null Sun 23 Dec 22:22:43 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 2pgc-2.5-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2pgc-2.5-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2pgc-2.5-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pgc-2.5-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/2pgc-2.5-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pgc-2.5-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 22:22:51 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/2pgc-2.5-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pgc-2.5-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 874 and 0 Target number of residues in the AU: 874 Target solvent content: 0.5950 Checking the provided sequence file Detected sequence length: 207 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 5 Adjusted target number of residues: 1035 Adjusted target solvent content: 0.52 Input MTZ file: 2pgc-2.5-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: 137.477 139.862 60.737 90.000 90.000 90.000 Input sequence file: 2pgc-2.5-parrot-hancs.fasta_lf Building free atoms model in initial map for 8280 target number of atoms Had to go as low as 0.75 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: 98.043 2.530 Wilson plot Bfac: 50.47 36493 reflections ( 98.58 % complete ) and 0 restraints for refining 9280 atoms. Observations/parameters ratio is 0.98 ------------------------------------------------------ Starting model: R = 0.3172 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2456 (Rfree = 0.000) for 9280 atoms. Found 98 (162 requested) and removed 94 (81 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.77 2.70 NCS extension: 0 residues added, 9284 seeds are put forward Round 1: 662 peptides, 95 chains. Longest chain 22 peptides. Score 0.556 Round 2: 738 peptides, 76 chains. Longest chain 26 peptides. Score 0.707 Round 3: 803 peptides, 73 chains. Longest chain 36 peptides. Score 0.763 Round 4: 838 peptides, 60 chains. Longest chain 43 peptides. Score 0.820 Round 5: 839 peptides, 55 chains. Longest chain 42 peptides. Score 0.833 Taking the results from Round 5 Chains 71, Residues 784, Estimated correctness of the model 94.3 % 24 chains (497 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 48 A and 54 A Built loop between residues 103 A and 112 A Built loop between residues 178 A and 184 A Built loop between residues 64 E and 68 E Built loop between residues 104 E and 114 E Built loop between residues 52 D and 56 D Built loop between residues 103 D and 109 D 58 chains (800 residues) following loop building 17 chains (535 residues) in sequence following loop building ------------------------------------------------------ 36493 reflections ( 98.58 % complete ) and 11444 restraints for refining 7998 atoms. 6271 conditional restraints added. Observations/parameters ratio is 1.14 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2784 (Rfree = 0.000) for 7998 atoms. Found 113 (140 requested) and removed 90 (70 requested) atoms. Cycle 2: After refmac, R = 0.2524 (Rfree = 0.000) for 7922 atoms. Found 86 (137 requested) and removed 81 (70 requested) atoms. Cycle 3: After refmac, R = 0.2396 (Rfree = 0.000) for 7886 atoms. Found 61 (132 requested) and removed 80 (69 requested) atoms. Cycle 4: After refmac, R = 0.2332 (Rfree = 0.000) for 7846 atoms. Found 72 (129 requested) and removed 72 (68 requested) atoms. Cycle 5: After refmac, R = 0.2213 (Rfree = 0.000) for 7827 atoms. Found 64 (126 requested) and removed 70 (68 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.74 2.67 NCS extension: 397 residues added (432 deleted due to clashes), 8276 seeds are put forward Round 1: 856 peptides, 52 chains. Longest chain 42 peptides. Score 0.847 Round 2: 875 peptides, 46 chains. Longest chain 72 peptides. Score 0.868 Round 3: 879 peptides, 47 chains. Longest chain 69 peptides. Score 0.867 Round 4: 881 peptides, 43 chains. Longest chain 72 peptides. Score 0.876 Round 5: 881 peptides, 47 chains. Longest chain 74 peptides. Score 0.868 Taking the results from Round 4 Chains 50, Residues 838, Estimated correctness of the model 96.7 % 17 chains (563 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 74 A and 85 A Built loop between residues 131 A and 137 A Built loop between residues 152 A and 157 A Built loop between residues 80 B and 86 B Built loop between residues 72 D and 78 D Built loop between residues 152 D and 156 D 41 chains (863 residues) following loop building 11 chains (595 residues) in sequence following loop building ------------------------------------------------------ 36493 reflections ( 98.58 % complete ) and 10526 restraints for refining 7863 atoms. 4781 conditional restraints added. Observations/parameters ratio is 1.16 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2406 (Rfree = 0.000) for 7863 atoms. Found 110 (123 requested) and removed 86 (68 requested) atoms. Cycle 7: After refmac, R = 0.2198 (Rfree = 0.000) for 7864 atoms. Found 60 (121 requested) and removed 72 (69 requested) atoms. Cycle 8: After refmac, R = 0.2079 (Rfree = 0.000) for 7847 atoms. Found 60 (118 requested) and removed 76 (68 requested) atoms. Cycle 9: After refmac, R = 0.1994 (Rfree = 0.000) for 7824 atoms. Found 49 (115 requested) and removed 69 (68 requested) atoms. Cycle 10: After refmac, R = 0.1968 (Rfree = 0.000) for 7801 atoms. Found 46 (112 requested) and removed 71 (68 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.75 2.68 NCS extension: 1120 residues added (1053 deleted due to clashes), 8926 seeds are put forward Round 1: 891 peptides, 44 chains. Longest chain 88 peptides. Score 0.878 Round 2: 903 peptides, 38 chains. Longest chain 96 peptides. Score 0.893 Round 3: 905 peptides, 42 chains. Longest chain 60 peptides. Score 0.886 Round 4: 895 peptides, 48 chains. Longest chain 75 peptides. Score 0.871 Round 5: 889 peptides, 48 chains. Longest chain 64 peptides. Score 0.869 Taking the results from Round 2 Chains 39, Residues 865, Estimated correctness of the model 97.5 % 20 chains (666 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 53 A and 56 A Built loop between residues 15 B and 18 B Built loop between residues 45 B and 48 B Built loop between residues 113 B and 116 B Built loop between residues 139 B and 142 B Built loop between residues 177 B and 185 B Built loop between residues 123 E and 130 E Built loop between residues 151 E and 155 E 29 chains (887 residues) following loop building 12 chains (692 residues) in sequence following loop building ------------------------------------------------------ 36493 reflections ( 98.58 % complete ) and 9790 restraints for refining 7853 atoms. 3593 conditional restraints added. Observations/parameters ratio is 1.16 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2283 (Rfree = 0.000) for 7853 atoms. Found 106 (110 requested) and removed 77 (68 requested) atoms. Cycle 12: After refmac, R = 0.2055 (Rfree = 0.000) for 7867 atoms. Found 57 (108 requested) and removed 76 (69 requested) atoms. Cycle 13: After refmac, R = 0.1993 (Rfree = 0.000) for 7840 atoms. Found 44 (104 requested) and removed 75 (68 requested) atoms. Cycle 14: After refmac, R = 0.1937 (Rfree = 0.000) for 7805 atoms. Found 50 (101 requested) and removed 69 (68 requested) atoms. Cycle 15: After refmac, R = 0.1901 (Rfree = 0.000) for 7777 atoms. Found 40 (98 requested) and removed 69 (68 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.74 2.67 NCS extension: 888 residues added (962 deleted due to clashes), 8661 seeds are put forward Round 1: 928 peptides, 36 chains. Longest chain 120 peptides. Score 0.904 Round 2: 926 peptides, 35 chains. Longest chain 116 peptides. Score 0.905 Round 3: 935 peptides, 35 chains. Longest chain 119 peptides. Score 0.907 Round 4: 925 peptides, 45 chains. Longest chain 89 peptides. Score 0.887 Round 5: 918 peptides, 40 chains. Longest chain 92 peptides. Score 0.894 Taking the results from Round 3 Chains 38, Residues 900, Estimated correctness of the model 98.1 % 21 chains (760 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 16 A and 23 A Built loop between residues 37 A and 40 A Built loop between residues 113 A and 116 A Built loop between residues 132 A and 136 A Built loop between residues 176 A and 185 A Built loop between residues 66 C and 73 C Built loop between residues 123 C and 126 C Built loop between residues 181 C and 189 C Built loop between residues 67 B and 72 B Built loop between residues 189 E and 192 E 27 chains (937 residues) following loop building 11 chains (802 residues) in sequence following loop building ------------------------------------------------------ 36493 reflections ( 98.58 % complete ) and 9243 restraints for refining 8069 atoms. 2404 conditional restraints added. Observations/parameters ratio is 1.13 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2327 (Rfree = 0.000) for 8069 atoms. Found 99 (99 requested) and removed 105 (70 requested) atoms. Cycle 17: After refmac, R = 0.2114 (Rfree = 0.000) for 8049 atoms. Found 88 (96 requested) and removed 72 (70 requested) atoms. Cycle 18: After refmac, R = 0.2013 (Rfree = 0.000) for 8061 atoms. Found 63 (93 requested) and removed 72 (70 requested) atoms. Cycle 19: After refmac, R = 0.1950 (Rfree = 0.000) for 8049 atoms. Found 56 (90 requested) and removed 72 (70 requested) atoms. Cycle 20: After refmac, R = 0.1877 (Rfree = 0.000) for 8031 atoms. Found 55 (87 requested) and removed 75 (70 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.73 2.66 NCS extension: 1193 residues added (1313 deleted due to clashes), 9236 seeds are put forward Round 1: 939 peptides, 35 chains. Longest chain 114 peptides. Score 0.908 Round 2: 951 peptides, 31 chains. Longest chain 108 peptides. Score 0.918 Round 3: 939 peptides, 31 chains. Longest chain 139 peptides. Score 0.915 Round 4: 929 peptides, 44 chains. Longest chain 64 peptides. Score 0.890 Round 5: 923 peptides, 37 chains. Longest chain 105 peptides. Score 0.901 Taking the results from Round 2 Chains 35, Residues 920, Estimated correctness of the model 98.5 % 19 chains (803 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 138 A and 147 A Built loop between residues 16 C and 21 C Built loop between residues 73 C and 76 C Built loop between residues 138 C and 141 C Built loop between residues 45 B and 55 B Built loop between residues 131 B and 135 B Built loop between residues 155 B and 159 B Built loop between residues 182 E and 185 E Built loop between residues 44 D and 47 D Built loop between residues 96 D and 99 D 24 chains (952 residues) following loop building 9 chains (840 residues) in sequence following loop building ------------------------------------------------------ 36493 reflections ( 98.58 % complete ) and 9165 restraints for refining 8158 atoms. 2069 conditional restraints added. Observations/parameters ratio is 1.12 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2190 (Rfree = 0.000) for 8158 atoms. Found 86 (86 requested) and removed 83 (71 requested) atoms. Cycle 22: After refmac, R = 0.1987 (Rfree = 0.000) for 8155 atoms. Found 83 (83 requested) and removed 73 (71 requested) atoms. Cycle 23: After refmac, R = 0.1903 (Rfree = 0.000) for 8163 atoms. Found 75 (80 requested) and removed 74 (71 requested) atoms. Cycle 24: After refmac, R = 0.1858 (Rfree = 0.000) for 8160 atoms. Found 58 (77 requested) and removed 71 (71 requested) atoms. Cycle 25: After refmac, R = 0.1821 (Rfree = 0.000) for 8144 atoms. Found 69 (74 requested) and removed 75 (71 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.72 2.65 NCS extension: 589 residues added (751 deleted due to clashes), 8747 seeds are put forward Round 1: 961 peptides, 19 chains. Longest chain 180 peptides. Score 0.938 Round 2: 964 peptides, 29 chains. Longest chain 119 peptides. Score 0.924 Round 3: 944 peptides, 33 chains. Longest chain 122 peptides. Score 0.913 Round 4: 926 peptides, 42 chains. Longest chain 71 peptides. Score 0.893 Round 5: 944 peptides, 35 chains. Longest chain 86 peptides. Score 0.910 Taking the results from Round 1 Chains 25, Residues 942, Estimated correctness of the model 99.1 % 16 chains (892 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 37 A and 40 A Built loop between residues 138 A and 141 A Built loop between residues 173 B and 179 B Built loop between residues 138 E and 145 E Built loop between residues 178 E and 181 E Built loop between residues 182 D and 192 D 18 chains (965 residues) following loop building 10 chains (918 residues) in sequence following loop building ------------------------------------------------------ 36493 reflections ( 98.58 % complete ) and 8608 restraints for refining 8182 atoms. 1126 conditional restraints added. Observations/parameters ratio is 1.12 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2103 (Rfree = 0.000) for 8182 atoms. Found 71 (71 requested) and removed 87 (71 requested) atoms. Cycle 27: After refmac, R = 0.1912 (Rfree = 0.000) for 8155 atoms. Found 71 (71 requested) and removed 73 (71 requested) atoms. Cycle 28: After refmac, R = 0.1834 (Rfree = 0.000) for 8147 atoms. Found 71 (71 requested) and removed 76 (71 requested) atoms. Cycle 29: After refmac, R = 0.1788 (Rfree = 0.000) for 8138 atoms. Found 71 (71 requested) and removed 75 (71 requested) atoms. Cycle 30: After refmac, R = 0.1773 (Rfree = 0.000) for 8134 atoms. Found 71 (71 requested) and removed 74 (71 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.73 2.66 NCS extension: 260 residues added (750 deleted due to clashes), 8407 seeds are put forward Round 1: 966 peptides, 21 chains. Longest chain 132 peptides. Score 0.936 Round 2: 967 peptides, 26 chains. Longest chain 121 peptides. Score 0.929 Round 3: 964 peptides, 23 chains. Longest chain 201 peptides. Score 0.932 Round 4: 942 peptides, 39 chains. Longest chain 66 peptides. Score 0.903 Round 5: 927 peptides, 40 chains. Longest chain 76 peptides. Score 0.897 Taking the results from Round 1 Chains 23, Residues 945, Estimated correctness of the model 99.0 % 18 chains (915 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 65 A and 68 A Built loop between residues 139 A and 142 A Built loop between residues 15 C and 18 C Built loop between residues 84 C and 88 C Built loop between residues 137 B and 145 B Built loop between residues 178 B and 181 B Built loop between residues 134 E and 138 E Built loop between residues 155 E and 159 E Built loop between residues 183 E and 188 E Built loop between residues 15 D and 18 D Built loop between residues 82 D and 91 D Built loop between residues 139 D and 142 D 10 chains (982 residues) following loop building 6 chains (955 residues) in sequence following loop building ------------------------------------------------------ 36493 reflections ( 98.58 % complete ) and 8555 restraints for refining 8284 atoms. 860 conditional restraints added. Observations/parameters ratio is 1.10 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2066 (Rfree = 0.000) for 8284 atoms. Found 72 (72 requested) and removed 87 (72 requested) atoms. Cycle 32: After refmac, R = 0.1881 (Rfree = 0.000) for 8260 atoms. Found 72 (72 requested) and removed 78 (72 requested) atoms. Cycle 33: After refmac, R = 0.1806 (Rfree = 0.000) for 8249 atoms. Found 72 (72 requested) and removed 75 (72 requested) atoms. Cycle 34: After refmac, R = 0.1765 (Rfree = 0.000) for 8244 atoms. Found 72 (72 requested) and removed 73 (72 requested) atoms. Cycle 35: After refmac, R = 0.1754 (Rfree = 0.000) for 8241 atoms. Found 72 (72 requested) and removed 79 (72 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.73 2.66 NCS extension: 42 residues added (45 deleted due to clashes), 8289 seeds are put forward Round 1: 950 peptides, 22 chains. Longest chain 166 peptides. Score 0.931 Round 2: 963 peptides, 24 chains. Longest chain 118 peptides. Score 0.931 Round 3: 959 peptides, 29 chains. Longest chain 190 peptides. Score 0.923 Round 4: 946 peptides, 32 chains. Longest chain 114 peptides. Score 0.915 Round 5: 935 peptides, 43 chains. Longest chain 60 peptides. Score 0.894 Taking the results from Round 2 Chains 26, Residues 939, Estimated correctness of the model 98.9 % 18 chains (890 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 38 A and 41 A Built loop between residues 66 A and 76 A Built loop between residues 141 A and 144 A Built loop between residues 80 C and 91 C Built loop between residues 44 B and 47 B Built loop between residues 133 B and 136 B Built loop between residues 179 B and 186 B Built loop between residues 133 E and 143 E Built loop between residues 180 E and 183 E Built loop between residues 20 D and 23 D Built loop between residues 74 D and 77 D Built loop between residues 123 D and 126 D 11 chains (976 residues) following loop building 6 chains (940 residues) in sequence following loop building ------------------------------------------------------ 36493 reflections ( 98.58 % complete ) and 8726 restraints for refining 8278 atoms. 1115 conditional restraints added. Observations/parameters ratio is 1.10 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2120 (Rfree = 0.000) for 8278 atoms. Found 72 (72 requested) and removed 90 (72 requested) atoms. Cycle 37: After refmac, R = 0.1872 (Rfree = 0.000) for 8255 atoms. Found 72 (72 requested) and removed 76 (72 requested) atoms. Cycle 38: After refmac, R = 0.1794 (Rfree = 0.000) for 8250 atoms. Found 72 (72 requested) and removed 78 (72 requested) atoms. Cycle 39: After refmac, R = 0.1743 (Rfree = 0.000) for 8243 atoms. Found 72 (72 requested) and removed 73 (72 requested) atoms. Cycle 40: After refmac, R = 0.1715 (Rfree = 0.000) for 8242 atoms. Found 72 (72 requested) and removed 77 (72 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.73 2.66 NCS extension: 70 residues added (131 deleted due to clashes), 8319 seeds are put forward Round 1: 957 peptides, 20 chains. Longest chain 136 peptides. Score 0.935 Round 2: 965 peptides, 22 chains. Longest chain 203 peptides. Score 0.934 Round 3: 951 peptides, 30 chains. Longest chain 100 peptides. Score 0.919 Round 4: 938 peptides, 36 chains. Longest chain 90 peptides. Score 0.906 Round 5: 946 peptides, 31 chains. Longest chain 126 peptides. Score 0.917 Taking the results from Round 1 Chains 20, Residues 937, Estimated correctness of the model 99.0 % 16 chains (914 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 75 A and 78 A Built loop between residues 133 A and 136 A Built loop between residues 155 A and 159 A Built loop between residues 72 C and 76 C Built loop between residues 133 B and 139 B Built loop between residues 179 B and 183 B Built loop between residues 138 E and 145 E Built loop between residues 83 D and 93 D Built loop between residues 137 D and 140 D 11 chains (972 residues) following loop building 7 chains (949 residues) in sequence following loop building ------------------------------------------------------ 36493 reflections ( 98.58 % complete ) and 8605 restraints for refining 8238 atoms. 974 conditional restraints added. Observations/parameters ratio is 1.11 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2223 (Rfree = 0.000) for 8238 atoms. Found 72 (72 requested) and removed 95 (72 requested) atoms. Cycle 42: After refmac, R = 0.1890 (Rfree = 0.000) for 8207 atoms. Found 72 (72 requested) and removed 75 (72 requested) atoms. Cycle 43: After refmac, R = 0.1794 (Rfree = 0.000) for 8199 atoms. Found 71 (71 requested) and removed 76 (71 requested) atoms. Cycle 44: After refmac, R = 0.1750 (Rfree = 0.000) for 8193 atoms. Found 71 (71 requested) and removed 75 (71 requested) atoms. Cycle 45: After refmac, R = 0.1722 (Rfree = 0.000) for 8189 atoms. Found 70 (71 requested) and removed 73 (71 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.73 2.66 NCS extension: 37 residues added (97 deleted due to clashes), 8232 seeds are put forward Round 1: 956 peptides, 22 chains. Longest chain 204 peptides. Score 0.932 Round 2: 962 peptides, 28 chains. Longest chain 122 peptides. Score 0.925 Round 3: 951 peptides, 31 chains. Longest chain 130 peptides. Score 0.918 Round 4: 950 peptides, 35 chains. Longest chain 124 peptides. Score 0.911 Round 5: 940 peptides, 36 chains. Longest chain 153 peptides. Score 0.907 Taking the results from Round 1 Last building cycle: Chain fragments will be rearranged Chains 24, Residues 934, Estimated correctness of the model 98.9 % 16 chains (827 residues) have been docked in sequence Sequence coverage is 88 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 182 A and 186 A Built loop between residues 139 C and 142 C Built loop between residues 133 B and 140 B Built loop between residues 179 B and 185 B Built loop between residues 73 E and 78 E Built loop between residues 126 E and 130 E Built loop between residues 155 E and 159 E Built loop between residues 182 E and 193 E 13 chains (964 residues) following loop building 8 chains (863 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 36493 reflections ( 98.58 % complete ) and 7285 restraints for refining 7173 atoms. Observations/parameters ratio is 1.27 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3010 (Rfree = 0.000) for 7173 atoms. Found 38 (62 requested) and removed 0 (62 requested) atoms. Cycle 47: After refmac, R = 0.2761 (Rfree = 0.000) for 7173 atoms. Found 34 (63 requested) and removed 0 (63 requested) atoms. Cycle 48: After refmac, R = 0.2656 (Rfree = 0.000) for 7173 atoms. Found 17 (63 requested) and removed 6 (63 requested) atoms. Cycle 49: After refmac, R = 0.2618 (Rfree = 0.000) for 7173 atoms. Found 10 (63 requested) and removed 8 (63 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 00:30:11 GMT 2018 Job finished. TimeTaking 127.47 Used memory is bytes: 18441512