Mon 24 Dec 00:10:36 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 2hr2-2.5-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2hr2-2.5-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2hr2-2.5-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2hr2-2.5-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/2hr2-2.5-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2hr2-2.5-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 00:10:41 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/2hr2-2.5-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2hr2-2.5-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 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-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: 19 Cell parameters: 89.090 91.280 176.170 90.000 90.000 90.000 Input sequence file: 2hr2-2.5-parrot-mrncs.fasta_lf Building free atoms model in initial map for 7632 target number of atoms Had to go as low as 0.80 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 8535 atoms. Observations/parameters ratio is 1.40 ------------------------------------------------------ Starting model: R = 0.3141 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2375 (Rfree = 0.000) for 8535 atoms. Found 107 (149 requested) and removed 91 (74 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.75 2.27 NCS extension: 0 residues added, 8551 seeds are put forward Round 1: 709 peptides, 90 chains. Longest chain 20 peptides. Score 0.569 Round 2: 804 peptides, 61 chains. Longest chain 43 peptides. Score 0.740 Round 3: 822 peptides, 53 chains. Longest chain 43 peptides. Score 0.773 Round 4: 842 peptides, 45 chains. Longest chain 59 peptides. Score 0.804 Round 5: 836 peptides, 51 chains. Longest chain 68 peptides. Score 0.786 Taking the results from Round 4 Chains 55, Residues 797, Estimated correctness of the model 92.4 % 27 chains (652 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 69 C and 73 C Built loop between residues 111 C and 119 C Built loop between residues 134 C and 137 C Built loop between residues 114 E and 118 E Built loop between residues 133 E and 138 E Built loop between residues 45 D and 55 D Built loop between residues 130 D and 133 D 45 chains (821 residues) following loop building 20 chains (682 residues) in sequence following loop building ------------------------------------------------------ 47715 reflections ( 99.08 % complete ) and 9392 restraints for refining 7745 atoms. 3596 conditional restraints added. Observations/parameters ratio is 1.54 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2570 (Rfree = 0.000) for 7745 atoms. Found 136 (136 requested) and removed 101 (68 requested) atoms. Cycle 2: After refmac, R = 0.2402 (Rfree = 0.000) for 7647 atoms. Found 87 (133 requested) and removed 78 (68 requested) atoms. Cycle 3: After refmac, R = 0.2281 (Rfree = 0.000) for 7608 atoms. Found 79 (129 requested) and removed 72 (67 requested) atoms. Cycle 4: After refmac, R = 0.2208 (Rfree = 0.000) for 7584 atoms. Found 47 (125 requested) and removed 71 (66 requested) atoms. Cycle 5: After refmac, R = 0.2190 (Rfree = 0.000) for 7535 atoms. Found 65 (121 requested) and removed 66 (66 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.75 2.27 NCS extension: 431 residues added (470 deleted due to clashes), 7988 seeds are put forward Round 1: 865 peptides, 31 chains. Longest chain 114 peptides. Score 0.846 Round 2: 879 peptides, 28 chains. Longest chain 100 peptides. Score 0.858 Round 3: 862 peptides, 34 chains. Longest chain 93 peptides. Score 0.838 Round 4: 848 peptides, 41 chains. Longest chain 50 peptides. Score 0.816 Round 5: 858 peptides, 42 chains. Longest chain 77 peptides. Score 0.818 Taking the results from Round 2 Chains 39, Residues 851, Estimated correctness of the model 95.8 % 24 chains (767 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 15 A and 18 A Built loop between residues 116 A and 119 A Built loop between residues 51 C and 54 C Built loop between residues 78 C and 81 C Built loop between residues 115 C and 118 C Built loop between residues 133 C and 137 C Built loop between residues 24 B and 27 B Built loop between residues 41 B and 45 B Built loop between residues 94 B and 98 B Built loop between residues 38 E and 45 E Built loop between residues 110 D and 117 D Built loop between residues 135 D and 139 D Built loop between residues 39 F and 46 F 21 chains (881 residues) following loop building 11 chains (809 residues) in sequence following loop building ------------------------------------------------------ 47715 reflections ( 99.08 % complete ) and 8317 restraints for refining 7676 atoms. 1736 conditional restraints added. Observations/parameters ratio is 1.55 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2397 (Rfree = 0.000) for 7676 atoms. Found 121 (121 requested) and removed 105 (67 requested) atoms. Cycle 7: After refmac, R = 0.2175 (Rfree = 0.000) for 7627 atoms. Found 101 (118 requested) and removed 73 (67 requested) atoms. Cycle 8: After refmac, R = 0.2064 (Rfree = 0.000) for 7633 atoms. Found 88 (115 requested) and removed 75 (67 requested) atoms. Cycle 9: After refmac, R = 0.2009 (Rfree = 0.000) for 7630 atoms. Found 81 (113 requested) and removed 76 (67 requested) atoms. Cycle 10: After refmac, R = 0.1955 (Rfree = 0.000) for 7623 atoms. Found 80 (109 requested) and removed 75 (66 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.75 2.27 NCS extension: 734 residues added (359 deleted due to clashes), 8382 seeds are put forward Round 1: 893 peptides, 24 chains. Longest chain 154 peptides. Score 0.870 Round 2: 908 peptides, 19 chains. Longest chain 164 peptides. Score 0.885 Round 3: 888 peptides, 28 chains. Longest chain 109 peptides. Score 0.861 Round 4: 880 peptides, 34 chains. Longest chain 92 peptides. Score 0.845 Round 5: 851 peptides, 38 chains. Longest chain 77 peptides. Score 0.825 Taking the results from Round 2 Chains 27, Residues 889, Estimated correctness of the model 97.1 % 18 chains (834 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 116 C and 119 C Built loop between residues 82 B and 86 B Built loop between residues 133 B and 136 B Built loop between residues 57 E and 60 E Built loop between residues 100 E and 104 E Built loop between residues 116 D and 123 D 19 chains (901 residues) following loop building 12 chains (852 residues) in sequence following loop building ------------------------------------------------------ 47715 reflections ( 99.08 % complete ) and 8052 restraints for refining 7650 atoms. 1201 conditional restraints added. Observations/parameters ratio is 1.56 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2272 (Rfree = 0.000) for 7650 atoms. Found 107 (107 requested) and removed 101 (67 requested) atoms. Failed to save intermediate PDB Cycle 12: After refmac, R = 0.2027 (Rfree = 0.000) for 7611 atoms. Found 105 (105 requested) and removed 73 (67 requested) atoms. Cycle 13: After refmac, R = 0.1907 (Rfree = 0.000) for 7629 atoms. Found 90 (102 requested) and removed 74 (67 requested) atoms. Cycle 14: After refmac, R = 0.1841 (Rfree = 0.000) for 7629 atoms. Found 97 (99 requested) and removed 85 (67 requested) atoms. Cycle 15: After refmac, R = 0.1807 (Rfree = 0.000) for 7631 atoms. Found 87 (96 requested) and removed 79 (67 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.74 2.26 NCS extension: 108 residues added (402 deleted due to clashes), 7763 seeds are put forward Round 1: 891 peptides, 24 chains. Longest chain 141 peptides. Score 0.870 Round 2: 895 peptides, 16 chains. Longest chain 139 peptides. Score 0.887 Round 3: 898 peptides, 20 chains. Longest chain 112 peptides. Score 0.880 Round 4: 875 peptides, 27 chains. Longest chain 71 peptides. Score 0.858 Round 5: 874 peptides, 33 chains. Longest chain 91 peptides. Score 0.845 Taking the results from Round 2 Chains 25, Residues 879, Estimated correctness of the model 97.2 % 18 chains (835 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 41 A and 48 A Built loop between residues 74 C and 77 C Built loop between residues 106 C and 110 C Built loop between residues 47 B and 55 B Built loop between residues 63 B and 66 B Built loop between residues 107 B and 110 B Built loop between residues 118 E and 125 E Built loop between residues 44 D and 51 D Built loop between residues 75 D and 79 D Built loop between residues 54 F and 61 F Built loop between residues 116 F and 120 F 10 chains (905 residues) following loop building 7 chains (881 residues) in sequence following loop building ------------------------------------------------------ 47715 reflections ( 99.08 % complete ) and 7864 restraints for refining 7622 atoms. 861 conditional restraints added. Observations/parameters ratio is 1.57 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2255 (Rfree = 0.000) for 7622 atoms. Found 93 (93 requested) and removed 95 (66 requested) atoms. Cycle 17: After refmac, R = 0.1974 (Rfree = 0.000) for 7590 atoms. Found 90 (90 requested) and removed 74 (66 requested) atoms. Cycle 18: After refmac, R = 0.1884 (Rfree = 0.000) for 7598 atoms. Found 88 (88 requested) and removed 73 (66 requested) atoms. Cycle 19: After refmac, R = 0.1841 (Rfree = 0.000) for 7604 atoms. Found 85 (85 requested) and removed 75 (66 requested) atoms. Cycle 20: After refmac, R = 0.1835 (Rfree = 0.000) for 7604 atoms. Found 82 (82 requested) and removed 73 (66 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.75 2.27 NCS extension: 49 residues added (430 deleted due to clashes), 7688 seeds are put forward Round 1: 907 peptides, 14 chains. Longest chain 142 peptides. Score 0.894 Round 2: 905 peptides, 15 chains. Longest chain 150 peptides. Score 0.891 Round 3: 888 peptides, 25 chains. Longest chain 120 peptides. Score 0.867 Round 4: 880 peptides, 31 chains. Longest chain 78 peptides. Score 0.852 Round 5: 858 peptides, 41 chains. Longest chain 74 peptides. Score 0.821 Taking the results from Round 1 Chains 16, Residues 893, Estimated correctness of the model 97.5 % 14 chains (877 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 37 A and 41 A Built loop between residues 86 A and 90 A Built loop between residues 43 C and 50 C Built loop between residues 108 C and 111 C Built loop between residues 15 B and 18 B Built loop between residues 60 E and 63 E Built loop between residues 104 E and 109 E Built loop between residues 45 D and 50 D 7 chains (914 residues) following loop building 6 chains (903 residues) in sequence following loop building ------------------------------------------------------ 47715 reflections ( 99.08 % complete ) and 7733 restraints for refining 7646 atoms. 601 conditional restraints added. Observations/parameters ratio is 1.56 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2143 (Rfree = 0.000) for 7646 atoms. Found 80 (80 requested) and removed 97 (67 requested) atoms. Cycle 22: After refmac, R = 0.1929 (Rfree = 0.000) for 7608 atoms. Found 77 (77 requested) and removed 68 (66 requested) atoms. Cycle 23: After refmac, R = 0.1840 (Rfree = 0.000) for 7608 atoms. Found 74 (74 requested) and removed 69 (66 requested) atoms. Cycle 24: After refmac, R = 0.1816 (Rfree = 0.000) for 7607 atoms. Found 72 (72 requested) and removed 74 (66 requested) atoms. Cycle 25: After refmac, R = 0.1808 (Rfree = 0.000) for 7600 atoms. Found 69 (69 requested) and removed 72 (66 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.74 2.26 NCS extension: 9 residues added (7 deleted due to clashes), 7613 seeds are put forward Round 1: 906 peptides, 17 chains. Longest chain 120 peptides. Score 0.888 Round 2: 901 peptides, 17 chains. Longest chain 120 peptides. Score 0.886 Round 3: 904 peptides, 24 chains. Longest chain 101 peptides. Score 0.874 Round 4: 872 peptides, 35 chains. Longest chain 71 peptides. Score 0.840 Round 5: 885 peptides, 37 chains. Longest chain 85 peptides. Score 0.841 Taking the results from Round 1 Chains 18, Residues 889, Estimated correctness of the model 97.3 % 15 chains (872 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 15 A and 18 A Built loop between residues 127 A and 130 A Built loop between residues 45 C and 49 C Built loop between residues 44 B and 48 B Built loop between residues 108 B and 111 B Built loop between residues 52 E and 63 E Built loop between residues 104 E and 109 E Built loop between residues 124 D and 127 D Built loop between residues 34 F and 39 F 8 chains (917 residues) following loop building 6 chains (904 residues) in sequence following loop building ------------------------------------------------------ 47715 reflections ( 99.08 % complete ) and 7707 restraints for refining 7630 atoms. 561 conditional restraints added. Observations/parameters ratio is 1.56 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2119 (Rfree = 0.000) for 7630 atoms. Found 66 (66 requested) and removed 91 (66 requested) atoms. Cycle 27: After refmac, R = 0.1922 (Rfree = 0.000) for 7586 atoms. Found 66 (66 requested) and removed 66 (66 requested) atoms. Cycle 28: After refmac, R = 0.1856 (Rfree = 0.000) for 7581 atoms. Found 66 (66 requested) and removed 69 (66 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.1821 (Rfree = 0.000) for 7572 atoms. Found 66 (66 requested) and removed 69 (66 requested) atoms. Cycle 30: After refmac, R = 0.1815 (Rfree = 0.000) for 7564 atoms. Found 66 (66 requested) and removed 74 (66 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.75 2.27 NCS extension: 5 residues added (12 deleted due to clashes), 7573 seeds are put forward Round 1: 896 peptides, 17 chains. Longest chain 110 peptides. Score 0.885 Round 2: 906 peptides, 22 chains. Longest chain 82 peptides. Score 0.879 Round 3: 891 peptides, 22 chains. Longest chain 85 peptides. Score 0.874 Round 4: 869 peptides, 34 chains. Longest chain 99 peptides. Score 0.841 Round 5: 873 peptides, 40 chains. Longest chain 112 peptides. Score 0.829 Taking the results from Round 1 Chains 19, Residues 879, Estimated correctness of the model 97.1 % 15 chains (809 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 13 A and 17 A Built loop between residues 47 A and 55 A Built loop between residues 47 C and 51 C Built loop between residues 45 B and 49 B Built loop between residues 36 E and 42 E Built loop between residues 49 D and 56 D Built loop between residues 104 D and 109 D Built loop between residues 45 F and 49 F 10 chains (909 residues) following loop building 7 chains (843 residues) in sequence following loop building ------------------------------------------------------ 47715 reflections ( 99.08 % complete ) and 7996 restraints for refining 7542 atoms. 1131 conditional restraints added. Observations/parameters ratio is 1.58 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2153 (Rfree = 0.000) for 7542 atoms. Found 66 (66 requested) and removed 84 (66 requested) atoms. Cycle 32: After refmac, R = 0.1952 (Rfree = 0.000) for 7512 atoms. Found 66 (66 requested) and removed 69 (66 requested) atoms. Cycle 33: After refmac, R = 0.1876 (Rfree = 0.000) for 7505 atoms. Found 65 (65 requested) and removed 65 (65 requested) atoms. Cycle 34: After refmac, R = 0.1859 (Rfree = 0.000) for 7501 atoms. Found 65 (65 requested) and removed 69 (65 requested) atoms. Cycle 35: After refmac, R = 0.1849 (Rfree = 0.000) for 7495 atoms. Found 65 (65 requested) and removed 74 (65 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.74 2.26 NCS extension: 7 residues added (90 deleted due to clashes), 7501 seeds are put forward Round 1: 891 peptides, 18 chains. Longest chain 110 peptides. Score 0.882 Round 2: 904 peptides, 18 chains. Longest chain 115 peptides. Score 0.885 Round 3: 892 peptides, 19 chains. Longest chain 151 peptides. Score 0.880 Round 4: 887 peptides, 31 chains. Longest chain 120 peptides. Score 0.854 Round 5: 874 peptides, 34 chains. Longest chain 86 peptides. Score 0.843 Taking the results from Round 2 Chains 19, Residues 886, Estimated correctness of the model 97.1 % 17 chains (878 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 36 A and 42 A Built loop between residues 89 A and 92 A Built loop between residues 117 A and 122 A Built loop between residues 61 C and 65 C Built loop between residues 104 C and 107 C Built loop between residues 117 C and 120 C Built loop between residues 46 B and 49 B Built loop between residues 110 E and 114 E Built loop between residues 118 D and 121 D Built loop between residues 44 F and 49 F Built loop between residues 100 F and 103 F 7 chains (916 residues) following loop building 6 chains (909 residues) in sequence following loop building ------------------------------------------------------ 47715 reflections ( 99.08 % complete ) and 7608 restraints for refining 7611 atoms. 434 conditional restraints added. Observations/parameters ratio is 1.57 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2143 (Rfree = 0.000) for 7611 atoms. Found 66 (66 requested) and removed 93 (66 requested) atoms. Cycle 37: After refmac, R = 0.1922 (Rfree = 0.000) for 7570 atoms. Found 66 (66 requested) and removed 72 (66 requested) atoms. Cycle 38: After refmac, R = 0.1857 (Rfree = 0.000) for 7560 atoms. Found 66 (66 requested) and removed 69 (66 requested) atoms. Failed to save intermediate PDB Cycle 39: After refmac, R = 0.1833 (Rfree = 0.000) for 7549 atoms. Found 66 (66 requested) and removed 71 (66 requested) atoms. Cycle 40: After refmac, R = 0.1828 (Rfree = 0.000) for 7540 atoms. Found 66 (66 requested) and removed 73 (66 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.75 2.27 NCS extension: 5 residues added (4 deleted due to clashes), 7541 seeds are put forward Round 1: 894 peptides, 20 chains. Longest chain 151 peptides. Score 0.879 Round 2: 907 peptides, 18 chains. Longest chain 138 peptides. Score 0.886 Round 3: 894 peptides, 24 chains. Longest chain 119 peptides. Score 0.871 Round 4: 880 peptides, 31 chains. Longest chain 65 peptides. Score 0.852 Round 5: 880 peptides, 32 chains. Longest chain 114 peptides. Score 0.850 Taking the results from Round 2 Chains 25, Residues 889, Estimated correctness of the model 97.2 % 17 chains (856 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 39 A and 42 A Built loop between residues 117 A and 120 A Built loop between residues 79 C and 83 C Built loop between residues 106 C and 110 C Built loop between residues 41 B and 45 B Built loop between residues 118 B and 125 B Built loop between residues 46 D and 53 D Built loop between residues 76 D and 79 D Built loop between residues 87 D and 94 D Built loop between residues 54 F and 63 F Built loop between residues 103 F and 106 F 10 chains (916 residues) following loop building 6 chains (899 residues) in sequence following loop building ------------------------------------------------------ 47715 reflections ( 99.08 % complete ) and 7741 restraints for refining 7633 atoms. 619 conditional restraints added. Observations/parameters ratio is 1.56 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2168 (Rfree = 0.000) for 7633 atoms. Found 66 (66 requested) and removed 88 (66 requested) atoms. Cycle 42: After refmac, R = 0.1961 (Rfree = 0.000) for 7587 atoms. Found 66 (66 requested) and removed 67 (66 requested) atoms. Cycle 43: After refmac, R = 0.1882 (Rfree = 0.000) for 7578 atoms. Found 66 (66 requested) and removed 70 (66 requested) atoms. Cycle 44: After refmac, R = 0.1864 (Rfree = 0.000) for 7566 atoms. Found 66 (66 requested) and removed 68 (66 requested) atoms. Cycle 45: After refmac, R = 0.1840 (Rfree = 0.000) for 7559 atoms. Found 66 (66 requested) and removed 73 (66 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.74 2.26 NCS extension: 4 residues added (9 deleted due to clashes), 7566 seeds are put forward Round 1: 898 peptides, 23 chains. Longest chain 86 peptides. Score 0.874 Round 2: 905 peptides, 19 chains. Longest chain 149 peptides. Score 0.884 Round 3: 880 peptides, 29 chains. Longest chain 104 peptides. Score 0.856 Round 4: 895 peptides, 32 chains. Longest chain 72 peptides. Score 0.855 Round 5: 871 peptides, 39 chains. Longest chain 69 peptides. Score 0.831 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 20, Residues 886, Estimated correctness of the model 97.1 % 16 chains (868 residues) have been docked in sequence Sequence coverage is 97 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 54 A and 61 A Built loop between residues 73 A and 77 A Built loop between residues 114 A and 117 A Built loop between residues 76 C and 79 C Built loop between residues 94 C and 103 C Built loop between residues 43 B and 49 B Built loop between residues 69 B and 72 B Built loop between residues 108 D and 114 D Built loop between residues 79 F and 82 F Built loop between residues 103 F and 106 F 8 chains (916 residues) following loop building 6 chains (905 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 47715 reflections ( 99.08 % complete ) and 7149 restraints for refining 7029 atoms. Observations/parameters ratio is 1.70 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2412 (Rfree = 0.000) for 7029 atoms. Found 56 (61 requested) and removed 0 (61 requested) atoms. Cycle 47: After refmac, R = 0.2185 (Rfree = 0.000) for 7029 atoms. Found 33 (62 requested) and removed 3 (62 requested) atoms. Cycle 48: After refmac, R = 0.2108 (Rfree = 0.000) for 7029 atoms. Found 19 (62 requested) and removed 3 (62 requested) atoms. Cycle 49: After refmac, R = 0.2071 (Rfree = 0.000) for 7029 atoms. Found 11 (62 requested) and removed 10 (62 requested) atoms. Writing output files ... TimeTaking 97.32