null Mon 24 Dec 00:32:12 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 2otm-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2otm-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2otm-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2otm-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/2otm-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2otm-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 00:32:16 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/2otm-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2otm-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 396 and 0 Target number of residues in the AU: 396 Target solvent content: 0.6127 Checking the provided sequence file Detected sequence length: 154 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 3 Adjusted target number of residues: 462 Adjusted target solvent content: 0.55 Input MTZ file: 2otm-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: 5 Cell parameters: 112.035 62.893 78.663 90.000 93.262 90.000 Input sequence file: 2otm-3.2-parrot-mrncs.fasta_lf Building free atoms model in initial map for 3696 target number of atoms Had to go as low as 0.75 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: 78.536 3.200 Wilson plot Bfac: 57.84 9162 reflections ( 99.84 % complete ) and 0 restraints for refining 4110 atoms. Observations/parameters ratio is 0.56 ------------------------------------------------------ Starting model: R = 0.2942 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2530 (Rfree = 0.000) for 4110 atoms. Found 36 (36 requested) and removed 26 (18 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.03 2.83 Search for helices and strands: 0 residues in 0 chains, 4196 seeds are put forward NCS extension: 0 residues added, 4196 seeds are put forward Round 1: 295 peptides, 50 chains. Longest chain 13 peptides. Score 0.456 Round 2: 315 peptides, 41 chains. Longest chain 16 peptides. Score 0.598 Round 3: 335 peptides, 33 chains. Longest chain 27 peptides. Score 0.706 Round 4: 352 peptides, 36 chains. Longest chain 21 peptides. Score 0.711 Round 5: 357 peptides, 31 chains. Longest chain 36 peptides. Score 0.755 Taking the results from Round 5 Chains 34, Residues 326, Estimated correctness of the model 76.0 % 10 chains (172 residues) have been docked in sequence Building loops using Loopy2018 34 chains (326 residues) following loop building 10 chains (172 residues) in sequence following loop building ------------------------------------------------------ 9162 reflections ( 99.84 % complete ) and 5712 restraints for refining 3530 atoms. 3784 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2660 (Rfree = 0.000) for 3530 atoms. Found 24 (31 requested) and removed 47 (15 requested) atoms. Cycle 2: After refmac, R = 0.2413 (Rfree = 0.000) for 3475 atoms. Found 16 (30 requested) and removed 19 (15 requested) atoms. Cycle 3: After refmac, R = 0.2224 (Rfree = 0.000) for 3449 atoms. Found 7 (30 requested) and removed 19 (15 requested) atoms. Cycle 4: After refmac, R = 0.2115 (Rfree = 0.000) for 3420 atoms. Found 8 (28 requested) and removed 19 (15 requested) atoms. Cycle 5: After refmac, R = 0.2066 (Rfree = 0.000) for 3397 atoms. Found 9 (28 requested) and removed 16 (15 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.03 2.83 Search for helices and strands: 0 residues in 0 chains, 3487 seeds are put forward NCS extension: 24 residues added (29 deleted due to clashes), 3511 seeds are put forward Round 1: 356 peptides, 35 chains. Longest chain 30 peptides. Score 0.725 Round 2: 369 peptides, 29 chains. Longest chain 36 peptides. Score 0.784 Round 3: 364 peptides, 29 chains. Longest chain 37 peptides. Score 0.777 Round 4: 372 peptides, 29 chains. Longest chain 39 peptides. Score 0.787 Round 5: 380 peptides, 27 chains. Longest chain 37 peptides. Score 0.809 Taking the results from Round 5 Chains 30, Residues 353, Estimated correctness of the model 84.8 % 9 chains (185 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 51 A and 56 A Built loop between residues 22 C and 30 C 25 chains (360 residues) following loop building 7 chains (196 residues) in sequence following loop building ------------------------------------------------------ 9162 reflections ( 99.84 % complete ) and 5225 restraints for refining 3413 atoms. 3071 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2585 (Rfree = 0.000) for 3413 atoms. Found 27 (27 requested) and removed 45 (15 requested) atoms. Cycle 7: After refmac, R = 0.2244 (Rfree = 0.000) for 3379 atoms. Found 14 (26 requested) and removed 25 (15 requested) atoms. Cycle 8: After refmac, R = 0.2104 (Rfree = 0.000) for 3361 atoms. Found 11 (26 requested) and removed 23 (15 requested) atoms. Cycle 9: After refmac, R = 0.2061 (Rfree = 0.000) for 3345 atoms. Found 5 (25 requested) and removed 18 (15 requested) atoms. Cycle 10: After refmac, R = 0.2052 (Rfree = 0.000) for 3329 atoms. Found 4 (24 requested) and removed 16 (14 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.02 2.82 Search for helices and strands: 0 residues in 0 chains, 3418 seeds are put forward NCS extension: 17 residues added (19 deleted due to clashes), 3435 seeds are put forward Round 1: 354 peptides, 36 chains. Longest chain 27 peptides. Score 0.714 Round 2: 375 peptides, 26 chains. Longest chain 33 peptides. Score 0.809 Round 3: 384 peptides, 32 chains. Longest chain 35 peptides. Score 0.784 Round 4: 373 peptides, 30 chains. Longest chain 35 peptides. Score 0.783 Round 5: 374 peptides, 29 chains. Longest chain 39 peptides. Score 0.790 Taking the results from Round 2 Chains 34, Residues 349, Estimated correctness of the model 84.8 % 12 chains (201 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 40 A and 43 A Built loop between residues 47 B and 56 B Built loop between residues 71 B and 75 B 30 chains (357 residues) following loop building 9 chains (214 residues) in sequence following loop building ------------------------------------------------------ 9162 reflections ( 99.84 % complete ) and 4961 restraints for refining 3375 atoms. 2709 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2471 (Rfree = 0.000) for 3375 atoms. Found 19 (24 requested) and removed 32 (15 requested) atoms. Cycle 12: After refmac, R = 0.2249 (Rfree = 0.000) for 3342 atoms. Found 14 (23 requested) and removed 23 (15 requested) atoms. Cycle 13: After refmac, R = 0.2040 (Rfree = 0.000) for 3321 atoms. Found 17 (22 requested) and removed 18 (14 requested) atoms. Cycle 14: After refmac, R = 0.1920 (Rfree = 0.000) for 3315 atoms. Found 9 (21 requested) and removed 18 (14 requested) atoms. Cycle 15: After refmac, R = 0.1853 (Rfree = 0.000) for 3304 atoms. Found 9 (21 requested) and removed 18 (14 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.04 2.84 Search for helices and strands: 0 residues in 0 chains, 3400 seeds are put forward NCS extension: 66 residues added (93 deleted due to clashes), 3466 seeds are put forward Round 1: 373 peptides, 29 chains. Longest chain 37 peptides. Score 0.789 Round 2: 385 peptides, 29 chains. Longest chain 35 peptides. Score 0.803 Round 3: 382 peptides, 29 chains. Longest chain 29 peptides. Score 0.799 Round 4: 377 peptides, 29 chains. Longest chain 31 peptides. Score 0.794 Round 5: 368 peptides, 26 chains. Longest chain 38 peptides. Score 0.801 Taking the results from Round 2 Chains 34, Residues 356, Estimated correctness of the model 83.9 % 12 chains (227 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 44 A and 49 A Built loop between residues 68 A and 71 A Built loop between residues 83 A and 88 A Built loop between residues 45 C and 49 C Built loop between residues 61 C and 64 C Built loop between residues 72 C and 80 C 25 chains (373 residues) following loop building 6 chains (249 residues) in sequence following loop building ------------------------------------------------------ 9162 reflections ( 99.84 % complete ) and 4610 restraints for refining 3375 atoms. 2176 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2394 (Rfree = 0.000) for 3375 atoms. Found 21 (21 requested) and removed 45 (15 requested) atoms. Cycle 17: After refmac, R = 0.2264 (Rfree = 0.000) for 3335 atoms. Found 18 (20 requested) and removed 23 (15 requested) atoms. Cycle 18: After refmac, R = 0.2180 (Rfree = 0.000) for 3320 atoms. Found 19 (19 requested) and removed 17 (14 requested) atoms. Cycle 19: After refmac, R = 0.1924 (Rfree = 0.000) for 3315 atoms. Found 12 (19 requested) and removed 19 (14 requested) atoms. Cycle 20: After refmac, R = 0.2004 (Rfree = 0.000) for 3303 atoms. Found 11 (18 requested) and removed 16 (14 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.04 2.84 Search for helices and strands: 0 residues in 0 chains, 3403 seeds are put forward NCS extension: 34 residues added (85 deleted due to clashes), 3437 seeds are put forward Round 1: 362 peptides, 27 chains. Longest chain 40 peptides. Score 0.787 Round 2: 381 peptides, 26 chains. Longest chain 37 peptides. Score 0.816 Round 3: 394 peptides, 26 chains. Longest chain 39 peptides. Score 0.829 Round 4: 375 peptides, 32 chains. Longest chain 30 peptides. Score 0.772 Round 5: 385 peptides, 28 chains. Longest chain 41 peptides. Score 0.809 Taking the results from Round 3 Chains 31, Residues 368, Estimated correctness of the model 87.6 % 12 chains (239 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 45 A and 49 A Built loop between residues 103 A and 114 A Built loop between residues 61 C and 64 C 27 chains (380 residues) following loop building 9 chains (254 residues) in sequence following loop building ------------------------------------------------------ 9162 reflections ( 99.84 % complete ) and 4592 restraints for refining 3377 atoms. 2102 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2347 (Rfree = 0.000) for 3377 atoms. Found 18 (18 requested) and removed 34 (15 requested) atoms. Cycle 22: After refmac, R = 0.2125 (Rfree = 0.000) for 3344 atoms. Found 17 (17 requested) and removed 26 (15 requested) atoms. Cycle 23: After refmac, R = 0.2162 (Rfree = 0.000) for 3327 atoms. Found 16 (16 requested) and removed 25 (14 requested) atoms. Cycle 24: After refmac, R = 0.2109 (Rfree = 0.000) for 3314 atoms. Found 16 (16 requested) and removed 20 (14 requested) atoms. Cycle 25: After refmac, R = 0.2041 (Rfree = 0.000) for 3303 atoms. Found 15 (15 requested) and removed 16 (14 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.03 2.83 Search for helices and strands: 0 residues in 0 chains, 3393 seeds are put forward NCS extension: 11 residues added (39 deleted due to clashes), 3404 seeds are put forward Round 1: 365 peptides, 32 chains. Longest chain 42 peptides. Score 0.759 Round 2: 375 peptides, 26 chains. Longest chain 42 peptides. Score 0.809 Round 3: 379 peptides, 33 chains. Longest chain 30 peptides. Score 0.771 Round 4: 379 peptides, 29 chains. Longest chain 27 peptides. Score 0.796 Round 5: 378 peptides, 31 chains. Longest chain 46 peptides. Score 0.783 Taking the results from Round 2 Chains 29, Residues 349, Estimated correctness of the model 84.8 % 9 chains (196 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 75 A and 79 A Built loop between residues 61 C and 63 C 27 chains (352 residues) following loop building 7 chains (200 residues) in sequence following loop building ------------------------------------------------------ 9162 reflections ( 99.84 % complete ) and 5189 restraints for refining 3375 atoms. 3044 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2275 (Rfree = 0.000) for 3375 atoms. Found 15 (15 requested) and removed 36 (15 requested) atoms. Cycle 27: After refmac, R = 0.2257 (Rfree = 0.000) for 3336 atoms. Found 15 (15 requested) and removed 27 (15 requested) atoms. Cycle 28: After refmac, R = 0.2057 (Rfree = 0.000) for 3315 atoms. Found 9 (14 requested) and removed 17 (14 requested) atoms. Cycle 29: After refmac, R = 0.1967 (Rfree = 0.000) for 3305 atoms. Found 5 (14 requested) and removed 17 (14 requested) atoms. Cycle 30: After refmac, R = 0.1933 (Rfree = 0.000) for 3289 atoms. Found 7 (14 requested) and removed 15 (14 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.03 2.83 Search for helices and strands: 0 residues in 0 chains, 3386 seeds are put forward NCS extension: 15 residues added (44 deleted due to clashes), 3401 seeds are put forward Round 1: 363 peptides, 29 chains. Longest chain 35 peptides. Score 0.776 Round 2: 389 peptides, 25 chains. Longest chain 36 peptides. Score 0.829 Round 3: 379 peptides, 30 chains. Longest chain 32 peptides. Score 0.790 Round 4: 379 peptides, 28 chains. Longest chain 37 peptides. Score 0.802 Round 5: 358 peptides, 30 chains. Longest chain 31 peptides. Score 0.763 Taking the results from Round 2 Chains 33, Residues 364, Estimated correctness of the model 87.6 % 15 chains (273 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 46 A and 49 A Built loop between residues 74 A and 77 A Built loop between residues 60 C and 63 C Built loop between residues 62 B and 66 B Built loop between residues 76 B and 81 B 27 chains (374 residues) following loop building 10 chains (286 residues) in sequence following loop building ------------------------------------------------------ 9162 reflections ( 99.84 % complete ) and 4332 restraints for refining 3375 atoms. 1764 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2404 (Rfree = 0.000) for 3375 atoms. Found 15 (15 requested) and removed 43 (15 requested) atoms. Cycle 32: After refmac, R = 0.2216 (Rfree = 0.000) for 3333 atoms. Found 15 (15 requested) and removed 25 (15 requested) atoms. Cycle 33: After refmac, R = 0.2029 (Rfree = 0.000) for 3319 atoms. Found 14 (14 requested) and removed 18 (14 requested) atoms. Cycle 34: After refmac, R = 0.1955 (Rfree = 0.000) for 3311 atoms. Found 14 (14 requested) and removed 15 (14 requested) atoms. Cycle 35: After refmac, R = 0.1922 (Rfree = 0.000) for 3308 atoms. Found 5 (14 requested) and removed 17 (14 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.05 2.85 Search for helices and strands: 0 residues in 0 chains, 3398 seeds are put forward NCS extension: 15 residues added (58 deleted due to clashes), 3413 seeds are put forward Round 1: 349 peptides, 30 chains. Longest chain 36 peptides. Score 0.750 Round 2: 362 peptides, 24 chains. Longest chain 37 peptides. Score 0.806 Round 3: 362 peptides, 27 chains. Longest chain 38 peptides. Score 0.787 Round 4: 361 peptides, 25 chains. Longest chain 38 peptides. Score 0.799 Round 5: 347 peptides, 32 chains. Longest chain 35 peptides. Score 0.733 Taking the results from Round 2 Chains 26, Residues 338, Estimated correctness of the model 84.3 % 9 chains (218 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 60 A and 63 A Built loop between residues 80 A and 87 A 24 chains (346 residues) following loop building 7 chains (226 residues) in sequence following loop building ------------------------------------------------------ 9162 reflections ( 99.84 % complete ) and 4902 restraints for refining 3375 atoms. 2628 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2328 (Rfree = 0.000) for 3375 atoms. Found 15 (15 requested) and removed 37 (15 requested) atoms. Cycle 37: After refmac, R = 0.2124 (Rfree = 0.000) for 3345 atoms. Found 15 (15 requested) and removed 23 (15 requested) atoms. Cycle 38: After refmac, R = 0.2065 (Rfree = 0.000) for 3336 atoms. Found 12 (14 requested) and removed 14 (14 requested) atoms. Cycle 39: After refmac, R = 0.2035 (Rfree = 0.000) for 3331 atoms. Found 7 (14 requested) and removed 14 (14 requested) atoms. Cycle 40: After refmac, R = 0.2178 (Rfree = 0.000) for 3323 atoms. Found 14 (14 requested) and removed 15 (14 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.04 2.84 Search for helices and strands: 0 residues in 0 chains, 3401 seeds are put forward NCS extension: 11 residues added (45 deleted due to clashes), 3412 seeds are put forward Round 1: 335 peptides, 33 chains. Longest chain 30 peptides. Score 0.706 Round 2: 356 peptides, 28 chains. Longest chain 36 peptides. Score 0.773 Round 3: 354 peptides, 34 chains. Longest chain 33 peptides. Score 0.729 Round 4: 352 peptides, 31 chains. Longest chain 35 peptides. Score 0.747 Round 5: 348 peptides, 31 chains. Longest chain 29 peptides. Score 0.741 Taking the results from Round 2 Chains 30, Residues 328, Estimated correctness of the model 79.1 % 8 chains (171 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 60 C and 63 C Built loop between residues 80 C and 86 C 27 chains (334 residues) following loop building 6 chains (178 residues) in sequence following loop building ------------------------------------------------------ 9162 reflections ( 99.84 % complete ) and 5413 restraints for refining 3374 atoms. 3428 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2387 (Rfree = 0.000) for 3374 atoms. Found 15 (15 requested) and removed 37 (15 requested) atoms. Cycle 42: After refmac, R = 0.2168 (Rfree = 0.000) for 3349 atoms. Found 13 (15 requested) and removed 20 (15 requested) atoms. Cycle 43: After refmac, R = 0.2086 (Rfree = 0.000) for 3334 atoms. Found 6 (14 requested) and removed 19 (14 requested) atoms. Cycle 44: After refmac, R = 0.2068 (Rfree = 0.000) for 3316 atoms. Found 4 (14 requested) and removed 16 (14 requested) atoms. Cycle 45: After refmac, R = 0.2029 (Rfree = 0.000) for 3299 atoms. Found 8 (14 requested) and removed 15 (14 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.03 2.83 Search for helices and strands: 0 residues in 0 chains, 3384 seeds are put forward NCS extension: 35 residues added (54 deleted due to clashes), 3419 seeds are put forward Round 1: 327 peptides, 34 chains. Longest chain 29 peptides. Score 0.684 Round 2: 357 peptides, 30 chains. Longest chain 36 peptides. Score 0.761 Round 3: 367 peptides, 34 chains. Longest chain 33 peptides. Score 0.748 Round 4: 354 peptides, 28 chains. Longest chain 37 peptides. Score 0.771 Round 5: 361 peptides, 31 chains. Longest chain 40 peptides. Score 0.760 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 32, Residues 326, Estimated correctness of the model 78.8 % 8 chains (157 residues) have been docked in sequence Sequence coverage is 48 % Consider running further cycles of model building using 2otm-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 17 C and 27 C 30 chains (334 residues) following loop building 7 chains (166 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 9162 reflections ( 99.84 % complete ) and 5577 restraints for refining 3375 atoms. 3660 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2414 (Rfree = 0.000) for 3375 atoms. Found 0 (15 requested) and removed 15 (15 requested) atoms. Cycle 47: After refmac, R = 0.2284 (Rfree = 0.000) for 3352 atoms. Found 0 (15 requested) and removed 13 (15 requested) atoms. Cycle 48: After refmac, R = 0.2260 (Rfree = 0.000) for 3331 atoms. Found 0 (14 requested) and removed 9 (14 requested) atoms. Cycle 49: After refmac, R = 0.2217 (Rfree = 0.000) for 3322 atoms. Found 0 (14 requested) and removed 11 (14 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:13:07 GMT 2018 Job finished. TimeTaking 40.91 Used memory is bytes: 3015352