Mon 24 Dec 00:21:30 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 1vkz-2.9-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vkz-2.9-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vkz-2.9-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkz-2.9-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/1vkz-2.9-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkz-2.9-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 00:21:35 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/1vkz-2.9-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkz-2.9-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 777 and 0 Target number of residues in the AU: 777 Target solvent content: 0.5035 Checking the provided sequence file Detected sequence length: 412 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 824 Adjusted target solvent content: 0.47 Input MTZ file: 1vkz-2.9-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: 4 Cell parameters: 63.745 78.443 85.018 90.000 95.062 90.000 Input sequence file: 1vkz-2.9-parrot-mrncs.fasta_lf Building free atoms model in initial map for 6592 target number of atoms Had to go as low as 0.50 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: 19.959 2.900 Wilson plot Bfac: 24.19 17874 reflections ( 95.70 % complete ) and 0 restraints for refining 7332 atoms. Observations/parameters ratio is 0.61 ------------------------------------------------------ Starting model: R = 0.2959 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2262 (Rfree = 0.000) for 7332 atoms. Found 74 (87 requested) and removed 87 (43 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.41 2.51 Search for helices and strands: 0 residues in 0 chains, 7468 seeds are put forward NCS extension: 0 residues added, 7468 seeds are put forward Round 1: 419 peptides, 75 chains. Longest chain 13 peptides. Score 0.409 Round 2: 509 peptides, 74 chains. Longest chain 21 peptides. Score 0.565 Round 3: 531 peptides, 63 chains. Longest chain 24 peptides. Score 0.661 Round 4: 520 peptides, 59 chains. Longest chain 30 peptides. Score 0.669 Round 5: 549 peptides, 59 chains. Longest chain 36 peptides. Score 0.702 Taking the results from Round 5 Chains 60, Residues 490, Estimated correctness of the model 74.8 % 12 chains (186 residues) have been docked in sequence Building loops using Loopy2018 60 chains (490 residues) following loop building 12 chains (186 residues) in sequence following loop building ------------------------------------------------------ 17874 reflections ( 95.70 % complete ) and 11083 restraints for refining 6070 atoms. 8470 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2752 (Rfree = 0.000) for 6070 atoms. Found 72 (72 requested) and removed 71 (36 requested) atoms. Cycle 2: After refmac, R = 0.2589 (Rfree = 0.000) for 5986 atoms. Found 44 (71 requested) and removed 51 (36 requested) atoms. Cycle 3: After refmac, R = 0.2465 (Rfree = 0.000) for 5937 atoms. Found 31 (68 requested) and removed 41 (35 requested) atoms. Cycle 4: After refmac, R = 0.2375 (Rfree = 0.000) for 5896 atoms. Found 30 (66 requested) and removed 39 (35 requested) atoms. Cycle 5: After refmac, R = 0.2302 (Rfree = 0.000) for 5860 atoms. Found 29 (63 requested) and removed 36 (34 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.43 2.53 Search for helices and strands: 0 residues in 0 chains, 6005 seeds are put forward NCS extension: 8 residues added (25 deleted due to clashes), 6013 seeds are put forward Round 1: 527 peptides, 64 chains. Longest chain 26 peptides. Score 0.650 Round 2: 581 peptides, 60 chains. Longest chain 26 peptides. Score 0.731 Round 3: 600 peptides, 62 chains. Longest chain 47 peptides. Score 0.740 Round 4: 596 peptides, 53 chains. Longest chain 40 peptides. Score 0.775 Round 5: 614 peptides, 56 chains. Longest chain 36 peptides. Score 0.777 Taking the results from Round 5 Chains 63, Residues 558, Estimated correctness of the model 85.2 % 14 chains (186 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 235 A and 238 A 62 chains (558 residues) following loop building 13 chains (188 residues) in sequence following loop building ------------------------------------------------------ 17874 reflections ( 95.70 % complete ) and 10956 restraints for refining 6068 atoms. 8112 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2780 (Rfree = 0.000) for 6068 atoms. Found 65 (65 requested) and removed 79 (36 requested) atoms. Cycle 7: After refmac, R = 0.2565 (Rfree = 0.000) for 6005 atoms. Found 56 (62 requested) and removed 44 (35 requested) atoms. Cycle 8: After refmac, R = 0.2476 (Rfree = 0.000) for 5991 atoms. Found 41 (61 requested) and removed 42 (35 requested) atoms. Cycle 9: After refmac, R = 0.2379 (Rfree = 0.000) for 5966 atoms. Found 24 (60 requested) and removed 37 (35 requested) atoms. Cycle 10: After refmac, R = 0.2322 (Rfree = 0.000) for 5929 atoms. Found 35 (57 requested) and removed 36 (35 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.44 2.54 Search for helices and strands: 0 residues in 0 chains, 6069 seeds are put forward NCS extension: 15 residues added (20 deleted due to clashes), 6084 seeds are put forward Round 1: 559 peptides, 61 chains. Longest chain 26 peptides. Score 0.703 Round 2: 606 peptides, 54 chains. Longest chain 40 peptides. Score 0.779 Round 3: 607 peptides, 61 chains. Longest chain 42 peptides. Score 0.751 Round 4: 617 peptides, 52 chains. Longest chain 44 peptides. Score 0.795 Round 5: 605 peptides, 53 chains. Longest chain 44 peptides. Score 0.782 Taking the results from Round 4 Chains 56, Residues 565, Estimated correctness of the model 87.3 % 13 chains (259 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 255 A and 261 A 54 chains (568 residues) following loop building 12 chains (264 residues) in sequence following loop building ------------------------------------------------------ 17874 reflections ( 95.70 % complete ) and 10083 restraints for refining 6070 atoms. 6876 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2643 (Rfree = 0.000) for 6070 atoms. Found 58 (58 requested) and removed 75 (36 requested) atoms. Failed to save intermediate PDB Cycle 12: After refmac, R = 0.2415 (Rfree = 0.000) for 6029 atoms. Found 41 (55 requested) and removed 39 (35 requested) atoms. Cycle 13: After refmac, R = 0.2313 (Rfree = 0.000) for 6013 atoms. Found 34 (54 requested) and removed 35 (35 requested) atoms. Cycle 14: After refmac, R = 0.2262 (Rfree = 0.000) for 5994 atoms. Found 31 (53 requested) and removed 36 (35 requested) atoms. Cycle 15: After refmac, R = 0.2204 (Rfree = 0.000) for 5973 atoms. Found 20 (51 requested) and removed 35 (35 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.43 2.53 Search for helices and strands: 0 residues in 0 chains, 6082 seeds are put forward NCS extension: 29 residues added (32 deleted due to clashes), 6111 seeds are put forward Round 1: 586 peptides, 61 chains. Longest chain 41 peptides. Score 0.731 Round 2: 613 peptides, 50 chains. Longest chain 51 peptides. Score 0.800 Round 3: 612 peptides, 48 chains. Longest chain 38 peptides. Score 0.806 Round 4: 626 peptides, 50 chains. Longest chain 51 peptides. Score 0.809 Round 5: 607 peptides, 46 chains. Longest chain 48 peptides. Score 0.810 Taking the results from Round 5 Chains 54, Residues 561, Estimated correctness of the model 88.9 % 14 chains (250 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 363 A and 366 A 53 chains (562 residues) following loop building 13 chains (252 residues) in sequence following loop building ------------------------------------------------------ 17874 reflections ( 95.70 % complete ) and 10067 restraints for refining 6070 atoms. 6930 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2661 (Rfree = 0.000) for 6070 atoms. Found 50 (50 requested) and removed 79 (36 requested) atoms. Cycle 17: After refmac, R = 0.2491 (Rfree = 0.000) for 6015 atoms. Found 48 (48 requested) and removed 39 (35 requested) atoms. Cycle 18: After refmac, R = 0.2380 (Rfree = 0.000) for 6008 atoms. Found 39 (47 requested) and removed 39 (35 requested) atoms. Cycle 19: After refmac, R = 0.2297 (Rfree = 0.000) for 5996 atoms. Found 31 (45 requested) and removed 37 (35 requested) atoms. Cycle 20: After refmac, R = 0.2221 (Rfree = 0.000) for 5976 atoms. Found 27 (44 requested) and removed 35 (35 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.43 2.53 Search for helices and strands: 0 residues in 0 chains, 6121 seeds are put forward NCS extension: 12 residues added (36 deleted due to clashes), 6133 seeds are put forward Round 1: 586 peptides, 57 chains. Longest chain 50 peptides. Score 0.749 Round 2: 613 peptides, 48 chains. Longest chain 40 peptides. Score 0.807 Round 3: 610 peptides, 58 chains. Longest chain 35 peptides. Score 0.766 Round 4: 606 peptides, 47 chains. Longest chain 48 peptides. Score 0.806 Round 5: 606 peptides, 53 chains. Longest chain 40 peptides. Score 0.783 Taking the results from Round 2 Chains 56, Residues 565, Estimated correctness of the model 88.6 % 16 chains (288 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 255 A and 259 A Built loop between residues 287 A and 290 A Built loop between residues 371 A and 374 A 53 chains (572 residues) following loop building 13 chains (295 residues) in sequence following loop building ------------------------------------------------------ 17874 reflections ( 95.70 % complete ) and 9585 restraints for refining 6069 atoms. 6182 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2503 (Rfree = 0.000) for 6069 atoms. Found 43 (43 requested) and removed 55 (36 requested) atoms. Cycle 22: After refmac, R = 0.2333 (Rfree = 0.000) for 6033 atoms. Found 34 (41 requested) and removed 37 (35 requested) atoms. Cycle 23: After refmac, R = 0.2253 (Rfree = 0.000) for 6008 atoms. Found 35 (40 requested) and removed 35 (35 requested) atoms. Cycle 24: After refmac, R = 0.2221 (Rfree = 0.000) for 5997 atoms. Found 27 (38 requested) and removed 35 (35 requested) atoms. Cycle 25: After refmac, R = 0.2176 (Rfree = 0.000) for 5976 atoms. Found 30 (37 requested) and removed 35 (35 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.45 2.55 Search for helices and strands: 0 residues in 0 chains, 6098 seeds are put forward NCS extension: 18 residues added (100 deleted due to clashes), 6116 seeds are put forward Round 1: 562 peptides, 53 chains. Longest chain 41 peptides. Score 0.744 Round 2: 611 peptides, 49 chains. Longest chain 50 peptides. Score 0.802 Round 3: 622 peptides, 48 chains. Longest chain 59 peptides. Score 0.814 Round 4: 596 peptides, 47 chains. Longest chain 40 peptides. Score 0.798 Round 5: 619 peptides, 55 chains. Longest chain 57 peptides. Score 0.785 Taking the results from Round 3 Chains 56, Residues 574, Estimated correctness of the model 89.4 % 15 chains (328 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 258 A and 269 A Built loop between residues 370 A and 374 A Built loop between residues 370 B and 373 B 51 chains (581 residues) following loop building 11 chains (343 residues) in sequence following loop building ------------------------------------------------------ 17874 reflections ( 95.70 % complete ) and 9082 restraints for refining 6070 atoms. 5438 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2602 (Rfree = 0.000) for 6070 atoms. Found 36 (36 requested) and removed 86 (36 requested) atoms. Cycle 27: After refmac, R = 0.2436 (Rfree = 0.000) for 5986 atoms. Found 35 (35 requested) and removed 39 (35 requested) atoms. Cycle 28: After refmac, R = 0.2356 (Rfree = 0.000) for 5968 atoms. Found 35 (35 requested) and removed 36 (35 requested) atoms. Cycle 29: After refmac, R = 0.2286 (Rfree = 0.000) for 5953 atoms. Found 22 (35 requested) and removed 36 (35 requested) atoms. Cycle 30: After refmac, R = 0.2248 (Rfree = 0.000) for 5922 atoms. Found 24 (35 requested) and removed 36 (35 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.41 2.51 Search for helices and strands: 0 residues in 0 chains, 6037 seeds are put forward NCS extension: 17 residues added (96 deleted due to clashes), 6054 seeds are put forward Round 1: 581 peptides, 47 chains. Longest chain 49 peptides. Score 0.786 Round 2: 589 peptides, 48 chains. Longest chain 40 peptides. Score 0.789 Round 3: 590 peptides, 52 chains. Longest chain 52 peptides. Score 0.774 Round 4: 606 peptides, 47 chains. Longest chain 47 peptides. Score 0.806 Round 5: 584 peptides, 53 chains. Longest chain 34 peptides. Score 0.764 Taking the results from Round 4 Chains 50, Residues 559, Estimated correctness of the model 88.5 % 15 chains (289 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 236 A and 243 A Built loop between residues 361 A and 365 A Built loop between residues 245 B and 256 B 46 chains (569 residues) following loop building 12 chains (308 residues) in sequence following loop building ------------------------------------------------------ 17874 reflections ( 95.70 % complete ) and 9533 restraints for refining 6068 atoms. 6128 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2649 (Rfree = 0.000) for 6068 atoms. Found 36 (36 requested) and removed 89 (36 requested) atoms. Cycle 32: After refmac, R = 0.2472 (Rfree = 0.000) for 5982 atoms. Found 35 (35 requested) and removed 38 (35 requested) atoms. Cycle 33: After refmac, R = 0.2373 (Rfree = 0.000) for 5960 atoms. Found 35 (35 requested) and removed 38 (35 requested) atoms. Cycle 34: After refmac, R = 0.2344 (Rfree = 0.000) for 5943 atoms. Found 35 (35 requested) and removed 36 (35 requested) atoms. Cycle 35: After refmac, R = 0.2280 (Rfree = 0.000) for 5933 atoms. Found 30 (35 requested) and removed 35 (35 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.41 2.51 Search for helices and strands: 0 residues in 0 chains, 6068 seeds are put forward NCS extension: 10 residues added (34 deleted due to clashes), 6078 seeds are put forward Round 1: 548 peptides, 53 chains. Longest chain 45 peptides. Score 0.731 Round 2: 594 peptides, 44 chains. Longest chain 55 peptides. Score 0.808 Round 3: 583 peptides, 50 chains. Longest chain 50 peptides. Score 0.776 Round 4: 584 peptides, 46 chains. Longest chain 41 peptides. Score 0.793 Round 5: 588 peptides, 48 chains. Longest chain 45 peptides. Score 0.788 Taking the results from Round 2 Chains 49, Residues 550, Estimated correctness of the model 88.7 % 16 chains (330 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 276 A and 280 A Built loop between residues 297 A and 301 A Built loop between residues 384 A and 387 A 44 chains (552 residues) following loop building 13 chains (338 residues) in sequence following loop building ------------------------------------------------------ 17874 reflections ( 95.70 % complete ) and 9297 restraints for refining 6070 atoms. 5826 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2523 (Rfree = 0.000) for 6070 atoms. Found 36 (36 requested) and removed 69 (36 requested) atoms. Cycle 37: After refmac, R = 0.2370 (Rfree = 0.000) for 6016 atoms. Found 35 (35 requested) and removed 39 (35 requested) atoms. Cycle 38: After refmac, R = 0.2271 (Rfree = 0.000) for 5998 atoms. Found 35 (35 requested) and removed 35 (35 requested) atoms. Cycle 39: After refmac, R = 0.2215 (Rfree = 0.000) for 5985 atoms. Found 33 (35 requested) and removed 35 (35 requested) atoms. Cycle 40: After refmac, R = 0.2170 (Rfree = 0.000) for 5971 atoms. Found 20 (35 requested) and removed 35 (35 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.42 2.52 Search for helices and strands: 0 residues in 0 chains, 6078 seeds are put forward NCS extension: 26 residues added (76 deleted due to clashes), 6104 seeds are put forward Round 1: 528 peptides, 50 chains. Longest chain 28 peptides. Score 0.725 Round 2: 564 peptides, 47 chains. Longest chain 44 peptides. Score 0.772 Round 3: 587 peptides, 45 chains. Longest chain 51 peptides. Score 0.799 Round 4: 586 peptides, 46 chains. Longest chain 47 peptides. Score 0.794 Round 5: 575 peptides, 45 chains. Longest chain 50 peptides. Score 0.790 Taking the results from Round 3 Chains 50, Residues 542, Estimated correctness of the model 87.7 % 17 chains (369 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 287 A and 290 A Built loop between residues 384 A and 387 A Built loop between residues 277 B and 282 B Built loop between residues 379 B and 383 B 44 chains (548 residues) following loop building 13 chains (380 residues) in sequence following loop building ------------------------------------------------------ 17874 reflections ( 95.70 % complete ) and 8795 restraints for refining 6070 atoms. 5140 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2500 (Rfree = 0.000) for 6070 atoms. Found 36 (36 requested) and removed 79 (36 requested) atoms. Cycle 42: After refmac, R = 0.2340 (Rfree = 0.000) for 5999 atoms. Found 35 (35 requested) and removed 38 (35 requested) atoms. Cycle 43: After refmac, R = 0.2261 (Rfree = 0.000) for 5981 atoms. Found 32 (35 requested) and removed 35 (35 requested) atoms. Cycle 44: After refmac, R = 0.2204 (Rfree = 0.000) for 5969 atoms. Found 19 (35 requested) and removed 36 (35 requested) atoms. Failed to save intermediate PDB Cycle 45: After refmac, R = 0.2174 (Rfree = 0.000) for 5946 atoms. Found 23 (35 requested) and removed 35 (35 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.40 2.50 Search for helices and strands: 0 residues in 0 chains, 6045 seeds are put forward NCS extension: 11 residues added (36 deleted due to clashes), 6056 seeds are put forward Round 1: 533 peptides, 48 chains. Longest chain 40 peptides. Score 0.739 Round 2: 584 peptides, 35 chains. Longest chain 56 peptides. Score 0.833 Round 3: 567 peptides, 48 chains. Longest chain 40 peptides. Score 0.771 Round 4: 584 peptides, 45 chains. Longest chain 57 peptides. Score 0.797 Round 5: 570 peptides, 53 chains. Longest chain 40 peptides. Score 0.752 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 40, Residues 549, Estimated correctness of the model 91.3 % 16 chains (393 residues) have been docked in sequence Sequence coverage is 71 % Consider running further cycles of model building using 1vkz-2_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 34 A and 46 A Built loop between residues 284 A and 288 A Built loop between residues 256 B and 261 B Built loop between residues 276 B and 280 B 34 chains (562 residues) following loop building 12 chains (414 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 17874 reflections ( 95.70 % complete ) and 8258 restraints for refining 6069 atoms. 4312 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2479 (Rfree = 0.000) for 6069 atoms. Found 0 (36 requested) and removed 15 (36 requested) atoms. Cycle 47: After refmac, R = 0.2366 (Rfree = 0.000) for 6023 atoms. Found 0 (35 requested) and removed 8 (35 requested) atoms. Cycle 48: After refmac, R = 0.2326 (Rfree = 0.000) for 6002 atoms. Found 0 (35 requested) and removed 1 (35 requested) atoms. Cycle 49: After refmac, R = 0.2300 (Rfree = 0.000) for 5993 atoms. TimeTaking 65.67