null Mon 24 Dec 07:30:23 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 2hx1-2.1-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2hx1-2.1-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2hx1-2.1-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2hx1-2.1-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/2hx1-2.1-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2hx1-2.1-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 07:30:28 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/2hx1-2.1-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2hx1-2.1-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 1161 and 0 Target number of residues in the AU: 1161 Target solvent content: 0.4702 Checking the provided sequence file Detected sequence length: 284 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1136 Adjusted target solvent content: 0.48 Input MTZ file: 2hx1-2.1-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: 65.624 119.462 151.274 90.000 90.000 90.000 Input sequence file: 2hx1-2.1-parrot-noncs.fasta_lf Building free atoms model in initial map for 9088 target number of atoms Had to go as low as 0.50 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 1 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: 93.753 2.100 Wilson plot Bfac: 17.81 70128 reflections ( 99.92 % complete ) and 0 restraints for refining 10115 atoms. Observations/parameters ratio is 1.73 ------------------------------------------------------ Starting model: R = 0.3391 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2947 (Rfree = 0.000) for 10115 atoms. Found 232 (301 requested) and removed 165 (150 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.99 2.04 NCS extension: 0 residues added, 10182 seeds are put forward Round 1: 804 peptides, 115 chains. Longest chain 24 peptides. Score 0.607 Round 2: 925 peptides, 74 chains. Longest chain 42 peptides. Score 0.823 Round 3: 974 peptides, 54 chains. Longest chain 62 peptides. Score 0.883 Round 4: 1008 peptides, 52 chains. Longest chain 66 peptides. Score 0.896 Round 5: 1034 peptides, 45 chains. Longest chain 97 peptides. Score 0.913 Taking the results from Round 5 Chains 47, Residues 989, Estimated correctness of the model 99.1 % 20 chains (763 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 43 A and 46 A Built loop between residues 197 A and 206 A Built loop between residues 236 C and 239 C Built loop between residues 253 C and 256 C Built loop between residues 39 B and 45 B Built loop between residues 67 B and 72 B Built loop between residues 214 B and 223 B Built loop between residues 262 B and 265 B 38 chains (1017 residues) following loop building 12 chains (796 residues) in sequence following loop building ------------------------------------------------------ 70128 reflections ( 99.92 % complete ) and 11479 restraints for refining 9470 atoms. 4370 conditional restraints added. Observations/parameters ratio is 1.85 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3294 (Rfree = 0.000) for 9470 atoms. Found 282 (282 requested) and removed 166 (141 requested) atoms. Cycle 2: After refmac, R = 0.3109 (Rfree = 0.000) for 9543 atoms. Found 220 (279 requested) and removed 142 (142 requested) atoms. Cycle 3: After refmac, R = 0.2937 (Rfree = 0.000) for 9581 atoms. Found 188 (275 requested) and removed 91 (143 requested) atoms. Cycle 4: After refmac, R = 0.2855 (Rfree = 0.000) for 9605 atoms. Found 146 (276 requested) and removed 39 (144 requested) atoms. Cycle 5: After refmac, R = 0.2775 (Rfree = 0.000) for 9684 atoms. Found 112 (277 requested) and removed 28 (144 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.95 2.00 NCS extension: 9 residues added (41 deleted due to clashes), 9797 seeds are put forward Round 1: 1040 peptides, 42 chains. Longest chain 93 peptides. Score 0.919 Round 2: 1060 peptides, 32 chains. Longest chain 111 peptides. Score 0.936 Round 3: 1069 peptides, 30 chains. Longest chain 94 peptides. Score 0.940 Round 4: 1080 peptides, 33 chains. Longest chain 89 peptides. Score 0.938 Round 5: 1090 peptides, 25 chains. Longest chain 111 peptides. Score 0.949 Taking the results from Round 5 Chains 27, Residues 1065, Estimated correctness of the model 99.6 % 15 chains (895 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 112 A and 117 A Built loop between residues 68 C and 72 C Built loop between residues 195 D and 206 D 21 chains (1077 residues) following loop building 12 chains (912 residues) in sequence following loop building ------------------------------------------------------ 70128 reflections ( 99.92 % complete ) and 11037 restraints for refining 9809 atoms. 3174 conditional restraints added. Observations/parameters ratio is 1.79 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2955 (Rfree = 0.000) for 9809 atoms. Found 269 (280 requested) and removed 179 (146 requested) atoms. Cycle 7: After refmac, R = 0.2819 (Rfree = 0.000) for 9884 atoms. Found 160 (277 requested) and removed 131 (147 requested) atoms. Cycle 8: After refmac, R = 0.2661 (Rfree = 0.000) for 9893 atoms. Found 118 (271 requested) and removed 55 (147 requested) atoms. Cycle 9: After refmac, R = 0.2607 (Rfree = 0.000) for 9899 atoms. Found 147 (272 requested) and removed 29 (148 requested) atoms. Cycle 10: After refmac, R = 0.2540 (Rfree = 0.000) for 9997 atoms. Found 117 (274 requested) and removed 25 (149 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.96 2.01 NCS extension: 17 residues added (9 deleted due to clashes), 10121 seeds are put forward Round 1: 1076 peptides, 28 chains. Longest chain 111 peptides. Score 0.943 Round 2: 1077 peptides, 27 chains. Longest chain 111 peptides. Score 0.945 Round 3: 1075 peptides, 31 chains. Longest chain 95 peptides. Score 0.940 Round 4: 1076 peptides, 24 chains. Longest chain 99 peptides. Score 0.948 Round 5: 1086 peptides, 24 chains. Longest chain 109 peptides. Score 0.949 Taking the results from Round 5 Chains 25, Residues 1062, Estimated correctness of the model 99.6 % 19 chains (1023 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 95 A and 98 A Built loop between residues 254 A and 257 A Built loop between residues 65 C and 69 C Built loop between residues 113 C and 117 C Built loop between residues 200 C and 208 C Built loop between residues 111 B and 117 B Built loop between residues 253 B and 256 B Built loop between residues 96 D and 100 D Built loop between residues 112 D and 118 D Built loop between residues 195 D and 205 D Built loop between residues 232 D and 235 D 12 chains (1098 residues) following loop building 8 chains (1066 residues) in sequence following loop building ------------------------------------------------------ 70128 reflections ( 99.92 % complete ) and 10146 restraints for refining 10048 atoms. 1595 conditional restraints added. Observations/parameters ratio is 1.74 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2720 (Rfree = 0.000) for 10048 atoms. Found 263 (275 requested) and removed 170 (149 requested) atoms. Cycle 12: After refmac, R = 0.2607 (Rfree = 0.000) for 10122 atoms. Found 170 (272 requested) and removed 92 (151 requested) atoms. Cycle 13: After refmac, R = 0.2536 (Rfree = 0.000) for 10183 atoms. Found 159 (268 requested) and removed 46 (152 requested) atoms. Cycle 14: After refmac, R = 0.2463 (Rfree = 0.000) for 10280 atoms. Found 108 (269 requested) and removed 36 (153 requested) atoms. Cycle 15: After refmac, R = 0.2344 (Rfree = 0.000) for 10327 atoms. Found 119 (271 requested) and removed 35 (154 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.94 1.99 NCS extension: 17 residues added (182 deleted due to clashes), 10433 seeds are put forward Round 1: 1092 peptides, 24 chains. Longest chain 111 peptides. Score 0.950 Round 2: 1103 peptides, 20 chains. Longest chain 141 peptides. Score 0.956 Round 3: 1102 peptides, 22 chains. Longest chain 113 peptides. Score 0.954 Round 4: 1100 peptides, 24 chains. Longest chain 131 peptides. Score 0.951 Round 5: 1098 peptides, 23 chains. Longest chain 111 peptides. Score 0.952 Taking the results from Round 2 Chains 24, Residues 1083, Estimated correctness of the model 99.7 % 17 chains (1023 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 203 A and 206 A Built loop between residues 144 C and 147 C Built loop between residues 28 B and 31 B Built loop between residues 66 B and 69 B Built loop between residues 218 B and 226 B Built loop between residues 142 D and 145 D Built loop between residues 194 D and 205 D 16 chains (1106 residues) following loop building 10 chains (1050 residues) in sequence following loop building ------------------------------------------------------ 70128 reflections ( 99.92 % complete ) and 10504 restraints for refining 10218 atoms. 1998 conditional restraints added. Observations/parameters ratio is 1.72 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2445 (Rfree = 0.000) for 10218 atoms. Found 268 (268 requested) and removed 159 (152 requested) atoms. Cycle 17: After refmac, R = 0.2312 (Rfree = 0.000) for 10290 atoms. Found 206 (264 requested) and removed 78 (153 requested) atoms. Cycle 18: After refmac, R = 0.2217 (Rfree = 0.000) for 10392 atoms. Found 154 (267 requested) and removed 67 (155 requested) atoms. Cycle 19: After refmac, R = 0.2151 (Rfree = 0.000) for 10457 atoms. Found 136 (268 requested) and removed 53 (156 requested) atoms. Cycle 20: After refmac, R = 0.2097 (Rfree = 0.000) for 10516 atoms. Found 146 (270 requested) and removed 59 (157 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.93 1.98 NCS extension: 22 residues added (156 deleted due to clashes), 10631 seeds are put forward Round 1: 1102 peptides, 21 chains. Longest chain 111 peptides. Score 0.955 Round 2: 1110 peptides, 16 chains. Longest chain 202 peptides. Score 0.961 Round 3: 1100 peptides, 25 chains. Longest chain 99 peptides. Score 0.950 Round 4: 1111 peptides, 18 chains. Longest chain 113 peptides. Score 0.959 Round 5: 1108 peptides, 21 chains. Longest chain 132 peptides. Score 0.956 Taking the results from Round 2 Chains 25, Residues 1094, Estimated correctness of the model 99.8 % 14 chains (1051 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 112 A and 117 A Built loop between residues 204 A and 209 A Built loop between residues 222 A and 227 A Built loop between residues 44 C and 47 C Built loop between residues 204 B and 210 B Built loop between residues 201 D and 207 D 16 chains (1113 residues) following loop building 8 chains (1075 residues) in sequence following loop building ------------------------------------------------------ 70128 reflections ( 99.92 % complete ) and 10297 restraints for refining 10345 atoms. 1678 conditional restraints added. Observations/parameters ratio is 1.69 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2309 (Rfree = 0.000) for 10345 atoms. Found 265 (265 requested) and removed 163 (154 requested) atoms. Cycle 22: After refmac, R = 0.2188 (Rfree = 0.000) for 10424 atoms. Found 181 (261 requested) and removed 93 (155 requested) atoms. Cycle 23: After refmac, R = 0.2109 (Rfree = 0.000) for 10502 atoms. Found 165 (257 requested) and removed 66 (156 requested) atoms. Cycle 24: After refmac, R = 0.2065 (Rfree = 0.000) for 10586 atoms. Found 147 (259 requested) and removed 68 (158 requested) atoms. Cycle 25: After refmac, R = 0.2064 (Rfree = 0.000) for 10646 atoms. Found 142 (260 requested) and removed 76 (158 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.93 1.98 NCS extension: 14 residues added (190 deleted due to clashes), 10735 seeds are put forward Round 1: 1105 peptides, 19 chains. Longest chain 113 peptides. Score 0.957 Round 2: 1112 peptides, 14 chains. Longest chain 204 peptides. Score 0.963 Round 3: 1100 peptides, 22 chains. Longest chain 111 peptides. Score 0.954 Round 4: 1108 peptides, 16 chains. Longest chain 166 peptides. Score 0.961 Round 5: 1091 peptides, 27 chains. Longest chain 141 peptides. Score 0.947 Taking the results from Round 2 Chains 16, Residues 1098, Estimated correctness of the model 99.8 % 12 chains (1074 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 112 C and 117 C Built loop between residues 111 B and 117 B Built loop between residues 113 D and 117 D Built loop between residues 200 D and 206 D 11 chains (1112 residues) following loop building 8 chains (1091 residues) in sequence following loop building ------------------------------------------------------ 70128 reflections ( 99.92 % complete ) and 10122 restraints for refining 10330 atoms. 1452 conditional restraints added. Observations/parameters ratio is 1.70 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2218 (Rfree = 0.000) for 10330 atoms. Found 246 (246 requested) and removed 157 (153 requested) atoms. Cycle 27: After refmac, R = 0.2109 (Rfree = 0.000) for 10395 atoms. Found 198 (242 requested) and removed 66 (155 requested) atoms. Cycle 28: After refmac, R = 0.2046 (Rfree = 0.000) for 10520 atoms. Found 149 (244 requested) and removed 71 (156 requested) atoms. Cycle 29: After refmac, R = 0.1995 (Rfree = 0.000) for 10576 atoms. Found 152 (246 requested) and removed 65 (157 requested) atoms. Cycle 30: After refmac, R = 0.1958 (Rfree = 0.000) for 10651 atoms. Found 140 (247 requested) and removed 66 (158 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.93 1.98 NCS extension: 9 residues added (353 deleted due to clashes), 10737 seeds are put forward Round 1: 1105 peptides, 19 chains. Longest chain 113 peptides. Score 0.957 Round 2: 1108 peptides, 17 chains. Longest chain 113 peptides. Score 0.960 Round 3: 1107 peptides, 21 chains. Longest chain 113 peptides. Score 0.956 Round 4: 1104 peptides, 20 chains. Longest chain 113 peptides. Score 0.956 Round 5: 1106 peptides, 19 chains. Longest chain 113 peptides. Score 0.957 Taking the results from Round 2 Chains 20, Residues 1091, Estimated correctness of the model 99.8 % 15 chains (1000 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 128 A and 131 A Built loop between residues 203 A and 206 A Built loop between residues 44 C and 47 C Built loop between residues 112 B and 117 B Built loop between residues 204 B and 207 B Built loop between residues 220 B and 225 B Built loop between residues 95 D and 99 D Built loop between residues 202 D and 206 D Built loop between residues 269 D and 272 D 10 chains (1114 residues) following loop building 6 chains (1024 residues) in sequence following loop building ------------------------------------------------------ 70128 reflections ( 99.92 % complete ) and 10578 restraints for refining 10339 atoms. 2139 conditional restraints added. Observations/parameters ratio is 1.70 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2284 (Rfree = 0.000) for 10339 atoms. Found 240 (240 requested) and removed 158 (154 requested) atoms. Cycle 32: After refmac, R = 0.2188 (Rfree = 0.000) for 10407 atoms. Found 206 (236 requested) and removed 48 (155 requested) atoms. Cycle 33: After refmac, R = 0.2127 (Rfree = 0.000) for 10555 atoms. Found 150 (239 requested) and removed 50 (157 requested) atoms. Cycle 34: After refmac, R = 0.2076 (Rfree = 0.000) for 10640 atoms. Found 121 (241 requested) and removed 51 (158 requested) atoms. Cycle 35: After refmac, R = 0.2034 (Rfree = 0.000) for 10705 atoms. Found 105 (242 requested) and removed 40 (159 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.94 1.99 NCS extension: 17 residues added (100 deleted due to clashes), 10789 seeds are put forward Round 1: 1109 peptides, 15 chains. Longest chain 114 peptides. Score 0.962 Round 2: 1109 peptides, 17 chains. Longest chain 175 peptides. Score 0.960 Round 3: 1098 peptides, 23 chains. Longest chain 113 peptides. Score 0.952 Round 4: 1108 peptides, 16 chains. Longest chain 113 peptides. Score 0.961 Round 5: 1104 peptides, 22 chains. Longest chain 204 peptides. Score 0.954 Taking the results from Round 1 Chains 15, Residues 1094, Estimated correctness of the model 99.8 % 15 chains (1094 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 114 A and 117 A Built loop between residues 95 C and 99 C Built loop between residues 203 C and 206 C Built loop between residues 111 B and 117 B Built loop between residues 112 D and 117 D Built loop between residues 203 D and 206 D Built loop between residues 254 D and 257 D 8 chains (1114 residues) following loop building 8 chains (1114 residues) in sequence following loop building ------------------------------------------------------ 70128 reflections ( 99.92 % complete ) and 10008 restraints for refining 10463 atoms. 1215 conditional restraints added. Observations/parameters ratio is 1.68 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2235 (Rfree = 0.000) for 10463 atoms. Found 236 (236 requested) and removed 157 (155 requested) atoms. Cycle 37: After refmac, R = 0.2150 (Rfree = 0.000) for 10529 atoms. Found 189 (232 requested) and removed 42 (157 requested) atoms. Cycle 38: After refmac, R = 0.2090 (Rfree = 0.000) for 10661 atoms. Found 121 (235 requested) and removed 46 (159 requested) atoms. Cycle 39: After refmac, R = 0.2046 (Rfree = 0.000) for 10726 atoms. Found 133 (237 requested) and removed 48 (160 requested) atoms. Cycle 40: After refmac, R = 0.2006 (Rfree = 0.000) for 10800 atoms. Found 126 (238 requested) and removed 60 (161 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.94 1.99 NCS extension: 40 residues added (355 deleted due to clashes), 10906 seeds are put forward Round 1: 1106 peptides, 18 chains. Longest chain 114 peptides. Score 0.958 Round 2: 1108 peptides, 19 chains. Longest chain 106 peptides. Score 0.958 Round 3: 1102 peptides, 22 chains. Longest chain 113 peptides. Score 0.954 Round 4: 1103 peptides, 22 chains. Longest chain 111 peptides. Score 0.954 Round 5: 1107 peptides, 20 chains. Longest chain 113 peptides. Score 0.957 Taking the results from Round 2 Chains 20, Residues 1089, Estimated correctness of the model 99.7 % 15 chains (968 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 82 A and 85 A Built loop between residues 112 A and 117 A Built loop between residues 33 C and 36 C Built loop between residues 111 C and 117 C Built loop between residues 33 B and 36 B Built loop between residues 114 B and 117 B Built loop between residues 269 B and 272 B Built loop between residues 96 D and 99 D Built loop between residues 202 D and 207 D 10 chains (1113 residues) following loop building 6 chains (993 residues) in sequence following loop building ------------------------------------------------------ 70128 reflections ( 99.92 % complete ) and 11062 restraints for refining 10487 atoms. 2763 conditional restraints added. Observations/parameters ratio is 1.67 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2129 (Rfree = 0.000) for 10487 atoms. Found 231 (231 requested) and removed 146 (156 requested) atoms. Cycle 42: After refmac, R = 0.2013 (Rfree = 0.000) for 10548 atoms. Found 208 (227 requested) and removed 38 (157 requested) atoms. Cycle 43: After refmac, R = 0.1986 (Rfree = 0.000) for 10706 atoms. Found 147 (230 requested) and removed 64 (159 requested) atoms. Cycle 44: After refmac, R = 0.1962 (Rfree = 0.000) for 10782 atoms. Found 134 (231 requested) and removed 52 (160 requested) atoms. Cycle 45: After refmac, R = 0.1927 (Rfree = 0.000) for 10858 atoms. Found 123 (233 requested) and removed 65 (161 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.93 1.98 NCS extension: 55 residues added (227 deleted due to clashes), 10974 seeds are put forward Round 1: 1097 peptides, 20 chains. Longest chain 109 peptides. Score 0.955 Round 2: 1107 peptides, 17 chains. Longest chain 109 peptides. Score 0.960 Round 3: 1102 peptides, 23 chains. Longest chain 111 peptides. Score 0.953 Round 4: 1108 peptides, 17 chains. Longest chain 113 peptides. Score 0.960 Round 5: 1106 peptides, 19 chains. Longest chain 113 peptides. Score 0.957 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 18, Residues 1091, Estimated correctness of the model 99.8 % 16 chains (1080 residues) have been docked in sequence Sequence coverage is 98 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 113 A and 117 A Built loop between residues 204 A and 210 A Built loop between residues 29 C and 32 C Built loop between residues 44 C and 47 C Built loop between residues 111 C and 117 C Built loop between residues 254 C and 257 C Built loop between residues 113 B and 117 B Built loop between residues 204 B and 207 B Built loop between residues 235 B and 238 B Built loop between residues 94 D and 98 D Built loop between residues 203 D and 206 D 8 chains (1121 residues) following loop building 5 chains (1111 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 70128 reflections ( 99.92 % complete ) and 8805 restraints for refining 8663 atoms. Observations/parameters ratio is 2.02 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2744 (Rfree = 0.000) for 8663 atoms. Found 151 (181 requested) and removed 0 (181 requested) atoms. Cycle 47: After refmac, R = 0.2550 (Rfree = 0.000) for 8663 atoms. Found 57 (183 requested) and removed 1 (131 requested) atoms. Cycle 48: After refmac, R = 0.2490 (Rfree = 0.000) for 8663 atoms. Found 31 (185 requested) and removed 3 (132 requested) atoms. Cycle 49: After refmac, R = 0.2444 (Rfree = 0.000) for 8663 atoms. Found 19 (185 requested) and removed 0 (132 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 09:39:47 GMT 2018 Job finished. TimeTaking 129.39 Used memory is bytes: 14861840