain 60 peptides. Score 0.713 Taking the results from Round 2 Chains 31, Residues 439, Estimated correctness of the model 77.0 % 11 chains (330 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 52 A and 59 A Built loop between residues 242 B and 245 B Built loop between residues 280 B and 291 B 27 chains (452 residues) following loop building 8 chains (348 residues) in sequence following loop building ------------------------------------------------------ 19666 reflections ( 99.68 % complete ) and 6717 restraints for refining 5095 atoms. 3440 conditional restraints added. Observations/parameters ratio is 0.96 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2323 (Rfree = 0.000) for 5095 atoms. Found 32 (32 requested) and removed 56 (27 requested) atoms. Cycle 42: After refmac, R = 0.2138 (Rfree = 0.000) for 5056 atoms. Found 31 (31 requested) and removed 28 (27 requested) atoms. Cycle 43: After refmac, R = 0.2042 (Rfree = 0.000) for 5044 atoms. Found 30 (30 requested) and removed 31 (27 requested) atoms. Cycle 44: After refmac, R = 0.1998 (Rfree = 0.000) for 5031 atoms. Found 29 (29 requested) and removed 32 (27 requested) atoms. Cycle 45: After refmac, R = 0.1963 (Rfree = 0.000) for 5021 atoms. Found 28 (28 requested) and removed 30 (27 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.67 2.30 Search for helices and strands: 0 residues in 0 chains, 5129 seeds are put forward NCS extension: 22 residues added (47 deleted due to clashes), 5151 seeds are put forward Round 1: 450 peptides, 31 chains. Longest chain 61 peptides. Score 0.701 Round 2: 456 peptides, 31 chains. Longest chain 58 peptides. Score 0.708 Round 3: 447 peptides, 36 chains. Longest chain 49 peptides. Score 0.672 Round 4: 458 peptides, 39 chains. Longest chain 41 peptides. Score 0.668 Round 5: 478 peptides, 32 chains. Longest chain 51 peptides. Score 0.724 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 36, Residues 446, Estimated correctness of the model 75.6 % 11 chains (283 residues) have been docked in sequence Sequence coverage is 63 % Consider running further cycles of model building using 1vky-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 273 A and 276 A Built loop between residues 187 B and 191 B Built loop between residues 242 B and 245 B Built loop between residues 259 B and 262 B Built loop between residues 311 B and 319 B 28 chains (458 residues) following loop building 6 chains (299 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 19666 reflections ( 99.68 % complete ) and 7302 restraints for refining 5095 atoms. 4240 conditional restraints added. Observations/parameters ratio is 0.96 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2352 (Rfree = 0.000) for 5095 atoms. Found 0 (27 requested) and removed 4 (27 requested) atoms. Cycle 47: After refmac, R = 0.2201 (Rfree = 0.000) for 5073 atoms. Found 0 (27 requested) and removed 4 (27 requested) atoms. Cycle 48: After refmac, R = 0.2128 (Rfree = 0.000) for 5063 atoms. Found 0 (27 requested) and removed 2 (27 requested) atoms. Cycle 49: After refmac, R = 0.2092 (Rfree = 0.000) for 5061 atoms. TimeTaking 73.17