Mon 24 Dec 07:47:36 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 2hr2-2.5-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2hr2-2.5-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2hr2-2.5-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2hr2-2.5-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/2hr2-2.5-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2hr2-2.5-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 07:47:40 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/2hr2-2.5-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2hr2-2.5-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 1076 and 0 Target number of residues in the AU: 1076 Target solvent content: 0.5935 Checking the provided sequence file Detected sequence length: 159 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 6 Adjusted target number of residues: 954 Adjusted target solvent content: 0.64 Input MTZ file: 2hr2-2.5-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: 19 Cell parameters: 89.090 91.280 176.170 90.000 90.000 90.000 Input sequence file: 2hr2-2.5-parrot-noncs.fasta_lf Building free atoms model in initial map for 7632 target number of atoms Had to go as low as 0.85 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: 88.085 2.529 Wilson plot Bfac: 49.98 47715 reflections ( 99.08 % complete ) and 0 restraints for refining 8461 atoms. Observations/parameters ratio is 1.41 ------------------------------------------------------ Starting model: R = 0.3277 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2494 (Rfree = 0.000) for 8461 atoms. Found 112 (148 requested) and removed 89 (74 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.73 2.25 NCS extension: 0 residues added, 8484 seeds are put forward Round 1: 668 peptides, 96 chains. Longest chain 22 peptides. Score 0.506 Round 2: 734 peptides, 74 chains. Longest chain 26 peptides. Score 0.651 Round 3: 749 peptides, 64 chains. Longest chain 34 peptides. Score 0.696 Round 4: 752 peptides, 67 chains. Longest chain 28 peptides. Score 0.688 Round 5: 786 peptides, 64 chains. Longest chain 35 peptides. Score 0.720 Taking the results from Round 5 Chains 73, Residues 722, Estimated correctness of the model 85.4 % 27 chains (405 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 17 A and 28 A Built loop between residues 51 A and 55 A Built loop between residues 64 C and 67 C Built loop between residues 139 C and 142 C Built loop between residues 70 D and 74 D 66 chains (736 residues) following loop building 22 chains (425 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 47715 reflections ( 99.08 % complete ) and 10878 restraints for refining 7490 atoms. 6378 conditional restraints added. Observations/parameters ratio is 1.59 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2889 (Rfree = 0.000) for 7490 atoms. Found 131 (131 requested) and removed 95 (65 requested) atoms. Cycle 2: After refmac, R = 0.2703 (Rfree = 0.000) for 7421 atoms. Found 91 (129 requested) and removed 75 (66 requested) atoms. Cycle 3: After refmac, R = 0.2596 (Rfree = 0.000) for 7369 atoms. Found 94 (125 requested) and removed 77 (65 requested) atoms. Cycle 4: After refmac, R = 0.2466 (Rfree = 0.000) for 7355 atoms. Found 76 (121 requested) and removed 65 (64 requested) atoms. Cycle 5: After refmac, R = 0.2416 (Rfree = 0.000) for 7321 atoms. Found 72 (119 requested) and removed 68 (64 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.76 2.28 NCS extension: 208 residues added (64 deleted due to clashes), 7563 seeds are put forward Round 1: 774 peptides, 60 chains. Longest chain 45 peptides. Score 0.725 Round 2: 816 peptides, 51 chains. Longest chain 75 peptides. Score 0.775 Round 3: 817 peptides, 55 chains. Longest chain 60 peptides. Score 0.765 Round 4: 808 peptides, 51 chains. Longest chain 51 peptides. Score 0.771 Round 5: 805 peptides, 48 chains. Longest chain 54 peptides. Score 0.778 Taking the results from Round 5 Chains 57, Residues 757, Estimated correctness of the model 90.5 % 24 chains (529 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 15 A and 19 A Built loop between residues 78 A and 84 A Built loop between residues 117 C and 120 C Built loop between residues 24 B and 27 B Built loop between residues 71 B and 76 B Built loop between residues 124 B and 128 B 50 chains (775 residues) following loop building 18 chains (548 residues) in sequence following loop building ------------------------------------------------------ 47715 reflections ( 99.08 % complete ) and 9573 restraints for refining 7256 atoms. 4471 conditional restraints added. Observations/parameters ratio is 1.64 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2610 (Rfree = 0.000) for 7256 atoms. Found 114 (114 requested) and removed 78 (63 requested) atoms. Cycle 7: After refmac, R = 0.2377 (Rfree = 0.000) for 7240 atoms. Found 76 (112 requested) and removed 64 (63 requested) atoms. Cycle 8: After refmac, R = 0.2291 (Rfree = 0.000) for 7217 atoms. Found 66 (109 requested) and removed 63 (63 requested) atoms. Cycle 9: After refmac, R = 0.2225 (Rfree = 0.000) for 7209 atoms. Found 50 (106 requested) and removed 65 (63 requested) atoms. Cycle 10: After refmac, R = 0.2203 (Rfree = 0.000) for 7179 atoms. Found 67 (103 requested) and removed 66 (63 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.75 2.27 NCS extension: 91 residues added (49 deleted due to clashes), 7295 seeds are put forward Round 1: 810 peptides, 48 chains. Longest chain 54 peptides. Score 0.780 Round 2: 829 peptides, 41 chains. Longest chain 55 peptides. Score 0.808 Round 3: 838 peptides, 34 chains. Longest chain 106 peptides. Score 0.829 Round 4: 827 peptides, 43 chains. Longest chain 75 peptides. Score 0.802 Round 5: 811 peptides, 46 chains. Longest chain 59 peptides. Score 0.786 Taking the results from Round 3 Chains 46, Residues 804, Estimated correctness of the model 94.1 % 20 chains (661 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 17 A and 20 A Built loop between residues 48 C and 55 C 43 chains (810 residues) following loop building 18 chains (669 residues) in sequence following loop building ------------------------------------------------------ 47715 reflections ( 99.08 % complete ) and 8769 restraints for refining 7318 atoms. 3007 conditional restraints added. Observations/parameters ratio is 1.63 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2429 (Rfree = 0.000) for 7318 atoms. Found 102 (102 requested) and removed 80 (64 requested) atoms. Cycle 12: After refmac, R = 0.2226 (Rfree = 0.000) for 7310 atoms. Found 100 (100 requested) and removed 68 (64 requested) atoms. Cycle 13: After refmac, R = 0.2162 (Rfree = 0.000) for 7326 atoms. Found 70 (97 requested) and removed 66 (64 requested) atoms. Cycle 14: After refmac, R = 0.2136 (Rfree = 0.000) for 7315 atoms. Found 58 (95 requested) and removed 72 (64 requested) atoms. Cycle 15: After refmac, R = 0.2127 (Rfree = 0.000) for 7293 atoms. Found 66 (92 requested) and removed 71 (64 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.75 2.27 NCS extension: 381 residues added (323 deleted due to clashes), 7683 seeds are put forward Round 1: 854 peptides, 37 chains. Longest chain 99 peptides. Score 0.828 Round 2: 861 peptides, 36 chains. Longest chain 76 peptides. Score 0.833 Round 3: 840 peptides, 36 chains. Longest chain 81 peptides. Score 0.825 Round 4: 838 peptides, 40 chains. Longest chain 61 peptides. Score 0.814 Round 5: 833 peptides, 42 chains. Longest chain 69 peptides. Score 0.807 Taking the results from Round 2 Chains 42, Residues 825, Estimated correctness of the model 94.3 % 27 chains (760 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 24 A and 27 A Built loop between residues 44 A and 49 A Built loop between residues 59 A and 63 A Built loop between residues 89 A and 94 A Built loop between residues 46 C and 49 C Built loop between residues 77 C and 80 C Built loop between residues 100 C and 103 C Built loop between residues 108 E and 111 E Built loop between residues 133 E and 137 E Built loop between residues 78 D and 81 D Built loop between residues 131 D and 134 D Built loop between residues 83 F and 86 F Built loop between residues 135 F and 142 F 26 chains (855 residues) following loop building 14 chains (796 residues) in sequence following loop building ------------------------------------------------------ 47715 reflections ( 99.08 % complete ) and 8297 restraints for refining 7542 atoms. 1821 conditional restraints added. Observations/parameters ratio is 1.58 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2323 (Rfree = 0.000) for 7542 atoms. Found 92 (92 requested) and removed 95 (66 requested) atoms. Cycle 17: After refmac, R = 0.2098 (Rfree = 0.000) for 7508 atoms. Found 90 (90 requested) and removed 75 (66 requested) atoms. Cycle 18: After refmac, R = 0.1991 (Rfree = 0.000) for 7509 atoms. Found 65 (87 requested) and removed 69 (66 requested) atoms. Cycle 19: After refmac, R = 0.1938 (Rfree = 0.000) for 7492 atoms. Found 63 (84 requested) and removed 75 (65 requested) atoms. Cycle 20: After refmac, R = 0.1893 (Rfree = 0.000) for 7463 atoms. Found 74 (81 requested) and removed 68 (65 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.74 2.26 NCS extension: 318 residues added (1253 deleted due to clashes), 7801 seeds are put forward Round 1: 905 peptides, 17 chains. Longest chain 152 peptides. Score 0.888 Round 2: 904 peptides, 20 chains. Longest chain 153 peptides. Score 0.882 Round 3: 893 peptides, 27 chains. Longest chain 153 peptides. Score 0.864 Round 4: 872 peptides, 33 chains. Longest chain 82 peptides. Score 0.844 Round 5: 862 peptides, 36 chains. Longest chain 80 peptides. Score 0.834 Taking the results from Round 1 Chains 17, Residues 888, Estimated correctness of the model 97.3 % 15 chains (878 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 15 A and 18 A Built loop between residues 44 C and 48 C Built loop between residues 108 C and 111 C Built loop between residues 46 B and 49 B Built loop between residues 133 E and 139 E Built loop between residues 59 F and 63 F Built loop between residues 89 F and 97 F Built loop between residues 110 F and 113 F 8 chains (911 residues) following loop building 7 chains (904 residues) in sequence following loop building ------------------------------------------------------ 47715 reflections ( 99.08 % complete ) and 7686 restraints for refining 7710 atoms. 546 conditional restraints added. Observations/parameters ratio is 1.55 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2162 (Rfree = 0.000) for 7710 atoms. Found 81 (81 requested) and removed 90 (67 requested) atoms. Cycle 22: After refmac, R = 0.1960 (Rfree = 0.000) for 7679 atoms. Found 78 (78 requested) and removed 72 (67 requested) atoms. Cycle 23: After refmac, R = 0.1911 (Rfree = 0.000) for 7671 atoms. Found 75 (75 requested) and removed 69 (67 requested) atoms. Cycle 24: After refmac, R = 0.1873 (Rfree = 0.000) for 7660 atoms. Found 72 (72 requested) and removed 70 (67 requested) atoms. Cycle 25: After refmac, R = 0.1852 (Rfree = 0.000) for 7652 atoms. Found 70 (70 requested) and removed 69 (67 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.75 2.27 NCS extension: 0 residues added, 7655 seeds are put forward Round 1: 894 peptides, 19 chains. Longest chain 151 peptides. Score 0.881 Round 2: 897 peptides, 25 chains. Longest chain 153 peptides. Score 0.870 Round 3: 893 peptides, 21 chains. Longest chain 153 peptides. Score 0.876 Round 4: 871 peptides, 32 chains. Longest chain 101 peptides. Score 0.846 Round 5: 863 peptides, 39 chains. Longest chain 84 peptides. Score 0.827 Taking the results from Round 1 Chains 23, Residues 875, Estimated correctness of the model 97.0 % 17 chains (841 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 45 A and 48 A Built loop between residues 73 A and 77 A Built loop between residues 46 C and 52 C Built loop between residues 82 C and 86 C Built loop between residues 105 C and 109 C Built loop between residues 135 C and 139 C Built loop between residues 36 B and 40 B Built loop between residues 40 F and 47 F 15 chains (903 residues) following loop building 9 chains (869 residues) in sequence following loop building ------------------------------------------------------ 47715 reflections ( 99.08 % complete ) and 7891 restraints for refining 7599 atoms. 935 conditional restraints added. Observations/parameters ratio is 1.57 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2242 (Rfree = 0.000) for 7599 atoms. Found 66 (66 requested) and removed 90 (66 requested) atoms. Cycle 27: After refmac, R = 0.2022 (Rfree = 0.000) for 7563 atoms. Found 66 (66 requested) and removed 69 (66 requested) atoms. Cycle 28: After refmac, R = 0.1937 (Rfree = 0.000) for 7553 atoms. Found 66 (66 requested) and removed 67 (66 requested) atoms. Cycle 29: After refmac, R = 0.1896 (Rfree = 0.000) for 7546 atoms. Found 66 (66 requested) and removed 69 (66 requested) atoms. Cycle 30: After refmac, R = 0.1888 (Rfree = 0.000) for 7528 atoms. Found 66 (66 requested) and removed 71 (66 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.75 2.27 NCS extension: 139 residues added (333 deleted due to clashes), 7669 seeds are put forward Round 1: 882 peptides, 21 chains. Longest chain 150 peptides. Score 0.873 Round 2: 896 peptides, 17 chains. Longest chain 150 peptides. Score 0.885 Round 3: 869 peptides, 29 chains. Longest chain 120 peptides. Score 0.852 Round 4: 869 peptides, 32 chains. Longest chain 101 peptides. Score 0.845 Round 5: 872 peptides, 34 chains. Longest chain 83 peptides. Score 0.842 Taking the results from Round 2 Chains 22, Residues 879, Estimated correctness of the model 97.1 % 19 chains (866 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 15 A and 18 A Built loop between residues 109 A and 112 A Built loop between residues 41 C and 47 C Built loop between residues 84 C and 95 C Built loop between residues 106 C and 112 C Built loop between residues 36 B and 40 B Built loop between residues 92 B and 95 B Built loop between residues 105 B and 110 B Built loop between residues 135 B and 139 B Built loop between residues 115 E and 122 E Built loop between residues 44 F and 49 F Built loop between residues 100 F and 103 F 8 chains (915 residues) following loop building 7 chains (914 residues) in sequence following loop building ------------------------------------------------------ 47715 reflections ( 99.08 % complete ) and 7568 restraints for refining 7632 atoms. 381 conditional restraints added. Observations/parameters ratio is 1.56 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2146 (Rfree = 0.000) for 7632 atoms. Found 66 (66 requested) and removed 89 (66 requested) atoms. Cycle 32: After refmac, R = 0.1958 (Rfree = 0.000) for 7587 atoms. Found 66 (66 requested) and removed 72 (66 requested) atoms. Cycle 33: After refmac, R = 0.1898 (Rfree = 0.000) for 7574 atoms. Found 66 (66 requested) and removed 70 (66 requested) atoms. Cycle 34: After refmac, R = 0.1869 (Rfree = 0.000) for 7561 atoms. Found 66 (66 requested) and removed 68 (66 requested) atoms. Cycle 35: After refmac, R = 0.1837 (Rfree = 0.000) for 7555 atoms. Found 66 (66 requested) and removed 71 (66 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.75 2.27 NCS extension: 1 residues added (2 deleted due to clashes), 7562 seeds are put forward Round 1: 894 peptides, 23 chains. Longest chain 103 peptides. Score 0.873 Round 2: 901 peptides, 15 chains. Longest chain 151 peptides. Score 0.890 Round 3: 885 peptides, 30 chains. Longest chain 119 peptides. Score 0.856 Round 4: 876 peptides, 30 chains. Longest chain 108 peptides. Score 0.852 Round 5: 857 peptides, 40 chains. Longest chain 89 peptides. Score 0.823 Taking the results from Round 2 Chains 21, Residues 886, Estimated correctness of the model 97.4 % 14 chains (850 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 77 A and 81 A Built loop between residues 44 C and 51 C Built loop between residues 75 C and 79 C Built loop between residues 44 B and 48 B Built loop between residues 111 D and 115 D Built loop between residues 39 F and 42 F 14 chains (901 residues) following loop building 8 chains (870 residues) in sequence following loop building ------------------------------------------------------ 47715 reflections ( 99.08 % complete ) and 7823 restraints for refining 7548 atoms. 854 conditional restraints added. Observations/parameters ratio is 1.58 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2211 (Rfree = 0.000) for 7548 atoms. Found 66 (66 requested) and removed 87 (66 requested) atoms. Cycle 37: After refmac, R = 0.1986 (Rfree = 0.000) for 7507 atoms. Found 66 (66 requested) and removed 68 (66 requested) atoms. Cycle 38: After refmac, R = 0.1911 (Rfree = 0.000) for 7492 atoms. Found 65 (65 requested) and removed 70 (65 requested) atoms. Cycle 39: After refmac, R = 0.1875 (Rfree = 0.000) for 7477 atoms. Found 65 (65 requested) and removed 66 (65 requested) atoms. Cycle 40: After refmac, R = 0.1839 (Rfree = 0.000) for 7472 atoms. Found 65 (65 requested) and removed 68 (65 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.75 2.27 NCS extension: 42 residues added (216 deleted due to clashes), 7517 seeds are put forward Round 1: 901 peptides, 19 chains. Longest chain 138 peptides. Score 0.883 Round 2: 897 peptides, 20 chains. Longest chain 150 peptides. Score 0.880 Round 3: 886 peptides, 31 chains. Longest chain 150 peptides. Score 0.854 Round 4: 879 peptides, 27 chains. Longest chain 109 peptides. Score 0.860 Round 5: 861 peptides, 39 chains. Longest chain 83 peptides. Score 0.827 Taking the results from Round 1 Chains 20, Residues 882, Estimated correctness of the model 97.0 % 16 chains (865 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 15 A and 18 A Built loop between residues 75 A and 79 A Built loop between residues 44 B and 48 B Built loop between residues 108 B and 111 B Built loop between residues 48 E and 51 E Built loop between residues 143 D and 146 D Built loop between residues 38 F and 43 F 12 chains (899 residues) following loop building 9 chains (883 residues) in sequence following loop building ------------------------------------------------------ 47715 reflections ( 99.08 % complete ) and 7879 restraints for refining 7552 atoms. 892 conditional restraints added. Observations/parameters ratio is 1.58 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2119 (Rfree = 0.000) for 7552 atoms. Found 66 (66 requested) and removed 87 (66 requested) atoms. Cycle 42: After refmac, R = 0.1930 (Rfree = 0.000) for 7516 atoms. Found 66 (66 requested) and removed 68 (66 requested) atoms. Failed to save intermediate PDB Cycle 43: After refmac, R = 0.1860 (Rfree = 0.000) for 7505 atoms. Found 65 (65 requested) and removed 73 (65 requested) atoms. Cycle 44: After refmac, R = 0.1845 (Rfree = 0.000) for 7490 atoms. Found 65 (65 requested) and removed 66 (65 requested) atoms. Cycle 45: After refmac, R = 0.1831 (Rfree = 0.000) for 7486 atoms. Found 65 (65 requested) and removed 66 (65 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.74 2.26 NCS extension: 43 residues added (376 deleted due to clashes), 7534 seeds are put forward Round 1: 906 peptides, 15 chains. Longest chain 155 peptides. Score 0.892 Round 2: 901 peptides, 17 chains. Longest chain 146 peptides. Score 0.886 Round 3: 883 peptides, 22 chains. Longest chain 142 peptides. Score 0.871 Round 4: 874 peptides, 31 chains. Longest chain 108 peptides. Score 0.849 Round 5: 871 peptides, 36 chains. Longest chain 110 peptides. Score 0.837 Taking the results from Round 1 Last building cycle: Chain fragments will be rearranged Chains 20, Residues 891, Estimated correctness of the model 97.4 % 16 chains (863 residues) have been docked in sequence Sequence coverage is 96 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 108 A and 111 A Built loop between residues 40 C and 43 C Built loop between residues 105 C and 108 C Built loop between residues 125 C and 129 C Built loop between residues 48 B and 55 B Built loop between residues 115 E and 122 E Built loop between residues 136 E and 146 E Built loop between residues 51 F and 54 F Built loop between residues 108 F and 111 F 8 chains (908 residues) following loop building 7 chains (897 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 47715 reflections ( 99.08 % complete ) and 7088 restraints for refining 6973 atoms. Observations/parameters ratio is 1.71 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2401 (Rfree = 0.000) for 6973 atoms. Found 60 (61 requested) and removed 0 (61 requested) atoms. Cycle 47: After refmac, R = 0.2176 (Rfree = 0.000) for 6973 atoms. Found 26 (61 requested) and removed 4 (61 requested) atoms. Cycle 48: After refmac, R = 0.2115 (Rfree = 0.000) for 6973 atoms. Found 12 (61 requested) and removed 4 (61 requested) atoms. Cycle 49: After refmac, R = 0.2087 (Rfree = 0.000) for 6973 atoms. TimeTaking 98.17