null Tue 25 Dec 19:27:57 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 2nuj-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2nuj-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2nuj-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2nuj-3.2-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/2nuj-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2nuj-3.2-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 ============================================================ Tue 25 Dec 19:28:12 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/2nuj-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2nuj-3.2-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 337 and 0 Target number of residues in the AU: 337 Target solvent content: 0.6081 Checking the provided sequence file Detected sequence length: 163 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 326 Adjusted target solvent content: 0.62 Input MTZ file: 2nuj-3.2-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: 91 Cell parameters: 78.401 78.401 151.418 90.000 90.000 90.000 Input sequence file: 2nuj-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 2608 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: 78.401 3.200 Wilson plot Bfac: 55.75 8166 reflections ( 97.97 % complete ) and 0 restraints for refining 2908 atoms. Observations/parameters ratio is 0.70 ------------------------------------------------------ Starting model: R = 0.3153 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3085 (Rfree = 0.000) for 2908 atoms. Found 26 (26 requested) and removed 24 (13 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.04 2.58 Search for helices and strands: 0 residues in 0 chains, 2952 seeds are put forward NCS extension: 0 residues added, 2952 seeds are put forward Round 1: 206 peptides, 35 chains. Longest chain 19 peptides. Score 0.417 Round 2: 241 peptides, 31 chains. Longest chain 24 peptides. Score 0.576 Round 3: 233 peptides, 29 chains. Longest chain 24 peptides. Score 0.579 Round 4: 239 peptides, 25 chains. Longest chain 21 peptides. Score 0.641 Round 5: 247 peptides, 22 chains. Longest chain 28 peptides. Score 0.691 Taking the results from Round 5 Chains 24, Residues 225, Estimated correctness of the model 63.2 % 3 chains (68 residues) have been docked in sequence ------------------------------------------------------ 8166 reflections ( 97.97 % complete ) and 4245 restraints for refining 2487 atoms. 3071 conditional restraints added. Observations/parameters ratio is 0.82 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2841 (Rfree = 0.000) for 2487 atoms. Found 19 (22 requested) and removed 18 (11 requested) atoms. Cycle 2: After refmac, R = 0.2656 (Rfree = 0.000) for 2466 atoms. Found 8 (22 requested) and removed 20 (11 requested) atoms. Cycle 3: After refmac, R = 0.2625 (Rfree = 0.000) for 2442 atoms. Found 14 (22 requested) and removed 12 (11 requested) atoms. Cycle 4: After refmac, R = 0.2558 (Rfree = 0.000) for 2431 atoms. Found 10 (21 requested) and removed 16 (10 requested) atoms. Cycle 5: After refmac, R = 0.2508 (Rfree = 0.000) for 2423 atoms. Found 6 (21 requested) and removed 13 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.03 2.57 Search for helices and strands: 0 residues in 0 chains, 2484 seeds are put forward NCS extension: 40 residues added (2 deleted due to clashes), 2524 seeds are put forward Round 1: 227 peptides, 26 chains. Longest chain 26 peptides. Score 0.600 Round 2: 249 peptides, 23 chains. Longest chain 49 peptides. Score 0.685 Round 3: 248 peptides, 22 chains. Longest chain 51 peptides. Score 0.693 Round 4: 262 peptides, 19 chains. Longest chain 51 peptides. Score 0.749 Round 5: 253 peptides, 21 chains. Longest chain 51 peptides. Score 0.713 Taking the results from Round 4 Chains 20, Residues 243, Estimated correctness of the model 74.9 % 6 chains (155 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 19 B and 24 B Built loop between residues 69 B and 76 B 17 chains (251 residues) following loop building 4 chains (165 residues) in sequence following loop building ------------------------------------------------------ 8166 reflections ( 97.97 % complete ) and 3405 restraints for refining 2492 atoms. 1715 conditional restraints added. Observations/parameters ratio is 0.82 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3059 (Rfree = 0.000) for 2492 atoms. Found 22 (22 requested) and removed 25 (11 requested) atoms. Cycle 7: After refmac, R = 0.2826 (Rfree = 0.000) for 2471 atoms. Found 22 (22 requested) and removed 23 (11 requested) atoms. Cycle 8: After refmac, R = 0.2705 (Rfree = 0.000) for 2457 atoms. Found 18 (21 requested) and removed 22 (11 requested) atoms. Cycle 9: After refmac, R = 0.2501 (Rfree = 0.000) for 2442 atoms. Found 19 (21 requested) and removed 17 (11 requested) atoms. Cycle 10: After refmac, R = 0.2687 (Rfree = 0.000) for 2435 atoms. Found 19 (19 requested) and removed 14 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.07 2.61 Search for helices and strands: 0 residues in 0 chains, 2513 seeds are put forward NCS extension: 90 residues added (8 deleted due to clashes), 2603 seeds are put forward Round 1: 238 peptides, 23 chains. Longest chain 28 peptides. Score 0.661 Round 2: 258 peptides, 21 chains. Longest chain 47 peptides. Score 0.723 Round 3: 275 peptides, 17 chains. Longest chain 51 peptides. Score 0.787 Round 4: 266 peptides, 14 chains. Longest chain 54 peptides. Score 0.797 Round 5: 262 peptides, 14 chains. Longest chain 51 peptides. Score 0.791 Taking the results from Round 4 Chains 19, Residues 252, Estimated correctness of the model 83.0 % 8 chains (185 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 67 A and 73 A Built loop between residues 39 B and 49 B Built loop between residues 69 B and 76 B Built loop between residues 124 B and 127 B Built loop between residues 137 B and 142 B 11 chains (265 residues) following loop building 3 chains (211 residues) in sequence following loop building ------------------------------------------------------ 8166 reflections ( 97.97 % complete ) and 3333 restraints for refining 2602 atoms. 1375 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2797 (Rfree = 0.000) for 2602 atoms. Found 21 (21 requested) and removed 37 (11 requested) atoms. Cycle 12: After refmac, R = 0.2539 (Rfree = 0.000) for 2574 atoms. Found 16 (20 requested) and removed 13 (11 requested) atoms. Cycle 13: After refmac, R = 0.2423 (Rfree = 0.000) for 2568 atoms. Found 10 (20 requested) and removed 11 (11 requested) atoms. Cycle 14: After refmac, R = 0.2342 (Rfree = 0.000) for 2564 atoms. Found 3 (19 requested) and removed 13 (11 requested) atoms. Cycle 15: After refmac, R = 0.2326 (Rfree = 0.000) for 2552 atoms. Found 6 (18 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.08 2.62 Search for helices and strands: 0 residues in 0 chains, 2616 seeds are put forward NCS extension: 192 residues added (35 deleted due to clashes), 2808 seeds are put forward Round 1: 247 peptides, 20 chains. Longest chain 50 peptides. Score 0.711 Round 2: 254 peptides, 19 chains. Longest chain 57 peptides. Score 0.734 Round 3: 269 peptides, 21 chains. Longest chain 46 peptides. Score 0.744 Round 4: 264 peptides, 17 chains. Longest chain 82 peptides. Score 0.770 Round 5: 259 peptides, 18 chains. Longest chain 48 peptides. Score 0.752 Taking the results from Round 4 Chains 22, Residues 247, Estimated correctness of the model 78.6 % 5 chains (144 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 69 A and 76 A 20 chains (248 residues) following loop building 4 chains (150 residues) in sequence following loop building ------------------------------------------------------ 8166 reflections ( 97.97 % complete ) and 3531 restraints for refining 2404 atoms. 1991 conditional restraints added. Observations/parameters ratio is 0.85 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2994 (Rfree = 0.000) for 2404 atoms. Found 17 (17 requested) and removed 24 (10 requested) atoms. Cycle 17: After refmac, R = 0.2818 (Rfree = 0.000) for 2390 atoms. Found 16 (16 requested) and removed 13 (10 requested) atoms. Cycle 18: After refmac, R = 0.2680 (Rfree = 0.000) for 2384 atoms. Found 14 (16 requested) and removed 13 (10 requested) atoms. Cycle 19: After refmac, R = 0.2518 (Rfree = 0.000) for 2382 atoms. Found 13 (16 requested) and removed 15 (10 requested) atoms. Cycle 20: After refmac, R = 0.2407 (Rfree = 0.000) for 2375 atoms. Found 9 (15 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.08 2.62 Search for helices and strands: 0 residues in 0 chains, 2440 seeds are put forward NCS extension: 88 residues added (25 deleted due to clashes), 2528 seeds are put forward Round 1: 244 peptides, 21 chains. Longest chain 50 peptides. Score 0.695 Round 2: 261 peptides, 16 chains. Longest chain 72 peptides. Score 0.773 Round 3: 263 peptides, 21 chains. Longest chain 53 peptides. Score 0.733 Round 4: 256 peptides, 18 chains. Longest chain 62 peptides. Score 0.747 Round 5: 267 peptides, 17 chains. Longest chain 70 peptides. Score 0.775 Taking the results from Round 5 Chains 19, Residues 250, Estimated correctness of the model 79.4 % 3 chains (125 residues) have been docked in sequence Building loops using Loopy2018 19 chains (250 residues) following loop building 3 chains (125 residues) in sequence following loop building ------------------------------------------------------ 8166 reflections ( 97.97 % complete ) and 3631 restraints for refining 2394 atoms. 2104 conditional restraints added. Observations/parameters ratio is 0.85 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2961 (Rfree = 0.000) for 2394 atoms. Found 15 (15 requested) and removed 24 (10 requested) atoms. Cycle 22: After refmac, R = 0.2741 (Rfree = 0.000) for 2378 atoms. Found 14 (14 requested) and removed 13 (10 requested) atoms. Cycle 23: After refmac, R = 0.2801 (Rfree = 0.000) for 2377 atoms. Found 14 (14 requested) and removed 15 (10 requested) atoms. Cycle 24: After refmac, R = 0.2554 (Rfree = 0.000) for 2368 atoms. Found 11 (13 requested) and removed 11 (10 requested) atoms. Cycle 25: After refmac, R = 0.2488 (Rfree = 0.000) for 2364 atoms. Found 13 (13 requested) and removed 13 (10 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.06 2.60 Search for helices and strands: 0 residues in 0 chains, 2427 seeds are put forward NCS extension: 6 residues added (15 deleted due to clashes), 2433 seeds are put forward Round 1: 252 peptides, 22 chains. Longest chain 48 peptides. Score 0.702 Round 2: 254 peptides, 19 chains. Longest chain 48 peptides. Score 0.734 Round 3: 261 peptides, 15 chains. Longest chain 73 peptides. Score 0.782 Round 4: 263 peptides, 14 chains. Longest chain 73 peptides. Score 0.793 Round 5: 264 peptides, 22 chains. Longest chain 48 peptides. Score 0.725 Taking the results from Round 4 Chains 17, Residues 249, Estimated correctness of the model 82.3 % 3 chains (134 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 65 A and 71 A 16 chains (254 residues) following loop building 2 chains (139 residues) in sequence following loop building ------------------------------------------------------ 8166 reflections ( 97.97 % complete ) and 3401 restraints for refining 2380 atoms. 1822 conditional restraints added. Observations/parameters ratio is 0.86 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3026 (Rfree = 0.000) for 2380 atoms. Found 13 (13 requested) and removed 24 (10 requested) atoms. Cycle 27: After refmac, R = 0.2916 (Rfree = 0.000) for 2355 atoms. Found 12 (12 requested) and removed 17 (10 requested) atoms. Cycle 28: After refmac, R = 0.2771 (Rfree = 0.000) for 2338 atoms. Found 12 (12 requested) and removed 14 (10 requested) atoms. Cycle 29: After refmac, R = 0.2842 (Rfree = 0.000) for 2330 atoms. Found 11 (11 requested) and removed 11 (10 requested) atoms. Cycle 30: After refmac, R = 0.2545 (Rfree = 0.000) for 2321 atoms. Found 10 (10 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.07 2.61 Search for helices and strands: 0 residues in 0 chains, 2396 seeds are put forward NCS extension: 93 residues added (21 deleted due to clashes), 2489 seeds are put forward Round 1: 232 peptides, 23 chains. Longest chain 38 peptides. Score 0.647 Round 2: 254 peptides, 18 chains. Longest chain 50 peptides. Score 0.744 Round 3: 262 peptides, 19 chains. Longest chain 49 peptides. Score 0.749 Round 4: 256 peptides, 23 chains. Longest chain 54 peptides. Score 0.700 Round 5: 260 peptides, 25 chains. Longest chain 37 peptides. Score 0.688 Taking the results from Round 3 Chains 20, Residues 243, Estimated correctness of the model 74.9 % 5 chains (137 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 67 A and 71 A Built loop between residues 104 B and 109 B 17 chains (248 residues) following loop building 3 chains (144 residues) in sequence following loop building ------------------------------------------------------ 8166 reflections ( 97.97 % complete ) and 3523 restraints for refining 2381 atoms. 1946 conditional restraints added. Observations/parameters ratio is 0.86 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3004 (Rfree = 0.000) for 2381 atoms. Found 10 (10 requested) and removed 18 (10 requested) atoms. Cycle 32: After refmac, R = 0.2704 (Rfree = 0.000) for 2360 atoms. Found 10 (10 requested) and removed 12 (10 requested) atoms. Cycle 33: After refmac, R = 0.2586 (Rfree = 0.000) for 2353 atoms. Found 10 (10 requested) and removed 16 (10 requested) atoms. Cycle 34: After refmac, R = 0.2516 (Rfree = 0.000) for 2341 atoms. Found 10 (10 requested) and removed 15 (10 requested) atoms. Cycle 35: After refmac, R = 0.2455 (Rfree = 0.000) for 2333 atoms. Found 10 (10 requested) and removed 13 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.05 2.59 Search for helices and strands: 0 residues in 0 chains, 2386 seeds are put forward NCS extension: 92 residues added (27 deleted due to clashes), 2478 seeds are put forward Round 1: 266 peptides, 20 chains. Longest chain 47 peptides. Score 0.747 Round 2: 272 peptides, 16 chains. Longest chain 51 peptides. Score 0.791 Round 3: 272 peptides, 15 chains. Longest chain 68 peptides. Score 0.798 Round 4: 262 peptides, 18 chains. Longest chain 65 peptides. Score 0.758 Round 5: 270 peptides, 17 chains. Longest chain 68 peptides. Score 0.779 Taking the results from Round 3 Chains 21, Residues 257, Estimated correctness of the model 83.1 % 6 chains (161 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 44 A and 51 A Built loop between residues 69 A and 76 A 18 chains (264 residues) following loop building 4 chains (173 residues) in sequence following loop building ------------------------------------------------------ 8166 reflections ( 97.97 % complete ) and 3200 restraints for refining 2381 atoms. 1434 conditional restraints added. Observations/parameters ratio is 0.86 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2910 (Rfree = 0.000) for 2381 atoms. Found 10 (10 requested) and removed 23 (10 requested) atoms. Cycle 37: After refmac, R = 0.2663 (Rfree = 0.000) for 2357 atoms. Found 10 (10 requested) and removed 13 (10 requested) atoms. Cycle 38: After refmac, R = 0.2553 (Rfree = 0.000) for 2350 atoms. Found 10 (10 requested) and removed 17 (10 requested) atoms. Cycle 39: After refmac, R = 0.2554 (Rfree = 0.000) for 2340 atoms. Found 10 (10 requested) and removed 15 (10 requested) atoms. Cycle 40: After refmac, R = 0.2541 (Rfree = 0.000) for 2327 atoms. Found 10 (10 requested) and removed 14 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.04 2.58 Search for helices and strands: 0 residues in 0 chains, 2392 seeds are put forward NCS extension: 79 residues added (71 deleted due to clashes), 2471 seeds are put forward Round 1: 261 peptides, 22 chains. Longest chain 37 peptides. Score 0.719 Round 2: 265 peptides, 15 chains. Longest chain 51 peptides. Score 0.788 Round 3: 265 peptides, 21 chains. Longest chain 38 peptides. Score 0.736 Round 4: 275 peptides, 17 chains. Longest chain 42 peptides. Score 0.787 Round 5: 261 peptides, 15 chains. Longest chain 46 peptides. Score 0.782 Taking the results from Round 2 Chains 17, Residues 250, Estimated correctness of the model 81.6 % 6 chains (164 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 19 B and 24 B 16 chains (254 residues) following loop building 5 chains (168 residues) in sequence following loop building ------------------------------------------------------ 8166 reflections ( 97.97 % complete ) and 3470 restraints for refining 2381 atoms. 1794 conditional restraints added. Observations/parameters ratio is 0.86 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2772 (Rfree = 0.000) for 2381 atoms. Found 10 (10 requested) and removed 18 (10 requested) atoms. Cycle 42: After refmac, R = 0.2547 (Rfree = 0.000) for 2364 atoms. Found 10 (10 requested) and removed 11 (10 requested) atoms. Cycle 43: After refmac, R = 0.2466 (Rfree = 0.000) for 2359 atoms. Found 10 (10 requested) and removed 11 (10 requested) atoms. Cycle 44: After refmac, R = 0.2324 (Rfree = 0.000) for 2357 atoms. Found 3 (10 requested) and removed 11 (10 requested) atoms. Cycle 45: After refmac, R = 0.2361 (Rfree = 0.000) for 2346 atoms. Found 6 (10 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.04 2.58 Search for helices and strands: 0 residues in 0 chains, 2401 seeds are put forward NCS extension: 61 residues added (32 deleted due to clashes), 2462 seeds are put forward Round 1: 261 peptides, 21 chains. Longest chain 37 peptides. Score 0.729 Round 2: 269 peptides, 16 chains. Longest chain 48 peptides. Score 0.786 Round 3: 249 peptides, 18 chains. Longest chain 48 peptides. Score 0.734 Round 4: 258 peptides, 16 chains. Longest chain 70 peptides. Score 0.768 Round 5: 259 peptides, 16 chains. Longest chain 50 peptides. Score 0.770 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 17, Residues 253, Estimated correctness of the model 81.2 % 7 chains (175 residues) have been docked in sequence Sequence coverage is 68 % Consider running further cycles of model building using 2nuj-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 45 A and 49 A Built loop between residues 60 A and 72 A Built loop between residues 19 B and 24 B Built loop between residues 46 B and 49 B Built loop between residues 68 B and 75 B 11 chains (274 residues) following loop building 2 chains (201 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8166 reflections ( 97.97 % complete ) and 3025 restraints for refining 2459 atoms. 1057 conditional restraints added. Observations/parameters ratio is 0.83 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2727 (Rfree = 0.000) for 2459 atoms. Found 0 (11 requested) and removed 5 (11 requested) atoms. Cycle 47: After refmac, R = 0.2543 (Rfree = 0.000) for 2443 atoms. Found 0 (11 requested) and removed 2 (11 requested) atoms. Cycle 48: After refmac, R = 0.2438 (Rfree = 0.000) for 2436 atoms. Found 0 (10 requested) and removed 2 (10 requested) atoms. Cycle 49: After refmac, R = 0.2400 (Rfree = 0.000) for 2430 atoms. Found 0 (10 requested) and removed 1 (10 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:38:06 GMT 2018 Job finished. TimeTaking 70.15 Used memory is bytes: 8406328