Sun 23 Dec 22:22:55 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 2hr2-2.5-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2hr2-2.5-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2hr2-2.5-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hr2-2.5-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/2hr2-2.5-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hr2-2.5-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 22:23:05 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hr2-2.5-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hr2-2.5-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 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-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: 19 Cell parameters: 89.090 91.280 176.170 90.000 90.000 90.000 Input sequence file: 2hr2-2.5-parrot-hancs.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 8568 atoms. Observations/parameters ratio is 1.39 ------------------------------------------------------ Starting model: R = 0.3141 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2281 (Rfree = 0.000) for 8568 atoms. Found 136 (150 requested) and removed 87 (75 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.75 2.27 NCS extension: 0 residues added, 8617 seeds are put forward Round 1: 733 peptides, 89 chains. Longest chain 26 peptides. Score 0.594 Round 2: 798 peptides, 61 chains. Longest chain 34 peptides. Score 0.737 Round 3: 823 peptides, 54 chains. Longest chain 39 peptides. Score 0.771 Round 4: 826 peptides, 46 chains. Longest chain 62 peptides. Score 0.794 Round 5: 843 peptides, 44 chains. Longest chain 77 peptides. Score 0.807 Taking the results from Round 5 Chains 54, Residues 799, Estimated correctness of the model 92.6 % 25 chains (622 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 44 A and 51 A Built loop between residues 77 A and 87 A Built loop between residues 46 B and 53 B Built loop between residues 117 B and 125 B Built loop between residues 12 E and 23 E Built loop between residues 70 E and 74 E Built loop between residues 16 D and 19 D 42 chains (828 residues) following loop building 18 chains (665 residues) in sequence following loop building ------------------------------------------------------ 47715 reflections ( 99.08 % complete ) and 9621 restraints for refining 7772 atoms. 3835 conditional restraints added. Observations/parameters ratio is 1.53 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2612 (Rfree = 0.000) for 7772 atoms. Found 136 (136 requested) and removed 96 (68 requested) atoms. Cycle 2: After refmac, R = 0.2365 (Rfree = 0.000) for 7693 atoms. Found 85 (134 requested) and removed 73 (68 requested) atoms. Cycle 3: After refmac, R = 0.2269 (Rfree = 0.000) for 7633 atoms. Found 73 (130 requested) and removed 70 (67 requested) atoms. Cycle 4: After refmac, R = 0.2215 (Rfree = 0.000) for 7594 atoms. Found 64 (126 requested) and removed 68 (67 requested) atoms. Cycle 5: After refmac, R = 0.2165 (Rfree = 0.000) for 7566 atoms. Found 50 (122 requested) and removed 68 (66 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.74 2.26 NCS extension: 623 residues added (548 deleted due to clashes), 8194 seeds are put forward Round 1: 870 peptides, 35 chains. Longest chain 73 peptides. Score 0.839 Round 2: 883 peptides, 23 chains. Longest chain 149 peptides. Score 0.869 Round 3: 883 peptides, 28 chains. Longest chain 99 peptides. Score 0.859 Round 4: 843 peptides, 38 chains. Longest chain 57 peptides. Score 0.821 Round 5: 859 peptides, 38 chains. Longest chain 80 peptides. Score 0.828 Taking the results from Round 2 Chains 31, Residues 860, Estimated correctness of the model 96.4 % 20 chains (811 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 47 A and 52 A Built loop between residues 71 C and 74 C Built loop between residues 115 C and 120 C Built loop between residues 100 B and 103 B Built loop between residues 43 E and 50 E Built loop between residues 69 E and 75 E Built loop between residues 86 E and 90 E Built loop between residues 115 E and 120 E Built loop between residues 46 F and 54 F 18 chains (884 residues) following loop building 11 chains (848 residues) in sequence following loop building ------------------------------------------------------ 47715 reflections ( 99.08 % complete ) and 8024 restraints for refining 7750 atoms. 1222 conditional restraints added. Observations/parameters ratio is 1.54 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2326 (Rfree = 0.000) for 7750 atoms. Found 122 (122 requested) and removed 93 (68 requested) atoms. Cycle 7: After refmac, R = 0.2100 (Rfree = 0.000) for 7710 atoms. Found 103 (120 requested) and removed 75 (68 requested) atoms. Cycle 8: After refmac, R = 0.2021 (Rfree = 0.000) for 7706 atoms. Found 90 (116 requested) and removed 72 (67 requested) atoms. Cycle 9: After refmac, R = 0.1973 (Rfree = 0.000) for 7701 atoms. Found 80 (113 requested) and removed 73 (67 requested) atoms. Cycle 10: After refmac, R = 0.1939 (Rfree = 0.000) for 7692 atoms. Found 83 (111 requested) and removed 76 (67 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.75 2.27 NCS extension: 134 residues added (907 deleted due to clashes), 7851 seeds are put forward Round 1: 885 peptides, 25 chains. Longest chain 82 peptides. Score 0.866 Round 2: 885 peptides, 22 chains. Longest chain 111 peptides. Score 0.872 Round 3: 865 peptides, 34 chains. Longest chain 77 peptides. Score 0.839 Round 4: 895 peptides, 30 chains. Longest chain 100 peptides. Score 0.859 Round 5: 860 peptides, 42 chains. Longest chain 72 peptides. Score 0.819 Taking the results from Round 2 Chains 27, Residues 863, Estimated correctness of the model 96.5 % 18 chains (789 residues) have been docked in sequence Building loops using Loopy2018 Failed to save intermediate PDB Built loop between residues 54 C and 58 C Built loop between residues 124 C and 127 C Built loop between residues 42 B and 45 B Built loop between residues 45 E and 52 E Built loop between residues 77 E and 82 E Built loop between residues 116 E and 120 E Built loop between residues 133 E and 138 E Built loop between residues 111 D and 116 D Built loop between residues 136 D and 140 D 15 chains (891 residues) following loop building 9 chains (820 residues) in sequence following loop building ------------------------------------------------------ 47715 reflections ( 99.08 % complete ) and 8282 restraints for refining 7612 atoms. 1558 conditional restraints added. Observations/parameters ratio is 1.57 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2243 (Rfree = 0.000) for 7612 atoms. Found 106 (106 requested) and removed 93 (66 requested) atoms. Cycle 12: After refmac, R = 0.2019 (Rfree = 0.000) for 7599 atoms. Found 91 (104 requested) and removed 72 (66 requested) atoms. Cycle 13: After refmac, R = 0.1950 (Rfree = 0.000) for 7604 atoms. Found 81 (101 requested) and removed 69 (66 requested) atoms. Cycle 14: After refmac, R = 0.1925 (Rfree = 0.000) for 7606 atoms. Found 69 (98 requested) and removed 72 (66 requested) atoms. Cycle 15: After refmac, R = 0.1888 (Rfree = 0.000) for 7593 atoms. Found 65 (96 requested) and removed 72 (66 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.75 2.27 NCS extension: 30 residues added (317 deleted due to clashes), 7626 seeds are put forward Round 1: 883 peptides, 24 chains. Longest chain 134 peptides. Score 0.867 Round 2: 900 peptides, 19 chains. Longest chain 147 peptides. Score 0.882 Round 3: 886 peptides, 30 chains. Longest chain 92 peptides. Score 0.856 Round 4: 863 peptides, 30 chains. Longest chain 118 peptides. Score 0.848 Round 5: 855 peptides, 40 chains. Longest chain 73 peptides. Score 0.822 Taking the results from Round 2 Chains 30, Residues 881, Estimated correctness of the model 97.0 % 18 chains (824 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 44 A and 47 A Built loop between residues 135 A and 138 A Built loop between residues 113 C and 119 C Built loop between residues 42 B and 49 B Built loop between residues 107 B and 116 B Built loop between residues 128 B and 132 B Built loop between residues 52 E and 54 E Built loop between residues 113 E and 120 E Built loop between residues 86 D and 90 D Built loop between residues 118 D and 125 D 16 chains (905 residues) following loop building 8 chains (866 residues) in sequence following loop building ------------------------------------------------------ 47715 reflections ( 99.08 % complete ) and 8022 restraints for refining 7657 atoms. 1102 conditional restraints added. Observations/parameters ratio is 1.56 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2311 (Rfree = 0.000) for 7657 atoms. Found 94 (94 requested) and removed 99 (67 requested) atoms. Cycle 17: After refmac, R = 0.2056 (Rfree = 0.000) for 7618 atoms. Found 91 (91 requested) and removed 70 (67 requested) atoms. Cycle 18: After refmac, R = 0.1948 (Rfree = 0.000) for 7623 atoms. Found 83 (88 requested) and removed 71 (67 requested) atoms. Cycle 19: After refmac, R = 0.1900 (Rfree = 0.000) for 7627 atoms. Found 84 (85 requested) and removed 67 (66 requested) atoms. Cycle 20: After refmac, R = 0.1868 (Rfree = 0.000) for 7638 atoms. Found 76 (83 requested) and removed 70 (67 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.75 2.27 NCS extension: 17 residues added (88 deleted due to clashes), 7681 seeds are put forward Round 1: 887 peptides, 25 chains. Longest chain 139 peptides. Score 0.867 Round 2: 904 peptides, 16 chains. Longest chain 152 peptides. Score 0.889 Round 3: 878 peptides, 29 chains. Longest chain 82 peptides. Score 0.855 Round 4: 874 peptides, 37 chains. Longest chain 57 peptides. Score 0.836 Round 5: 864 peptides, 35 chains. Longest chain 88 peptides. Score 0.837 Taking the results from Round 2 Chains 20, Residues 888, Estimated correctness of the model 97.3 % 16 chains (870 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 23 A and 26 A Built loop between residues 101 A and 104 A Built loop between residues 54 C and 57 C Built loop between residues 115 C and 119 C Built loop between residues 47 B and 50 B Built loop between residues 15 E and 19 E Built loop between residues 40 E and 47 E Built loop between residues 115 E and 122 E Built loop between residues 118 D and 125 D Built loop between residues 45 F and 52 F 8 chains (920 residues) following loop building 6 chains (908 residues) in sequence following loop building ------------------------------------------------------ 47715 reflections ( 99.08 % complete ) and 7670 restraints for refining 7659 atoms. 500 conditional restraints added. Observations/parameters ratio is 1.56 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2199 (Rfree = 0.000) for 7659 atoms. Found 80 (80 requested) and removed 94 (67 requested) atoms. Cycle 22: After refmac, R = 0.1979 (Rfree = 0.000) for 7624 atoms. Found 78 (78 requested) and removed 73 (67 requested) atoms. Cycle 23: After refmac, R = 0.1887 (Rfree = 0.000) for 7619 atoms. Found 74 (74 requested) and removed 67 (66 requested) atoms. Cycle 24: After refmac, R = 0.1835 (Rfree = 0.000) for 7623 atoms. Found 72 (72 requested) and removed 72 (66 requested) atoms. Cycle 25: After refmac, R = 0.1810 (Rfree = 0.000) for 7616 atoms. Found 69 (69 requested) and removed 71 (66 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.75 2.27 NCS extension: 0 residues added (6 deleted due to clashes), 7621 seeds are put forward Round 1: 890 peptides, 22 chains. Longest chain 115 peptides. Score 0.873 Round 2: 898 peptides, 18 chains. Longest chain 150 peptides. Score 0.884 Round 3: 888 peptides, 31 chains. Longest chain 112 peptides. Score 0.855 Round 4: 880 peptides, 28 chains. Longest chain 100 peptides. Score 0.858 Round 5: 857 peptides, 39 chains. Longest chain 77 peptides. Score 0.825 Taking the results from Round 2 Chains 23, Residues 880, Estimated correctness of the model 97.1 % 17 chains (854 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 38 A and 44 A Built loop between residues 107 A and 110 A Built loop between residues 116 A and 121 A Built loop between residues 49 C and 53 C Built loop between residues 115 C and 118 C Built loop between residues 45 B and 52 B Built loop between residues 91 B and 94 B Built loop between residues 115 E and 122 E Built loop between residues 111 D and 115 D Built loop between residues 47 F and 57 F Built loop between residues 93 F and 103 F 8 chains (915 residues) following loop building 6 chains (905 residues) in sequence following loop building ------------------------------------------------------ 47715 reflections ( 99.08 % complete ) and 7688 restraints for refining 7648 atoms. 540 conditional restraints added. Observations/parameters ratio is 1.56 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2162 (Rfree = 0.000) for 7648 atoms. Found 67 (67 requested) and removed 94 (67 requested) atoms. Cycle 27: After refmac, R = 0.1947 (Rfree = 0.000) for 7602 atoms. Found 66 (66 requested) and removed 68 (66 requested) atoms. Cycle 28: After refmac, R = 0.1874 (Rfree = 0.000) for 7596 atoms. Found 66 (66 requested) and removed 68 (66 requested) atoms. Cycle 29: After refmac, R = 0.1827 (Rfree = 0.000) for 7589 atoms. Found 66 (66 requested) and removed 68 (66 requested) atoms. Cycle 30: After refmac, R = 0.1811 (Rfree = 0.000) for 7583 atoms. Found 66 (66 requested) and removed 67 (66 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.75 2.27 NCS extension: 2 residues added (12 deleted due to clashes), 7597 seeds are put forward Round 1: 889 peptides, 22 chains. Longest chain 141 peptides. Score 0.873 Round 2: 897 peptides, 18 chains. Longest chain 157 peptides. Score 0.883 Round 3: 887 peptides, 25 chains. Longest chain 107 peptides. Score 0.867 Round 4: 890 peptides, 29 chains. Longest chain 83 peptides. Score 0.859 Round 5: 865 peptides, 45 chains. Longest chain 78 peptides. Score 0.814 Taking the results from Round 2 Chains 25, Residues 879, Estimated correctness of the model 97.0 % 17 chains (842 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 15 A and 19 A Built loop between residues 46 C and 53 C Built loop between residues 87 C and 90 C Built loop between residues 47 B and 51 B Built loop between residues 75 B and 79 B Built loop between residues 108 B and 110 B Built loop between residues 116 D and 125 D Built loop between residues 46 F and 53 F 14 chains (899 residues) following loop building 9 chains (874 residues) in sequence following loop building ------------------------------------------------------ 47715 reflections ( 99.08 % complete ) and 7949 restraints for refining 7561 atoms. 1010 conditional restraints added. Observations/parameters ratio is 1.58 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2171 (Rfree = 0.000) for 7561 atoms. Found 66 (66 requested) and removed 89 (66 requested) atoms. Cycle 32: After refmac, R = 0.1951 (Rfree = 0.000) for 7517 atoms. Found 66 (66 requested) and removed 67 (66 requested) atoms. Cycle 33: After refmac, R = 0.1855 (Rfree = 0.000) for 7508 atoms. Found 65 (65 requested) and removed 69 (65 requested) atoms. Cycle 34: After refmac, R = 0.1831 (Rfree = 0.000) for 7498 atoms. Found 65 (65 requested) and removed 71 (65 requested) atoms. Cycle 35: After refmac, R = 0.1812 (Rfree = 0.000) for 7488 atoms. Found 65 (65 requested) and removed 68 (65 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.75 2.27 NCS extension: 43 residues added (385 deleted due to clashes), 7544 seeds are put forward Round 1: 906 peptides, 21 chains. Longest chain 151 peptides. Score 0.880 Round 2: 907 peptides, 17 chains. Longest chain 153 peptides. Score 0.888 Round 3: 885 peptides, 30 chains. Longest chain 77 peptides. Score 0.856 Round 4: 884 peptides, 29 chains. Longest chain 100 peptides. Score 0.857 Round 5: 880 peptides, 39 chains. Longest chain 75 peptides. Score 0.834 Taking the results from Round 2 Chains 18, Residues 890, Estimated correctness of the model 97.3 % 16 chains (886 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 14 A and 18 A Built loop between residues 37 A and 42 A Built loop between residues 84 A and 90 A Built loop between residues 106 A and 109 A Built loop between residues 116 A and 120 A Built loop between residues 76 C and 79 C Built loop between residues 114 C and 117 C Built loop between residues 44 B and 48 B Built loop between residues 135 B and 138 B Built loop between residues 111 D and 115 D 8 chains (919 residues) following loop building 6 chains (915 residues) in sequence following loop building ------------------------------------------------------ 47715 reflections ( 99.08 % complete ) and 7621 restraints for refining 7635 atoms. 417 conditional restraints added. Observations/parameters ratio is 1.56 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2151 (Rfree = 0.000) for 7635 atoms. Found 66 (66 requested) and removed 90 (66 requested) atoms. Cycle 37: After refmac, R = 0.1948 (Rfree = 0.000) for 7593 atoms. Found 66 (66 requested) and removed 71 (66 requested) atoms. Cycle 38: After refmac, R = 0.1894 (Rfree = 0.000) for 7581 atoms. Found 66 (66 requested) and removed 67 (66 requested) atoms. Cycle 39: After refmac, R = 0.1867 (Rfree = 0.000) for 7575 atoms. Found 66 (66 requested) and removed 72 (66 requested) atoms. Cycle 40: After refmac, R = 0.1852 (Rfree = 0.000) for 7562 atoms. Found 66 (66 requested) and removed 73 (66 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.75 2.27 NCS extension: 0 residues added, 7561 seeds are put forward Round 1: 888 peptides, 27 chains. Longest chain 78 peptides. Score 0.863 Round 2: 901 peptides, 21 chains. Longest chain 157 peptides. Score 0.879 Round 3: 874 peptides, 33 chains. Longest chain 71 peptides. Score 0.845 Round 4: 867 peptides, 35 chains. Longest chain 80 peptides. Score 0.838 Round 5: 856 peptides, 40 chains. Longest chain 53 peptides. Score 0.822 Taking the results from Round 2 Chains 30, Residues 880, Estimated correctness of the model 96.9 % 20 chains (851 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 12 A and 18 A Built loop between residues 37 A and 41 A Built loop between residues 84 A and 92 A Built loop between residues 116 A and 122 A Built loop between residues 136 C and 139 C Built loop between residues 43 B and 46 B Built loop between residues 121 B and 125 B Built loop between residues 125 E and 130 E Built loop between residues 50 D and 53 D Built loop between residues 118 D and 121 D Built loop between residues 45 F and 48 F Built loop between residues 108 F and 111 F 15 chains (912 residues) following loop building 8 chains (890 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 47715 reflections ( 99.08 % complete ) and 7684 restraints for refining 7571 atoms. 622 conditional restraints added. Observations/parameters ratio is 1.58 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2163 (Rfree = 0.000) for 7571 atoms. Found 66 (66 requested) and removed 91 (66 requested) atoms. Cycle 42: After refmac, R = 0.1962 (Rfree = 0.000) for 7527 atoms. Found 66 (66 requested) and removed 67 (66 requested) atoms. Cycle 43: After refmac, R = 0.1896 (Rfree = 0.000) for 7520 atoms. Found 66 (66 requested) and removed 69 (66 requested) atoms. Cycle 44: After refmac, R = 0.1865 (Rfree = 0.000) for 7514 atoms. Found 65 (65 requested) and removed 68 (65 requested) atoms. Cycle 45: After refmac, R = 0.1827 (Rfree = 0.000) for 7504 atoms. Found 65 (65 requested) and removed 77 (65 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.75 2.27 NCS extension: 21 residues added (150 deleted due to clashes), 7522 seeds are put forward Round 1: 895 peptides, 21 chains. Longest chain 112 peptides. Score 0.877 Round 2: 905 peptides, 19 chains. Longest chain 119 peptides. Score 0.884 Round 3: 889 peptides, 29 chains. Longest chain 83 peptides. Score 0.859 Round 4: 872 peptides, 43 chains. Longest chain 72 peptides. Score 0.822 Round 5: 886 peptides, 37 chains. Longest chain 60 peptides. Score 0.841 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 22, Residues 886, Estimated correctness of the model 97.1 % 18 chains (871 residues) have been docked in sequence Sequence coverage is 98 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 17 A and 20 A Built loop between residues 95 A and 99 A Built loop between residues 116 A and 121 A Built loop between residues 54 C and 57 C Built loop between residues 36 B and 40 B Built loop between residues 47 E and 50 E Built loop between residues 108 E and 111 E Built loop between residues 136 E and 139 E Built loop between residues 118 D and 121 D Built loop between residues 46 F and 53 F Built loop between residues 77 F and 82 F Built loop between residues 100 F and 103 F 8 chains (913 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 7028 atoms. Observations/parameters ratio is 1.70 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2469 (Rfree = 0.000) for 7028 atoms. Found 48 (61 requested) and removed 0 (61 requested) atoms. Cycle 47: After refmac, R = 0.2247 (Rfree = 0.000) for 7028 atoms. Found 29 (62 requested) and removed 2 (62 requested) atoms. Cycle 48: After refmac, R = 0.2160 (Rfree = 0.000) for 7028 atoms. Found 13 (62 requested) and removed 10 (62 requested) atoms. Cycle 49: After refmac, R = 0.2145 (Rfree = 0.000) for 7028 atoms. Found 11 (62 requested) and removed 3 (62 requested) atoms. Writing output files ... TimeTaking 123.02