Sun 23 Dec 23:45:14 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 2opk-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2opk-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2opk-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2opk-3.4-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/2opk-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2opk-3.4-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 ============================================================ Sun 23 Dec 23:45:18 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/2opk-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2opk-3.4-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 418 and 0 Target number of residues in the AU: 418 Target solvent content: 0.6018 Checking the provided sequence file Detected sequence length: 112 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 448 Adjusted target solvent content: 0.57 Input MTZ file: 2opk-3.4-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: 96 Cell parameters: 75.570 75.570 198.970 90.000 90.000 90.000 Input sequence file: 2opk-3.4-parrot-mrncs.fasta_lf Building free atoms model in initial map for 3584 target number of atoms Had to go as low as 0.80 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: 28.177 3.400 Wilson plot Bfac: 53.33 8484 reflections ( 99.60 % complete ) and 0 restraints for refining 3956 atoms. Observations/parameters ratio is 0.54 ------------------------------------------------------ Starting model: R = 0.2905 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2588 (Rfree = 0.000) for 3956 atoms. Found 29 (29 requested) and removed 32 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.14 2.86 Search for helices and strands: 0 residues in 0 chains, 3989 seeds are put forward NCS extension: 0 residues added, 3989 seeds are put forward Round 1: 284 peptides, 47 chains. Longest chain 19 peptides. Score 0.455 Round 2: 339 peptides, 38 chains. Longest chain 25 peptides. Score 0.665 Round 3: 351 peptides, 37 chains. Longest chain 27 peptides. Score 0.694 Round 4: 354 peptides, 33 chains. Longest chain 32 peptides. Score 0.729 Round 5: 366 peptides, 30 chains. Longest chain 69 peptides. Score 0.766 Taking the results from Round 5 Chains 34, Residues 336, Estimated correctness of the model 73.3 % 6 chains (129 residues) have been docked in sequence Building loops using Loopy2018 34 chains (336 residues) following loop building 6 chains (129 residues) in sequence following loop building ------------------------------------------------------ 8484 reflections ( 99.60 % complete ) and 5260 restraints for refining 3255 atoms. 3433 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2608 (Rfree = 0.000) for 3255 atoms. Found 24 (24 requested) and removed 28 (12 requested) atoms. Cycle 2: After refmac, R = 0.2432 (Rfree = 0.000) for 3217 atoms. Found 17 (24 requested) and removed 18 (12 requested) atoms. Cycle 3: After refmac, R = 0.2364 (Rfree = 0.000) for 3200 atoms. Found 13 (23 requested) and removed 18 (12 requested) atoms. Cycle 4: After refmac, R = 0.2251 (Rfree = 0.000) for 3182 atoms. Found 10 (23 requested) and removed 15 (12 requested) atoms. Cycle 5: After refmac, R = 0.2192 (Rfree = 0.000) for 3171 atoms. Found 8 (21 requested) and removed 14 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.15 2.87 Search for helices and strands: 0 residues in 0 chains, 3225 seeds are put forward NCS extension: 13 residues added (21 deleted due to clashes), 3238 seeds are put forward Round 1: 329 peptides, 34 chains. Longest chain 24 peptides. Score 0.680 Round 2: 361 peptides, 28 chains. Longest chain 51 peptides. Score 0.773 Round 3: 362 peptides, 29 chains. Longest chain 43 peptides. Score 0.768 Round 4: 372 peptides, 26 chains. Longest chain 30 peptides. Score 0.799 Round 5: 367 peptides, 27 chains. Longest chain 38 peptides. Score 0.787 Taking the results from Round 4 Chains 30, Residues 346, Estimated correctness of the model 79.8 % 8 chains (157 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 64 B and 72 B Built loop between residues 86 B and 89 B 28 chains (355 residues) following loop building 6 chains (166 residues) in sequence following loop building ------------------------------------------------------ 8484 reflections ( 99.60 % complete ) and 5086 restraints for refining 3258 atoms. 3031 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2633 (Rfree = 0.000) for 3258 atoms. Found 22 (22 requested) and removed 25 (12 requested) atoms. Cycle 7: After refmac, R = 0.2393 (Rfree = 0.000) for 3236 atoms. Found 16 (21 requested) and removed 21 (12 requested) atoms. Cycle 8: After refmac, R = 0.2244 (Rfree = 0.000) for 3224 atoms. Found 7 (21 requested) and removed 14 (12 requested) atoms. Cycle 9: After refmac, R = 0.2159 (Rfree = 0.000) for 3212 atoms. Found 3 (20 requested) and removed 16 (12 requested) atoms. Cycle 10: After refmac, R = 0.2098 (Rfree = 0.000) for 3193 atoms. Found 6 (20 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.10 2.82 Search for helices and strands: 0 residues in 0 chains, 3263 seeds are put forward NCS extension: 47 residues added (31 deleted due to clashes), 3310 seeds are put forward Round 1: 350 peptides, 31 chains. Longest chain 30 peptides. Score 0.737 Round 2: 382 peptides, 25 chains. Longest chain 40 peptides. Score 0.816 Round 3: 377 peptides, 28 chains. Longest chain 38 peptides. Score 0.793 Round 4: 370 peptides, 29 chains. Longest chain 32 peptides. Score 0.778 Round 5: 379 peptides, 24 chains. Longest chain 36 peptides. Score 0.818 Taking the results from Round 5 Chains 30, Residues 355, Estimated correctness of the model 83.1 % 8 chains (174 residues) have been docked in sequence Building loops using Loopy2018 30 chains (355 residues) following loop building 8 chains (174 residues) in sequence following loop building ------------------------------------------------------ 8484 reflections ( 99.60 % complete ) and 4908 restraints for refining 3258 atoms. 2797 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2752 (Rfree = 0.000) for 3258 atoms. Found 19 (19 requested) and removed 38 (12 requested) atoms. Cycle 12: After refmac, R = 0.2514 (Rfree = 0.000) for 3218 atoms. Found 18 (19 requested) and removed 20 (12 requested) atoms. Cycle 13: After refmac, R = 0.2351 (Rfree = 0.000) for 3208 atoms. Found 11 (18 requested) and removed 15 (12 requested) atoms. Cycle 14: After refmac, R = 0.2241 (Rfree = 0.000) for 3201 atoms. Found 9 (18 requested) and removed 15 (12 requested) atoms. Cycle 15: After refmac, R = 0.2192 (Rfree = 0.000) for 3190 atoms. Found 7 (17 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.10 2.82 Search for helices and strands: 0 residues in 0 chains, 3237 seeds are put forward NCS extension: 10 residues added (16 deleted due to clashes), 3247 seeds are put forward Round 1: 344 peptides, 32 chains. Longest chain 34 peptides. Score 0.721 Round 2: 370 peptides, 23 chains. Longest chain 44 peptides. Score 0.814 Round 3: 346 peptides, 27 chains. Longest chain 40 peptides. Score 0.759 Round 4: 372 peptides, 27 chains. Longest chain 45 peptides. Score 0.793 Round 5: 374 peptides, 28 chains. Longest chain 39 peptides. Score 0.789 Taking the results from Round 2 Chains 26, Residues 347, Estimated correctness of the model 82.4 % 9 chains (195 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 85 A and 88 A 25 chains (348 residues) following loop building 8 chains (197 residues) in sequence following loop building ------------------------------------------------------ 8484 reflections ( 99.60 % complete ) and 4916 restraints for refining 3258 atoms. 2794 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2585 (Rfree = 0.000) for 3258 atoms. Found 17 (17 requested) and removed 38 (12 requested) atoms. Cycle 17: After refmac, R = 0.2285 (Rfree = 0.000) for 3231 atoms. Found 14 (16 requested) and removed 15 (12 requested) atoms. Cycle 18: After refmac, R = 0.2168 (Rfree = 0.000) for 3227 atoms. Found 6 (16 requested) and removed 14 (12 requested) atoms. Cycle 19: After refmac, R = 0.2142 (Rfree = 0.000) for 3215 atoms. Found 9 (15 requested) and removed 15 (12 requested) atoms. Cycle 20: After refmac, R = 0.2084 (Rfree = 0.000) for 3207 atoms. Found 11 (15 requested) and removed 14 (12 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.12 2.84 Search for helices and strands: 0 residues in 0 chains, 3257 seeds are put forward NCS extension: 64 residues added (64 deleted due to clashes), 3321 seeds are put forward Round 1: 332 peptides, 29 chains. Longest chain 36 peptides. Score 0.725 Round 2: 351 peptides, 25 chains. Longest chain 41 peptides. Score 0.779 Round 3: 355 peptides, 25 chains. Longest chain 45 peptides. Score 0.784 Round 4: 367 peptides, 28 chains. Longest chain 53 peptides. Score 0.780 Round 5: 353 peptides, 25 chains. Longest chain 61 peptides. Score 0.782 Taking the results from Round 3 Chains 30, Residues 330, Estimated correctness of the model 76.9 % 9 chains (173 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 78 A and 81 A Built loop between residues 98 C and 104 C Built loop between residues 83 B and 88 B 25 chains (336 residues) following loop building 6 chains (184 residues) in sequence following loop building ------------------------------------------------------ 8484 reflections ( 99.60 % complete ) and 5009 restraints for refining 3258 atoms. 2951 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2571 (Rfree = 0.000) for 3258 atoms. Found 14 (14 requested) and removed 37 (12 requested) atoms. Cycle 22: After refmac, R = 0.2343 (Rfree = 0.000) for 3221 atoms. Found 14 (14 requested) and removed 21 (12 requested) atoms. Cycle 23: After refmac, R = 0.2239 (Rfree = 0.000) for 3212 atoms. Found 12 (13 requested) and removed 18 (12 requested) atoms. Cycle 24: After refmac, R = 0.2175 (Rfree = 0.000) for 3200 atoms. Found 7 (13 requested) and removed 14 (12 requested) atoms. Cycle 25: After refmac, R = 0.2143 (Rfree = 0.000) for 3188 atoms. Found 8 (12 requested) and removed 15 (12 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.15 2.87 Search for helices and strands: 0 residues in 0 chains, 3255 seeds are put forward NCS extension: 38 residues added (56 deleted due to clashes), 3293 seeds are put forward Round 1: 330 peptides, 34 chains. Longest chain 26 peptides. Score 0.682 Round 2: 344 peptides, 29 chains. Longest chain 38 peptides. Score 0.743 Round 3: 346 peptides, 30 chains. Longest chain 36 peptides. Score 0.738 Round 4: 358 peptides, 28 chains. Longest chain 43 peptides. Score 0.769 Round 5: 350 peptides, 29 chains. Longest chain 33 peptides. Score 0.751 Taking the results from Round 4 Chains 32, Residues 330, Estimated correctness of the model 73.9 % 7 chains (159 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 38 A and 43 A Built loop between residues 84 A and 89 A Built loop between residues 65 C and 68 C 29 chains (340 residues) following loop building 4 chains (169 residues) in sequence following loop building ------------------------------------------------------ 8484 reflections ( 99.60 % complete ) and 5102 restraints for refining 3258 atoms. 3083 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2636 (Rfree = 0.000) for 3258 atoms. Found 12 (12 requested) and removed 33 (12 requested) atoms. Cycle 27: After refmac, R = 0.2426 (Rfree = 0.000) for 3223 atoms. Found 12 (12 requested) and removed 18 (12 requested) atoms. Cycle 28: After refmac, R = 0.2283 (Rfree = 0.000) for 3214 atoms. Found 11 (12 requested) and removed 15 (12 requested) atoms. Cycle 29: After refmac, R = 0.2211 (Rfree = 0.000) for 3209 atoms. Found 2 (12 requested) and removed 13 (12 requested) atoms. Cycle 30: After refmac, R = 0.2170 (Rfree = 0.000) for 3196 atoms. Found 5 (12 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.15 2.87 Search for helices and strands: 0 residues in 0 chains, 3251 seeds are put forward NCS extension: 99 residues added (72 deleted due to clashes), 3350 seeds are put forward Round 1: 321 peptides, 36 chains. Longest chain 25 peptides. Score 0.649 Round 2: 358 peptides, 28 chains. Longest chain 51 peptides. Score 0.769 Round 3: 360 peptides, 32 chains. Longest chain 32 peptides. Score 0.745 Round 4: 350 peptides, 28 chains. Longest chain 51 peptides. Score 0.758 Round 5: 344 peptides, 32 chains. Longest chain 35 peptides. Score 0.721 Taking the results from Round 2 Chains 30, Residues 330, Estimated correctness of the model 73.9 % 7 chains (156 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 63 D and 70 D Built loop between residues 79 D and 88 D 26 chains (336 residues) following loop building 5 chains (170 residues) in sequence following loop building ------------------------------------------------------ 8484 reflections ( 99.60 % complete ) and 5149 restraints for refining 3258 atoms. 3162 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2549 (Rfree = 0.000) for 3258 atoms. Found 12 (12 requested) and removed 42 (12 requested) atoms. Cycle 32: After refmac, R = 0.2352 (Rfree = 0.000) for 3215 atoms. Found 10 (12 requested) and removed 19 (12 requested) atoms. Cycle 33: After refmac, R = 0.2296 (Rfree = 0.000) for 3199 atoms. Found 7 (12 requested) and removed 13 (12 requested) atoms. Cycle 34: After refmac, R = 0.2219 (Rfree = 0.000) for 3190 atoms. Found 6 (12 requested) and removed 13 (12 requested) atoms. Cycle 35: After refmac, R = 0.2165 (Rfree = 0.000) for 3178 atoms. Found 4 (12 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.12 2.84 Search for helices and strands: 0 residues in 0 chains, 3244 seeds are put forward NCS extension: 52 residues added (40 deleted due to clashes), 3296 seeds are put forward Round 1: 313 peptides, 37 chains. Longest chain 19 peptides. Score 0.624 Round 2: 345 peptides, 32 chains. Longest chain 40 peptides. Score 0.722 Round 3: 345 peptides, 34 chains. Longest chain 40 peptides. Score 0.707 Round 4: 344 peptides, 35 chains. Longest chain 26 peptides. Score 0.698 Round 5: 341 peptides, 35 chains. Longest chain 38 peptides. Score 0.693 Taking the results from Round 2 Chains 36, Residues 313, Estimated correctness of the model 63.4 % 6 chains (117 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 46 A and 53 A 32 chains (314 residues) following loop building 5 chains (123 residues) in sequence following loop building ------------------------------------------------------ 8484 reflections ( 99.60 % complete ) and 5772 restraints for refining 3258 atoms. 4066 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2564 (Rfree = 0.000) for 3258 atoms. Found 12 (12 requested) and removed 30 (12 requested) atoms. Cycle 37: After refmac, R = 0.2357 (Rfree = 0.000) for 3232 atoms. Found 11 (12 requested) and removed 16 (12 requested) atoms. Cycle 38: After refmac, R = 0.2269 (Rfree = 0.000) for 3225 atoms. Found 6 (12 requested) and removed 14 (12 requested) atoms. Cycle 39: After refmac, R = 0.2222 (Rfree = 0.000) for 3215 atoms. Found 10 (12 requested) and removed 13 (12 requested) atoms. Cycle 40: After refmac, R = 0.2176 (Rfree = 0.000) for 3209 atoms. Found 9 (12 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.12 2.84 Search for helices and strands: 0 residues in 0 chains, 3261 seeds are put forward NCS extension: 24 residues added (26 deleted due to clashes), 3285 seeds are put forward Round 1: 297 peptides, 40 chains. Longest chain 20 peptides. Score 0.561 Round 2: 330 peptides, 31 chains. Longest chain 25 peptides. Score 0.706 Round 3: 324 peptides, 33 chains. Longest chain 25 peptides. Score 0.680 Round 4: 322 peptides, 34 chains. Longest chain 28 peptides. Score 0.668 Round 5: 334 peptides, 34 chains. Longest chain 38 peptides. Score 0.689 Taking the results from Round 2 Chains 33, Residues 299, Estimated correctness of the model 59.4 % 4 chains (77 residues) have been docked in sequence Building loops using Loopy2018 33 chains (299 residues) following loop building 4 chains (77 residues) in sequence following loop building ------------------------------------------------------ 8484 reflections ( 99.60 % complete ) and 6170 restraints for refining 3258 atoms. 4686 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2509 (Rfree = 0.000) for 3258 atoms. Found 12 (12 requested) and removed 21 (12 requested) atoms. Cycle 42: After refmac, R = 0.2390 (Rfree = 0.000) for 3235 atoms. Found 12 (12 requested) and removed 16 (12 requested) atoms. Cycle 43: After refmac, R = 0.2317 (Rfree = 0.000) for 3228 atoms. Found 12 (12 requested) and removed 12 (12 requested) atoms. Cycle 44: After refmac, R = 0.2248 (Rfree = 0.000) for 3220 atoms. Found 12 (12 requested) and removed 14 (12 requested) atoms. Cycle 45: After refmac, R = 0.2166 (Rfree = 0.000) for 3215 atoms. Found 9 (12 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.16 2.88 Search for helices and strands: 0 residues in 0 chains, 3248 seeds are put forward NCS extension: 10 residues added (8 deleted due to clashes), 3258 seeds are put forward Round 1: 291 peptides, 39 chains. Longest chain 22 peptides. Score 0.558 Round 2: 326 peptides, 30 chains. Longest chain 25 peptides. Score 0.707 Round 3: 316 peptides, 31 chains. Longest chain 27 peptides. Score 0.682 Round 4: 316 peptides, 29 chains. Longest chain 30 peptides. Score 0.699 Round 5: 310 peptides, 28 chains. Longest chain 26 peptides. Score 0.697 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 32, Residues 296, Estimated correctness of the model 59.7 % 6 chains (107 residues) have been docked in sequence Sequence coverage is 36 % Consider running further cycles of model building using 2opk-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 39 B and 53 B 31 chains (304 residues) following loop building 5 chains (120 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8484 reflections ( 99.60 % complete ) and 5677 restraints for refining 3258 atoms. 4008 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2543 (Rfree = 0.000) for 3258 atoms. Found 0 (12 requested) and removed 10 (12 requested) atoms. Cycle 47: After refmac, R = 0.2426 (Rfree = 0.000) for 3238 atoms. Found 0 (12 requested) and removed 5 (12 requested) atoms. Cycle 48: After refmac, R = 0.2324 (Rfree = 0.000) for 3224 atoms. Found 0 (12 requested) and removed 4 (12 requested) atoms. Cycle 49: After refmac, R = 0.2302 (Rfree = 0.000) for 3215 atoms. TimeTaking 44.23