Mon 24 Dec 00:52:33 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 2opk-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2opk-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2opk-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2opk-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/2opk-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2opk-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 00:52:38 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/2opk-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2opk-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 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-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: 96 Cell parameters: 75.570 75.570 198.970 90.000 90.000 90.000 Input sequence file: 2opk-3.2-parrot-mrncs.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 4009 atoms. Observations/parameters ratio is 0.63 ------------------------------------------------------ Starting model: R = 0.2885 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2290 (Rfree = 0.000) for 4009 atoms. Found 35 (35 requested) and removed 28 (17 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.96 2.69 Search for helices and strands: 0 residues in 0 chains, 4070 seeds are put forward NCS extension: 0 residues added, 4070 seeds are put forward Round 1: 307 peptides, 41 chains. Longest chain 21 peptides. Score 0.574 Round 2: 349 peptides, 31 chains. Longest chain 27 peptides. Score 0.736 Round 3: 376 peptides, 33 chains. Longest chain 26 peptides. Score 0.760 Round 4: 374 peptides, 26 chains. Longest chain 28 peptides. Score 0.801 Round 5: 388 peptides, 22 chains. Longest chain 40 peptides. Score 0.838 Taking the results from Round 5 Chains 24, Residues 366, Estimated correctness of the model 88.7 % 10 chains (261 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 37 A and 47 A Built loop between residues 77 A and 88 A Built loop between residues 68 C and 75 C 20 chains (389 residues) following loop building 7 chains (286 residues) in sequence following loop building ------------------------------------------------------ 10119 reflections ( 99.61 % complete ) and 4686 restraints for refining 3672 atoms. 1981 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2616 (Rfree = 0.000) for 3672 atoms. Found 32 (32 requested) and removed 67 (16 requested) atoms. Cycle 2: After refmac, R = 0.2386 (Rfree = 0.000) for 3583 atoms. Found 19 (31 requested) and removed 24 (16 requested) atoms. Cycle 3: After refmac, R = 0.2250 (Rfree = 0.000) for 3555 atoms. Found 14 (31 requested) and removed 21 (16 requested) atoms. Cycle 4: After refmac, R = 0.2152 (Rfree = 0.000) for 3535 atoms. Found 17 (29 requested) and removed 15 (15 requested) atoms. Cycle 5: After refmac, R = 0.2042 (Rfree = 0.000) for 3523 atoms. Found 11 (29 requested) and removed 15 (15 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.96 2.69 Search for helices and strands: 0 residues in 0 chains, 3593 seeds are put forward NCS extension: 32 residues added (65 deleted due to clashes), 3625 seeds are put forward Round 1: 374 peptides, 26 chains. Longest chain 51 peptides. Score 0.801 Round 2: 405 peptides, 19 chains. Longest chain 65 peptides. Score 0.867 Round 3: 406 peptides, 20 chains. Longest chain 70 peptides. Score 0.863 Round 4: 406 peptides, 16 chains. Longest chain 84 peptides. Score 0.881 Round 5: 405 peptides, 23 chains. Longest chain 51 peptides. Score 0.848 Taking the results from Round 4 Chains 19, Residues 390, Estimated correctness of the model 93.6 % 11 chains (341 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 40 C and 46 C Built loop between residues 78 C and 84 C Built loop between residues 68 B and 72 B Built loop between residues 99 B and 102 B Built loop between residues 86 D and 93 D 14 chains (410 residues) following loop building 6 chains (362 residues) in sequence following loop building ------------------------------------------------------ 10119 reflections ( 99.61 % complete ) and 4092 restraints for refining 3591 atoms. 1001 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2486 (Rfree = 0.000) for 3591 atoms. Found 29 (29 requested) and removed 49 (16 requested) atoms. Cycle 7: After refmac, R = 0.2274 (Rfree = 0.000) for 3556 atoms. Found 22 (28 requested) and removed 25 (16 requested) atoms. Cycle 8: After refmac, R = 0.2146 (Rfree = 0.000) for 3547 atoms. Found 10 (27 requested) and removed 26 (15 requested) atoms. Cycle 9: After refmac, R = 0.2094 (Rfree = 0.000) for 3525 atoms. Found 13 (26 requested) and removed 15 (15 requested) atoms. Cycle 10: After refmac, R = 0.2033 (Rfree = 0.000) for 3520 atoms. Found 15 (25 requested) and removed 17 (15 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.98 2.71 Search for helices and strands: 0 residues in 0 chains, 3589 seeds are put forward NCS extension: 26 residues added (89 deleted due to clashes), 3615 seeds are put forward Round 1: 401 peptides, 17 chains. Longest chain 55 peptides. Score 0.873 Round 2: 405 peptides, 16 chains. Longest chain 67 peptides. Score 0.880 Round 3: 408 peptides, 17 chains. Longest chain 56 peptides. Score 0.878 Round 4: 396 peptides, 20 chains. Longest chain 51 peptides. Score 0.855 Round 5: 405 peptides, 16 chains. Longest chain 61 peptides. Score 0.880 Taking the results from Round 5 Chains 19, Residues 389, Estimated correctness of the model 93.5 % 11 chains (341 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 61 A and 64 A Built loop between residues 84 A and 89 A Built loop between residues 60 C and 71 C Built loop between residues 82 C and 86 C Built loop between residues 66 B and 72 B Built loop between residues 42 D and 46 D Built loop between residues 68 D and 75 D 9 chains (414 residues) following loop building 4 chains (374 residues) in sequence following loop building ------------------------------------------------------ 10119 reflections ( 99.61 % complete ) and 3983 restraints for refining 3539 atoms. 804 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2445 (Rfree = 0.000) for 3539 atoms. Found 25 (25 requested) and removed 54 (15 requested) atoms. Cycle 12: After refmac, R = 0.2241 (Rfree = 0.000) for 3485 atoms. Found 24 (24 requested) and removed 28 (15 requested) atoms. Cycle 13: After refmac, R = 0.2096 (Rfree = 0.000) for 3470 atoms. Found 16 (24 requested) and removed 17 (15 requested) atoms. Cycle 14: After refmac, R = 0.2022 (Rfree = 0.000) for 3464 atoms. Found 16 (23 requested) and removed 19 (15 requested) atoms. Cycle 15: After refmac, R = 0.2020 (Rfree = 0.000) for 3458 atoms. Found 12 (22 requested) and removed 19 (15 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.97 2.70 Search for helices and strands: 0 residues in 0 chains, 3515 seeds are put forward NCS extension: 15 residues added (31 deleted due to clashes), 3530 seeds are put forward Round 1: 394 peptides, 20 chains. Longest chain 57 peptides. Score 0.853 Round 2: 401 peptides, 20 chains. Longest chain 58 peptides. Score 0.859 Round 3: 400 peptides, 16 chains. Longest chain 70 peptides. Score 0.876 Round 4: 402 peptides, 15 chains. Longest chain 85 peptides. Score 0.882 Round 5: 396 peptides, 21 chains. Longest chain 45 peptides. Score 0.850 Taking the results from Round 4 Chains 20, Residues 387, Estimated correctness of the model 93.7 % 10 chains (313 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 39 A and 47 A Built loop between residues 58 A and 61 A Built loop between residues 60 C and 63 C Built loop between residues 78 C and 89 C Built loop between residues 37 B and 42 B 12 chains (401 residues) following loop building 5 chains (338 residues) in sequence following loop building ------------------------------------------------------ 10119 reflections ( 99.61 % complete ) and 3872 restraints for refining 3382 atoms. 940 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2605 (Rfree = 0.000) for 3382 atoms. Found 21 (21 requested) and removed 50 (15 requested) atoms. Cycle 17: After refmac, R = 0.2362 (Rfree = 0.000) for 3340 atoms. Found 20 (20 requested) and removed 20 (15 requested) atoms. Cycle 18: After refmac, R = 0.2187 (Rfree = 0.000) for 3336 atoms. Found 19 (19 requested) and removed 15 (14 requested) atoms. Cycle 19: After refmac, R = 0.2079 (Rfree = 0.000) for 3339 atoms. Found 12 (19 requested) and removed 17 (14 requested) atoms. Cycle 20: After refmac, R = 0.2030 (Rfree = 0.000) for 3329 atoms. Found 16 (18 requested) and removed 17 (14 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.96 2.69 Search for helices and strands: 0 residues in 0 chains, 3412 seeds are put forward NCS extension: 39 residues added (108 deleted due to clashes), 3451 seeds are put forward Round 1: 379 peptides, 25 chains. Longest chain 55 peptides. Score 0.812 Round 2: 401 peptides, 18 chains. Longest chain 53 peptides. Score 0.868 Round 3: 402 peptides, 23 chains. Longest chain 68 peptides. Score 0.846 Round 4: 382 peptides, 24 chains. Longest chain 42 peptides. Score 0.821 Round 5: 396 peptides, 23 chains. Longest chain 50 peptides. Score 0.840 Taking the results from Round 2 Chains 21, Residues 383, Estimated correctness of the model 92.2 % 8 chains (271 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 34 A and 40 A Built loop between residues 68 A and 72 A Built loop between residues 86 C and 90 C 16 chains (391 residues) following loop building 5 chains (282 residues) in sequence following loop building ------------------------------------------------------ 10119 reflections ( 99.61 % complete ) and 4094 restraints for refining 3271 atoms. 1414 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2522 (Rfree = 0.000) for 3271 atoms. Found 17 (17 requested) and removed 39 (14 requested) atoms. Cycle 22: After refmac, R = 0.2259 (Rfree = 0.000) for 3245 atoms. Found 17 (17 requested) and removed 17 (14 requested) atoms. Cycle 23: After refmac, R = 0.2161 (Rfree = 0.000) for 3242 atoms. Found 16 (16 requested) and removed 15 (14 requested) atoms. Cycle 24: After refmac, R = 0.2117 (Rfree = 0.000) for 3241 atoms. Found 16 (16 requested) and removed 14 (14 requested) atoms. Cycle 25: After refmac, R = 0.2064 (Rfree = 0.000) for 3240 atoms. Found 13 (15 requested) and removed 18 (14 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.02 2.75 Search for helices and strands: 0 residues in 0 chains, 3293 seeds are put forward NCS extension: 25 residues added (80 deleted due to clashes), 3318 seeds are put forward Round 1: 372 peptides, 28 chains. Longest chain 52 peptides. Score 0.787 Round 2: 381 peptides, 22 chains. Longest chain 51 peptides. Score 0.831 Round 3: 391 peptides, 22 chains. Longest chain 45 peptides. Score 0.840 Round 4: 393 peptides, 21 chains. Longest chain 60 peptides. Score 0.847 Round 5: 378 peptides, 27 chains. Longest chain 33 peptides. Score 0.800 Taking the results from Round 4 Chains 27, Residues 372, Estimated correctness of the model 89.8 % 10 chains (267 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 44 A and 48 A Built loop between residues 78 C and 82 C Built loop between residues 78 B and 81 B Built loop between residues 43 D and 50 D 21 chains (381 residues) following loop building 6 chains (281 residues) in sequence following loop building ------------------------------------------------------ 10119 reflections ( 99.61 % complete ) and 4115 restraints for refining 3272 atoms. 1495 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2515 (Rfree = 0.000) for 3272 atoms. Found 14 (14 requested) and removed 38 (14 requested) atoms. Cycle 27: After refmac, R = 0.2279 (Rfree = 0.000) for 3238 atoms. Found 14 (14 requested) and removed 15 (14 requested) atoms. Cycle 28: After refmac, R = 0.2155 (Rfree = 0.000) for 3237 atoms. Found 14 (14 requested) and removed 14 (14 requested) atoms. Cycle 29: After refmac, R = 0.2086 (Rfree = 0.000) for 3237 atoms. Found 14 (14 requested) and removed 14 (14 requested) atoms. Cycle 30: After refmac, R = 0.2076 (Rfree = 0.000) for 3235 atoms. Found 7 (14 requested) and removed 15 (14 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.98 2.71 Search for helices and strands: 0 residues in 0 chains, 3310 seeds are put forward NCS extension: 26 residues added (97 deleted due to clashes), 3336 seeds are put forward Round 1: 351 peptides, 27 chains. Longest chain 34 peptides. Score 0.766 Round 2: 382 peptides, 23 chains. Longest chain 40 peptides. Score 0.827 Round 3: 379 peptides, 22 chains. Longest chain 68 peptides. Score 0.829 Round 4: 382 peptides, 26 chains. Longest chain 38 peptides. Score 0.810 Round 5: 380 peptides, 24 chains. Longest chain 67 peptides. Score 0.819 Taking the results from Round 3 Chains 24, Residues 357, Estimated correctness of the model 87.6 % 10 chains (264 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 35 A and 45 A Built loop between residues 38 C and 43 C Built loop between residues 68 C and 75 C Built loop between residues 67 B and 70 B Built loop between residues 45 D and 49 D 17 chains (375 residues) following loop building 5 chains (288 residues) in sequence following loop building ------------------------------------------------------ 10119 reflections ( 99.61 % complete ) and 4233 restraints for refining 3320 atoms. 1578 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2686 (Rfree = 0.000) for 3320 atoms. Found 14 (14 requested) and removed 52 (14 requested) atoms. Cycle 32: After refmac, R = 0.2461 (Rfree = 0.000) for 3271 atoms. Found 14 (14 requested) and removed 18 (14 requested) atoms. Cycle 33: After refmac, R = 0.2332 (Rfree = 0.000) for 3263 atoms. Found 11 (14 requested) and removed 16 (14 requested) atoms. Cycle 34: After refmac, R = 0.2221 (Rfree = 0.000) for 3258 atoms. Found 12 (14 requested) and removed 16 (14 requested) atoms. Cycle 35: After refmac, R = 0.2145 (Rfree = 0.000) for 3253 atoms. Found 7 (14 requested) and removed 18 (14 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.99 2.72 Search for helices and strands: 0 residues in 0 chains, 3323 seeds are put forward NCS extension: 23 residues added (57 deleted due to clashes), 3346 seeds are put forward Round 1: 351 peptides, 29 chains. Longest chain 66 peptides. Score 0.753 Round 2: 364 peptides, 27 chains. Longest chain 37 peptides. Score 0.783 Round 3: 366 peptides, 28 chains. Longest chain 34 peptides. Score 0.779 Round 4: 368 peptides, 24 chains. Longest chain 37 peptides. Score 0.806 Round 5: 375 peptides, 25 chains. Longest chain 39 peptides. Score 0.808 Taking the results from Round 5 Chains 31, Residues 350, Estimated correctness of the model 84.6 % 10 chains (229 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 86 A and 91 A Built loop between residues 38 C and 45 C 28 chains (357 residues) following loop building 8 chains (239 residues) in sequence following loop building ------------------------------------------------------ 10119 reflections ( 99.61 % complete ) and 4618 restraints for refining 3272 atoms. 2257 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2640 (Rfree = 0.000) for 3272 atoms. Found 14 (14 requested) and removed 35 (14 requested) atoms. Cycle 37: After refmac, R = 0.2426 (Rfree = 0.000) for 3243 atoms. Found 14 (14 requested) and removed 15 (14 requested) atoms. Cycle 38: After refmac, R = 0.2293 (Rfree = 0.000) for 3235 atoms. Found 12 (14 requested) and removed 15 (14 requested) atoms. Failed to save intermediate PDB Cycle 39: After refmac, R = 0.2251 (Rfree = 0.000) for 3225 atoms. Found 5 (14 requested) and removed 15 (14 requested) atoms. Cycle 40: After refmac, R = 0.2210 (Rfree = 0.000) for 3212 atoms. Found 12 (14 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.01 2.74 Search for helices and strands: 0 residues in 0 chains, 3265 seeds are put forward NCS extension: 43 residues added (62 deleted due to clashes), 3308 seeds are put forward Round 1: 355 peptides, 29 chains. Longest chain 29 peptides. Score 0.758 Round 2: 373 peptides, 21 chains. Longest chain 42 peptides. Score 0.828 Round 3: 356 peptides, 24 chains. Longest chain 40 peptides. Score 0.792 Round 4: 347 peptides, 23 chains. Longest chain 39 peptides. Score 0.787 Round 5: 359 peptides, 18 chains. Longest chain 70 peptides. Score 0.830 Taking the results from Round 5 Chains 23, Residues 341, Estimated correctness of the model 87.7 % 9 chains (213 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 39 A and 46 A Built loop between residues 50 B and 53 B Built loop between residues 66 B and 77 B 19 chains (352 residues) following loop building 6 chains (231 residues) in sequence following loop building ------------------------------------------------------ 10119 reflections ( 99.61 % complete ) and 4531 restraints for refining 3271 atoms. 2214 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2520 (Rfree = 0.000) for 3271 atoms. Found 14 (14 requested) and removed 39 (14 requested) atoms. Cycle 42: After refmac, R = 0.2346 (Rfree = 0.000) for 3235 atoms. Found 14 (14 requested) and removed 18 (14 requested) atoms. Cycle 43: After refmac, R = 0.2220 (Rfree = 0.000) for 3222 atoms. Found 14 (14 requested) and removed 16 (14 requested) atoms. Cycle 44: After refmac, R = 0.2136 (Rfree = 0.000) for 3216 atoms. Found 14 (14 requested) and removed 14 (14 requested) atoms. Cycle 45: After refmac, R = 0.2115 (Rfree = 0.000) for 3213 atoms. Found 13 (14 requested) and removed 16 (14 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.99 2.72 Search for helices and strands: 0 residues in 0 chains, 3284 seeds are put forward NCS extension: 47 residues added (28 deleted due to clashes), 3331 seeds are put forward Round 1: 341 peptides, 35 chains. Longest chain 23 peptides. Score 0.693 Round 2: 352 peptides, 25 chains. Longest chain 35 peptides. Score 0.781 Round 3: 357 peptides, 25 chains. Longest chain 38 peptides. Score 0.787 Round 4: 356 peptides, 26 chains. Longest chain 28 peptides. Score 0.779 Round 5: 372 peptides, 27 chains. Longest chain 37 peptides. Score 0.793 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 34, Residues 345, Estimated correctness of the model 82.3 % 9 chains (174 residues) have been docked in sequence Sequence coverage is 50 % Consider running further cycles of model building using 2opk-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 39 A and 43 A Built loop between residues 44 C and 47 C Built loop between residues 45 B and 56 B 30 chains (353 residues) following loop building 6 chains (189 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 10119 reflections ( 99.61 % complete ) and 4865 restraints for refining 3272 atoms. 2726 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2504 (Rfree = 0.000) for 3272 atoms. Found 0 (14 requested) and removed 7 (14 requested) atoms. Cycle 47: After refmac, R = 0.2385 (Rfree = 0.000) for 3252 atoms. Found 0 (14 requested) and removed 3 (14 requested) atoms. Cycle 48: After refmac, R = 0.2269 (Rfree = 0.000) for 3246 atoms. Found 0 (14 requested) and removed 2 (14 requested) atoms. Cycle 49: After refmac, R = 0.2269 (Rfree = 0.000) for 3243 atoms. TimeTaking 52.53