Sun 23 Dec 22:23:05 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 2p8j-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2p8j-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2p8j-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p8j-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/2p8j-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p8j-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 ============================================================ Sun 23 Dec 22:23:13 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/2p8j-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p8j-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 439 and 0 Target number of residues in the AU: 439 Target solvent content: 0.6324 Checking the provided sequence file Detected sequence length: 209 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 418 Adjusted target solvent content: 0.65 Input MTZ file: 2p8j-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: 152 Cell parameters: 83.860 83.860 159.200 90.000 90.000 120.000 Input sequence file: 2p8j-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 3344 target number of atoms Had to go as low as 1.05 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: 72.625 3.201 Wilson plot Bfac: 67.57 11083 reflections ( 98.96 % complete ) and 0 restraints for refining 3694 atoms. Observations/parameters ratio is 0.75 ------------------------------------------------------ Starting model: R = 0.3264 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2510 (Rfree = 0.000) for 3694 atoms. Found 33 (33 requested) and removed 19 (16 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.18 2.59 Search for helices and strands: 0 residues in 0 chains, 3784 seeds are put forward NCS extension: 0 residues added, 3784 seeds are put forward Round 1: 272 peptides, 40 chains. Longest chain 16 peptides. Score 0.473 Round 2: 311 peptides, 34 chains. Longest chain 31 peptides. Score 0.610 Round 3: 332 peptides, 30 chains. Longest chain 38 peptides. Score 0.678 Round 4: 332 peptides, 31 chains. Longest chain 32 peptides. Score 0.671 Round 5: 328 peptides, 27 chains. Longest chain 51 peptides. Score 0.695 Taking the results from Round 5 Chains 27, Residues 301, Estimated correctness of the model 64.1 % 2 chains (66 residues) have been docked in sequence ------------------------------------------------------ 11083 reflections ( 98.96 % complete ) and 5952 restraints for refining 3212 atoms. 4510 conditional restraints added. Observations/parameters ratio is 0.86 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2646 (Rfree = 0.000) for 3212 atoms. Found 28 (28 requested) and removed 44 (14 requested) atoms. Cycle 2: After refmac, R = 0.2490 (Rfree = 0.000) for 3165 atoms. Found 17 (28 requested) and removed 22 (14 requested) atoms. Cycle 3: After refmac, R = 0.2687 (Rfree = 0.000) for 3145 atoms. Found 28 (28 requested) and removed 19 (14 requested) atoms. Cycle 4: After refmac, R = 0.2693 (Rfree = 0.000) for 3141 atoms. Found 28 (28 requested) and removed 18 (14 requested) atoms. Cycle 5: After refmac, R = 0.2325 (Rfree = 0.000) for 3132 atoms. Found 20 (28 requested) and removed 15 (14 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.21 2.61 Search for helices and strands: 0 residues in 0 chains, 3228 seeds are put forward NCS extension: 58 residues added (27 deleted due to clashes), 3286 seeds are put forward Round 1: 314 peptides, 27 chains. Longest chain 26 peptides. Score 0.673 Round 2: 326 peptides, 27 chains. Longest chain 56 peptides. Score 0.692 Round 3: 336 peptides, 25 chains. Longest chain 38 peptides. Score 0.721 Round 4: 335 peptides, 28 chains. Longest chain 50 peptides. Score 0.698 Round 5: 339 peptides, 25 chains. Longest chain 54 peptides. Score 0.725 Taking the results from Round 5 Chains 26, Residues 314, Estimated correctness of the model 70.3 % 6 chains (184 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 57 B and 67 B Built loop between residues 185 B and 190 B 23 chains (323 residues) following loop building 4 chains (197 residues) in sequence following loop building ------------------------------------------------------ 11083 reflections ( 98.96 % complete ) and 4817 restraints for refining 3287 atoms. 2684 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2698 (Rfree = 0.000) for 3287 atoms. Found 29 (29 requested) and removed 36 (14 requested) atoms. Cycle 7: After refmac, R = 0.2635 (Rfree = 0.000) for 3261 atoms. Found 28 (28 requested) and removed 27 (14 requested) atoms. Cycle 8: After refmac, R = 0.2317 (Rfree = 0.000) for 3246 atoms. Found 10 (28 requested) and removed 21 (14 requested) atoms. Cycle 9: After refmac, R = 0.2218 (Rfree = 0.000) for 3230 atoms. Found 8 (27 requested) and removed 17 (14 requested) atoms. Cycle 10: After refmac, R = 0.2135 (Rfree = 0.000) for 3218 atoms. Found 8 (26 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.19 2.60 Search for helices and strands: 0 residues in 0 chains, 3319 seeds are put forward NCS extension: 38 residues added (73 deleted due to clashes), 3357 seeds are put forward Round 1: 323 peptides, 25 chains. Longest chain 40 peptides. Score 0.702 Round 2: 348 peptides, 23 chains. Longest chain 46 peptides. Score 0.751 Round 3: 343 peptides, 24 chains. Longest chain 50 peptides. Score 0.737 Round 4: 333 peptides, 27 chains. Longest chain 28 peptides. Score 0.702 Round 5: 338 peptides, 26 chains. Longest chain 51 peptides. Score 0.717 Taking the results from Round 2 Chains 24, Residues 325, Estimated correctness of the model 75.2 % 7 chains (158 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 184 A and 192 A Built loop between residues 113 B and 120 B 22 chains (338 residues) following loop building 5 chains (171 residues) in sequence following loop building ------------------------------------------------------ 11083 reflections ( 98.96 % complete ) and 4840 restraints for refining 3236 atoms. 2732 conditional restraints added. Observations/parameters ratio is 0.86 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2659 (Rfree = 0.000) for 3236 atoms. Found 26 (26 requested) and removed 38 (14 requested) atoms. Cycle 12: After refmac, R = 0.2511 (Rfree = 0.000) for 3211 atoms. Found 25 (25 requested) and removed 29 (14 requested) atoms. Cycle 13: After refmac, R = 0.2478 (Rfree = 0.000) for 3198 atoms. Found 24 (24 requested) and removed 20 (14 requested) atoms. Cycle 14: After refmac, R = 0.2422 (Rfree = 0.000) for 3194 atoms. Found 24 (24 requested) and removed 17 (14 requested) atoms. Cycle 15: After refmac, R = 0.2375 (Rfree = 0.000) for 3185 atoms. Found 23 (23 requested) and removed 18 (14 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.18 2.59 Search for helices and strands: 0 residues in 0 chains, 3322 seeds are put forward NCS extension: 40 residues added (42 deleted due to clashes), 3362 seeds are put forward Round 1: 336 peptides, 28 chains. Longest chain 40 peptides. Score 0.699 Round 2: 350 peptides, 20 chains. Longest chain 43 peptides. Score 0.772 Round 3: 361 peptides, 23 chains. Longest chain 55 peptides. Score 0.767 Round 4: 361 peptides, 18 chains. Longest chain 44 peptides. Score 0.797 Round 5: 362 peptides, 23 chains. Longest chain 43 peptides. Score 0.768 Taking the results from Round 4 Chains 20, Residues 343, Estimated correctness of the model 82.9 % 10 chains (239 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 62 B and 69 B Built loop between residues 143 B and 148 B Built loop between residues 162 B and 168 B 16 chains (357 residues) following loop building 7 chains (254 residues) in sequence following loop building ------------------------------------------------------ 11083 reflections ( 98.96 % complete ) and 4469 restraints for refining 3399 atoms. 1952 conditional restraints added. Observations/parameters ratio is 0.82 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2761 (Rfree = 0.000) for 3399 atoms. Found 24 (24 requested) and removed 55 (15 requested) atoms. Cycle 17: After refmac, R = 0.2508 (Rfree = 0.000) for 3345 atoms. Found 23 (23 requested) and removed 27 (15 requested) atoms. Cycle 18: After refmac, R = 0.2432 (Rfree = 0.000) for 3333 atoms. Found 22 (22 requested) and removed 24 (14 requested) atoms. Cycle 19: After refmac, R = 0.2339 (Rfree = 0.000) for 3316 atoms. Found 21 (21 requested) and removed 20 (14 requested) atoms. Cycle 20: After refmac, R = 0.2209 (Rfree = 0.000) for 3310 atoms. Found 14 (21 requested) and removed 16 (14 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.20 2.60 Search for helices and strands: 0 residues in 0 chains, 3399 seeds are put forward NCS extension: 67 residues added (77 deleted due to clashes), 3466 seeds are put forward Round 1: 359 peptides, 19 chains. Longest chain 54 peptides. Score 0.789 Round 2: 359 peptides, 18 chains. Longest chain 66 peptides. Score 0.795 Round 3: 353 peptides, 22 chains. Longest chain 61 peptides. Score 0.763 Round 4: 347 peptides, 26 chains. Longest chain 61 peptides. Score 0.729 Round 5: 353 peptides, 22 chains. Longest chain 73 peptides. Score 0.763 Taking the results from Round 2 Chains 22, Residues 341, Estimated correctness of the model 82.6 % 6 chains (216 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 59 A and 67 A Built loop between residues 61 B and 70 B Built loop between residues 110 B and 113 B 17 chains (354 residues) following loop building 3 chains (233 residues) in sequence following loop building ------------------------------------------------------ 11083 reflections ( 98.96 % complete ) and 4559 restraints for refining 3330 atoms. 2171 conditional restraints added. Observations/parameters ratio is 0.83 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2741 (Rfree = 0.000) for 3330 atoms. Found 20 (20 requested) and removed 49 (14 requested) atoms. Cycle 22: After refmac, R = 0.2444 (Rfree = 0.000) for 3289 atoms. Found 20 (20 requested) and removed 32 (14 requested) atoms. Cycle 23: After refmac, R = 0.2313 (Rfree = 0.000) for 3264 atoms. Found 19 (19 requested) and removed 25 (14 requested) atoms. Cycle 24: After refmac, R = 0.2252 (Rfree = 0.000) for 3248 atoms. Found 19 (19 requested) and removed 22 (14 requested) atoms. Cycle 25: After refmac, R = 0.2217 (Rfree = 0.000) for 3233 atoms. Found 18 (18 requested) and removed 23 (14 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.18 2.59 Search for helices and strands: 0 residues in 0 chains, 3304 seeds are put forward NCS extension: 98 residues added (89 deleted due to clashes), 3402 seeds are put forward Round 1: 348 peptides, 24 chains. Longest chain 27 peptides. Score 0.744 Round 2: 353 peptides, 15 chains. Longest chain 49 peptides. Score 0.806 Round 3: 353 peptides, 28 chains. Longest chain 32 peptides. Score 0.724 Round 4: 347 peptides, 20 chains. Longest chain 60 peptides. Score 0.769 Round 5: 351 peptides, 23 chains. Longest chain 45 peptides. Score 0.754 Taking the results from Round 2 Chains 16, Residues 338, Estimated correctness of the model 84.3 % 8 chains (262 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 58 A and 68 A Built loop between residues 58 B and 65 B Built loop between residues 109 B and 113 B Built loop between residues 135 B and 138 B Built loop between residues 185 B and 191 B 10 chains (361 residues) following loop building 3 chains (287 residues) in sequence following loop building ------------------------------------------------------ 11083 reflections ( 98.96 % complete ) and 4140 restraints for refining 3379 atoms. 1466 conditional restraints added. Observations/parameters ratio is 0.82 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2581 (Rfree = 0.000) for 3379 atoms. Found 18 (18 requested) and removed 41 (15 requested) atoms. Cycle 27: After refmac, R = 0.2340 (Rfree = 0.000) for 3335 atoms. Found 17 (17 requested) and removed 27 (15 requested) atoms. Cycle 28: After refmac, R = 0.2238 (Rfree = 0.000) for 3314 atoms. Found 16 (16 requested) and removed 20 (14 requested) atoms. Cycle 29: After refmac, R = 0.2136 (Rfree = 0.000) for 3305 atoms. Found 16 (16 requested) and removed 16 (14 requested) atoms. Cycle 30: After refmac, R = 0.2024 (Rfree = 0.000) for 3299 atoms. Found 15 (15 requested) and removed 19 (14 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.20 2.60 Search for helices and strands: 0 residues in 0 chains, 3395 seeds are put forward NCS extension: 180 residues added (134 deleted due to clashes), 3575 seeds are put forward Round 1: 349 peptides, 24 chains. Longest chain 42 peptides. Score 0.745 Round 2: 354 peptides, 20 chains. Longest chain 48 peptides. Score 0.777 Round 3: 345 peptides, 26 chains. Longest chain 38 peptides. Score 0.727 Round 4: 352 peptides, 24 chains. Longest chain 33 peptides. Score 0.749 Round 5: 339 peptides, 22 chains. Longest chain 66 peptides. Score 0.746 Taking the results from Round 2 Chains 26, Residues 334, Estimated correctness of the model 79.7 % 9 chains (235 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 55 B and 65 B Built loop between residues 111 B and 115 B Built loop between residues 136 B and 139 B 22 chains (346 residues) following loop building 6 chains (249 residues) in sequence following loop building ------------------------------------------------------ 11083 reflections ( 98.96 % complete ) and 4427 restraints for refining 3283 atoms. 1974 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2376 (Rfree = 0.000) for 3283 atoms. Found 14 (14 requested) and removed 38 (14 requested) atoms. Cycle 32: After refmac, R = 0.2187 (Rfree = 0.000) for 3242 atoms. Found 14 (14 requested) and removed 19 (14 requested) atoms. Cycle 33: After refmac, R = 0.2104 (Rfree = 0.000) for 3229 atoms. Found 14 (14 requested) and removed 20 (14 requested) atoms. Cycle 34: After refmac, R = 0.2096 (Rfree = 0.000) for 3219 atoms. Found 14 (14 requested) and removed 15 (14 requested) atoms. Cycle 35: After refmac, R = 0.2045 (Rfree = 0.000) for 3212 atoms. Found 14 (14 requested) and removed 15 (14 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.21 2.61 Search for helices and strands: 0 residues in 0 chains, 3307 seeds are put forward NCS extension: 110 residues added (157 deleted due to clashes), 3417 seeds are put forward Round 1: 351 peptides, 20 chains. Longest chain 48 peptides. Score 0.773 Round 2: 337 peptides, 25 chains. Longest chain 38 peptides. Score 0.722 Round 3: 335 peptides, 25 chains. Longest chain 36 peptides. Score 0.720 Round 4: 340 peptides, 28 chains. Longest chain 39 peptides. Score 0.705 Round 5: 339 peptides, 30 chains. Longest chain 27 peptides. Score 0.689 Taking the results from Round 1 Chains 21, Residues 331, Estimated correctness of the model 79.1 % 11 chains (262 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 32 A and 41 A Built loop between residues 54 A and 65 A Built loop between residues 86 A and 89 A Built loop between residues 162 A and 165 A Built loop between residues 104 B and 115 B Built loop between residues 187 B and 191 B 14 chains (362 residues) following loop building 5 chains (297 residues) in sequence following loop building ------------------------------------------------------ 11083 reflections ( 98.96 % complete ) and 4162 restraints for refining 3385 atoms. 1444 conditional restraints added. Observations/parameters ratio is 0.82 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2418 (Rfree = 0.000) for 3385 atoms. Found 15 (15 requested) and removed 43 (15 requested) atoms. Cycle 37: After refmac, R = 0.2299 (Rfree = 0.000) for 3345 atoms. Found 15 (15 requested) and removed 22 (15 requested) atoms. Cycle 38: After refmac, R = 0.2242 (Rfree = 0.000) for 3323 atoms. Found 14 (14 requested) and removed 24 (14 requested) atoms. Cycle 39: After refmac, R = 0.2011 (Rfree = 0.000) for 3304 atoms. Found 14 (14 requested) and removed 15 (14 requested) atoms. Cycle 40: After refmac, R = 0.1905 (Rfree = 0.000) for 3300 atoms. Found 14 (14 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.18 2.59 Search for helices and strands: 0 residues in 0 chains, 3378 seeds are put forward NCS extension: 53 residues added (109 deleted due to clashes), 3431 seeds are put forward Round 1: 334 peptides, 28 chains. Longest chain 28 peptides. Score 0.696 Round 2: 338 peptides, 26 chains. Longest chain 30 peptides. Score 0.717 Round 3: 348 peptides, 23 chains. Longest chain 50 peptides. Score 0.751 Round 4: 327 peptides, 29 chains. Longest chain 40 peptides. Score 0.678 Round 5: 350 peptides, 26 chains. Longest chain 38 peptides. Score 0.733 Taking the results from Round 3 Chains 25, Residues 325, Estimated correctness of the model 75.2 % 7 chains (184 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 107 A and 114 A Built loop between residues 162 A and 165 A 23 chains (332 residues) following loop building 5 chains (192 residues) in sequence following loop building ------------------------------------------------------ 11083 reflections ( 98.96 % complete ) and 4835 restraints for refining 3179 atoms. 2680 conditional restraints added. Observations/parameters ratio is 0.87 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2486 (Rfree = 0.000) for 3179 atoms. Found 14 (14 requested) and removed 23 (14 requested) atoms. Cycle 42: After refmac, R = 0.2384 (Rfree = 0.000) for 3163 atoms. Found 14 (14 requested) and removed 24 (14 requested) atoms. Cycle 43: After refmac, R = 0.2310 (Rfree = 0.000) for 3147 atoms. Found 14 (14 requested) and removed 19 (14 requested) atoms. Cycle 44: After refmac, R = 0.2261 (Rfree = 0.000) for 3138 atoms. Found 14 (14 requested) and removed 17 (14 requested) atoms. Cycle 45: After refmac, R = 0.2239 (Rfree = 0.000) for 3130 atoms. Found 14 (14 requested) and removed 16 (14 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.17 2.58 Search for helices and strands: 0 residues in 0 chains, 3214 seeds are put forward NCS extension: 61 residues added (111 deleted due to clashes), 3275 seeds are put forward Round 1: 332 peptides, 23 chains. Longest chain 34 peptides. Score 0.729 Round 2: 359 peptides, 18 chains. Longest chain 52 peptides. Score 0.795 Round 3: 352 peptides, 20 chains. Longest chain 40 peptides. Score 0.775 Round 4: 353 peptides, 24 chains. Longest chain 50 peptides. Score 0.751 Round 5: 345 peptides, 25 chains. Longest chain 57 peptides. Score 0.733 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 21, Residues 341, Estimated correctness of the model 82.6 % 10 chains (279 residues) have been docked in sequence Sequence coverage is 81 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 108 A and 113 A Built loop between residues 30 B and 38 B Built loop between residues 57 B and 71 B Built loop between residues 108 B and 112 B Built loop between residues 187 B and 190 B 15 chains (366 residues) following loop building 5 chains (308 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 11083 reflections ( 98.96 % complete ) and 2775 restraints for refining 2744 atoms. Observations/parameters ratio is 1.01 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3166 (Rfree = 0.000) for 2744 atoms. Found 12 (12 requested) and removed 0 (12 requested) atoms. Cycle 47: After refmac, R = 0.2916 (Rfree = 0.000) for 2744 atoms. Found 9 (12 requested) and removed 1 (12 requested) atoms. Cycle 48: After refmac, R = 0.2787 (Rfree = 0.000) for 2744 atoms. Found 7 (12 requested) and removed 1 (12 requested) atoms. Cycle 49: After refmac, R = 0.2709 (Rfree = 0.000) for 2744 atoms. TimeTaking 66.83