null Mon 24 Dec 08:03:00 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vr5-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vr5-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vr5-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vr5-3.2-parrot-noncs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vr5-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vr5-3.2-parrot-noncs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Mon 24 Dec 08:03:05 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vr5-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vr5-3.2-parrot-noncs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 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-noncs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 18 Cell parameters: 140.030 96.640 115.780 90.000 90.000 90.000 Input sequence file: 1vr5-3.2-parrot-noncs.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 9651 atoms. Observations/parameters ratio is 0.69 ------------------------------------------------------ Starting model: R = 0.3121 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2680 (Rfree = 0.000) for 9651 atoms. Found 86 (86 requested) and removed 55 (43 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.20 2.72 Search for helices and strands: 0 residues in 0 chains, 9853 seeds are put forward NCS extension: 0 residues added, 9853 seeds are put forward Round 1: 739 peptides, 105 chains. Longest chain 22 peptides. Score 0.513 Round 2: 827 peptides, 94 chains. Longest chain 26 peptides. Score 0.625 Round 3: 872 peptides, 82 chains. Longest chain 30 peptides. Score 0.693 Round 4: 854 peptides, 78 chains. Longest chain 48 peptides. Score 0.694 Round 5: 859 peptides, 70 chains. Longest chain 57 peptides. Score 0.720 Taking the results from Round 5 Chains 80, Residues 789, Estimated correctness of the model 69.3 % 19 chains (341 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 162 A and 172 A 77 chains (793 residues) following loop building 18 chains (350 residues) in sequence following loop building ------------------------------------------------------ 26515 reflections ( 99.70 % complete ) and 14532 restraints for refining 8646 atoms. 9910 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2693 (Rfree = 0.000) for 8646 atoms. Found 77 (77 requested) and removed 81 (38 requested) atoms. Cycle 2: After refmac, R = 0.2428 (Rfree = 0.000) for 8523 atoms. Found 75 (75 requested) and removed 61 (38 requested) atoms. Cycle 3: After refmac, R = 0.2218 (Rfree = 0.000) for 8472 atoms. Found 48 (73 requested) and removed 48 (38 requested) atoms. Cycle 4: After refmac, R = 0.2087 (Rfree = 0.000) for 8449 atoms. Found 33 (71 requested) and removed 52 (38 requested) atoms. Cycle 5: After refmac, R = 0.2066 (Rfree = 0.000) for 8416 atoms. Found 32 (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, 8641 seeds are put forward NCS extension: 52 residues added (54 deleted due to clashes), 8693 seeds are put forward Round 1: 836 peptides, 85 chains. Longest chain 27 peptides. Score 0.660 Round 2: 890 peptides, 70 chains. Longest chain 44 peptides. Score 0.737 Round 3: 898 peptides, 67 chains. Longest chain 61 peptides. Score 0.749 Round 4: 907 peptides, 57 chains. Longest chain 95 peptides. Score 0.779 Round 5: 881 peptides, 68 chains. Longest chain 64 peptides. Score 0.738 Taking the results from Round 4 Chains 65, Residues 850, Estimated correctness of the model 80.1 % 18 chains (504 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 41 B and 44 B Built loop between residues 137 B and 143 B Built loop between residues 163 B and 172 B Built loop between residues 378 B and 389 B Built loop between residues 404 B and 413 B 58 chains (878 residues) following loop building 13 chains (537 residues) in sequence following loop building ------------------------------------------------------ 26515 reflections ( 99.70 % complete ) and 12594 restraints for refining 8754 atoms. 6674 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2608 (Rfree = 0.000) for 8754 atoms. Found 70 (70 requested) and removed 101 (39 requested) atoms. Cycle 7: After refmac, R = 0.2306 (Rfree = 0.000) for 8665 atoms. Found 50 (69 requested) and removed 50 (39 requested) atoms. Cycle 8: After refmac, R = 0.2197 (Rfree = 0.000) for 8643 atoms. Found 40 (66 requested) and removed 42 (38 requested) atoms. Cycle 9: After refmac, R = 0.2136 (Rfree = 0.000) for 8626 atoms. Found 20 (65 requested) and removed 41 (38 requested) atoms. Cycle 10: After refmac, R = 0.2116 (Rfree = 0.000) for 8598 atoms. Found 15 (63 requested) and removed 39 (38 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.21 2.73 Search for helices and strands: 0 residues in 0 chains, 8767 seeds are put forward NCS extension: 142 residues added (93 deleted due to clashes), 8909 seeds are put forward Round 1: 846 peptides, 70 chains. Longest chain 45 peptides. Score 0.712 Round 2: 895 peptides, 65 chains. Longest chain 57 peptides. Score 0.753 Round 3: 910 peptides, 71 chains. Longest chain 53 peptides. Score 0.745 Round 4: 887 peptides, 61 chains. Longest chain 54 peptides. Score 0.759 Round 5: 906 peptides, 59 chains. Longest chain 65 peptides. Score 0.774 Taking the results from Round 5 Chains 69, Residues 847, Estimated correctness of the model 79.3 % 14 chains (325 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 28 A and 32 A Built loop between residues 126 A and 129 A Built loop between residues 218 B and 224 B 65 chains (856 residues) following loop building 11 chains (335 residues) in sequence following loop building ------------------------------------------------------ 26515 reflections ( 99.70 % complete ) and 13663 restraints for refining 8305 atoms. 8773 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2510 (Rfree = 0.000) for 8305 atoms. Found 59 (59 requested) and removed 69 (37 requested) atoms. Cycle 12: After refmac, R = 0.2340 (Rfree = 0.000) for 8257 atoms. Found 58 (58 requested) and removed 45 (37 requested) atoms. Cycle 13: After refmac, R = 0.2225 (Rfree = 0.000) for 8249 atoms. Found 36 (56 requested) and removed 39 (37 requested) atoms. Cycle 14: After refmac, R = 0.2209 (Rfree = 0.000) for 8236 atoms. Found 28 (55 requested) and removed 38 (37 requested) atoms. Cycle 15: After refmac, R = 0.2132 (Rfree = 0.000) for 8215 atoms. Found 25 (53 requested) and removed 37 (36 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.19 2.71 Search for helices and strands: 0 residues in 0 chains, 8371 seeds are put forward NCS extension: 34 residues added (68 deleted due to clashes), 8405 seeds are put forward Round 1: 868 peptides, 77 chains. Longest chain 55 peptides. Score 0.705 Round 2: 898 peptides, 63 chains. Longest chain 61 peptides. Score 0.760 Round 3: 915 peptides, 65 chains. Longest chain 82 peptides. Score 0.763 Round 4: 875 peptides, 68 chains. Longest chain 68 peptides. Score 0.734 Round 5: 905 peptides, 67 chains. Longest chain 54 peptides. Score 0.753 Taking the results from Round 3 Chains 70, Residues 850, Estimated correctness of the model 77.4 % 14 chains (361 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 176 B and 179 B 69 chains (850 residues) following loop building 13 chains (363 residues) in sequence following loop building ------------------------------------------------------ 26515 reflections ( 99.70 % complete ) and 13304 restraints for refining 8131 atoms. 8410 conditional restraints added. Observations/parameters ratio is 0.82 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2540 (Rfree = 0.000) for 8131 atoms. Found 50 (50 requested) and removed 58 (36 requested) atoms. Cycle 17: After refmac, R = 0.2304 (Rfree = 0.000) for 8103 atoms. Found 49 (49 requested) and removed 40 (36 requested) atoms. Cycle 18: After refmac, R = 0.2359 (Rfree = 0.000) for 8101 atoms. Found 48 (48 requested) and removed 38 (36 requested) atoms. Cycle 19: After refmac, R = 0.2390 (Rfree = 0.000) for 8091 atoms. Found 46 (46 requested) and removed 39 (36 requested) atoms. Cycle 20: After refmac, R = 0.2367 (Rfree = 0.000) for 8067 atoms. Found 45 (45 requested) and removed 48 (36 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.19 2.71 Search for helices and strands: 0 residues in 0 chains, 8285 seeds are put forward NCS extension: 19 residues added (27 deleted due to clashes), 8304 seeds are put forward Round 1: 869 peptides, 76 chains. Longest chain 46 peptides. Score 0.708 Round 2: 908 peptides, 71 chains. Longest chain 46 peptides. Score 0.744 Round 3: 907 peptides, 55 chains. Longest chain 95 peptides. Score 0.784 Round 4: 923 peptides, 59 chains. Longest chain 69 peptides. Score 0.782 Round 5: 912 peptides, 66 chains. Longest chain 50 peptides. Score 0.759 Taking the results from Round 3 Chains 64, Residues 852, Estimated correctness of the model 80.9 % 17 chains (417 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 64 A and 69 A Built loop between residues 56 B and 65 B Built loop between residues 74 B and 80 B Built loop between residues 161 B and 165 B Built loop between residues 487 B and 495 B 56 chains (873 residues) following loop building 12 chains (444 residues) in sequence following loop building ------------------------------------------------------ 26515 reflections ( 99.70 % complete ) and 12678 restraints for refining 8327 atoms. 7260 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2592 (Rfree = 0.000) for 8327 atoms. Found 44 (44 requested) and removed 73 (37 requested) atoms. Cycle 22: After refmac, R = 0.2509 (Rfree = 0.000) for 8253 atoms. Found 43 (43 requested) and removed 58 (37 requested) atoms. Cycle 23: After refmac, R = 0.2199 (Rfree = 0.000) for 8216 atoms. Found 41 (41 requested) and removed 43 (36 requested) atoms. Cycle 24: After refmac, R = 0.2103 (Rfree = 0.000) for 8205 atoms. Found 33 (39 requested) and removed 37 (36 requested) atoms. Cycle 25: After refmac, R = 0.2076 (Rfree = 0.000) for 8194 atoms. Found 17 (38 requested) and removed 36 (36 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.23 2.74 Search for helices and strands: 0 residues in 0 chains, 8366 seeds are put forward NCS extension: 111 residues added (64 deleted due to clashes), 8477 seeds are put forward Round 1: 834 peptides, 76 chains. Longest chain 51 peptides. Score 0.687 Round 2: 892 peptides, 57 chains. Longest chain 51 peptides. Score 0.772 Round 3: 888 peptides, 63 chains. Longest chain 56 peptides. Score 0.755 Round 4: 892 peptides, 69 chains. Longest chain 56 peptides. Score 0.741 Round 5: 885 peptides, 63 chains. Longest chain 62 peptides. Score 0.753 Taking the results from Round 2 Chains 68, Residues 835, Estimated correctness of the model 78.9 % 21 chains (431 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 155 A and 162 A Built loop between residues 510 A and 520 A Built loop between residues 60 B and 63 B Built loop between residues 81 B and 85 B Built loop between residues 405 B and 413 B Built loop between residues 515 B and 519 B 59 chains (855 residues) following loop building 15 chains (461 residues) in sequence following loop building ------------------------------------------------------ 26515 reflections ( 99.70 % complete ) and 11859 restraints for refining 8037 atoms. 6619 conditional restraints added. Observations/parameters ratio is 0.82 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2650 (Rfree = 0.000) for 8037 atoms. Found 36 (36 requested) and removed 64 (36 requested) atoms. Cycle 27: After refmac, R = 0.2404 (Rfree = 0.000) for 7977 atoms. Found 35 (35 requested) and removed 45 (35 requested) atoms. Cycle 28: After refmac, R = 0.2277 (Rfree = 0.000) for 7950 atoms. Found 35 (35 requested) and removed 35 (35 requested) atoms. Cycle 29: After refmac, R = 0.2197 (Rfree = 0.000) for 7945 atoms. Found 35 (35 requested) and removed 35 (35 requested) atoms. Cycle 30: After refmac, R = 0.2174 (Rfree = 0.000) for 7937 atoms. Found 27 (35 requested) and removed 35 (35 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.23 2.74 Search for helices and strands: 0 residues in 0 chains, 8126 seeds are put forward NCS extension: 42 residues added (27 deleted due to clashes), 8168 seeds are put forward Round 1: 817 peptides, 78 chains. Longest chain 36 peptides. Score 0.670 Round 2: 851 peptides, 62 chains. Longest chain 51 peptides. Score 0.738 Round 3: 878 peptides, 68 chains. Longest chain 62 peptides. Score 0.736 Round 4: 880 peptides, 62 chains. Longest chain 45 peptides. Score 0.753 Round 5: 851 peptides, 66 chains. Longest chain 50 peptides. Score 0.726 Taking the results from Round 4 Chains 70, Residues 818, Estimated correctness of the model 75.6 % 18 chains (360 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 34 A and 45 A Built loop between residues 58 A and 65 A 67 chains (826 residues) following loop building 16 chains (376 residues) in sequence following loop building ------------------------------------------------------ 26515 reflections ( 99.70 % complete ) and 12761 restraints for refining 8012 atoms. 7852 conditional restraints added. Observations/parameters ratio is 0.83 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2528 (Rfree = 0.000) for 8012 atoms. Found 35 (35 requested) and removed 54 (35 requested) atoms. Cycle 32: After refmac, R = 0.2324 (Rfree = 0.000) for 7964 atoms. Found 35 (35 requested) and removed 41 (35 requested) atoms. Cycle 33: After refmac, R = 0.2221 (Rfree = 0.000) for 7938 atoms. Found 30 (35 requested) and removed 35 (35 requested) atoms. Cycle 34: After refmac, R = 0.2144 (Rfree = 0.000) for 7924 atoms. Found 19 (35 requested) and removed 35 (35 requested) atoms. Cycle 35: After refmac, R = 0.2099 (Rfree = 0.000) for 7903 atoms. Found 19 (35 requested) and removed 35 (35 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.21 2.73 Search for helices and strands: 0 residues in 0 chains, 8088 seeds are put forward NCS extension: 42 residues added (22 deleted due to clashes), 8130 seeds are put forward Round 1: 806 peptides, 77 chains. Longest chain 40 peptides. Score 0.666 Round 2: 853 peptides, 66 chains. Longest chain 39 peptides. Score 0.728 Round 3: 847 peptides, 70 chains. Longest chain 48 peptides. Score 0.713 Round 4: 856 peptides, 65 chains. Longest chain 39 peptides. Score 0.732 Round 5: 858 peptides, 69 chains. Longest chain 33 peptides. Score 0.722 Taking the results from Round 4 Chains 71, Residues 791, Estimated correctness of the model 71.7 % 18 chains (322 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 37 A and 42 A 70 chains (793 residues) following loop building 17 chains (326 residues) in sequence following loop building ------------------------------------------------------ 26515 reflections ( 99.70 % complete ) and 13310 restraints for refining 7989 atoms. 8824 conditional restraints added. Observations/parameters ratio is 0.83 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2506 (Rfree = 0.000) for 7989 atoms. Found 35 (35 requested) and removed 66 (35 requested) atoms. Cycle 37: After refmac, R = 0.2333 (Rfree = 0.000) for 7926 atoms. Found 35 (35 requested) and removed 38 (35 requested) atoms. Cycle 38: After refmac, R = 0.2256 (Rfree = 0.000) for 7915 atoms. Found 35 (35 requested) and removed 37 (35 requested) atoms. Cycle 39: After refmac, R = 0.2164 (Rfree = 0.000) for 7909 atoms. Found 33 (35 requested) and removed 37 (35 requested) atoms. Cycle 40: After refmac, R = 0.2100 (Rfree = 0.000) for 7897 atoms. Found 17 (35 requested) and removed 35 (35 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.21 2.73 Search for helices and strands: 0 residues in 0 chains, 8062 seeds are put forward NCS extension: 37 residues added (26 deleted due to clashes), 8099 seeds are put forward Round 1: 782 peptides, 74 chains. Longest chain 31 peptides. Score 0.659 Round 2: 832 peptides, 70 chains. Longest chain 50 peptides. Score 0.704 Round 3: 846 peptides, 66 chains. Longest chain 35 peptides. Score 0.724 Round 4: 846 peptides, 69 chains. Longest chain 36 peptides. Score 0.715 Round 5: 849 peptides, 73 chains. Longest chain 41 peptides. Score 0.705 Taking the results from Round 3 Chains 81, Residues 780, Estimated correctness of the model 70.1 % 16 chains (285 residues) have been docked in sequence Building loops using Loopy2018 81 chains (780 residues) following loop building 16 chains (285 residues) in sequence following loop building ------------------------------------------------------ 26515 reflections ( 99.70 % complete ) and 13801 restraints for refining 8024 atoms. 9476 conditional restraints added. Observations/parameters ratio is 0.83 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2483 (Rfree = 0.000) for 8024 atoms. Found 36 (36 requested) and removed 68 (36 requested) atoms. Cycle 42: After refmac, R = 0.2354 (Rfree = 0.000) for 7966 atoms. Found 35 (35 requested) and removed 40 (35 requested) atoms. Cycle 43: After refmac, R = 0.2249 (Rfree = 0.000) for 7947 atoms. Found 25 (35 requested) and removed 36 (35 requested) atoms. Cycle 44: After refmac, R = 0.2213 (Rfree = 0.000) for 7924 atoms. Found 20 (35 requested) and removed 35 (35 requested) atoms. Cycle 45: After refmac, R = 0.2078 (Rfree = 0.000) for 7901 atoms. Found 22 (35 requested) and removed 36 (35 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.21 2.73 Search for helices and strands: 0 residues in 0 chains, 8063 seeds are put forward NCS extension: 13 residues added (14 deleted due to clashes), 8076 seeds are put forward Round 1: 766 peptides, 80 chains. Longest chain 45 peptides. Score 0.627 Round 2: 819 peptides, 75 chains. Longest chain 41 peptides. Score 0.680 Round 3: 816 peptides, 70 chains. Longest chain 54 peptides. Score 0.694 Round 4: 816 peptides, 65 chains. Longest chain 46 peptides. Score 0.709 Round 5: 805 peptides, 70 chains. Longest chain 36 peptides. Score 0.687 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 74, Residues 751, Estimated correctness of the model 67.1 % 13 chains (302 residues) have been docked in sequence Sequence coverage is 40 % Consider running further cycles of model building using 1vr5-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 177 A and 180 A Built loop between residues 35 B and 40 B 71 chains (756 residues) following loop building 11 chains (308 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 26515 reflections ( 99.70 % complete ) and 13764 restraints for refining 7990 atoms. 9462 conditional restraints added. Observations/parameters ratio is 0.83 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2448 (Rfree = 0.000) for 7990 atoms. Found 0 (35 requested) and removed 35 (35 requested) atoms. Cycle 47: After refmac, R = 0.2311 (Rfree = 0.000) for 7936 atoms. Found 0 (35 requested) and removed 24 (35 requested) atoms. Cycle 48: After refmac, R = 0.2322 (Rfree = 0.000) for 7903 atoms. Found 0 (35 requested) and removed 14 (35 requested) atoms. Cycle 49: After refmac, R = 0.2198 (Rfree = 0.000) for 7883 atoms. Found 0 (35 requested) and removed 8 (35 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 09:52:16 GMT 2018 Job finished. TimeTaking 109.27 Used memory is bytes: 10353552