null Mon 24 Dec 00:46:13 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 2hx1-2.1-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2hx1-2.1-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2hx1-2.1-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2hx1-2.1-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/2hx1-2.1-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2hx1-2.1-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 00:46:18 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/2hx1-2.1-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2hx1-2.1-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 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-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: 65.624 119.462 151.274 90.000 90.000 90.000 Input sequence file: 2hx1-2.1-parrot-mrncs.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 10085 atoms. Observations/parameters ratio is 1.74 ------------------------------------------------------ Starting model: R = 0.3473 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2938 (Rfree = 0.000) for 10085 atoms. Found 300 (300 requested) and removed 161 (150 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.99 2.04 NCS extension: 0 residues added, 10224 seeds are put forward Round 1: 853 peptides, 101 chains. Longest chain 27 peptides. Score 0.702 Round 2: 978 peptides, 61 chains. Longest chain 51 peptides. Score 0.871 Round 3: 1021 peptides, 45 chains. Longest chain 91 peptides. Score 0.910 Round 4: 1060 peptides, 32 chains. Longest chain 92 peptides. Score 0.936 Round 5: 1077 peptides, 26 chains. Longest chain 91 peptides. Score 0.946 Taking the results from Round 5 Chains 28, Residues 1051, Estimated correctness of the model 99.6 % 20 chains (930 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 38 C and 41 C Built loop between residues 93 C and 96 C Built loop between residues 112 C and 118 C Built loop between residues 160 C and 163 C Built loop between residues 195 C and 206 C Built loop between residues 254 C and 257 C Built loop between residues 20 B and 23 B Built loop between residues 201 B and 207 B Built loop between residues 219 B and 222 B Built loop between residues 93 D and 99 D Built loop between residues 145 D and 151 D Built loop between residues 220 D and 223 D Built loop between residues 238 D and 243 D 12 chains (1092 residues) following loop building 7 chains (978 residues) in sequence following loop building ------------------------------------------------------ 70128 reflections ( 99.92 % complete ) and 10422 restraints for refining 9645 atoms. 2286 conditional restraints added. Observations/parameters ratio is 1.82 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3084 (Rfree = 0.000) for 9645 atoms. Found 287 (287 requested) and removed 161 (143 requested) atoms. Cycle 2: After refmac, R = 0.2872 (Rfree = 0.000) for 9738 atoms. Found 190 (285 requested) and removed 145 (145 requested) atoms. Cycle 3: After refmac, R = 0.2751 (Rfree = 0.000) for 9751 atoms. Found 192 (279 requested) and removed 54 (145 requested) atoms. Cycle 4: After refmac, R = 0.2664 (Rfree = 0.000) for 9865 atoms. Found 129 (282 requested) and removed 43 (147 requested) atoms. Cycle 5: After refmac, R = 0.2589 (Rfree = 0.000) for 9927 atoms. Found 115 (284 requested) and removed 20 (148 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.95 2.00 NCS extension: 25 residues added (108 deleted due to clashes), 10066 seeds are put forward Round 1: 1085 peptides, 23 chains. Longest chain 111 peptides. Score 0.950 Round 2: 1102 peptides, 19 chains. Longest chain 111 peptides. Score 0.957 Round 3: 1097 peptides, 20 chains. Longest chain 132 peptides. Score 0.955 Round 4: 1097 peptides, 25 chains. Longest chain 99 peptides. Score 0.950 Round 5: 1095 peptides, 24 chains. Longest chain 113 peptides. Score 0.951 Taking the results from Round 2 Chains 21, Residues 1083, Estimated correctness of the model 99.7 % 15 chains (1027 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 112 A and 117 A Built loop between residues 64 C and 68 C Built loop between residues 204 C and 207 C Built loop between residues 218 C and 225 C Built loop between residues 31 B and 34 B Built loop between residues 112 B and 117 B Built loop between residues 94 D and 98 D Built loop between residues 197 D and 207 D 11 chains (1112 residues) following loop building 7 chains (1060 residues) in sequence following loop building ------------------------------------------------------ 70128 reflections ( 99.92 % complete ) and 10125 restraints for refining 9986 atoms. 1582 conditional restraints added. Observations/parameters ratio is 1.76 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2693 (Rfree = 0.000) for 9986 atoms. Found 249 (285 requested) and removed 157 (148 requested) atoms. Cycle 7: After refmac, R = 0.2561 (Rfree = 0.000) for 10063 atoms. Found 170 (282 requested) and removed 91 (150 requested) atoms. Cycle 8: After refmac, R = 0.2474 (Rfree = 0.000) for 10127 atoms. Found 123 (278 requested) and removed 35 (151 requested) atoms. Cycle 9: After refmac, R = 0.2386 (Rfree = 0.000) for 10206 atoms. Found 105 (280 requested) and removed 27 (152 requested) atoms. Cycle 10: After refmac, R = 0.2320 (Rfree = 0.000) for 10267 atoms. Found 117 (282 requested) and removed 24 (153 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.95 2.00 NCS extension: 39 residues added (273 deleted due to clashes), 10408 seeds are put forward Round 1: 1094 peptides, 21 chains. Longest chain 111 peptides. Score 0.954 Round 2: 1102 peptides, 15 chains. Longest chain 194 peptides. Score 0.961 Round 3: 1098 peptides, 24 chains. Longest chain 205 peptides. Score 0.951 Round 4: 1098 peptides, 21 chains. Longest chain 129 peptides. Score 0.954 Round 5: 1093 peptides, 26 chains. Longest chain 94 peptides. Score 0.948 Taking the results from Round 2 Chains 16, Residues 1087, Estimated correctness of the model 99.8 % 12 chains (984 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 112 A and 117 A Built loop between residues 131 A and 134 A Built loop between residues 202 A and 207 A Built loop between residues 29 C and 36 C Built loop between residues 113 C and 117 C Built loop between residues 95 D and 99 D Built loop between residues 197 D and 207 D 7 chains (1113 residues) following loop building 5 chains (1015 residues) in sequence following loop building ------------------------------------------------------ 70128 reflections ( 99.92 % complete ) and 10720 restraints for refining 10200 atoms. 2358 conditional restraints added. Observations/parameters ratio is 1.72 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2511 (Rfree = 0.000) for 10200 atoms. Found 224 (280 requested) and removed 167 (152 requested) atoms. Cycle 12: After refmac, R = 0.2412 (Rfree = 0.000) for 10238 atoms. Found 181 (274 requested) and removed 55 (152 requested) atoms. Cycle 13: After refmac, R = 0.2331 (Rfree = 0.000) for 10358 atoms. Found 126 (277 requested) and removed 45 (154 requested) atoms. Cycle 14: After refmac, R = 0.2271 (Rfree = 0.000) for 10422 atoms. Found 121 (280 requested) and removed 41 (155 requested) atoms. Cycle 15: After refmac, R = 0.2224 (Rfree = 0.000) for 10492 atoms. Found 107 (282 requested) and removed 38 (156 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.94 1.99 NCS extension: 12 residues added (116 deleted due to clashes), 10583 seeds are put forward Round 1: 1100 peptides, 18 chains. Longest chain 204 peptides. Score 0.958 Round 2: 1105 peptides, 16 chains. Longest chain 204 peptides. Score 0.960 Round 3: 1106 peptides, 18 chains. Longest chain 170 peptides. Score 0.958 Round 4: 1107 peptides, 19 chains. Longest chain 129 peptides. Score 0.958 Round 5: 1100 peptides, 22 chains. Longest chain 144 peptides. Score 0.954 Taking the results from Round 2 Chains 17, Residues 1089, Estimated correctness of the model 99.8 % 14 chains (1071 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 197 A and 200 A Built loop between residues 231 A and 234 A Built loop between residues 253 A and 256 A Built loop between residues 28 C and 31 C Built loop between residues 204 C and 207 C Built loop between residues 113 B and 117 B Built loop between residues 204 B and 207 B Built loop between residues 215 B and 221 B Built loop between residues 200 D and 207 D 7 chains (1111 residues) following loop building 5 chains (1097 residues) in sequence following loop building ------------------------------------------------------ 70128 reflections ( 99.92 % complete ) and 10188 restraints for refining 10381 atoms. 1485 conditional restraints added. Observations/parameters ratio is 1.69 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2419 (Rfree = 0.000) for 10381 atoms. Found 233 (278 requested) and removed 167 (154 requested) atoms. Cycle 17: After refmac, R = 0.2325 (Rfree = 0.000) for 10435 atoms. Found 144 (274 requested) and removed 58 (155 requested) atoms. Cycle 18: After refmac, R = 0.2258 (Rfree = 0.000) for 10504 atoms. Found 121 (275 requested) and removed 26 (156 requested) atoms. Cycle 19: After refmac, R = 0.2208 (Rfree = 0.000) for 10587 atoms. Found 100 (277 requested) and removed 34 (157 requested) atoms. Cycle 20: After refmac, R = 0.2168 (Rfree = 0.000) for 10635 atoms. Found 98 (279 requested) and removed 28 (158 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.95 2.00 NCS extension: 12 residues added (165 deleted due to clashes), 10724 seeds are put forward Round 1: 1101 peptides, 20 chains. Longest chain 204 peptides. Score 0.956 Round 2: 1108 peptides, 13 chains. Longest chain 178 peptides. Score 0.964 Round 3: 1097 peptides, 24 chains. Longest chain 172 peptides. Score 0.951 Round 4: 1106 peptides, 18 chains. Longest chain 211 peptides. Score 0.958 Round 5: 1100 peptides, 22 chains. Longest chain 203 peptides. Score 0.954 Taking the results from Round 2 Chains 14, Residues 1095, Estimated correctness of the model 99.8 % 13 chains (1092 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 81 A and 85 A Built loop between residues 138 A and 142 A Built loop between residues 25 C and 28 C Built loop between residues 201 C and 207 C Built loop between residues 113 B and 117 B Built loop between residues 204 B and 207 B Built loop between residues 216 B and 225 B Built loop between residues 129 D and 132 D Built loop between residues 203 D and 206 D 4 chains (1122 residues) following loop building 4 chains (1122 residues) in sequence following loop building ------------------------------------------------------ 70128 reflections ( 99.92 % complete ) and 9971 restraints for refining 10492 atoms. 1119 conditional restraints added. Observations/parameters ratio is 1.67 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2340 (Rfree = 0.000) for 10492 atoms. Found 273 (275 requested) and removed 168 (156 requested) atoms. Cycle 22: After refmac, R = 0.2259 (Rfree = 0.000) for 10586 atoms. Found 162 (271 requested) and removed 62 (157 requested) atoms. Cycle 23: After refmac, R = 0.2184 (Rfree = 0.000) for 10665 atoms. Found 131 (273 requested) and removed 32 (159 requested) atoms. Cycle 24: After refmac, R = 0.2129 (Rfree = 0.000) for 10749 atoms. Found 114 (275 requested) and removed 35 (160 requested) atoms. Cycle 25: After refmac, R = 0.2087 (Rfree = 0.000) for 10809 atoms. Found 119 (277 requested) and removed 41 (161 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.94 1.99 NCS extension: 16 residues added (111 deleted due to clashes), 10905 seeds are put forward Round 1: 1107 peptides, 18 chains. Longest chain 203 peptides. Score 0.959 Round 2: 1112 peptides, 15 chains. Longest chain 204 peptides. Score 0.962 Round 3: 1105 peptides, 23 chains. Longest chain 178 peptides. Score 0.953 Round 4: 1112 peptides, 14 chains. Longest chain 202 peptides. Score 0.963 Round 5: 1102 peptides, 25 chains. Longest chain 123 peptides. Score 0.951 Taking the results from Round 4 Chains 14, Residues 1098, Estimated correctness of the model 99.8 % 13 chains (1083 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 129 A and 132 A Built loop between residues 203 A and 206 A Built loop between residues 65 C and 69 C Built loop between residues 95 C and 99 C Built loop between residues 203 C and 206 C Built loop between residues 82 B and 85 B Built loop between residues 113 B and 117 B Built loop between residues 203 D and 207 D 6 chains (1118 residues) following loop building 5 chains (1103 residues) in sequence following loop building ------------------------------------------------------ 70128 reflections ( 99.92 % complete ) and 10108 restraints for refining 10520 atoms. 1365 conditional restraints added. Observations/parameters ratio is 1.67 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2313 (Rfree = 0.000) for 10520 atoms. Found 269 (269 requested) and removed 154 (156 requested) atoms. Cycle 27: After refmac, R = 0.2207 (Rfree = 0.000) for 10621 atoms. Found 170 (266 requested) and removed 51 (158 requested) atoms. Cycle 28: After refmac, R = 0.2076 (Rfree = 0.000) for 10729 atoms. Found 137 (269 requested) and removed 28 (160 requested) atoms. Cycle 29: After refmac, R = 0.2014 (Rfree = 0.000) for 10806 atoms. Found 154 (271 requested) and removed 50 (161 requested) atoms. Cycle 30: After refmac, R = 0.1961 (Rfree = 0.000) for 10880 atoms. Found 141 (273 requested) and removed 65 (162 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.93 1.98 NCS extension: 76 residues added (205 deleted due to clashes), 11034 seeds are put forward Round 1: 1107 peptides, 18 chains. Longest chain 114 peptides. Score 0.959 Round 2: 1108 peptides, 15 chains. Longest chain 199 peptides. Score 0.962 Round 3: 1103 peptides, 19 chains. Longest chain 204 peptides. Score 0.957 Round 4: 1104 peptides, 20 chains. Longest chain 122 peptides. Score 0.956 Round 5: 1104 peptides, 18 chains. Longest chain 204 peptides. Score 0.958 Taking the results from Round 2 Chains 17, Residues 1093, Estimated correctness of the model 99.8 % 14 chains (1081 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 114 A and 117 A Built loop between residues 200 A and 207 A Built loop between residues 82 C and 85 C Built loop between residues 81 B and 84 B Built loop between residues 113 B and 117 B Built loop between residues 204 B and 207 B Built loop between residues 216 B and 225 B Built loop between residues 254 B and 257 B Built loop between residues 112 D and 115 D Built loop between residues 203 D and 207 D 5 chains (1120 residues) following loop building 4 chains (1113 residues) in sequence following loop building ------------------------------------------------------ 70128 reflections ( 99.92 % complete ) and 10088 restraints for refining 10610 atoms. 1284 conditional restraints added. Observations/parameters ratio is 1.65 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2154 (Rfree = 0.000) for 10610 atoms. Found 265 (265 requested) and removed 170 (158 requested) atoms. Cycle 32: After refmac, R = 0.2116 (Rfree = 0.000) for 10668 atoms. Found 211 (262 requested) and removed 65 (159 requested) atoms. Cycle 33: After refmac, R = 0.2084 (Rfree = 0.000) for 10801 atoms. Found 177 (264 requested) and removed 59 (161 requested) atoms. Cycle 34: After refmac, R = 0.2037 (Rfree = 0.000) for 10913 atoms. Found 147 (266 requested) and removed 54 (162 requested) atoms. Cycle 35: After refmac, R = 0.2004 (Rfree = 0.000) for 10995 atoms. Found 141 (269 requested) and removed 69 (164 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.93 1.98 NCS extension: 19 residues added (109 deleted due to clashes), 11088 seeds are put forward Round 1: 1104 peptides, 18 chains. Longest chain 113 peptides. Score 0.958 Round 2: 1110 peptides, 14 chains. Longest chain 204 peptides. Score 0.963 Round 3: 1100 peptides, 26 chains. Longest chain 105 peptides. Score 0.949 Round 4: 1105 peptides, 20 chains. Longest chain 204 peptides. Score 0.956 Round 5: 1103 peptides, 21 chains. Longest chain 194 peptides. Score 0.955 Taking the results from Round 2 Chains 15, Residues 1096, Estimated correctness of the model 99.8 % 13 chains (1080 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 33 C and 36 C Built loop between residues 113 C and 117 C Built loop between residues 203 C and 207 C Built loop between residues 113 B and 117 B Built loop between residues 204 B and 207 B Built loop between residues 218 B and 224 B Built loop between residues 244 B and 247 B Built loop between residues 200 D and 207 D 6 chains (1118 residues) following loop building 5 chains (1106 residues) in sequence following loop building ------------------------------------------------------ 70128 reflections ( 99.92 % complete ) and 10240 restraints for refining 10648 atoms. 1460 conditional restraints added. Observations/parameters ratio is 1.65 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2143 (Rfree = 0.000) for 10648 atoms. Found 260 (260 requested) and removed 171 (158 requested) atoms. Cycle 37: After refmac, R = 0.2113 (Rfree = 0.000) for 10709 atoms. Found 240 (256 requested) and removed 68 (160 requested) atoms. Cycle 38: After refmac, R = 0.2067 (Rfree = 0.000) for 10874 atoms. Found 138 (259 requested) and removed 77 (162 requested) atoms. Cycle 39: After refmac, R = 0.2020 (Rfree = 0.000) for 10926 atoms. Found 150 (253 requested) and removed 73 (162 requested) atoms. Cycle 40: After refmac, R = 0.1991 (Rfree = 0.000) for 10993 atoms. Found 144 (256 requested) and removed 76 (164 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.94 1.99 NCS extension: 41 residues added (255 deleted due to clashes), 11103 seeds are put forward Round 1: 1107 peptides, 18 chains. Longest chain 204 peptides. Score 0.959 Round 2: 1111 peptides, 14 chains. Longest chain 178 peptides. Score 0.963 Round 3: 1107 peptides, 19 chains. Longest chain 194 peptides. Score 0.958 Round 4: 1113 peptides, 14 chains. Longest chain 204 peptides. Score 0.963 Round 5: 1112 peptides, 16 chains. Longest chain 205 peptides. Score 0.961 Taking the results from Round 4 Chains 16, Residues 1099, Estimated correctness of the model 99.8 % 12 chains (1079 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 113 A and 117 A Built loop between residues 204 A and 209 A Built loop between residues 43 C and 47 C Built loop between residues 200 C and 207 C Built loop between residues 204 B and 207 B Built loop between residues 219 B and 222 B Built loop between residues 131 D and 134 D 7 chains (1116 residues) following loop building 5 chains (1101 residues) in sequence following loop building ------------------------------------------------------ 70128 reflections ( 99.92 % complete ) and 10276 restraints for refining 10633 atoms. 1538 conditional restraints added. Observations/parameters ratio is 1.65 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2144 (Rfree = 0.000) for 10633 atoms. Found 240 (240 requested) and removed 158 (158 requested) atoms. Cycle 42: After refmac, R = 0.2095 (Rfree = 0.000) for 10698 atoms. Found 225 (236 requested) and removed 54 (159 requested) atoms. Cycle 43: After refmac, R = 0.2052 (Rfree = 0.000) for 10862 atoms. Found 149 (240 requested) and removed 65 (162 requested) atoms. Cycle 44: After refmac, R = 0.2010 (Rfree = 0.000) for 10938 atoms. Found 128 (241 requested) and removed 66 (163 requested) atoms. Cycle 45: After refmac, R = 0.1979 (Rfree = 0.000) for 10988 atoms. Found 141 (235 requested) and removed 66 (163 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.94 1.99 NCS extension: 58 residues added (236 deleted due to clashes), 11122 seeds are put forward Round 1: 1106 peptides, 17 chains. Longest chain 113 peptides. Score 0.960 Round 2: 1112 peptides, 15 chains. Longest chain 202 peptides. Score 0.962 Round 3: 1112 peptides, 15 chains. Longest chain 204 peptides. Score 0.962 Round 4: 1108 peptides, 18 chains. Longest chain 204 peptides. Score 0.959 Round 5: 1103 peptides, 22 chains. Longest chain 105 peptides. Score 0.954 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 16, Residues 1097, Estimated correctness of the model 99.8 % 15 chains (1093 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 113 A and 117 A Built loop between residues 231 A and 234 A Built loop between residues 253 A and 256 A Built loop between residues 96 C and 99 C Built loop between residues 231 C and 236 C Built loop between residues 253 C and 256 C Built loop between residues 113 B and 117 B Built loop between residues 254 B and 257 B Built loop between residues 200 D and 207 D 6 chains (1119 residues) following loop building 6 chains (1119 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 70128 reflections ( 99.92 % complete ) and 8826 restraints for refining 8682 atoms. Observations/parameters ratio is 2.02 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2723 (Rfree = 0.000) for 8682 atoms. Found 150 (186 requested) and removed 0 (186 requested) atoms. Cycle 47: After refmac, R = 0.2514 (Rfree = 0.000) for 8682 atoms. Found 68 (189 requested) and removed 2 (131 requested) atoms. Cycle 48: After refmac, R = 0.2396 (Rfree = 0.000) for 8682 atoms. Found 25 (191 requested) and removed 4 (132 requested) atoms. Cycle 49: After refmac, R = 0.2364 (Rfree = 0.000) for 8682 atoms. Found 21 (191 requested) and removed 5 (132 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 03:12:47 GMT 2018 Job finished. TimeTaking 146.57 Used memory is bytes: 10102400