Sun 23 Dec 23:55:48 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 2aj7-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2aj7-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2aj7-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2aj7-3.2-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/2aj7-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2aj7-3.2-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 ============================================================ Sun 23 Dec 23:55:52 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/2aj7-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2aj7-3.2-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 415 and 0 Target number of residues in the AU: 415 Target solvent content: 0.6032 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: 0.69 Input MTZ file: 2aj7-3.2-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: 173 Cell parameters: 108.801 108.801 82.811 90.000 90.000 120.000 Input sequence file: 2aj7-3.2-parrot-mrncs.fasta_lf Building free atoms model in initial map for 2608 target number of atoms Had to go as low as 1.10 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: 94.224 3.200 Wilson plot Bfac: 53.85 9297 reflections ( 99.95 % complete ) and 0 restraints for refining 2915 atoms. Observations/parameters ratio is 0.80 ------------------------------------------------------ Starting model: R = 0.3199 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2406 (Rfree = 0.000) for 2915 atoms. Found 26 (26 requested) and removed 53 (13 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.98 2.28 Search for helices and strands: 0 residues in 0 chains, 2930 seeds are put forward NCS extension: 0 residues added, 2930 seeds are put forward Round 1: 213 peptides, 27 chains. Longest chain 16 peptides. Score 0.502 Round 2: 246 peptides, 19 chains. Longest chain 51 peptides. Score 0.661 Round 3: 249 peptides, 24 chains. Longest chain 28 peptides. Score 0.618 Round 4: 262 peptides, 17 chains. Longest chain 44 peptides. Score 0.709 Round 5: 261 peptides, 17 chains. Longest chain 39 peptides. Score 0.707 Taking the results from Round 4 Chains 19, Residues 245, Estimated correctness of the model 67.1 % 5 chains (139 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 129 A and 140 A 17 chains (252 residues) following loop building 4 chains (149 residues) in sequence following loop building ------------------------------------------------------ 9297 reflections ( 99.95 % complete ) and 3373 restraints for refining 2429 atoms. 1776 conditional restraints added. Observations/parameters ratio is 0.96 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2635 (Rfree = 0.000) for 2429 atoms. Found 21 (21 requested) and removed 26 (10 requested) atoms. Cycle 2: After refmac, R = 0.2429 (Rfree = 0.000) for 2382 atoms. Found 21 (21 requested) and removed 17 (10 requested) atoms. Cycle 3: After refmac, R = 0.2302 (Rfree = 0.000) for 2368 atoms. Found 20 (20 requested) and removed 10 (10 requested) atoms. Cycle 4: After refmac, R = 0.2198 (Rfree = 0.000) for 2373 atoms. Found 7 (20 requested) and removed 13 (10 requested) atoms. Cycle 5: After refmac, R = 0.2142 (Rfree = 0.000) for 2357 atoms. Found 11 (20 requested) and removed 13 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.01 2.31 Search for helices and strands: 0 residues in 0 chains, 2423 seeds are put forward NCS extension: 32 residues added (21 deleted due to clashes), 2455 seeds are put forward Round 1: 260 peptides, 15 chains. Longest chain 45 peptides. Score 0.722 Round 2: 260 peptides, 15 chains. Longest chain 38 peptides. Score 0.722 Round 3: 269 peptides, 13 chains. Longest chain 46 peptides. Score 0.753 Round 4: 268 peptides, 15 chains. Longest chain 46 peptides. Score 0.735 Round 5: 266 peptides, 20 chains. Longest chain 36 peptides. Score 0.689 Taking the results from Round 3 Chains 15, Residues 256, Estimated correctness of the model 75.6 % 8 chains (214 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 52 A and 56 A Built loop between residues 38 B and 41 B Built loop between residues 55 B and 59 B Built loop between residues 113 B and 116 B 10 chains (265 residues) following loop building 4 chains (224 residues) in sequence following loop building ------------------------------------------------------ 9297 reflections ( 99.95 % complete ) and 2887 restraints for refining 2465 atoms. 936 conditional restraints added. Observations/parameters ratio is 0.94 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2303 (Rfree = 0.000) for 2465 atoms. Found 20 (20 requested) and removed 30 (11 requested) atoms. Cycle 7: After refmac, R = 0.2167 (Rfree = 0.000) for 2438 atoms. Found 20 (20 requested) and removed 21 (11 requested) atoms. Cycle 8: After refmac, R = 0.2146 (Rfree = 0.000) for 2422 atoms. Found 15 (18 requested) and removed 17 (10 requested) atoms. Cycle 9: After refmac, R = 0.2020 (Rfree = 0.000) for 2410 atoms. Found 16 (18 requested) and removed 13 (10 requested) atoms. Cycle 10: After refmac, R = 0.2030 (Rfree = 0.000) for 2403 atoms. Found 18 (18 requested) and removed 17 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.98 2.28 Search for helices and strands: 0 residues in 0 chains, 2460 seeds are put forward NCS extension: 72 residues added (18 deleted due to clashes), 2532 seeds are put forward Round 1: 275 peptides, 12 chains. Longest chain 45 peptides. Score 0.769 Round 2: 280 peptides, 13 chains. Longest chain 67 peptides. Score 0.769 Round 3: 283 peptides, 12 chains. Longest chain 51 peptides. Score 0.780 Round 4: 276 peptides, 15 chains. Longest chain 39 peptides. Score 0.748 Round 5: 269 peptides, 14 chains. Longest chain 50 peptides. Score 0.745 Taking the results from Round 3 Chains 14, Residues 271, Estimated correctness of the model 80.3 % 6 chains (198 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 37 B and 40 B Built loop between residues 80 B and 84 B 11 chains (274 residues) following loop building 4 chains (203 residues) in sequence following loop building ------------------------------------------------------ 9297 reflections ( 99.95 % complete ) and 3014 restraints for refining 2408 atoms. 1078 conditional restraints added. Observations/parameters ratio is 0.97 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2199 (Rfree = 0.000) for 2408 atoms. Found 17 (17 requested) and removed 23 (10 requested) atoms. Cycle 12: After refmac, R = 0.2096 (Rfree = 0.000) for 2389 atoms. Found 17 (17 requested) and removed 21 (10 requested) atoms. Cycle 13: After refmac, R = 0.2043 (Rfree = 0.000) for 2380 atoms. Found 16 (16 requested) and removed 17 (10 requested) atoms. Cycle 14: After refmac, R = 0.1936 (Rfree = 0.000) for 2377 atoms. Found 16 (16 requested) and removed 11 (10 requested) atoms. Cycle 15: After refmac, R = 0.1884 (Rfree = 0.000) for 2381 atoms. Found 12 (16 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.00 2.30 Search for helices and strands: 0 residues in 0 chains, 2430 seeds are put forward NCS extension: 40 residues added (26 deleted due to clashes), 2470 seeds are put forward Round 1: 262 peptides, 14 chains. Longest chain 48 peptides. Score 0.734 Round 2: 279 peptides, 11 chains. Longest chain 63 peptides. Score 0.782 Round 3: 272 peptides, 11 chains. Longest chain 74 peptides. Score 0.773 Round 4: 270 peptides, 11 chains. Longest chain 66 peptides. Score 0.770 Round 5: 269 peptides, 12 chains. Longest chain 37 peptides. Score 0.761 Taking the results from Round 2 Chains 13, Residues 268, Estimated correctness of the model 80.6 % 6 chains (203 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 113 A and 116 A Built loop between residues 74 B and 77 B 10 chains (271 residues) following loop building 4 chains (207 residues) in sequence following loop building ------------------------------------------------------ 9297 reflections ( 99.95 % complete ) and 3016 restraints for refining 2381 atoms. 1090 conditional restraints added. Observations/parameters ratio is 0.98 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2068 (Rfree = 0.000) for 2381 atoms. Found 15 (15 requested) and removed 19 (10 requested) atoms. Cycle 17: After refmac, R = 0.2027 (Rfree = 0.000) for 2371 atoms. Found 15 (15 requested) and removed 14 (10 requested) atoms. Cycle 18: After refmac, R = 0.1881 (Rfree = 0.000) for 2369 atoms. Found 14 (14 requested) and removed 11 (10 requested) atoms. Cycle 19: After refmac, R = 0.1914 (Rfree = 0.000) for 2372 atoms. Found 14 (14 requested) and removed 10 (10 requested) atoms. Cycle 20: After refmac, R = 0.1884 (Rfree = 0.000) for 2375 atoms. Found 13 (13 requested) and removed 12 (10 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.00 2.30 Search for helices and strands: 0 residues in 0 chains, 2432 seeds are put forward NCS extension: 52 residues added (101 deleted due to clashes), 2484 seeds are put forward Round 1: 273 peptides, 16 chains. Longest chain 38 peptides. Score 0.735 Round 2: 280 peptides, 14 chains. Longest chain 67 peptides. Score 0.761 Round 3: 277 peptides, 11 chains. Longest chain 45 peptides. Score 0.780 Round 4: 271 peptides, 13 chains. Longest chain 59 peptides. Score 0.756 Round 5: 269 peptides, 13 chains. Longest chain 54 peptides. Score 0.753 Taking the results from Round 3 Chains 16, Residues 266, Estimated correctness of the model 80.3 % 8 chains (213 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 37 B and 40 B Built loop between residues 92 B and 97 B 14 chains (272 residues) following loop building 6 chains (219 residues) in sequence following loop building ------------------------------------------------------ 9297 reflections ( 99.95 % complete ) and 3018 restraints for refining 2428 atoms. 1047 conditional restraints added. Observations/parameters ratio is 0.96 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2194 (Rfree = 0.000) for 2428 atoms. Found 13 (13 requested) and removed 29 (10 requested) atoms. Cycle 22: After refmac, R = 0.2092 (Rfree = 0.000) for 2408 atoms. Found 13 (13 requested) and removed 17 (10 requested) atoms. Cycle 23: After refmac, R = 0.2051 (Rfree = 0.000) for 2399 atoms. Found 12 (12 requested) and removed 13 (10 requested) atoms. Cycle 24: After refmac, R = 0.2039 (Rfree = 0.000) for 2397 atoms. Found 12 (12 requested) and removed 14 (10 requested) atoms. Cycle 25: After refmac, R = 0.1887 (Rfree = 0.000) for 2395 atoms. Found 11 (11 requested) and removed 12 (10 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.98 2.28 Search for helices and strands: 0 residues in 0 chains, 2451 seeds are put forward NCS extension: 19 residues added (27 deleted due to clashes), 2470 seeds are put forward Round 1: 275 peptides, 11 chains. Longest chain 58 peptides. Score 0.777 Round 2: 278 peptides, 11 chains. Longest chain 43 peptides. Score 0.781 Round 3: 284 peptides, 9 chains. Longest chain 85 peptides. Score 0.803 Round 4: 279 peptides, 12 chains. Longest chain 48 peptides. Score 0.775 Round 5: 273 peptides, 12 chains. Longest chain 51 peptides. Score 0.767 Taking the results from Round 3 Chains 11, Residues 275, Estimated correctness of the model 83.9 % 7 chains (240 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 74 B and 78 B Built loop between residues 113 B and 116 B Built loop between residues 129 B and 133 B 7 chains (282 residues) following loop building 3 chains (248 residues) in sequence following loop building ------------------------------------------------------ 9297 reflections ( 99.95 % complete ) and 2857 restraints for refining 2497 atoms. 700 conditional restraints added. Observations/parameters ratio is 0.93 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2279 (Rfree = 0.000) for 2497 atoms. Found 11 (11 requested) and removed 50 (11 requested) atoms. Cycle 27: After refmac, R = 0.2056 (Rfree = 0.000) for 2450 atoms. Found 11 (11 requested) and removed 24 (11 requested) atoms. Cycle 28: After refmac, R = 0.2093 (Rfree = 0.000) for 2432 atoms. Found 10 (10 requested) and removed 20 (10 requested) atoms. Cycle 29: After refmac, R = 0.2030 (Rfree = 0.000) for 2420 atoms. Found 10 (10 requested) and removed 15 (10 requested) atoms. Cycle 30: After refmac, R = 0.1841 (Rfree = 0.000) for 2410 atoms. Found 10 (10 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.00 2.30 Search for helices and strands: 0 residues in 0 chains, 2489 seeds are put forward NCS extension: 34 residues added (17 deleted due to clashes), 2523 seeds are put forward Round 1: 273 peptides, 11 chains. Longest chain 64 peptides. Score 0.774 Round 2: 286 peptides, 8 chains. Longest chain 66 peptides. Score 0.813 Round 3: 283 peptides, 12 chains. Longest chain 52 peptides. Score 0.780 Round 4: 282 peptides, 10 chains. Longest chain 120 peptides. Score 0.794 Round 5: 274 peptides, 15 chains. Longest chain 43 peptides. Score 0.745 Taking the results from Round 2 Chains 10, Residues 278, Estimated correctness of the model 85.3 % 5 chains (222 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 141 B and 145 B 9 chains (281 residues) following loop building 4 chains (225 residues) in sequence following loop building ------------------------------------------------------ 9297 reflections ( 99.95 % complete ) and 2909 restraints for refining 2412 atoms. 865 conditional restraints added. Observations/parameters ratio is 0.96 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2180 (Rfree = 0.000) for 2412 atoms. Found 10 (10 requested) and removed 23 (10 requested) atoms. Cycle 32: After refmac, R = 0.2014 (Rfree = 0.000) for 2395 atoms. Found 10 (10 requested) and removed 21 (10 requested) atoms. Cycle 33: After refmac, R = 0.1982 (Rfree = 0.000) for 2383 atoms. Found 10 (10 requested) and removed 17 (10 requested) atoms. Cycle 34: After refmac, R = 0.1956 (Rfree = 0.000) for 2375 atoms. Found 10 (10 requested) and removed 15 (10 requested) atoms. Cycle 35: After refmac, R = 0.1957 (Rfree = 0.000) for 2369 atoms. Found 10 (10 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.00 2.30 Search for helices and strands: 0 residues in 0 chains, 2438 seeds are put forward NCS extension: 44 residues added (23 deleted due to clashes), 2482 seeds are put forward Round 1: 269 peptides, 15 chains. Longest chain 38 peptides. Score 0.737 Round 2: 278 peptides, 11 chains. Longest chain 56 peptides. Score 0.781 Round 3: 287 peptides, 9 chains. Longest chain 71 peptides. Score 0.807 Round 4: 276 peptides, 13 chains. Longest chain 40 peptides. Score 0.763 Round 5: 270 peptides, 10 chains. Longest chain 65 peptides. Score 0.778 Taking the results from Round 3 Chains 12, Residues 278, Estimated correctness of the model 84.5 % 5 chains (219 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 83 B and 94 B 10 chains (284 residues) following loop building 4 chains (229 residues) in sequence following loop building ------------------------------------------------------ 9297 reflections ( 99.95 % complete ) and 2862 restraints for refining 2405 atoms. 794 conditional restraints added. Observations/parameters ratio is 0.97 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2161 (Rfree = 0.000) for 2405 atoms. Found 10 (10 requested) and removed 22 (10 requested) atoms. Cycle 37: After refmac, R = 0.2012 (Rfree = 0.000) for 2387 atoms. Found 10 (10 requested) and removed 12 (10 requested) atoms. Cycle 38: After refmac, R = 0.2018 (Rfree = 0.000) for 2382 atoms. Found 10 (10 requested) and removed 15 (10 requested) atoms. Cycle 39: After refmac, R = 0.1914 (Rfree = 0.000) for 2376 atoms. Found 10 (10 requested) and removed 12 (10 requested) atoms. Cycle 40: After refmac, R = 0.1877 (Rfree = 0.000) for 2374 atoms. Found 10 (10 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.98 2.28 Search for helices and strands: 0 residues in 0 chains, 2443 seeds are put forward NCS extension: 212 residues added (73 deleted due to clashes), 2655 seeds are put forward Round 1: 274 peptides, 16 chains. Longest chain 47 peptides. Score 0.737 Round 2: 283 peptides, 10 chains. Longest chain 55 peptides. Score 0.795 Round 3: 279 peptides, 12 chains. Longest chain 59 peptides. Score 0.775 Round 4: 272 peptides, 13 chains. Longest chain 50 peptides. Score 0.757 Round 5: 274 peptides, 14 chains. Longest chain 39 peptides. Score 0.753 Taking the results from Round 2 Chains 10, Residues 273, Estimated correctness of the model 82.7 % 8 chains (262 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 34 A and 41 A Built loop between residues 94 A and 98 A Built loop between residues 111 A and 115 A Built loop between residues 26 B and 29 B Built loop between residues 111 B and 117 B 4 chains (289 residues) following loop building 3 chains (281 residues) in sequence following loop building ------------------------------------------------------ 9297 reflections ( 99.95 % complete ) and 2626 restraints for refining 2496 atoms. 313 conditional restraints added. Observations/parameters ratio is 0.93 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2130 (Rfree = 0.000) for 2496 atoms. Found 11 (11 requested) and removed 32 (11 requested) atoms. Cycle 42: After refmac, R = 0.1911 (Rfree = 0.000) for 2466 atoms. Found 11 (11 requested) and removed 14 (11 requested) atoms. Cycle 43: After refmac, R = 0.1856 (Rfree = 0.000) for 2461 atoms. Found 11 (11 requested) and removed 17 (11 requested) atoms. Cycle 44: After refmac, R = 0.1810 (Rfree = 0.000) for 2452 atoms. Found 11 (11 requested) and removed 14 (11 requested) atoms. Cycle 45: After refmac, R = 0.1779 (Rfree = 0.000) for 2447 atoms. Found 10 (10 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.98 2.28 Search for helices and strands: 0 residues in 0 chains, 2511 seeds are put forward NCS extension: 80 residues added (84 deleted due to clashes), 2591 seeds are put forward Round 1: 271 peptides, 12 chains. Longest chain 65 peptides. Score 0.764 Round 2: 286 peptides, 9 chains. Longest chain 68 peptides. Score 0.806 Round 3: 287 peptides, 12 chains. Longest chain 48 peptides. Score 0.786 Round 4: 285 peptides, 12 chains. Longest chain 52 peptides. Score 0.783 Round 5: 285 peptides, 10 chains. Longest chain 66 peptides. Score 0.797 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 12, Residues 277, Estimated correctness of the model 84.3 % 7 chains (249 residues) have been docked in sequence Sequence coverage is 89 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 34 A and 41 A Built loop between residues 75 A and 78 A Built loop between residues 73 B and 78 B 8 chains (286 residues) following loop building 4 chains (261 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 9297 reflections ( 99.95 % complete ) and 2236 restraints for refining 2194 atoms. Observations/parameters ratio is 1.06 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2511 (Rfree = 0.000) for 2194 atoms. Found 9 (9 requested) and removed 0 (9 requested) atoms. Cycle 47: After refmac, R = 0.2310 (Rfree = 0.000) for 2194 atoms. Found 9 (9 requested) and removed 0 (9 requested) atoms. Cycle 48: After refmac, R = 0.2174 (Rfree = 0.000) for 2194 atoms. Found 9 (9 requested) and removed 0 (9 requested) atoms. Cycle 49: After refmac, R = 0.2115 (Rfree = 0.000) for 2194 atoms. Found 2 (9 requested) and removed 3 (9 requested) atoms. Writing output files ... TimeTaking 44.78