Sun 23 Dec 22:23:02 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vr5-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vr5-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vr5-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vr5-3.2-parrot-hancs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vr5-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vr5-3.2-parrot-hancs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Sun 23 Dec 22:23:12 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vr5-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vr5-3.2-parrot-hancs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 1068 and 0 Target number of residues in the AU: 1068 Target solvent content: 0.6311 Checking the provided sequence file Detected sequence length: 547 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 1094 Adjusted target solvent content: 0.62 Input MTZ file: 1vr5-3.2-parrot-hancs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 18 Cell parameters: 140.030 96.640 115.780 90.000 90.000 90.000 Input sequence file: 1vr5-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 8752 target number of atoms Had to go as low as 0.90 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: 115.780 3.200 Wilson plot Bfac: 67.10 26515 reflections ( 99.70 % complete ) and 0 restraints for refining 9665 atoms. Observations/parameters ratio is 0.69 ------------------------------------------------------ Starting model: R = 0.3065 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2739 (Rfree = 0.000) for 9665 atoms. Found 86 (86 requested) and removed 52 (43 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.19 2.71 Search for helices and strands: 0 residues in 0 chains, 9890 seeds are put forward NCS extension: 0 residues added, 9890 seeds are put forward Round 1: 741 peptides, 112 chains. Longest chain 23 peptides. Score 0.487 Round 2: 829 peptides, 92 chains. Longest chain 31 peptides. Score 0.633 Round 3: 887 peptides, 82 chains. Longest chain 38 peptides. Score 0.702 Round 4: 891 peptides, 74 chains. Longest chain 49 peptides. Score 0.727 Round 5: 881 peptides, 73 chains. Longest chain 43 peptides. Score 0.724 Taking the results from Round 4 Chains 81, Residues 817, Estimated correctness of the model 70.7 % 15 chains (289 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 294 B and 300 B 78 chains (818 residues) following loop building 14 chains (294 residues) in sequence following loop building ------------------------------------------------------ 26515 reflections ( 99.70 % complete ) and 14786 restraints for refining 8606 atoms. 10323 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2586 (Rfree = 0.000) for 8606 atoms. Found 77 (77 requested) and removed 73 (38 requested) atoms. Cycle 2: After refmac, R = 0.2425 (Rfree = 0.000) for 8474 atoms. Found 70 (75 requested) and removed 51 (38 requested) atoms. Cycle 3: After refmac, R = 0.2288 (Rfree = 0.000) for 8459 atoms. Found 30 (73 requested) and removed 40 (38 requested) atoms. Cycle 4: After refmac, R = 0.2249 (Rfree = 0.000) for 8416 atoms. Found 34 (70 requested) and removed 40 (37 requested) atoms. Cycle 5: After refmac, R = 0.2193 (Rfree = 0.000) for 8399 atoms. Found 25 (69 requested) and removed 39 (37 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.16 2.68 Search for helices and strands: 0 residues in 0 chains, 8580 seeds are put forward NCS extension: 13 residues added (8 deleted due to clashes), 8593 seeds are put forward Round 1: 837 peptides, 77 chains. Longest chain 44 peptides. Score 0.686 Round 2: 879 peptides, 72 chains. Longest chain 31 peptides. Score 0.726 Round 3: 864 peptides, 66 chains. Longest chain 39 peptides. Score 0.734 Round 4: 870 peptides, 70 chains. Longest chain 44 peptides. Score 0.726 Round 5: 885 peptides, 63 chains. Longest chain 74 peptides. Score 0.753 Taking the results from Round 5 Chains 69, Residues 822, Estimated correctness of the model 75.6 % 15 chains (378 residues) have been docked in sequence Building loops using Loopy2018 69 chains (822 residues) following loop building 15 chains (378 residues) in sequence following loop building ------------------------------------------------------ 26515 reflections ( 99.70 % complete ) and 13664 restraints for refining 8382 atoms. 8780 conditional restraints added. Observations/parameters ratio is 0.79 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2617 (Rfree = 0.000) for 8382 atoms. Found 67 (67 requested) and removed 61 (37 requested) atoms. Cycle 7: After refmac, R = 0.2369 (Rfree = 0.000) for 8307 atoms. Found 47 (66 requested) and removed 44 (37 requested) atoms. Cycle 8: After refmac, R = 0.2232 (Rfree = 0.000) for 8277 atoms. Found 29 (64 requested) and removed 57 (37 requested) atoms. Cycle 9: After refmac, R = 0.2132 (Rfree = 0.000) for 8225 atoms. Found 23 (62 requested) and removed 39 (37 requested) atoms. Cycle 10: After refmac, R = 0.2089 (Rfree = 0.000) for 8190 atoms. Found 35 (60 requested) and removed 37 (36 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.18 2.70 Search for helices and strands: 0 residues in 0 chains, 8371 seeds are put forward NCS extension: 34 residues added (23 deleted due to clashes), 8405 seeds are put forward Round 1: 850 peptides, 75 chains. Longest chain 39 peptides. Score 0.700 Round 2: 901 peptides, 72 chains. Longest chain 51 peptides. Score 0.738 Round 3: 910 peptides, 68 chains. Longest chain 54 peptides. Score 0.753 Round 4: 898 peptides, 72 chains. Longest chain 40 peptides. Score 0.736 Round 5: 898 peptides, 66 chains. Longest chain 50 peptides. Score 0.752 Taking the results from Round 3 Failed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDB Chains 79, Residues 842, Estimated correctness of the model 75.6 % 21 chains (466 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 134 A and 140 A Built loop between residues 242 A and 245 A Built loop between residues 302 A and 311 A Built loop between residues 55 B and 66 B Built loop between residues 494 B and 504 B 69 chains (863 residues) following loop building 16 chains (500 residues) in sequence following loop building ------------------------------------------------------ 26515 reflections ( 99.70 % complete ) and 12578 restraints for refining 8423 atoms. 6918 conditional restraints added. Observations/parameters ratio is 0.79 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2579 (Rfree = 0.000) for 8423 atoms. Found 60 (60 requested) and removed 73 (37 requested) atoms. Cycle 12: After refmac, R = 0.2430 (Rfree = 0.000) for 8384 atoms. Found 58 (58 requested) and removed 55 (37 requested) atoms. Cycle 13: After refmac, R = 0.2382 (Rfree = 0.000) for 8356 atoms. Found 57 (57 requested) and removed 52 (37 requested) atoms. Cycle 14: After refmac, R = 0.2390 (Rfree = 0.000) for 8327 atoms. Found 55 (55 requested) and removed 47 (37 requested) atoms. Cycle 15: After refmac, R = 0.2091 (Rfree = 0.000) for 8302 atoms. Found 34 (53 requested) and removed 48 (37 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.18 2.70 Search for helices and strands: 0 residues in 0 chains, 8484 seeds are put forward NCS extension: 15 residues added (40 deleted due to clashes), 8499 seeds are put forward Round 1: 896 peptides, 79 chains. Longest chain 43 peptides. Score 0.716 Round 2: 906 peptides, 69 chains. Longest chain 51 peptides. Score 0.748 Round 3: 905 peptides, 68 chains. Longest chain 45 peptides. Score 0.750 Round 4: 916 peptides, 75 chains. Longest chain 38 peptides. Score 0.738 Round 5: 937 peptides, 69 chains. Longest chain 58 peptides. Score 0.764 Taking the results from Round 5 Chains 83, Residues 868, Estimated correctness of the model 77.6 % 23 chains (482 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 30 B and 33 B Built loop between residues 41 B and 45 B Built loop between residues 94 B and 97 B Built loop between residues 111 B and 113 B Built loop between residues 169 B and 173 B 77 chains (875 residues) following loop building 18 chains (493 residues) in sequence following loop building ------------------------------------------------------ 26515 reflections ( 99.70 % complete ) and 12616 restraints for refining 8385 atoms. 6940 conditional restraints added. Observations/parameters ratio is 0.79 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2477 (Rfree = 0.000) for 8385 atoms. Found 52 (52 requested) and removed 72 (37 requested) atoms. Cycle 17: After refmac, R = 0.2331 (Rfree = 0.000) for 8331 atoms. Found 51 (51 requested) and removed 52 (37 requested) atoms. Cycle 18: After refmac, R = 0.2095 (Rfree = 0.000) for 8303 atoms. Found 33 (49 requested) and removed 44 (37 requested) atoms. Cycle 19: After refmac, R = 0.2003 (Rfree = 0.000) for 8279 atoms. Found 24 (47 requested) and removed 40 (37 requested) atoms. Cycle 20: After refmac, R = 0.2031 (Rfree = 0.000) for 8258 atoms. Found 33 (46 requested) and removed 40 (37 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.19 2.71 Search for helices and strands: 0 residues in 0 chains, 8491 seeds are put forward NCS extension: 40 residues added (73 deleted due to clashes), 8531 seeds are put forward Round 1: 874 peptides, 70 chains. Longest chain 80 peptides. Score 0.728 Round 2: 903 peptides, 62 chains. Longest chain 72 peptides. Score 0.765 Round 3: 904 peptides, 65 chains. Longest chain 62 peptides. Score 0.758 Round 4: 892 peptides, 70 chains. Longest chain 42 peptides. Score 0.738 Round 5: 873 peptides, 69 chains. Longest chain 54 peptides. Score 0.731 Taking the results from Round 2 Chains 75, Residues 841, Estimated correctness of the model 77.7 % 22 chains (504 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 40 A and 47 A Built loop between residues 224 A and 232 A Built loop between residues 39 B and 45 B Built loop between residues 55 B and 65 B Built loop between residues 95 B and 98 B Built loop between residues 120 B and 127 B Built loop between residues 497 B and 500 B 64 chains (862 residues) following loop building 15 chains (541 residues) in sequence following loop building ------------------------------------------------------ 26515 reflections ( 99.70 % complete ) and 12189 restraints for refining 8362 atoms. 6383 conditional restraints added. Observations/parameters ratio is 0.79 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2578 (Rfree = 0.000) for 8362 atoms. Found 45 (45 requested) and removed 85 (37 requested) atoms. Cycle 22: After refmac, R = 0.2389 (Rfree = 0.000) for 8283 atoms. Found 43 (43 requested) and removed 47 (37 requested) atoms. Cycle 23: After refmac, R = 0.2294 (Rfree = 0.000) for 8241 atoms. Found 41 (41 requested) and removed 53 (37 requested) atoms. Cycle 24: After refmac, R = 0.2269 (Rfree = 0.000) for 8201 atoms. Found 39 (39 requested) and removed 45 (36 requested) atoms. Cycle 25: After refmac, R = 0.2219 (Rfree = 0.000) for 8169 atoms. Found 38 (38 requested) and removed 42 (36 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.18 2.70 Search for helices and strands: 0 residues in 0 chains, 8363 seeds are put forward NCS extension: 24 residues added (90 deleted due to clashes), 8387 seeds are put forward Round 1: 893 peptides, 78 chains. Longest chain 41 peptides. Score 0.717 Round 2: 901 peptides, 68 chains. Longest chain 67 peptides. Score 0.748 Round 3: 899 peptides, 57 chains. Longest chain 65 peptides. Score 0.775 Round 4: 898 peptides, 59 chains. Longest chain 49 peptides. Score 0.770 Round 5: 907 peptides, 65 chains. Longest chain 69 peptides. Score 0.759 Taking the results from Round 3 Chains 64, Residues 842, Estimated correctness of the model 79.4 % 24 chains (551 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 109 A and 116 A Built loop between residues 221 A and 232 A Built loop between residues 518 A and 521 A Built loop between residues 63 B and 66 B Built loop between residues 92 B and 95 B Built loop between residues 503 B and 506 B 54 chains (856 residues) following loop building 18 chains (575 residues) in sequence following loop building ------------------------------------------------------ 26515 reflections ( 99.70 % complete ) and 11895 restraints for refining 8349 atoms. 5951 conditional restraints added. Observations/parameters ratio is 0.79 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2545 (Rfree = 0.000) for 8349 atoms. Found 37 (37 requested) and removed 85 (37 requested) atoms. Cycle 27: After refmac, R = 0.2252 (Rfree = 0.000) for 8271 atoms. Found 37 (37 requested) and removed 54 (37 requested) atoms. Cycle 28: After refmac, R = 0.2348 (Rfree = 0.000) for 8219 atoms. Found 37 (37 requested) and removed 54 (37 requested) atoms. Cycle 29: After refmac, R = 0.2117 (Rfree = 0.000) for 8176 atoms. Found 36 (36 requested) and removed 42 (36 requested) atoms. Cycle 30: After refmac, R = 0.1974 (Rfree = 0.000) for 8159 atoms. Found 36 (36 requested) and removed 44 (36 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.17 2.69 Search for helices and strands: 0 residues in 0 chains, 8352 seeds are put forward NCS extension: 70 residues added (112 deleted due to clashes), 8422 seeds are put forward Round 1: 849 peptides, 65 chains. Longest chain 51 peptides. Score 0.728 Round 2: 883 peptides, 56 chains. Longest chain 51 peptides. Score 0.770 Round 3: 892 peptides, 57 chains. Longest chain 68 peptides. Score 0.772 Round 4: 899 peptides, 54 chains. Longest chain 55 peptides. Score 0.783 Round 5: 877 peptides, 61 chains. Longest chain 61 peptides. Score 0.754 Taking the results from Round 4 Chains 67, Residues 845, Estimated correctness of the model 80.8 % 21 chains (513 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 41 A and 44 A Built loop between residues 219 A and 229 A Built loop between residues 502 A and 505 A Built loop between residues 514 A and 519 A Built loop between residues 195 B and 204 B Built loop between residues 222 B and 232 B Built loop between residues 488 B and 494 B 57 chains (877 residues) following loop building 14 chains (552 residues) in sequence following loop building ------------------------------------------------------ 26515 reflections ( 99.70 % complete ) and 11977 restraints for refining 8318 atoms. 6035 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2469 (Rfree = 0.000) for 8318 atoms. Found 37 (37 requested) and removed 76 (37 requested) atoms. Cycle 32: After refmac, R = 0.2292 (Rfree = 0.000) for 8246 atoms. Found 37 (37 requested) and removed 60 (37 requested) atoms. Cycle 33: After refmac, R = 0.2274 (Rfree = 0.000) for 8200 atoms. Found 36 (36 requested) and removed 53 (36 requested) atoms. Cycle 34: After refmac, R = 0.2272 (Rfree = 0.000) for 8177 atoms. Found 36 (36 requested) and removed 45 (36 requested) atoms. Cycle 35: After refmac, R = 0.2193 (Rfree = 0.000) for 8155 atoms. Found 36 (36 requested) and removed 47 (36 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.17 2.69 Search for helices and strands: 0 residues in 0 chains, 8333 seeds are put forward NCS extension: 36 residues added (41 deleted due to clashes), 8369 seeds are put forward Round 1: 858 peptides, 74 chains. Longest chain 36 peptides. Score 0.708 Round 2: 899 peptides, 63 chains. Longest chain 62 peptides. Score 0.760 Round 3: 909 peptides, 59 chains. Longest chain 52 peptides. Score 0.775 Round 4: 906 peptides, 58 chains. Longest chain 70 peptides. Score 0.776 Round 5: 882 peptides, 65 chains. Longest chain 51 peptides. Score 0.746 Taking the results from Round 4 Chains 66, Residues 848, Estimated correctness of the model 79.6 % 18 chains (443 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 519 A and 529 A 64 chains (852 residues) following loop building 17 chains (452 residues) in sequence following loop building ------------------------------------------------------ 26515 reflections ( 99.70 % complete ) and 12073 restraints for refining 8010 atoms. 6657 conditional restraints added. Observations/parameters ratio is 0.83 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2511 (Rfree = 0.000) for 8010 atoms. Found 35 (35 requested) and removed 68 (35 requested) atoms. Cycle 37: After refmac, R = 0.2253 (Rfree = 0.000) for 7958 atoms. Found 35 (35 requested) and removed 38 (35 requested) atoms. Cycle 38: After refmac, R = 0.2175 (Rfree = 0.000) for 7944 atoms. Found 35 (35 requested) and removed 41 (35 requested) atoms. Cycle 39: After refmac, R = 0.2302 (Rfree = 0.000) for 7924 atoms. Found 35 (35 requested) and removed 43 (35 requested) atoms. Cycle 40: After refmac, R = 0.2173 (Rfree = 0.000) for 7909 atoms. Found 35 (35 requested) and removed 37 (35 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.16 2.68 Search for helices and strands: 0 residues in 0 chains, 8127 seeds are put forward NCS extension: 26 residues added (72 deleted due to clashes), 8153 seeds are put forward Round 1: 844 peptides, 70 chains. Longest chain 44 peptides. Score 0.711 Round 2: 887 peptides, 64 chains. Longest chain 51 peptides. Score 0.752 Round 3: 889 peptides, 58 chains. Longest chain 58 peptides. Score 0.768 Round 4: 879 peptides, 62 chains. Longest chain 51 peptides. Score 0.753 Round 5: 869 peptides, 61 chains. Longest chain 58 peptides. Score 0.750 Taking the results from Round 3 Chains 66, Residues 831, Estimated correctness of the model 78.2 % 17 chains (395 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 87 A and 95 A 64 chains (835 residues) following loop building 16 chains (402 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 26515 reflections ( 99.70 % complete ) and 12791 restraints for refining 7989 atoms. 7751 conditional restraints added. Observations/parameters ratio is 0.83 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2492 (Rfree = 0.000) for 7989 atoms. Found 35 (35 requested) and removed 64 (35 requested) atoms. Cycle 42: After refmac, R = 0.2156 (Rfree = 0.000) for 7949 atoms. Found 35 (35 requested) and removed 46 (35 requested) atoms. Cycle 43: After refmac, R = 0.2110 (Rfree = 0.000) for 7930 atoms. Found 35 (35 requested) and removed 37 (35 requested) atoms. Cycle 44: After refmac, R = 0.2004 (Rfree = 0.000) for 7925 atoms. Found 35 (35 requested) and removed 36 (35 requested) atoms. Cycle 45: After refmac, R = 0.1960 (Rfree = 0.000) for 7920 atoms. Found 25 (35 requested) and removed 39 (35 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.18 2.70 Search for helices and strands: 0 residues in 0 chains, 8088 seeds are put forward NCS extension: 44 residues added (36 deleted due to clashes), 8132 seeds are put forward Round 1: 828 peptides, 72 chains. Longest chain 42 peptides. Score 0.695 Round 2: 880 peptides, 62 chains. Longest chain 64 peptides. Score 0.753 Round 3: 884 peptides, 63 chains. Longest chain 51 peptides. Score 0.753 Round 4: 874 peptides, 64 chains. Longest chain 54 peptides. Score 0.745 Round 5: 883 peptides, 63 chains. Longest chain 55 peptides. Score 0.752 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 71, Residues 821, Estimated correctness of the model 75.6 % 19 chains (412 residues) have been docked in sequence Sequence coverage is 50 % Consider running further cycles of model building using 1vr5-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 494 A and 505 A Built loop between residues 27 B and 40 B Built loop between residues 64 B and 67 B Built loop between residues 195 B and 205 B 63 chains (835 residues) following loop building 15 chains (445 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 26515 reflections ( 99.70 % complete ) and 12430 restraints for refining 8064 atoms. 7099 conditional restraints added. Observations/parameters ratio is 0.82 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2509 (Rfree = 0.000) for 8064 atoms. Found 0 (36 requested) and removed 34 (36 requested) atoms. Cycle 47: After refmac, R = 0.2220 (Rfree = 0.000) for 8007 atoms. Found 0 (36 requested) and removed 10 (36 requested) atoms. Cycle 48: After refmac, R = 0.2160 (Rfree = 0.000) for 7988 atoms. Found 0 (35 requested) and removed 10 (35 requested) atoms. Cycle 49: After refmac, R = 0.2281 (Rfree = 0.000) for 7971 atoms. TimeTaking 124.2