Mon 24 Dec 01:09:05 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 2nuj-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2nuj-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2nuj-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2nuj-3.2-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/2nuj-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2nuj-3.2-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 01:09:10 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/2nuj-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2nuj-3.2-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 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-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: 91 Cell parameters: 78.401 78.401 151.418 90.000 90.000 90.000 Input sequence file: 2nuj-3.2-parrot-mrncs.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 2889 atoms. Observations/parameters ratio is 0.71 ------------------------------------------------------ Starting model: R = 0.3123 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2970 (Rfree = 0.000) for 2889 atoms. Found 25 (25 requested) and removed 24 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.05 2.59 Search for helices and strands: 0 residues in 0 chains, 2946 seeds are put forward NCS extension: 0 residues added, 2946 seeds are put forward Round 1: 202 peptides, 30 chains. Longest chain 18 peptides. Score 0.475 Round 2: 234 peptides, 30 chains. Longest chain 24 peptides. Score 0.570 Round 3: 250 peptides, 31 chains. Longest chain 24 peptides. Score 0.600 Round 4: 255 peptides, 30 chains. Longest chain 42 peptides. Score 0.624 Round 5: 258 peptides, 25 chains. Longest chain 33 peptides. Score 0.684 Taking the results from Round 5 Chains 26, Residues 233, Estimated correctness of the model 61.7 % 5 chains (91 residues) have been docked in sequence ------------------------------------------------------ 8166 reflections ( 97.97 % complete ) and 4044 restraints for refining 2474 atoms. 2733 conditional restraints added. Observations/parameters ratio is 0.83 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3110 (Rfree = 0.000) for 2474 atoms. Found 22 (22 requested) and removed 17 (11 requested) atoms. Cycle 2: After refmac, R = 0.2666 (Rfree = 0.000) for 2428 atoms. Found 14 (22 requested) and removed 13 (11 requested) atoms. Cycle 3: After refmac, R = 0.2572 (Rfree = 0.000) for 2403 atoms. Found 19 (21 requested) and removed 10 (10 requested) atoms. Cycle 4: After refmac, R = 0.2442 (Rfree = 0.000) for 2404 atoms. Found 10 (21 requested) and removed 10 (10 requested) atoms. Cycle 5: After refmac, R = 0.2419 (Rfree = 0.000) for 2393 atoms. Found 7 (21 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.04 2.58 Search for helices and strands: 0 residues in 0 chains, 2443 seeds are put forward NCS extension: 40 residues added (5 deleted due to clashes), 2483 seeds are put forward Round 1: 240 peptides, 23 chains. Longest chain 42 peptides. Score 0.665 Round 2: 272 peptides, 24 chains. Longest chain 45 peptides. Score 0.722 Round 3: 277 peptides, 24 chains. Longest chain 46 peptides. Score 0.731 Round 4: 272 peptides, 24 chains. Longest chain 46 peptides. Score 0.722 Round 5: 285 peptides, 21 chains. Longest chain 65 peptides. Score 0.771 Taking the results from Round 5 Chains 23, Residues 264, Estimated correctness of the model 78.8 % 7 chains (156 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 89 A and 91 A 22 chains (264 residues) following loop building 6 chains (157 residues) in sequence following loop building ------------------------------------------------------ 8166 reflections ( 97.97 % complete ) and 3314 restraints for refining 2402 atoms. 1682 conditional restraints added. Observations/parameters ratio is 0.85 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2817 (Rfree = 0.000) for 2402 atoms. Found 21 (21 requested) and removed 14 (10 requested) atoms. Cycle 7: After refmac, R = 0.2607 (Rfree = 0.000) for 2386 atoms. Found 13 (21 requested) and removed 11 (10 requested) atoms. Cycle 8: After refmac, R = 0.2457 (Rfree = 0.000) for 2380 atoms. Found 11 (20 requested) and removed 10 (10 requested) atoms. Cycle 9: After refmac, R = 0.2343 (Rfree = 0.000) for 2376 atoms. Found 7 (20 requested) and removed 10 (10 requested) atoms. Cycle 10: After refmac, R = 0.2247 (Rfree = 0.000) for 2368 atoms. Found 3 (19 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.07 2.61 Search for helices and strands: 0 residues in 0 chains, 2399 seeds are put forward NCS extension: 66 residues added (54 deleted due to clashes), 2465 seeds are put forward Round 1: 252 peptides, 21 chains. Longest chain 51 peptides. Score 0.711 Round 2: 264 peptides, 21 chains. Longest chain 48 peptides. Score 0.734 Round 3: 281 peptides, 17 chains. Longest chain 78 peptides. Score 0.796 Round 4: 275 peptides, 18 chains. Longest chain 46 peptides. Score 0.779 Round 5: 270 peptides, 17 chains. Longest chain 47 peptides. Score 0.779 Taking the results from Round 3 Chains 20, Residues 264, Estimated correctness of the model 82.8 % 6 chains (179 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 69 A and 74 A Built loop between residues 118 A and 128 A 16 chains (271 residues) following loop building 4 chains (192 residues) in sequence following loop building ------------------------------------------------------ 8166 reflections ( 97.97 % complete ) and 3237 restraints for refining 2489 atoms. 1378 conditional restraints added. Observations/parameters ratio is 0.82 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2630 (Rfree = 0.000) for 2489 atoms. Found 20 (20 requested) and removed 22 (11 requested) atoms. Cycle 12: After refmac, R = 0.2374 (Rfree = 0.000) for 2477 atoms. Found 16 (19 requested) and removed 14 (11 requested) atoms. Cycle 13: After refmac, R = 0.2349 (Rfree = 0.000) for 2471 atoms. Found 15 (19 requested) and removed 12 (11 requested) atoms. Cycle 14: After refmac, R = 0.2143 (Rfree = 0.000) for 2466 atoms. Found 11 (18 requested) and removed 13 (11 requested) atoms. Cycle 15: After refmac, R = 0.2383 (Rfree = 0.000) for 2460 atoms. Found 18 (18 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.04 2.58 Search for helices and strands: 0 residues in 0 chains, 2533 seeds are put forward NCS extension: 49 residues added (60 deleted due to clashes), 2582 seeds are put forward Round 1: 260 peptides, 20 chains. Longest chain 46 peptides. Score 0.736 Round 2: 267 peptides, 16 chains. Longest chain 37 peptides. Score 0.783 Round 3: 267 peptides, 17 chains. Longest chain 75 peptides. Score 0.775 Round 4: 274 peptides, 14 chains. Longest chain 59 peptides. Score 0.809 Round 5: 254 peptides, 15 chains. Longest chain 49 peptides. Score 0.770 Taking the results from Round 4 Chains 22, Residues 260, Estimated correctness of the model 84.8 % 8 chains (191 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 118 A and 128 A Built loop between residues 139 A and 143 A Built loop between residues 45 B and 56 B Built loop between residues 69 B and 74 B Built loop between residues 102 B and 105 B 13 chains (279 residues) following loop building 3 chains (219 residues) in sequence following loop building ------------------------------------------------------ 8166 reflections ( 97.97 % complete ) and 3177 restraints for refining 2555 atoms. 1194 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2756 (Rfree = 0.000) for 2555 atoms. Found 18 (18 requested) and removed 27 (11 requested) atoms. Cycle 17: After refmac, R = 0.2667 (Rfree = 0.000) for 2534 atoms. Found 17 (17 requested) and removed 15 (11 requested) atoms. Cycle 18: After refmac, R = 0.2487 (Rfree = 0.000) for 2520 atoms. Found 17 (17 requested) and removed 14 (11 requested) atoms. Cycle 19: After refmac, R = 0.2414 (Rfree = 0.000) for 2509 atoms. Found 16 (16 requested) and removed 17 (11 requested) atoms. Cycle 20: After refmac, R = 0.2367 (Rfree = 0.000) for 2507 atoms. Found 16 (16 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.05 2.59 Search for helices and strands: 0 residues in 0 chains, 2587 seeds are put forward NCS extension: 89 residues added (16 deleted due to clashes), 2676 seeds are put forward Round 1: 259 peptides, 17 chains. Longest chain 67 peptides. Score 0.761 Round 2: 268 peptides, 13 chains. Longest chain 88 peptides. Score 0.808 Round 3: 263 peptides, 20 chains. Longest chain 54 peptides. Score 0.742 Round 4: 279 peptides, 18 chains. Longest chain 63 peptides. Score 0.785 Round 5: 281 peptides, 18 chains. Longest chain 51 peptides. Score 0.788 Taking the results from Round 2 Chains 17, Residues 255, Estimated correctness of the model 84.6 % 5 chains (177 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 97 B and 100 B 16 chains (257 residues) following loop building 4 chains (179 residues) in sequence following loop building ------------------------------------------------------ 8166 reflections ( 97.97 % complete ) and 3433 restraints for refining 2421 atoms. 1717 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2441 (Rfree = 0.000) for 2421 atoms. Found 15 (15 requested) and removed 16 (10 requested) atoms. Cycle 22: After refmac, R = 0.2211 (Rfree = 0.000) for 2414 atoms. Found 14 (14 requested) and removed 12 (10 requested) atoms. Cycle 23: After refmac, R = 0.2088 (Rfree = 0.000) for 2407 atoms. Found 14 (14 requested) and removed 11 (10 requested) atoms. Cycle 24: After refmac, R = 0.1977 (Rfree = 0.000) for 2408 atoms. Found 9 (13 requested) and removed 10 (10 requested) atoms. Cycle 25: After refmac, R = 0.1963 (Rfree = 0.000) for 2407 atoms. Found 6 (13 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.04 2.58 Search for helices and strands: 0 residues in 0 chains, 2473 seeds are put forward NCS extension: 61 residues added (3 deleted due to clashes), 2534 seeds are put forward Round 1: 271 peptides, 16 chains. Longest chain 78 peptides. Score 0.789 Round 2: 285 peptides, 14 chains. Longest chain 87 peptides. Score 0.824 Round 3: 275 peptides, 16 chains. Longest chain 75 peptides. Score 0.795 Round 4: 283 peptides, 11 chains. Longest chain 99 peptides. Score 0.842 Round 5: 278 peptides, 20 chains. Longest chain 71 peptides. Score 0.768 Taking the results from Round 4 Chains 16, Residues 272, Estimated correctness of the model 89.2 % 7 chains (228 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 19 B and 23 B Built loop between residues 39 B and 48 B Built loop between residues 69 B and 72 B 10 chains (282 residues) following loop building 4 chains (241 residues) in sequence following loop building ------------------------------------------------------ 8166 reflections ( 97.97 % complete ) and 3012 restraints for refining 2524 atoms. 918 conditional restraints added. Observations/parameters ratio is 0.81 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2315 (Rfree = 0.000) for 2524 atoms. Found 13 (13 requested) and removed 20 (11 requested) atoms. Cycle 27: After refmac, R = 0.2168 (Rfree = 0.000) for 2506 atoms. Found 13 (13 requested) and removed 14 (11 requested) atoms. Cycle 28: After refmac, R = 0.2133 (Rfree = 0.000) for 2497 atoms. Found 12 (12 requested) and removed 16 (11 requested) atoms. Cycle 29: After refmac, R = 0.1937 (Rfree = 0.000) for 2490 atoms. Found 12 (12 requested) and removed 14 (11 requested) atoms. Cycle 30: After refmac, R = 0.1879 (Rfree = 0.000) for 2485 atoms. Found 7 (11 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.03 2.57 Search for helices and strands: 0 residues in 0 chains, 2538 seeds are put forward NCS extension: 64 residues added (129 deleted due to clashes), 2602 seeds are put forward Round 1: 266 peptides, 19 chains. Longest chain 55 peptides. Score 0.756 Round 2: 280 peptides, 17 chains. Longest chain 76 peptides. Score 0.795 Round 3: 277 peptides, 15 chains. Longest chain 85 peptides. Score 0.806 Round 4: 280 peptides, 14 chains. Longest chain 81 peptides. Score 0.817 Round 5: 276 peptides, 15 chains. Longest chain 64 peptides. Score 0.804 Taking the results from Round 4 Chains 15, Residues 266, Estimated correctness of the model 85.9 % 6 chains (198 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 136 A and 142 A Built loop between residues 19 B and 27 B 12 chains (277 residues) following loop building 4 chains (210 residues) in sequence following loop building ------------------------------------------------------ 8166 reflections ( 97.97 % complete ) and 3241 restraints for refining 2465 atoms. 1316 conditional restraints added. Observations/parameters ratio is 0.83 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2631 (Rfree = 0.000) for 2465 atoms. Found 11 (11 requested) and removed 23 (11 requested) atoms. Cycle 32: After refmac, R = 0.2282 (Rfree = 0.000) for 2445 atoms. Found 11 (11 requested) and removed 12 (11 requested) atoms. Cycle 33: After refmac, R = 0.2313 (Rfree = 0.000) for 2439 atoms. Found 10 (10 requested) and removed 13 (10 requested) atoms. Cycle 34: After refmac, R = 0.2044 (Rfree = 0.000) for 2435 atoms. Found 10 (10 requested) and removed 11 (10 requested) atoms. Cycle 35: After refmac, R = 0.1956 (Rfree = 0.000) for 2432 atoms. Found 10 (10 requested) and removed 13 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.04 2.58 Search for helices and strands: 0 residues in 0 chains, 2477 seeds are put forward NCS extension: 72 residues added (19 deleted due to clashes), 2549 seeds are put forward Round 1: 275 peptides, 16 chains. Longest chain 75 peptides. Score 0.795 Round 2: 280 peptides, 16 chains. Longest chain 78 peptides. Score 0.802 Round 3: 289 peptides, 16 chains. Longest chain 78 peptides. Score 0.815 Round 4: 287 peptides, 15 chains. Longest chain 69 peptides. Score 0.819 Round 5: 280 peptides, 15 chains. Longest chain 84 peptides. Score 0.810 Taking the results from Round 4 Chains 15, Residues 272, Estimated correctness of the model 86.2 % 6 chains (198 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 13 A and 20 A Built loop between residues 19 B and 24 B 13 chains (282 residues) following loop building 4 chains (208 residues) in sequence following loop building ------------------------------------------------------ 8166 reflections ( 97.97 % complete ) and 3218 restraints for refining 2461 atoms. 1273 conditional restraints added. Observations/parameters ratio is 0.83 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2323 (Rfree = 0.000) for 2461 atoms. Found 11 (11 requested) and removed 21 (11 requested) atoms. Cycle 37: After refmac, R = 0.2260 (Rfree = 0.000) for 2442 atoms. Found 10 (10 requested) and removed 21 (10 requested) atoms. Cycle 38: After refmac, R = 0.2155 (Rfree = 0.000) for 2429 atoms. Found 10 (10 requested) and removed 11 (10 requested) atoms. Cycle 39: After refmac, R = 0.1974 (Rfree = 0.000) for 2422 atoms. Found 10 (10 requested) and removed 10 (10 requested) atoms. Cycle 40: After refmac, R = 0.2125 (Rfree = 0.000) for 2422 atoms. Found 10 (10 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.03 2.57 Search for helices and strands: 0 residues in 0 chains, 2474 seeds are put forward NCS extension: 33 residues added (8 deleted due to clashes), 2507 seeds are put forward Round 1: 274 peptides, 16 chains. Longest chain 46 peptides. Score 0.794 Round 2: 287 peptides, 10 chains. Longest chain 78 peptides. Score 0.853 Round 3: 286 peptides, 13 chains. Longest chain 90 peptides. Score 0.832 Round 4: 291 peptides, 14 chains. Longest chain 78 peptides. Score 0.831 Round 5: 279 peptides, 16 chains. Longest chain 70 peptides. Score 0.801 Taking the results from Round 2 Chains 12, Residues 277, Estimated correctness of the model 90.6 % 7 chains (254 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 23 A and 27 A Built loop between residues 135 A and 140 A Built loop between residues 20 B and 24 B Built loop between residues 68 B and 72 B 7 chains (289 residues) following loop building 3 chains (267 residues) in sequence following loop building ------------------------------------------------------ 8166 reflections ( 97.97 % complete ) and 2917 restraints for refining 2531 atoms. 698 conditional restraints added. Observations/parameters ratio is 0.81 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2350 (Rfree = 0.000) for 2531 atoms. Found 11 (11 requested) and removed 21 (11 requested) atoms. Cycle 42: After refmac, R = 0.2043 (Rfree = 0.000) for 2516 atoms. Found 11 (11 requested) and removed 14 (11 requested) atoms. Cycle 43: After refmac, R = 0.2078 (Rfree = 0.000) for 2505 atoms. Found 11 (11 requested) and removed 12 (11 requested) atoms. Cycle 44: After refmac, R = 0.1981 (Rfree = 0.000) for 2499 atoms. Found 11 (11 requested) and removed 11 (11 requested) atoms. Cycle 45: After refmac, R = 0.1815 (Rfree = 0.000) for 2497 atoms. Found 11 (11 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.06 2.60 Search for helices and strands: 0 residues in 0 chains, 2567 seeds are put forward NCS extension: 78 residues added (111 deleted due to clashes), 2645 seeds are put forward Round 1: 282 peptides, 15 chains. Longest chain 68 peptides. Score 0.813 Round 2: 285 peptides, 17 chains. Longest chain 66 peptides. Score 0.802 Round 3: 284 peptides, 14 chains. Longest chain 63 peptides. Score 0.822 Round 4: 281 peptides, 14 chains. Longest chain 72 peptides. Score 0.819 Round 5: 284 peptides, 13 chains. Longest chain 81 peptides. Score 0.830 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 14, Residues 271, Estimated correctness of the model 87.7 % 6 chains (226 residues) have been docked in sequence Sequence coverage is 83 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 19 B and 23 B Built loop between residues 46 B and 58 B Built loop between residues 66 B and 69 B 9 chains (279 residues) following loop building 3 chains (242 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 8166 reflections ( 97.97 % complete ) and 2095 restraints for refining 2053 atoms. Observations/parameters ratio is 0.99 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3325 (Rfree = 0.000) for 2053 atoms. Found 9 (9 requested) and removed 0 (9 requested) atoms. Cycle 47: After refmac, R = 0.3147 (Rfree = 0.000) for 2053 atoms. Found 6 (9 requested) and removed 1 (9 requested) atoms. Cycle 48: After refmac, R = 0.3068 (Rfree = 0.000) for 2053 atoms. Found 6 (9 requested) and removed 1 (9 requested) atoms. Cycle 49: After refmac, R = 0.3020 (Rfree = 0.000) for 2053 atoms. Found 2 (9 requested) and removed 0 (9 requested) atoms. Writing output files ... TimeTaking 45.03