null Mon 24 Dec 07:57:54 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2opk-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2opk-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2opk-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2opk-3.2-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2opk-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2opk-3.2-parrot-noncs ############### 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 07:57:58 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/noncs/ArpWArp/wArpResults/WorkingDir/2opk-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2opk-3.2-parrot-noncs/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 429 and 0 Target number of residues in the AU: 429 Target solvent content: 0.5913 Checking the provided sequence file Detected sequence length: 112 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 448 Adjusted target solvent content: 0.57 Input MTZ file: 2opk-3.2-parrot-noncs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 96 Cell parameters: 75.570 75.570 198.970 90.000 90.000 90.000 Input sequence file: 2opk-3.2-parrot-noncs.fasta_lf Building free atoms model in initial map for 3584 target number of atoms Had to go as low as 0.80 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 3 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 28.177 3.200 Wilson plot Bfac: 49.17 10119 reflections ( 99.61 % complete ) and 0 restraints for refining 3993 atoms. Observations/parameters ratio is 0.63 ------------------------------------------------------ Starting model: R = 0.2941 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2472 (Rfree = 0.000) for 3993 atoms. Found 35 (35 requested) and removed 35 (17 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.97 2.70 Search for helices and strands: 0 residues in 0 chains, 4039 seeds are put forward NCS extension: 0 residues added, 4039 seeds are put forward Round 1: 295 peptides, 46 chains. Longest chain 14 peptides. Score 0.494 Round 2: 338 peptides, 33 chains. Longest chain 27 peptides. Score 0.704 Round 3: 358 peptides, 32 chains. Longest chain 36 peptides. Score 0.742 Round 4: 370 peptides, 28 chains. Longest chain 40 peptides. Score 0.784 Round 5: 366 peptides, 32 chains. Longest chain 35 peptides. Score 0.753 Taking the results from Round 4 Chains 30, Residues 342, Estimated correctness of the model 80.9 % 5 chains (124 residues) have been docked in sequence Building loops using Loopy2018 30 chains (342 residues) following loop building 5 chains (124 residues) in sequence following loop building ------------------------------------------------------ 10119 reflections ( 99.61 % complete ) and 5538 restraints for refining 3358 atoms. 3693 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2674 (Rfree = 0.000) for 3358 atoms. Found 30 (30 requested) and removed 32 (15 requested) atoms. Cycle 2: After refmac, R = 0.2417 (Rfree = 0.000) for 3326 atoms. Found 16 (29 requested) and removed 22 (15 requested) atoms. Cycle 3: After refmac, R = 0.2287 (Rfree = 0.000) for 3298 atoms. Found 14 (28 requested) and removed 17 (14 requested) atoms. Cycle 4: After refmac, R = 0.2215 (Rfree = 0.000) for 3285 atoms. Found 15 (27 requested) and removed 17 (14 requested) atoms. Cycle 5: After refmac, R = 0.2136 (Rfree = 0.000) for 3277 atoms. Found 8 (27 requested) and removed 17 (14 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.00 2.73 Search for helices and strands: 0 residues in 0 chains, 3358 seeds are put forward NCS extension: 12 residues added (11 deleted due to clashes), 3370 seeds are put forward Round 1: 345 peptides, 34 chains. Longest chain 26 peptides. Score 0.707 Round 2: 357 peptides, 25 chains. Longest chain 35 peptides. Score 0.787 Round 3: 346 peptides, 27 chains. Longest chain 34 peptides. Score 0.759 Round 4: 347 peptides, 30 chains. Longest chain 28 peptides. Score 0.740 Round 5: 353 peptides, 29 chains. Longest chain 27 peptides. Score 0.755 Taking the results from Round 2 Chains 32, Residues 332, Estimated correctness of the model 81.4 % 10 chains (180 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 95 C and 99 C Built loop between residues 43 B and 48 B 30 chains (339 residues) following loop building 8 chains (187 residues) in sequence following loop building ------------------------------------------------------ 10119 reflections ( 99.61 % complete ) and 4909 restraints for refining 3272 atoms. 2795 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2598 (Rfree = 0.000) for 3272 atoms. Found 26 (26 requested) and removed 29 (14 requested) atoms. Cycle 7: After refmac, R = 0.2402 (Rfree = 0.000) for 3258 atoms. Found 23 (26 requested) and removed 18 (14 requested) atoms. Cycle 8: After refmac, R = 0.2292 (Rfree = 0.000) for 3258 atoms. Found 17 (25 requested) and removed 16 (14 requested) atoms. Cycle 9: After refmac, R = 0.2224 (Rfree = 0.000) for 3256 atoms. Found 10 (24 requested) and removed 17 (14 requested) atoms. Cycle 10: After refmac, R = 0.2206 (Rfree = 0.000) for 3242 atoms. Found 8 (24 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.03 2.76 Search for helices and strands: 0 residues in 0 chains, 3291 seeds are put forward NCS extension: 7 residues added (17 deleted due to clashes), 3298 seeds are put forward Round 1: 343 peptides, 38 chains. Longest chain 20 peptides. Score 0.672 Round 2: 355 peptides, 30 chains. Longest chain 36 peptides. Score 0.751 Round 3: 360 peptides, 27 chains. Longest chain 25 peptides. Score 0.778 Round 4: 356 peptides, 27 chains. Longest chain 39 peptides. Score 0.773 Round 5: 358 peptides, 27 chains. Longest chain 30 peptides. Score 0.775 Taking the results from Round 3 Chains 28, Residues 333, Estimated correctness of the model 79.9 % 10 chains (175 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 39 A and 47 A 27 chains (340 residues) following loop building 9 chains (182 residues) in sequence following loop building ------------------------------------------------------ 10119 reflections ( 99.61 % complete ) and 4921 restraints for refining 3272 atoms. 2814 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2593 (Rfree = 0.000) for 3272 atoms. Found 23 (23 requested) and removed 29 (14 requested) atoms. Cycle 12: After refmac, R = 0.2429 (Rfree = 0.000) for 3253 atoms. Found 17 (23 requested) and removed 16 (14 requested) atoms. Cycle 13: After refmac, R = 0.2332 (Rfree = 0.000) for 3245 atoms. Found 16 (22 requested) and removed 15 (14 requested) atoms. Cycle 14: After refmac, R = 0.2293 (Rfree = 0.000) for 3244 atoms. Found 8 (21 requested) and removed 17 (14 requested) atoms. Cycle 15: After refmac, R = 0.2221 (Rfree = 0.000) for 3227 atoms. Found 15 (21 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.00 2.73 Search for helices and strands: 0 residues in 0 chains, 3290 seeds are put forward NCS extension: 35 residues added (35 deleted due to clashes), 3325 seeds are put forward Round 1: 349 peptides, 30 chains. Longest chain 30 peptides. Score 0.743 Round 2: 370 peptides, 26 chains. Longest chain 49 peptides. Score 0.796 Round 3: 374 peptides, 20 chains. Longest chain 68 peptides. Score 0.835 Round 4: 365 peptides, 22 chains. Longest chain 38 peptides. Score 0.814 Round 5: 361 peptides, 27 chains. Longest chain 40 peptides. Score 0.779 Taking the results from Round 3 Chains 25, Residues 354, Estimated correctness of the model 88.3 % 10 chains (235 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 72 C and 75 C Built loop between residues 38 B and 43 B Built loop between residues 66 B and 74 B 21 chains (362 residues) following loop building 7 chains (248 residues) in sequence following loop building ------------------------------------------------------ 10119 reflections ( 99.61 % complete ) and 4497 restraints for refining 3304 atoms. 2086 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2677 (Rfree = 0.000) for 3304 atoms. Found 20 (20 requested) and removed 34 (14 requested) atoms. Cycle 17: After refmac, R = 0.2449 (Rfree = 0.000) for 3283 atoms. Found 20 (20 requested) and removed 16 (14 requested) atoms. Cycle 18: After refmac, R = 0.2286 (Rfree = 0.000) for 3283 atoms. Found 19 (19 requested) and removed 19 (14 requested) atoms. Cycle 19: After refmac, R = 0.2203 (Rfree = 0.000) for 3282 atoms. Found 6 (19 requested) and removed 14 (14 requested) atoms. Cycle 20: After refmac, R = 0.2182 (Rfree = 0.000) for 3273 atoms. Found 6 (18 requested) and removed 15 (14 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.03 2.76 Search for helices and strands: 0 residues in 0 chains, 3328 seeds are put forward NCS extension: 21 residues added (18 deleted due to clashes), 3349 seeds are put forward Round 1: 347 peptides, 33 chains. Longest chain 27 peptides. Score 0.718 Round 2: 373 peptides, 22 chains. Longest chain 38 peptides. Score 0.823 Round 3: 362 peptides, 26 chains. Longest chain 35 peptides. Score 0.787 Round 4: 357 peptides, 26 chains. Longest chain 35 peptides. Score 0.780 Round 5: 360 peptides, 26 chains. Longest chain 35 peptides. Score 0.784 Taking the results from Round 2 Chains 25, Residues 351, Estimated correctness of the model 86.7 % 10 chains (224 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 39 A and 45 A Built loop between residues 96 A and 99 A Built loop between residues 68 B and 75 B 21 chains (360 residues) following loop building 7 chains (237 residues) in sequence following loop building ------------------------------------------------------ 10119 reflections ( 99.61 % complete ) and 4508 restraints for refining 3272 atoms. 2181 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2663 (Rfree = 0.000) for 3272 atoms. Found 17 (17 requested) and removed 42 (14 requested) atoms. Cycle 22: After refmac, R = 0.2414 (Rfree = 0.000) for 3242 atoms. Found 17 (17 requested) and removed 19 (14 requested) atoms. Cycle 23: After refmac, R = 0.2302 (Rfree = 0.000) for 3237 atoms. Found 13 (16 requested) and removed 15 (14 requested) atoms. Cycle 24: After refmac, R = 0.2223 (Rfree = 0.000) for 3231 atoms. Found 9 (16 requested) and removed 15 (14 requested) atoms. Cycle 25: After refmac, R = 0.2182 (Rfree = 0.000) for 3224 atoms. Found 8 (15 requested) and removed 15 (14 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.99 2.72 Search for helices and strands: 0 residues in 0 chains, 3302 seeds are put forward NCS extension: 30 residues added (26 deleted due to clashes), 3332 seeds are put forward Round 1: 346 peptides, 28 chains. Longest chain 30 peptides. Score 0.752 Round 2: 357 peptides, 27 chains. Longest chain 34 peptides. Score 0.774 Round 3: 357 peptides, 26 chains. Longest chain 61 peptides. Score 0.780 Round 4: 354 peptides, 26 chains. Longest chain 29 peptides. Score 0.777 Round 5: 363 peptides, 22 chains. Longest chain 38 peptides. Score 0.812 Taking the results from Round 5 Chains 28, Residues 341, Estimated correctness of the model 85.2 % 10 chains (245 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 37 A and 42 A Built loop between residues 73 A and 81 A Built loop between residues 66 B and 75 B 21 chains (354 residues) following loop building 7 chains (264 residues) in sequence following loop building ------------------------------------------------------ 10119 reflections ( 99.61 % complete ) and 4338 restraints for refining 3272 atoms. 1907 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2683 (Rfree = 0.000) for 3272 atoms. Found 14 (14 requested) and removed 33 (14 requested) atoms. Cycle 27: After refmac, R = 0.2431 (Rfree = 0.000) for 3245 atoms. Found 14 (14 requested) and removed 17 (14 requested) atoms. Cycle 28: After refmac, R = 0.2309 (Rfree = 0.000) for 3237 atoms. Found 14 (14 requested) and removed 16 (14 requested) atoms. Cycle 29: After refmac, R = 0.2227 (Rfree = 0.000) for 3234 atoms. Found 11 (14 requested) and removed 15 (14 requested) atoms. Cycle 30: After refmac, R = 0.2144 (Rfree = 0.000) for 3228 atoms. Found 13 (14 requested) and removed 17 (14 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.97 2.70 Search for helices and strands: 0 residues in 0 chains, 3311 seeds are put forward NCS extension: 69 residues added (72 deleted due to clashes), 3380 seeds are put forward Round 1: 348 peptides, 29 chains. Longest chain 57 peptides. Score 0.748 Round 2: 368 peptides, 22 chains. Longest chain 60 peptides. Score 0.817 Round 3: 359 peptides, 29 chains. Longest chain 23 peptides. Score 0.764 Round 4: 361 peptides, 30 chains. Longest chain 63 peptides. Score 0.760 Round 5: 360 peptides, 29 chains. Longest chain 32 peptides. Score 0.765 Taking the results from Round 2 Chains 27, Residues 346, Estimated correctness of the model 85.9 % 12 chains (251 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 39 A and 49 A Built loop between residues 87 C and 93 C 25 chains (360 residues) following loop building 10 chains (265 residues) in sequence following loop building ------------------------------------------------------ 10119 reflections ( 99.61 % complete ) and 4343 restraints for refining 3293 atoms. 1831 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2515 (Rfree = 0.000) for 3293 atoms. Found 14 (14 requested) and removed 42 (14 requested) atoms. Cycle 32: After refmac, R = 0.2282 (Rfree = 0.000) for 3257 atoms. Found 14 (14 requested) and removed 17 (14 requested) atoms. Cycle 33: After refmac, R = 0.2062 (Rfree = 0.000) for 3250 atoms. Found 14 (14 requested) and removed 22 (14 requested) atoms. Cycle 34: After refmac, R = 0.1995 (Rfree = 0.000) for 3237 atoms. Found 14 (14 requested) and removed 14 (14 requested) atoms. Cycle 35: After refmac, R = 0.2174 (Rfree = 0.000) for 3234 atoms. Found 14 (14 requested) and removed 18 (14 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.95 2.69 Search for helices and strands: 0 residues in 0 chains, 3285 seeds are put forward NCS extension: 37 residues added (32 deleted due to clashes), 3322 seeds are put forward Round 1: 342 peptides, 33 chains. Longest chain 27 peptides. Score 0.710 Round 2: 363 peptides, 22 chains. Longest chain 51 peptides. Score 0.812 Round 3: 354 peptides, 25 chains. Longest chain 65 peptides. Score 0.783 Round 4: 368 peptides, 28 chains. Longest chain 44 peptides. Score 0.782 Round 5: 352 peptides, 30 chains. Longest chain 30 peptides. Score 0.747 Taking the results from Round 2 Chains 29, Residues 341, Estimated correctness of the model 85.2 % 10 chains (222 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 65 A and 72 A Built loop between residues 36 B and 43 B 25 chains (346 residues) following loop building 8 chains (234 residues) in sequence following loop building ------------------------------------------------------ 10119 reflections ( 99.61 % complete ) and 4592 restraints for refining 3272 atoms. 2256 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2547 (Rfree = 0.000) for 3272 atoms. Found 14 (14 requested) and removed 27 (14 requested) atoms. Cycle 37: After refmac, R = 0.2365 (Rfree = 0.000) for 3252 atoms. Found 14 (14 requested) and removed 15 (14 requested) atoms. Cycle 38: After refmac, R = 0.2232 (Rfree = 0.000) for 3248 atoms. Found 14 (14 requested) and removed 15 (14 requested) atoms. Cycle 39: After refmac, R = 0.2154 (Rfree = 0.000) for 3246 atoms. Found 12 (14 requested) and removed 15 (14 requested) atoms. Cycle 40: After refmac, R = 0.2092 (Rfree = 0.000) for 3241 atoms. Found 12 (14 requested) and removed 16 (14 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.98 2.71 Search for helices and strands: 0 residues in 0 chains, 3308 seeds are put forward NCS extension: 11 residues added (6 deleted due to clashes), 3319 seeds are put forward Round 1: 340 peptides, 29 chains. Longest chain 30 peptides. Score 0.737 Round 2: 347 peptides, 23 chains. Longest chain 36 peptides. Score 0.787 Round 3: 356 peptides, 26 chains. Longest chain 61 peptides. Score 0.779 Round 4: 379 peptides, 24 chains. Longest chain 36 peptides. Score 0.818 Round 5: 360 peptides, 27 chains. Longest chain 51 peptides. Score 0.778 Taking the results from Round 4 Chains 28, Residues 355, Estimated correctness of the model 86.0 % 11 chains (240 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 36 C and 45 C Built loop between residues 58 C and 61 C Built loop between residues 69 C and 80 C Built loop between residues 40 D and 46 D Built loop between residues 58 D and 61 D 21 chains (376 residues) following loop building 6 chains (267 residues) in sequence following loop building ------------------------------------------------------ 10119 reflections ( 99.61 % complete ) and 4239 restraints for refining 3290 atoms. 1685 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2632 (Rfree = 0.000) for 3290 atoms. Found 14 (14 requested) and removed 39 (14 requested) atoms. Cycle 42: After refmac, R = 0.2418 (Rfree = 0.000) for 3255 atoms. Found 14 (14 requested) and removed 18 (14 requested) atoms. Cycle 43: After refmac, R = 0.2265 (Rfree = 0.000) for 3248 atoms. Found 14 (14 requested) and removed 14 (14 requested) atoms. Cycle 44: After refmac, R = 0.2173 (Rfree = 0.000) for 3243 atoms. Found 9 (14 requested) and removed 17 (14 requested) atoms. Cycle 45: After refmac, R = 0.2121 (Rfree = 0.000) for 3228 atoms. Found 7 (14 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.96 2.69 Search for helices and strands: 0 residues in 0 chains, 3292 seeds are put forward NCS extension: 70 residues added (189 deleted due to clashes), 3362 seeds are put forward Round 1: 354 peptides, 28 chains. Longest chain 37 peptides. Score 0.763 Round 2: 371 peptides, 23 chains. Longest chain 41 peptides. Score 0.815 Round 3: 361 peptides, 23 chains. Longest chain 51 peptides. Score 0.804 Round 4: 363 peptides, 27 chains. Longest chain 43 peptides. Score 0.782 Round 5: 366 peptides, 24 chains. Longest chain 41 peptides. Score 0.804 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 24, Residues 348, Estimated correctness of the model 85.6 % 9 chains (229 residues) have been docked in sequence Sequence coverage is 65 % Consider running further cycles of model building using 2opk-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 43 B and 46 B 23 chains (348 residues) following loop building 8 chains (231 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 10119 reflections ( 99.61 % complete ) and 4774 restraints for refining 3271 atoms. 2480 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2401 (Rfree = 0.000) for 3271 atoms. Found 0 (14 requested) and removed 6 (14 requested) atoms. Cycle 47: After refmac, R = 0.2297 (Rfree = 0.000) for 3261 atoms. Found 0 (14 requested) and removed 3 (14 requested) atoms. Cycle 48: After refmac, R = 0.2260 (Rfree = 0.000) for 3257 atoms. Found 0 (14 requested) and removed 3 (14 requested) atoms. Cycle 49: After refmac, R = 0.2248 (Rfree = 0.000) for 3254 atoms. Found 0 (14 requested) and removed 2 (14 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:41:50 GMT 2018 Job finished. TimeTaking 43.93 Used memory is bytes: 8162592