Mon 24 Dec 00:39:05 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 1vr5-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vr5-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vr5-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vr5-3.2-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/1vr5-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vr5-3.2-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 00:39:10 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/1vr5-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vr5-3.2-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 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-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: 18 Cell parameters: 140.030 96.640 115.780 90.000 90.000 90.000 Input sequence file: 1vr5-3.2-parrot-mrncs.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 9643 atoms. Observations/parameters ratio is 0.69 ------------------------------------------------------ Starting model: R = 0.3101 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3019 (Rfree = 0.000) for 9643 atoms. Found 86 (86 requested) and removed 59 (43 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.25 2.76 Search for helices and strands: 0 residues in 0 chains, 9850 seeds are put forward NCS extension: 0 residues added, 9850 seeds are put forward Round 1: 713 peptides, 109 chains. Longest chain 26 peptides. Score 0.473 Round 2: 818 peptides, 91 chains. Longest chain 32 peptides. Score 0.628 Round 3: 845 peptides, 87 chains. Longest chain 29 peptides. Score 0.660 Round 4: 863 peptides, 72 chains. Longest chain 40 peptides. Score 0.716 Round 5: 873 peptides, 75 chains. Longest chain 36 peptides. Score 0.714 Taking the results from Round 4 Chains 81, Residues 791, Estimated correctness of the model 68.5 % 12 chains (274 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 497 A and 508 A 77 chains (795 residues) following loop building 11 chains (284 residues) in sequence following loop building ------------------------------------------------------ 26515 reflections ( 99.70 % complete ) and 14555 restraints for refining 8436 atoms. 10192 conditional restraints added. Observations/parameters ratio is 0.79 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2708 (Rfree = 0.000) for 8436 atoms. Found 75 (75 requested) and removed 69 (37 requested) atoms. Cycle 2: After refmac, R = 0.2478 (Rfree = 0.000) for 8324 atoms. Found 54 (73 requested) and removed 46 (37 requested) atoms. Failed to save intermediate PDB Cycle 3: After refmac, R = 0.2375 (Rfree = 0.000) for 8268 atoms. Found 49 (71 requested) and removed 42 (37 requested) atoms. Failed to save intermediate PDB Cycle 4: After refmac, R = 0.2304 (Rfree = 0.000) for 8241 atoms. Found 26 (70 requested) and removed 42 (37 requested) atoms. Cycle 5: After refmac, R = 0.2321 (Rfree = 0.000) for 8198 atoms. Found 34 (67 requested) and removed 39 (36 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.23 2.74 Search for helices and strands: 0 residues in 0 chains, 8390 seeds are put forward NCS extension: 51 residues added (35 deleted due to clashes), 8441 seeds are put forward Round 1: 837 peptides, 81 chains. Longest chain 40 peptides. Score 0.674 Round 2: 865 peptides, 77 chains. Longest chain 47 peptides. Score 0.703 Round 3: 886 peptides, 73 chains. Longest chain 49 peptides. Score 0.727 Round 4: 894 peptides, 67 chains. Longest chain 39 peptides. Score 0.747 Round 5: 872 peptides, 69 chains. Longest chain 71 peptides. Score 0.730 Taking the results from Round 4 Chains 83, Residues 827, Estimated correctness of the model 74.5 % 19 chains (343 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 95 B and 99 B 82 chains (830 residues) following loop building 18 chains (346 residues) in sequence following loop building ------------------------------------------------------ 26515 reflections ( 99.70 % complete ) and 13393 restraints for refining 8191 atoms. 8565 conditional restraints added. Observations/parameters ratio is 0.81 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2659 (Rfree = 0.000) for 8191 atoms. Found 66 (66 requested) and removed 77 (36 requested) atoms. Cycle 7: After refmac, R = 0.2447 (Rfree = 0.000) for 8140 atoms. Found 55 (64 requested) and removed 38 (36 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.2332 (Rfree = 0.000) for 8142 atoms. Found 20 (63 requested) and removed 37 (36 requested) atoms. Cycle 9: After refmac, R = 0.2266 (Rfree = 0.000) for 8107 atoms. Found 14 (60 requested) and removed 36 (36 requested) atoms. Cycle 10: After refmac, R = 0.2250 (Rfree = 0.000) for 8072 atoms. Found 17 (59 requested) and removed 37 (36 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.22 2.74 Search for helices and strands: 0 residues in 0 chains, 8242 seeds are put forward NCS extension: 27 residues added (31 deleted due to clashes), 8269 seeds are put forward Round 1: 837 peptides, 76 chains. Longest chain 64 peptides. Score 0.689 Round 2: 873 peptides, 77 chains. Longest chain 42 peptides. Score 0.708 Round 3: 850 peptides, 70 chains. Longest chain 30 peptides. Score 0.715 Round 4: 888 peptides, 76 chains. Longest chain 44 peptides. Score 0.720 Round 5: 890 peptides, 69 chains. Longest chain 68 peptides. Score 0.740 Taking the results from Round 5 Chains 76, Residues 821, Estimated correctness of the model 73.2 % 14 chains (300 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 40 B and 45 B 74 chains (824 residues) following loop building 13 chains (304 residues) in sequence following loop building ------------------------------------------------------ 26515 reflections ( 99.70 % complete ) and 13742 restraints for refining 8144 atoms. 9176 conditional restraints added. Observations/parameters ratio is 0.81 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2588 (Rfree = 0.000) for 8144 atoms. Found 58 (58 requested) and removed 67 (36 requested) atoms. Cycle 12: After refmac, R = 0.2346 (Rfree = 0.000) for 8093 atoms. Found 48 (57 requested) and removed 41 (36 requested) atoms. Cycle 13: After refmac, R = 0.2224 (Rfree = 0.000) for 8068 atoms. Found 32 (55 requested) and removed 39 (36 requested) atoms. Cycle 14: After refmac, R = 0.2179 (Rfree = 0.000) for 8048 atoms. Found 17 (53 requested) and removed 36 (36 requested) atoms. Cycle 15: After refmac, R = 0.2157 (Rfree = 0.000) for 8018 atoms. Found 17 (52 requested) and removed 37 (36 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.21 2.73 Search for helices and strands: 0 residues in 0 chains, 8208 seeds are put forward NCS extension: 50 residues added (23 deleted due to clashes), 8258 seeds are put forward Round 1: 856 peptides, 73 chains. Longest chain 72 peptides. Score 0.709 Round 2: 873 peptides, 68 chains. Longest chain 74 peptides. Score 0.733 Round 3: 887 peptides, 66 chains. Longest chain 49 peptides. Score 0.746 Round 4: 877 peptides, 73 chains. Longest chain 54 peptides. Score 0.722 Round 5: 892 peptides, 71 chains. Longest chain 58 peptides. Score 0.736 Taking the results from Round 3 Chains 72, Residues 821, Estimated correctness of the model 74.3 % 18 chains (357 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 57 A and 64 A 70 chains (824 residues) following loop building 17 chains (363 residues) in sequence following loop building ------------------------------------------------------ 26515 reflections ( 99.70 % complete ) and 13184 restraints for refining 8094 atoms. 8326 conditional restraints added. Observations/parameters ratio is 0.82 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2650 (Rfree = 0.000) for 8094 atoms. Found 50 (50 requested) and removed 66 (36 requested) atoms. Cycle 17: After refmac, R = 0.2402 (Rfree = 0.000) for 8034 atoms. Found 49 (49 requested) and removed 44 (36 requested) atoms. Cycle 18: After refmac, R = 0.2266 (Rfree = 0.000) for 8018 atoms. Found 38 (48 requested) and removed 38 (36 requested) atoms. Cycle 19: After refmac, R = 0.2150 (Rfree = 0.000) for 8001 atoms. Found 19 (45 requested) and removed 35 (35 requested) atoms. Cycle 20: After refmac, R = 0.2128 (Rfree = 0.000) for 7973 atoms. Found 29 (44 requested) and removed 35 (35 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.21 2.73 Search for helices and strands: 0 residues in 0 chains, 8167 seeds are put forward NCS extension: 21 residues added (26 deleted due to clashes), 8188 seeds are put forward Round 1: 831 peptides, 75 chains. Longest chain 35 peptides. Score 0.688 Round 2: 872 peptides, 63 chains. Longest chain 49 peptides. Score 0.746 Round 3: 884 peptides, 66 chains. Longest chain 51 peptides. Score 0.745 Round 4: 869 peptides, 70 chains. Longest chain 37 peptides. Score 0.725 Round 5: 862 peptides, 72 chains. Longest chain 51 peptides. Score 0.716 Taking the results from Round 2 Chains 67, Residues 809, Estimated correctness of the model 74.3 % 13 chains (301 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 39 B and 46 B Built loop between residues 501 B and 504 B 65 chains (815 residues) following loop building 11 chains (309 residues) in sequence following loop building ------------------------------------------------------ 26515 reflections ( 99.70 % complete ) and 13522 restraints for refining 7989 atoms. 8929 conditional restraints added. Observations/parameters ratio is 0.83 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2723 (Rfree = 0.000) for 7989 atoms. Found 43 (43 requested) and removed 58 (35 requested) atoms. Cycle 22: After refmac, R = 0.2382 (Rfree = 0.000) for 7929 atoms. Found 41 (41 requested) and removed 40 (35 requested) atoms. Cycle 23: After refmac, R = 0.2301 (Rfree = 0.000) for 7908 atoms. Found 40 (40 requested) and removed 40 (35 requested) atoms. Cycle 24: After refmac, R = 0.2183 (Rfree = 0.000) for 7897 atoms. Found 16 (38 requested) and removed 36 (35 requested) atoms. Cycle 25: After refmac, R = 0.2130 (Rfree = 0.000) for 7871 atoms. Found 20 (36 requested) and removed 37 (35 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.22 2.74 Search for helices and strands: 0 residues in 0 chains, 8054 seeds are put forward NCS extension: 18 residues added (49 deleted due to clashes), 8072 seeds are put forward Round 1: 822 peptides, 75 chains. Longest chain 46 peptides. Score 0.682 Round 2: 876 peptides, 70 chains. Longest chain 50 peptides. Score 0.729 Round 3: 861 peptides, 68 chains. Longest chain 38 peptides. Score 0.727 Round 4: 864 peptides, 67 chains. Longest chain 48 peptides. Score 0.731 Round 5: 870 peptides, 64 chains. Longest chain 46 peptides. Score 0.743 Taking the results from Round 5 Chains 69, Residues 806, Estimated correctness of the model 73.8 % 18 chains (372 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 88 A and 91 A Built loop between residues 32 B and 43 B Built loop between residues 134 B and 137 B 64 chains (811 residues) following loop building 15 chains (386 residues) in sequence following loop building ------------------------------------------------------ 26515 reflections ( 99.70 % complete ) and 12717 restraints for refining 8031 atoms. 7795 conditional restraints added. Observations/parameters ratio is 0.83 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2719 (Rfree = 0.000) for 8031 atoms. Found 36 (36 requested) and removed 60 (36 requested) atoms. Cycle 27: After refmac, R = 0.2442 (Rfree = 0.000) for 7954 atoms. Found 35 (35 requested) and removed 43 (35 requested) atoms. Cycle 28: After refmac, R = 0.2297 (Rfree = 0.000) for 7928 atoms. Found 33 (35 requested) and removed 39 (35 requested) atoms. Cycle 29: After refmac, R = 0.2221 (Rfree = 0.000) for 7909 atoms. Found 24 (35 requested) and removed 37 (35 requested) atoms. Cycle 30: After refmac, R = 0.2247 (Rfree = 0.000) for 7883 atoms. Found 21 (35 requested) and removed 35 (35 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.19 2.71 Search for helices and strands: 0 residues in 0 chains, 8037 seeds are put forward NCS extension: 55 residues added (63 deleted due to clashes), 8092 seeds are put forward Round 1: 819 peptides, 78 chains. Longest chain 43 peptides. Score 0.671 Round 2: 857 peptides, 75 chains. Longest chain 47 peptides. Score 0.704 Round 3: 862 peptides, 72 chains. Longest chain 38 peptides. Score 0.716 Round 4: 860 peptides, 69 chains. Longest chain 57 peptides. Score 0.723 Round 5: 847 peptides, 72 chains. Longest chain 42 peptides. Score 0.707 Taking the results from Round 4 Chains 80, Residues 791, Estimated correctness of the model 69.9 % 18 chains (318 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 242 A and 245 A Built loop between residues 253 A and 262 A 77 chains (800 residues) following loop building 16 chains (328 residues) in sequence following loop building ------------------------------------------------------ 26515 reflections ( 99.70 % complete ) and 13353 restraints for refining 7989 atoms. 8771 conditional restraints added. Observations/parameters ratio is 0.83 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2561 (Rfree = 0.000) for 7989 atoms. Found 35 (35 requested) and removed 53 (35 requested) atoms. Cycle 32: After refmac, R = 0.2368 (Rfree = 0.000) for 7938 atoms. Found 35 (35 requested) and removed 44 (35 requested) atoms. Cycle 33: After refmac, R = 0.2210 (Rfree = 0.000) for 7917 atoms. Found 34 (35 requested) and removed 35 (35 requested) atoms. Cycle 34: After refmac, R = 0.2241 (Rfree = 0.000) for 7899 atoms. Found 29 (35 requested) and removed 36 (35 requested) atoms. Cycle 35: After refmac, R = 0.2085 (Rfree = 0.000) for 7884 atoms. Found 20 (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, 8068 seeds are put forward NCS extension: 27 residues added (24 deleted due to clashes), 8095 seeds are put forward Round 1: 811 peptides, 82 chains. Longest chain 46 peptides. Score 0.653 Round 2: 871 peptides, 69 chains. Longest chain 53 peptides. Score 0.729 Round 3: 849 peptides, 68 chains. Longest chain 42 peptides. Score 0.720 Round 4: 840 peptides, 71 chains. Longest chain 55 peptides. Score 0.706 Round 5: 841 peptides, 72 chains. Longest chain 37 peptides. Score 0.703 Taking the results from Round 2 Chains 77, Residues 802, Estimated correctness of the model 71.1 % 15 chains (360 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 94 A and 102 A Built loop between residues 439 A and 449 A Built loop between residues 105 B and 115 B 72 chains (816 residues) following loop building 12 chains (385 residues) in sequence following loop building ------------------------------------------------------ 26515 reflections ( 99.70 % complete ) and 12688 restraints for refining 7990 atoms. 7802 conditional restraints added. Observations/parameters ratio is 0.83 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2581 (Rfree = 0.000) for 7990 atoms. Found 35 (35 requested) and removed 69 (35 requested) atoms. Cycle 37: After refmac, R = 0.2381 (Rfree = 0.000) for 7937 atoms. Found 35 (35 requested) and removed 55 (35 requested) atoms. Cycle 38: After refmac, R = 0.2248 (Rfree = 0.000) for 7903 atoms. Found 35 (35 requested) and removed 54 (35 requested) atoms. Cycle 39: After refmac, R = 0.2143 (Rfree = 0.000) for 7869 atoms. Found 24 (35 requested) and removed 41 (35 requested) atoms. Cycle 40: After refmac, R = 0.2212 (Rfree = 0.000) for 7833 atoms. Found 35 (35 requested) and removed 38 (35 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.20 2.72 Search for helices and strands: 0 residues in 0 chains, 8024 seeds are put forward NCS extension: 26 residues added (101 deleted due to clashes), 8050 seeds are put forward Round 1: 775 peptides, 79 chains. Longest chain 34 peptides. Score 0.637 Round 2: 860 peptides, 62 chains. Longest chain 54 peptides. Score 0.743 Round 3: 856 peptides, 67 chains. Longest chain 56 peptides. Score 0.727 Round 4: 869 peptides, 72 chains. Longest chain 54 peptides. Score 0.720 Round 5: 825 peptides, 72 chains. Longest chain 55 peptides. Score 0.693 Taking the results from Round 2 Chains 71, Residues 798, Estimated correctness of the model 73.8 % 16 chains (439 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 95 A and 100 A Built loop between residues 137 A and 144 A 67 chains (803 residues) following loop building 14 chains (449 residues) in sequence following loop building ------------------------------------------------------ 26515 reflections ( 99.70 % complete ) and 12045 restraints for refining 7988 atoms. 6902 conditional restraints added. Observations/parameters ratio is 0.83 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2571 (Rfree = 0.000) for 7988 atoms. Found 35 (35 requested) and removed 69 (35 requested) atoms. Cycle 42: After refmac, R = 0.2411 (Rfree = 0.000) for 7933 atoms. Found 35 (35 requested) and removed 40 (35 requested) atoms. Cycle 43: After refmac, R = 0.2283 (Rfree = 0.000) for 7905 atoms. Found 34 (35 requested) and removed 38 (35 requested) atoms. Cycle 44: After refmac, R = 0.2226 (Rfree = 0.000) for 7882 atoms. Found 35 (35 requested) and removed 38 (35 requested) atoms. Cycle 45: After refmac, R = 0.2185 (Rfree = 0.000) for 7873 atoms. Found 16 (35 requested) and removed 37 (35 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.16 2.68 Search for helices and strands: 0 residues in 0 chains, 8043 seeds are put forward NCS extension: 50 residues added (146 deleted due to clashes), 8093 seeds are put forward Round 1: 794 peptides, 73 chains. Longest chain 49 peptides. Score 0.670 Round 2: 849 peptides, 66 chains. Longest chain 57 peptides. Score 0.725 Round 3: 849 peptides, 61 chains. Longest chain 58 peptides. Score 0.739 Round 4: 860 peptides, 70 chains. Longest chain 60 peptides. Score 0.720 Round 5: 850 peptides, 71 chains. Longest chain 69 peptides. Score 0.712 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 70, Residues 788, Estimated correctness of the model 73.0 % 17 chains (399 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 194 A and 199 A Built loop between residues 222 A and 227 A Built loop between residues 405 A and 413 A Built loop between residues 104 B and 116 B 63 chains (806 residues) following loop building 13 chains (425 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 26515 reflections ( 99.70 % complete ) and 12317 restraints for refining 7989 atoms. 7331 conditional restraints added. Observations/parameters ratio is 0.83 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2623 (Rfree = 0.000) for 7989 atoms. Found 0 (35 requested) and removed 35 (35 requested) atoms. Failed to save intermediate PDB Cycle 47: After refmac, R = 0.2494 (Rfree = 0.000) for 7932 atoms. Found 0 (35 requested) and removed 28 (35 requested) atoms. Cycle 48: After refmac, R = 0.2409 (Rfree = 0.000) for 7883 atoms. Found 0 (35 requested) and removed 14 (35 requested) atoms. Cycle 49: After refmac, R = 0.2339 (Rfree = 0.000) for 7860 atoms. TimeTaking 111.08