Sun 23 Dec 22:22:43 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 1vp7-3.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vp7-3.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vp7-3.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vp7-3.0-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/1vp7-3.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vp7-3.0-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 22:22:53 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/1vp7-3.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vp7-3.0-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 625 and 0 Target number of residues in the AU: 625 Target solvent content: 0.5057 Checking the provided sequence file Detected sequence length: 100 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 6 Adjusted target number of residues: 600 Adjusted target solvent content: 0.53 Input MTZ file: 1vp7-3.0-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: 177 Cell parameters: 106.979 106.979 207.138 90.000 90.000 120.000 Input sequence file: 1vp7-3.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 4800 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: 207.138 3.000 Wilson plot Bfac: 24.67 14741 reflections ( 99.77 % complete ) and 0 restraints for refining 5309 atoms. Observations/parameters ratio is 0.69 ------------------------------------------------------ Starting model: R = 0.3196 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2628 (Rfree = 0.000) for 5309 atoms. Found 57 (57 requested) and removed 56 (28 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.45 2.35 Search for helices and strands: 0 residues in 0 chains, 5443 seeds are put forward NCS extension: 0 residues added, 5443 seeds are put forward Round 1: 283 peptides, 37 chains. Longest chain 22 peptides. Score 0.513 Round 2: 327 peptides, 34 chains. Longest chain 26 peptides. Score 0.622 Round 3: 335 peptides, 26 chains. Longest chain 29 peptides. Score 0.696 Round 4: 332 peptides, 32 chains. Longest chain 34 peptides. Score 0.646 Round 5: 334 peptides, 26 chains. Longest chain 50 peptides. Score 0.694 Taking the results from Round 3 Chains 32, Residues 309, Estimated correctness of the model 70.9 % 12 chains (224 residues) have been docked in sequence ------------------------------------------------------ 14741 reflections ( 99.77 % complete ) and 6808 restraints for refining 4403 atoms. 4730 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2841 (Rfree = 0.000) for 4403 atoms. Found 47 (47 requested) and removed 54 (23 requested) atoms. Cycle 2: After refmac, R = 0.2747 (Rfree = 0.000) for 4273 atoms. Found 47 (47 requested) and removed 52 (23 requested) atoms. Cycle 3: After refmac, R = 0.2639 (Rfree = 0.000) for 4215 atoms. Found 35 (46 requested) and removed 43 (23 requested) atoms. Cycle 4: After refmac, R = 0.2524 (Rfree = 0.000) for 4173 atoms. Found 31 (45 requested) and removed 31 (22 requested) atoms. Cycle 5: After refmac, R = 0.2509 (Rfree = 0.000) for 4153 atoms. Found 24 (45 requested) and removed 33 (22 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.49 2.39 Search for helices and strands: 0 residues in 0 chains, 4281 seeds are put forward NCS extension: 0 residues added, 4281 seeds are put forward Round 1: 310 peptides, 23 chains. Longest chain 37 peptides. Score 0.681 Round 2: 339 peptides, 25 chains. Longest chain 33 peptides. Score 0.708 Round 3: 342 peptides, 23 chains. Longest chain 39 peptides. Score 0.726 Round 4: 337 peptides, 26 chains. Longest chain 50 peptides. Score 0.698 Round 5: 342 peptides, 24 chains. Longest chain 40 peptides. Score 0.719 Taking the results from Round 3 Chains 25, Residues 319, Estimated correctness of the model 75.9 % 9 chains (218 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 44 C and 55 C Built loop between residues 46 E and 57 E 20 chains (331 residues) following loop building 7 chains (238 residues) in sequence following loop building ------------------------------------------------------ 14741 reflections ( 99.77 % complete ) and 6108 restraints for refining 4233 atoms. 3878 conditional restraints added. Observations/parameters ratio is 0.87 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2796 (Rfree = 0.000) for 4233 atoms. Found 45 (45 requested) and removed 56 (22 requested) atoms. Cycle 7: After refmac, R = 0.2647 (Rfree = 0.000) for 4185 atoms. Found 39 (44 requested) and removed 36 (22 requested) atoms. Cycle 8: After refmac, R = 0.2516 (Rfree = 0.000) for 4168 atoms. Found 29 (43 requested) and removed 27 (22 requested) atoms. Cycle 9: After refmac, R = 0.2533 (Rfree = 0.000) for 4145 atoms. Found 38 (41 requested) and removed 27 (22 requested) atoms. Cycle 10: After refmac, R = 0.2387 (Rfree = 0.000) for 4129 atoms. Found 39 (40 requested) and removed 24 (22 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.46 2.36 Search for helices and strands: 0 residues in 0 chains, 4254 seeds are put forward NCS extension: 15 residues added (27 deleted due to clashes), 4269 seeds are put forward Round 1: 343 peptides, 24 chains. Longest chain 39 peptides. Score 0.721 Round 2: 346 peptides, 23 chains. Longest chain 51 peptides. Score 0.731 Round 3: 339 peptides, 23 chains. Longest chain 66 peptides. Score 0.722 Round 4: 355 peptides, 25 chains. Longest chain 40 peptides. Score 0.730 Round 5: 349 peptides, 29 chains. Longest chain 30 peptides. Score 0.694 Taking the results from Round 2 Chains 25, Residues 323, Estimated correctness of the model 76.7 % 12 chains (258 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 46 C and 53 C Built loop between residues 62 C and 65 C Built loop between residues 35 B and 38 B 21 chains (332 residues) following loop building 9 chains (268 residues) in sequence following loop building ------------------------------------------------------ 14741 reflections ( 99.77 % complete ) and 5795 restraints for refining 4238 atoms. 3472 conditional restraints added. Observations/parameters ratio is 0.87 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2622 (Rfree = 0.000) for 4238 atoms. Found 40 (40 requested) and removed 55 (22 requested) atoms. Cycle 12: After refmac, R = 0.2428 (Rfree = 0.000) for 4197 atoms. Found 40 (40 requested) and removed 37 (22 requested) atoms. Cycle 13: After refmac, R = 0.2289 (Rfree = 0.000) for 4179 atoms. Found 32 (39 requested) and removed 27 (22 requested) atoms. Cycle 14: After refmac, R = 0.2218 (Rfree = 0.000) for 4167 atoms. Found 18 (38 requested) and removed 28 (22 requested) atoms. Cycle 15: After refmac, R = 0.2178 (Rfree = 0.000) for 4151 atoms. Found 16 (36 requested) and removed 24 (22 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.49 2.39 Search for helices and strands: 0 residues in 0 chains, 4274 seeds are put forward NCS extension: 23 residues added (27 deleted due to clashes), 4297 seeds are put forward Round 1: 342 peptides, 28 chains. Longest chain 58 peptides. Score 0.691 Round 2: 357 peptides, 27 chains. Longest chain 42 peptides. Score 0.719 Round 3: 352 peptides, 30 chains. Longest chain 51 peptides. Score 0.692 Round 4: 345 peptides, 27 chains. Longest chain 35 peptides. Score 0.703 Round 5: 358 peptides, 28 chains. Longest chain 51 peptides. Score 0.714 Taking the results from Round 2 Failed to save intermediate PDB Chains 28, Residues 330, Estimated correctness of the model 74.8 % 9 chains (224 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 35 B and 39 B 27 chains (333 residues) following loop building 8 chains (227 residues) in sequence following loop building ------------------------------------------------------ 14741 reflections ( 99.77 % complete ) and 6121 restraints for refining 4213 atoms. 3917 conditional restraints added. Observations/parameters ratio is 0.87 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2468 (Rfree = 0.000) for 4213 atoms. Found 36 (36 requested) and removed 41 (22 requested) atoms. Cycle 17: After refmac, R = 0.2311 (Rfree = 0.000) for 4194 atoms. Found 30 (35 requested) and removed 24 (22 requested) atoms. Cycle 18: After refmac, R = 0.2249 (Rfree = 0.000) for 4184 atoms. Found 15 (34 requested) and removed 28 (22 requested) atoms. Cycle 19: After refmac, R = 0.2217 (Rfree = 0.000) for 4163 atoms. Found 19 (33 requested) and removed 23 (22 requested) atoms. Cycle 20: After refmac, R = 0.2192 (Rfree = 0.000) for 4152 atoms. Found 11 (32 requested) and removed 25 (22 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.51 2.41 Search for helices and strands: 0 residues in 0 chains, 4284 seeds are put forward NCS extension: 9 residues added (24 deleted due to clashes), 4293 seeds are put forward Round 1: 334 peptides, 24 chains. Longest chain 43 peptides. Score 0.708 Round 2: 351 peptides, 28 chains. Longest chain 39 peptides. Score 0.704 Round 3: 349 peptides, 27 chains. Longest chain 37 peptides. Score 0.708 Round 4: 357 peptides, 28 chains. Longest chain 55 peptides. Score 0.713 Round 5: 354 peptides, 24 chains. Longest chain 41 peptides. Score 0.735 Taking the results from Round 5 Chains 27, Residues 330, Estimated correctness of the model 77.4 % 11 chains (235 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 42 B and 53 B 26 chains (332 residues) following loop building 10 chains (245 residues) in sequence following loop building ------------------------------------------------------ 14741 reflections ( 99.77 % complete ) and 6086 restraints for refining 4252 atoms. 3841 conditional restraints added. Observations/parameters ratio is 0.87 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2617 (Rfree = 0.000) for 4252 atoms. Found 31 (31 requested) and removed 55 (22 requested) atoms. Cycle 22: After refmac, R = 0.2459 (Rfree = 0.000) for 4211 atoms. Found 31 (31 requested) and removed 33 (22 requested) atoms. Cycle 23: After refmac, R = 0.2298 (Rfree = 0.000) for 4200 atoms. Found 19 (30 requested) and removed 27 (22 requested) atoms. Cycle 24: After refmac, R = 0.2272 (Rfree = 0.000) for 4181 atoms. Found 23 (29 requested) and removed 25 (22 requested) atoms. Cycle 25: After refmac, R = 0.2241 (Rfree = 0.000) for 4172 atoms. Found 18 (28 requested) and removed 23 (22 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.52 2.42 Search for helices and strands: 0 residues in 0 chains, 4299 seeds are put forward NCS extension: 18 residues added (9 deleted due to clashes), 4317 seeds are put forward Round 1: 347 peptides, 23 chains. Longest chain 40 peptides. Score 0.733 Round 2: 329 peptides, 26 chains. Longest chain 27 peptides. Score 0.687 Round 3: 336 peptides, 25 chains. Longest chain 38 peptides. Score 0.704 Round 4: 342 peptides, 26 chains. Longest chain 41 peptides. Score 0.705 Round 5: 332 peptides, 33 chains. Longest chain 24 peptides. Score 0.639 Taking the results from Round 1 Chains 26, Residues 324, Estimated correctness of the model 77.0 % 12 chains (250 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 47 C and 54 C Built loop between residues 67 C and 71 C Built loop between residues 69 E and 73 E Built loop between residues 62 D and 65 D 22 chains (338 residues) following loop building 8 chains (264 residues) in sequence following loop building ------------------------------------------------------ 14741 reflections ( 99.77 % complete ) and 5892 restraints for refining 4303 atoms. 3539 conditional restraints added. Observations/parameters ratio is 0.86 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2575 (Rfree = 0.000) for 4303 atoms. Found 28 (28 requested) and removed 43 (23 requested) atoms. Cycle 27: After refmac, R = 0.2431 (Rfree = 0.000) for 4272 atoms. Found 16 (27 requested) and removed 29 (23 requested) atoms. Cycle 28: After refmac, R = 0.2391 (Rfree = 0.000) for 4248 atoms. Found 18 (25 requested) and removed 22 (22 requested) atoms. Cycle 29: After refmac, R = 0.2378 (Rfree = 0.000) for 4237 atoms. Found 20 (24 requested) and removed 22 (22 requested) atoms. Cycle 30: After refmac, R = 0.2341 (Rfree = 0.000) for 4230 atoms. Found 10 (23 requested) and removed 26 (22 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.51 2.41 Search for helices and strands: 0 residues in 0 chains, 4365 seeds are put forward NCS extension: 0 residues added, 4365 seeds are put forward Round 1: 342 peptides, 21 chains. Longest chain 41 peptides. Score 0.739 Round 2: 345 peptides, 20 chains. Longest chain 40 peptides. Score 0.750 Round 3: 337 peptides, 30 chains. Longest chain 31 peptides. Score 0.669 Round 4: 352 peptides, 23 chains. Longest chain 40 peptides. Score 0.739 Round 5: 352 peptides, 24 chains. Longest chain 38 peptides. Score 0.732 Taking the results from Round 2 Chains 23, Residues 325, Estimated correctness of the model 79.7 % 11 chains (263 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 48 C and 54 C Built loop between residues 38 B and 41 B Built loop between residues 63 B and 66 B Built loop between residues 45 D and 56 D Built loop between residues 47 F and 54 F 16 chains (348 residues) following loop building 6 chains (288 residues) in sequence following loop building ------------------------------------------------------ 14741 reflections ( 99.77 % complete ) and 5634 restraints for refining 4318 atoms. 3147 conditional restraints added. Observations/parameters ratio is 0.85 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2523 (Rfree = 0.000) for 4318 atoms. Found 23 (23 requested) and removed 45 (23 requested) atoms. Cycle 32: After refmac, R = 0.2368 (Rfree = 0.000) for 4275 atoms. Found 23 (23 requested) and removed 29 (23 requested) atoms. Cycle 33: After refmac, R = 0.2331 (Rfree = 0.000) for 4264 atoms. Found 23 (23 requested) and removed 25 (23 requested) atoms. Cycle 34: After refmac, R = 0.2273 (Rfree = 0.000) for 4252 atoms. Found 21 (22 requested) and removed 25 (22 requested) atoms. Cycle 35: After refmac, R = 0.2236 (Rfree = 0.000) for 4241 atoms. Found 21 (22 requested) and removed 28 (22 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.50 2.40 Search for helices and strands: 0 residues in 0 chains, 4390 seeds are put forward NCS extension: 13 residues added (7 deleted due to clashes), 4403 seeds are put forward Round 1: 343 peptides, 22 chains. Longest chain 51 peptides. Score 0.734 Round 2: 338 peptides, 22 chains. Longest chain 39 peptides. Score 0.727 Round 3: 355 peptides, 26 chains. Longest chain 45 peptides. Score 0.723 Round 4: 338 peptides, 26 chains. Longest chain 41 peptides. Score 0.700 Round 5: 337 peptides, 28 chains. Longest chain 37 peptides. Score 0.684 Taking the results from Round 1 Chains 22, Residues 321, Estimated correctness of the model 77.2 % 9 chains (253 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 46 C and 55 C Built loop between residues 63 D and 71 D 19 chains (332 residues) following loop building 7 chains (268 residues) in sequence following loop building ------------------------------------------------------ 14741 reflections ( 99.77 % complete ) and 5877 restraints for refining 4287 atoms. 3518 conditional restraints added. Observations/parameters ratio is 0.86 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2363 (Rfree = 0.000) for 4287 atoms. Found 23 (23 requested) and removed 41 (23 requested) atoms. Cycle 37: After refmac, R = 0.2209 (Rfree = 0.000) for 4253 atoms. Found 18 (23 requested) and removed 28 (23 requested) atoms. Cycle 38: After refmac, R = 0.2172 (Rfree = 0.000) for 4235 atoms. Found 15 (22 requested) and removed 24 (22 requested) atoms. Cycle 39: After refmac, R = 0.2153 (Rfree = 0.000) for 4220 atoms. Found 16 (22 requested) and removed 25 (22 requested) atoms. Cycle 40: After refmac, R = 0.2169 (Rfree = 0.000) for 4207 atoms. Found 19 (22 requested) and removed 25 (22 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.48 2.38 Search for helices and strands: 0 residues in 0 chains, 4331 seeds are put forward NCS extension: 7 residues added (12 deleted due to clashes), 4338 seeds are put forward Round 1: 339 peptides, 22 chains. Longest chain 51 peptides. Score 0.729 Round 2: 357 peptides, 20 chains. Longest chain 68 peptides. Score 0.764 Round 3: 360 peptides, 21 chains. Longest chain 40 peptides. Score 0.761 Round 4: 358 peptides, 23 chains. Longest chain 54 peptides. Score 0.746 Round 5: 357 peptides, 25 chains. Longest chain 43 peptides. Score 0.732 Taking the results from Round 2 Chains 22, Residues 337, Estimated correctness of the model 81.7 % 8 chains (242 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 49 C and 56 C 20 chains (342 residues) following loop building 7 chains (248 residues) in sequence following loop building ------------------------------------------------------ 14741 reflections ( 99.77 % complete ) and 5907 restraints for refining 4244 atoms. 3606 conditional restraints added. Observations/parameters ratio is 0.87 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2344 (Rfree = 0.000) for 4244 atoms. Found 22 (22 requested) and removed 41 (22 requested) atoms. Cycle 42: After refmac, R = 0.2199 (Rfree = 0.000) for 4217 atoms. Found 18 (22 requested) and removed 25 (22 requested) atoms. Cycle 43: After refmac, R = 0.2132 (Rfree = 0.000) for 4197 atoms. Found 19 (22 requested) and removed 24 (22 requested) atoms. Cycle 44: After refmac, R = 0.2138 (Rfree = 0.000) for 4187 atoms. Found 13 (22 requested) and removed 26 (22 requested) atoms. Cycle 45: After refmac, R = 0.2095 (Rfree = 0.000) for 4168 atoms. Found 17 (22 requested) and removed 25 (22 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.53 2.43 Search for helices and strands: 0 residues in 0 chains, 4313 seeds are put forward NCS extension: 28 residues added (41 deleted due to clashes), 4341 seeds are put forward Round 1: 349 peptides, 20 chains. Longest chain 55 peptides. Score 0.754 Round 2: 348 peptides, 21 chains. Longest chain 43 peptides. Score 0.747 Round 3: 341 peptides, 26 chains. Longest chain 40 peptides. Score 0.704 Round 4: 346 peptides, 23 chains. Longest chain 40 peptides. Score 0.731 Round 5: 345 peptides, 25 chains. Longest chain 40 peptides. Score 0.716 Taking the results from Round 1 Last building cycle: Chain fragments will be rearranged Chains 20, Residues 329, Estimated correctness of the model 80.2 % 10 chains (270 residues) have been docked in sequence Sequence coverage is 81 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 50 C and 53 C Built loop between residues 36 B and 39 B Built loop between residues 42 F and 54 F 16 chains (340 residues) following loop building 7 chains (285 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 14741 reflections ( 99.77 % complete ) and 2437 restraints for refining 2427 atoms. Observations/parameters ratio is 1.52 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3441 (Rfree = 0.000) for 2427 atoms. Found 13 (13 requested) and removed 0 (13 requested) atoms. Cycle 47: After refmac, R = 0.3305 (Rfree = 0.000) for 2427 atoms. Found 13 (13 requested) and removed 0 (13 requested) atoms. Cycle 48: After refmac, R = 0.3198 (Rfree = 0.000) for 2427 atoms. Found 13 (13 requested) and removed 0 (13 requested) atoms. Cycle 49: After refmac, R = 0.3120 (Rfree = 0.000) for 2427 atoms. TimeTaking 93.07