Mon 24 Dec 07:53:44 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 2ash-2.1-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2ash-2.1-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2ash-2.1-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ash-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/2ash-2.1-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ash-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 07:53:48 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/2ash-2.1-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ash-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 1373 and 0 Target number of residues in the AU: 1373 Target solvent content: 0.5773 Checking the provided sequence file Detected sequence length: 381 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1524 Adjusted target solvent content: 0.53 Input MTZ file: 2ash-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: 5 Cell parameters: 170.109 99.745 124.866 90.000 123.929 90.000 Input sequence file: 2ash-2.1-parrot-noncs.fasta_lf Building free atoms model in initial map for 12192 target number of atoms Had to go as low as 0.75 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: 103.605 2.100 Wilson plot Bfac: 44.02 100147 reflections ( 99.19 % complete ) and 0 restraints for refining 13619 atoms. Observations/parameters ratio is 1.84 ------------------------------------------------------ Starting model: R = 0.3892 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3412 (Rfree = 0.000) for 13619 atoms. Found 204 (405 requested) and removed 240 (202 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.54 2.44 NCS extension: 0 residues added, 13583 seeds are put forward Round 1: 759 peptides, 147 chains. Longest chain 13 peptides. Score 0.342 Round 2: 854 peptides, 128 chains. Longest chain 21 peptides. Score 0.497 Round 3: 915 peptides, 126 chains. Longest chain 20 peptides. Score 0.551 Round 4: 947 peptides, 108 chains. Longest chain 37 peptides. Score 0.629 Round 5: 986 peptides, 106 chains. Longest chain 41 peptides. Score 0.659 Taking the results from Round 5 Chains 115, Residues 880, Estimated correctness of the model 88.4 % 24 chains (315 residues) have been docked in sequence ------------------------------------------------------ 100147 reflections ( 99.19 % complete ) and 21722 restraints for refining 11725 atoms. 17077 conditional restraints added. Observations/parameters ratio is 2.14 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3621 (Rfree = 0.000) for 11725 atoms. Found 293 (349 requested) and removed 213 (174 requested) atoms. Cycle 2: After refmac, R = 0.3398 (Rfree = 0.000) for 11770 atoms. Found 197 (351 requested) and removed 180 (175 requested) atoms. Cycle 3: After refmac, R = 0.3264 (Rfree = 0.000) for 11702 atoms. Found 170 (351 requested) and removed 175 (175 requested) atoms. Cycle 4: After refmac, R = 0.3177 (Rfree = 0.000) for 11659 atoms. Found 148 (348 requested) and removed 175 (174 requested) atoms. Cycle 5: After refmac, R = 0.3151 (Rfree = 0.000) for 11601 atoms. Found 153 (346 requested) and removed 173 (173 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.49 2.39 NCS extension: 21 residues added (9 deleted due to clashes), 11628 seeds are put forward Round 1: 941 peptides, 111 chains. Longest chain 28 peptides. Score 0.616 Round 2: 1013 peptides, 107 chains. Longest chain 38 peptides. Score 0.672 Round 3: 1042 peptides, 103 chains. Longest chain 43 peptides. Score 0.699 Round 4: 1039 peptides, 96 chains. Longest chain 60 peptides. Score 0.715 Round 5: 1062 peptides, 95 chains. Longest chain 51 peptides. Score 0.729 Taking the results from Round 5 Chains 108, Residues 967, Estimated correctness of the model 92.4 % 21 chains (415 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 341 A and 347 A 107 chains (972 residues) following loop building 20 chains (420 residues) in sequence following loop building ------------------------------------------------------ 100147 reflections ( 99.19 % complete ) and 20294 restraints for refining 11726 atoms. 14844 conditional restraints added. Observations/parameters ratio is 2.14 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3372 (Rfree = 0.000) for 11726 atoms. Found 273 (349 requested) and removed 206 (174 requested) atoms. Cycle 7: After refmac, R = 0.3191 (Rfree = 0.000) for 11746 atoms. Found 224 (344 requested) and removed 180 (175 requested) atoms. Cycle 8: After refmac, R = 0.3048 (Rfree = 0.000) for 11749 atoms. Found 180 (337 requested) and removed 178 (175 requested) atoms. Cycle 9: After refmac, R = 0.2955 (Rfree = 0.000) for 11715 atoms. Found 156 (329 requested) and removed 177 (175 requested) atoms. Cycle 10: After refmac, R = 0.2896 (Rfree = 0.000) for 11663 atoms. Found 130 (320 requested) and removed 171 (174 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.47 2.37 NCS extension: 27 residues added (32 deleted due to clashes), 11673 seeds are put forward Round 1: 1064 peptides, 103 chains. Longest chain 41 peptides. Score 0.711 Round 2: 1116 peptides, 89 chains. Longest chain 75 peptides. Score 0.767 Round 3: 1117 peptides, 89 chains. Longest chain 44 peptides. Score 0.768 Round 4: 1132 peptides, 82 chains. Longest chain 62 peptides. Score 0.788 Round 5: 1113 peptides, 87 chains. Longest chain 44 peptides. Score 0.770 Taking the results from Round 4 Chains 90, Residues 1050, Estimated correctness of the model 95.2 % 26 chains (630 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 208 A and 214 A Built loop between residues 339 C and 343 C 88 chains (1057 residues) following loop building 24 chains (638 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 100147 reflections ( 99.19 % complete ) and 17458 restraints for refining 11725 atoms. 10815 conditional restraints added. Observations/parameters ratio is 2.14 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3227 (Rfree = 0.000) for 11725 atoms. Found 280 (314 requested) and removed 198 (174 requested) atoms. Cycle 12: After refmac, R = 0.2998 (Rfree = 0.000) for 11775 atoms. Found 205 (309 requested) and removed 175 (175 requested) atoms. Cycle 13: After refmac, R = 0.2867 (Rfree = 0.000) for 11784 atoms. Found 178 (302 requested) and removed 119 (175 requested) atoms. Cycle 14: After refmac, R = 0.2786 (Rfree = 0.000) for 11827 atoms. Found 146 (296 requested) and removed 82 (176 requested) atoms. Failed to save intermediate PDB Cycle 15: After refmac, R = 0.2725 (Rfree = 0.000) for 11867 atoms. Found 136 (290 requested) and removed 72 (177 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.46 2.36 NCS extension: 14 residues added (14 deleted due to clashes), 11965 seeds are put forward Round 1: 1062 peptides, 86 chains. Longest chain 46 peptides. Score 0.750 Round 2: 1135 peptides, 72 chains. Longest chain 74 peptides. Score 0.809 Round 3: 1135 peptides, 74 chains. Longest chain 71 peptides. Score 0.805 Round 4: 1133 peptides, 75 chains. Longest chain 94 peptides. Score 0.802 Round 5: 1145 peptides, 81 chains. Longest chain 72 peptides. Score 0.795 Taking the results from Round 2 Chains 82, Residues 1063, Estimated correctness of the model 96.0 % 27 chains (720 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 76 A and 79 A Built loop between residues 260 A and 266 A Built loop between residues 308 C and 315 C Built loop between residues 54 B and 57 B Built loop between residues 75 B and 79 B Built loop between residues 157 B and 163 B Built loop between residues 324 B and 328 B 71 chains (1080 residues) following loop building 20 chains (746 residues) in sequence following loop building ------------------------------------------------------ 100147 reflections ( 99.19 % complete ) and 16575 restraints for refining 11843 atoms. 9275 conditional restraints added. Observations/parameters ratio is 2.11 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2960 (Rfree = 0.000) for 11843 atoms. Found 231 (282 requested) and removed 188 (176 requested) atoms. Cycle 17: After refmac, R = 0.2791 (Rfree = 0.000) for 11857 atoms. Found 177 (276 requested) and removed 149 (177 requested) atoms. Cycle 18: After refmac, R = 0.2692 (Rfree = 0.000) for 11867 atoms. Found 152 (269 requested) and removed 79 (177 requested) atoms. Cycle 19: After refmac, R = 0.2631 (Rfree = 0.000) for 11931 atoms. Found 128 (263 requested) and removed 76 (177 requested) atoms. Cycle 20: After refmac, R = 0.2587 (Rfree = 0.000) for 11972 atoms. Found 100 (257 requested) and removed 60 (178 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.45 2.35 NCS extension: 20 residues added (73 deleted due to clashes), 12051 seeds are put forward Round 1: 1119 peptides, 77 chains. Longest chain 114 peptides. Score 0.793 Round 2: 1168 peptides, 64 chains. Longest chain 97 peptides. Score 0.834 Round 3: 1166 peptides, 63 chains. Longest chain 88 peptides. Score 0.835 Round 4: 1160 peptides, 66 chains. Longest chain 86 peptides. Score 0.828 Round 5: 1153 peptides, 64 chains. Longest chain 81 peptides. Score 0.829 Taking the results from Round 3 Chains 71, Residues 1103, Estimated correctness of the model 96.9 % 28 chains (803 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 253 C and 258 C Built loop between residues 115 B and 118 B Built loop between residues 213 B and 216 B Built loop between residues 251 B and 258 B Built loop between residues 272 B and 275 B Built loop between residues 290 B and 293 B 63 chains (1117 residues) following loop building 22 chains (821 residues) in sequence following loop building ------------------------------------------------------ 100147 reflections ( 99.19 % complete ) and 15937 restraints for refining 11897 atoms. 8182 conditional restraints added. Observations/parameters ratio is 2.10 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2888 (Rfree = 0.000) for 11897 atoms. Found 248 (248 requested) and removed 196 (177 requested) atoms. Cycle 22: After refmac, R = 0.2687 (Rfree = 0.000) for 11924 atoms. Found 207 (242 requested) and removed 148 (178 requested) atoms. Cycle 23: After refmac, R = 0.2579 (Rfree = 0.000) for 11966 atoms. Found 150 (236 requested) and removed 65 (178 requested) atoms. Cycle 24: After refmac, R = 0.2506 (Rfree = 0.000) for 12034 atoms. Found 106 (237 requested) and removed 77 (179 requested) atoms. Cycle 25: After refmac, R = 0.2468 (Rfree = 0.000) for 12045 atoms. Found 110 (230 requested) and removed 60 (179 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.45 2.35 NCS extension: 109 residues added (70 deleted due to clashes), 12215 seeds are put forward Round 1: 1189 peptides, 64 chains. Longest chain 117 peptides. Score 0.841 Round 2: 1224 peptides, 57 chains. Longest chain 117 peptides. Score 0.862 Round 3: 1203 peptides, 60 chains. Longest chain 105 peptides. Score 0.851 Round 4: 1203 peptides, 60 chains. Longest chain 115 peptides. Score 0.851 Round 5: 1209 peptides, 64 chains. Longest chain 73 peptides. Score 0.847 Taking the results from Round 2 Chains 62, Residues 1167, Estimated correctness of the model 97.8 % 20 chains (880 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 46 A and 49 A Built loop between residues 75 A and 78 A Built loop between residues 158 A and 162 A Built loop between residues 254 A and 257 A Built loop between residues 74 C and 78 C Built loop between residues 75 B and 78 B Built loop between residues 195 B and 198 B 55 chains (1183 residues) following loop building 13 chains (896 residues) in sequence following loop building ------------------------------------------------------ 100147 reflections ( 99.19 % complete ) and 15093 restraints for refining 11900 atoms. 6791 conditional restraints added. Observations/parameters ratio is 2.10 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2733 (Rfree = 0.000) for 11900 atoms. Found 219 (219 requested) and removed 189 (177 requested) atoms. Cycle 27: After refmac, R = 0.2560 (Rfree = 0.000) for 11909 atoms. Found 183 (213 requested) and removed 119 (177 requested) atoms. Cycle 28: After refmac, R = 0.2476 (Rfree = 0.000) for 11965 atoms. Found 131 (206 requested) and removed 90 (178 requested) atoms. Cycle 29: After refmac, R = 0.2422 (Rfree = 0.000) for 11996 atoms. Found 153 (200 requested) and removed 107 (178 requested) atoms. Cycle 30: After refmac, R = 0.2385 (Rfree = 0.000) for 12033 atoms. Found 154 (193 requested) and removed 90 (179 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.45 2.35 NCS extension: 15 residues added (20 deleted due to clashes), 12119 seeds are put forward Round 1: 1194 peptides, 63 chains. Longest chain 106 peptides. Score 0.844 Round 2: 1236 peptides, 44 chains. Longest chain 121 peptides. Score 0.884 Round 3: 1237 peptides, 48 chains. Longest chain 155 peptides. Score 0.878 Round 4: 1235 peptides, 52 chains. Longest chain 95 peptides. Score 0.872 Round 5: 1219 peptides, 52 chains. Longest chain 112 peptides. Score 0.868 Taking the results from Round 2 Chains 48, Residues 1192, Estimated correctness of the model 98.4 % 22 chains (1008 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 158 A and 162 A Built loop between residues 74 C and 79 C Built loop between residues 54 B and 57 B Built loop between residues 157 B and 161 B Built loop between residues 253 B and 256 B Built loop between residues 205 D and 215 D 40 chains (1212 residues) following loop building 16 chains (1031 residues) in sequence following loop building ------------------------------------------------------ 100147 reflections ( 99.19 % complete ) and 14211 restraints for refining 11969 atoms. 5223 conditional restraints added. Observations/parameters ratio is 2.09 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2679 (Rfree = 0.000) for 11969 atoms. Found 185 (185 requested) and removed 195 (178 requested) atoms. Cycle 32: After refmac, R = 0.2510 (Rfree = 0.000) for 11929 atoms. Found 178 (178 requested) and removed 166 (178 requested) atoms. Cycle 33: After refmac, R = 0.2425 (Rfree = 0.000) for 11928 atoms. Found 177 (177 requested) and removed 86 (177 requested) atoms. Cycle 34: After refmac, R = 0.2373 (Rfree = 0.000) for 12010 atoms. Found 179 (179 requested) and removed 98 (179 requested) atoms. Cycle 35: After refmac, R = 0.2333 (Rfree = 0.000) for 12081 atoms. Found 162 (180 requested) and removed 107 (180 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.45 2.35 NCS extension: 88 residues added (102 deleted due to clashes), 12237 seeds are put forward Round 1: 1203 peptides, 52 chains. Longest chain 101 peptides. Score 0.864 Round 2: 1248 peptides, 45 chains. Longest chain 158 peptides. Score 0.885 Round 3: 1239 peptides, 51 chains. Longest chain 144 peptides. Score 0.874 Round 4: 1221 peptides, 59 chains. Longest chain 94 peptides. Score 0.858 Round 5: 1234 peptides, 57 chains. Longest chain 103 peptides. Score 0.864 Taking the results from Round 2 Chains 50, Residues 1203, Estimated correctness of the model 98.4 % 25 chains (1003 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 50 A and 53 A Built loop between residues 75 A and 78 A Built loop between residues 187 A and 190 A Built loop between residues 208 A and 212 A Built loop between residues 225 A and 230 A Built loop between residues 76 C and 79 C Built loop between residues 159 C and 163 C Built loop between residues 341 C and 344 C Built loop between residues 75 B and 78 B 40 chains (1224 residues) following loop building 16 chains (1025 residues) in sequence following loop building ------------------------------------------------------ 100147 reflections ( 99.19 % complete ) and 14202 restraints for refining 11941 atoms. 5206 conditional restraints added. Observations/parameters ratio is 2.10 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2675 (Rfree = 0.000) for 11941 atoms. Found 177 (177 requested) and removed 197 (177 requested) atoms. Cycle 37: After refmac, R = 0.2483 (Rfree = 0.000) for 11900 atoms. Found 177 (177 requested) and removed 165 (177 requested) atoms. Cycle 38: After refmac, R = 0.2385 (Rfree = 0.000) for 11900 atoms. Found 177 (177 requested) and removed 79 (177 requested) atoms. Cycle 39: After refmac, R = 0.2327 (Rfree = 0.000) for 11987 atoms. Found 145 (178 requested) and removed 90 (178 requested) atoms. Cycle 40: After refmac, R = 0.2284 (Rfree = 0.000) for 12033 atoms. Found 147 (179 requested) and removed 89 (179 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.44 2.34 NCS extension: 13 residues added (24 deleted due to clashes), 12119 seeds are put forward Round 1: 1216 peptides, 54 chains. Longest chain 129 peptides. Score 0.864 Round 2: 1232 peptides, 44 chains. Longest chain 117 peptides. Score 0.883 Round 3: 1230 peptides, 54 chains. Longest chain 142 peptides. Score 0.868 Round 4: 1235 peptides, 54 chains. Longest chain 204 peptides. Score 0.869 Round 5: 1240 peptides, 48 chains. Longest chain 119 peptides. Score 0.879 Taking the results from Round 2 Chains 50, Residues 1188, Estimated correctness of the model 98.4 % 26 chains (1035 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 31 A and 35 A Built loop between residues 72 A and 80 A Built loop between residues 158 A and 163 A Built loop between residues 223 A and 232 A Built loop between residues 341 A and 344 A Built loop between residues 75 B and 78 B Built loop between residues 207 B and 210 B 40 chains (1210 residues) following loop building 19 chains (1063 residues) in sequence following loop building ------------------------------------------------------ 100147 reflections ( 99.19 % complete ) and 14131 restraints for refining 11987 atoms. 4926 conditional restraints added. Observations/parameters ratio is 2.09 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2595 (Rfree = 0.000) for 11987 atoms. Found 178 (178 requested) and removed 192 (178 requested) atoms. Cycle 42: After refmac, R = 0.2411 (Rfree = 0.000) for 11957 atoms. Found 178 (178 requested) and removed 158 (178 requested) atoms. Cycle 43: After refmac, R = 0.2316 (Rfree = 0.000) for 11964 atoms. Found 178 (178 requested) and removed 106 (178 requested) atoms. Cycle 44: After refmac, R = 0.2263 (Rfree = 0.000) for 12030 atoms. Found 179 (179 requested) and removed 103 (179 requested) atoms. Cycle 45: After refmac, R = 0.2221 (Rfree = 0.000) for 12097 atoms. Found 180 (180 requested) and removed 118 (180 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.44 2.34 NCS extension: 66 residues added (80 deleted due to clashes), 12228 seeds are put forward Round 1: 1226 peptides, 48 chains. Longest chain 129 peptides. Score 0.876 Round 2: 1242 peptides, 45 chains. Longest chain 141 peptides. Score 0.884 Round 3: 1241 peptides, 46 chains. Longest chain 144 peptides. Score 0.882 Round 4: 1248 peptides, 49 chains. Longest chain 100 peptides. Score 0.879 Round 5: 1237 peptides, 55 chains. Longest chain 102 peptides. Score 0.868 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 50, Residues 1197, Estimated correctness of the model 98.4 % 28 chains (1078 residues) have been docked in sequence Sequence coverage is 89 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 31 A and 40 A Built loop between residues 70 A and 78 A Built loop between residues 157 A and 161 A Built loop between residues 183 A and 186 A Built loop between residues 201 A and 205 A Built loop between residues 253 A and 256 A Built loop between residues 37 C and 40 C Built loop between residues 84 C and 88 C Built loop between residues 104 C and 116 C Built loop between residues 158 C and 161 C Built loop between residues 253 C and 266 C Built loop between residues 37 B and 40 B Built loop between residues 53 B and 56 B Built loop between residues 73 B and 78 B Built loop between residues 183 B and 186 B Built loop between residues 226 B and 233 B Built loop between residues 47 D and 50 D Built loop between residues 177 D and 190 D Built loop between residues 205 D and 218 D 25 chains (1277 residues) following loop building 9 chains (1175 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 100147 reflections ( 99.19 % complete ) and 9867 restraints for refining 9690 atoms. Observations/parameters ratio is 2.58 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3380 (Rfree = 0.000) for 9690 atoms. Found 87 (144 requested) and removed 0 (144 requested) atoms. Cycle 47: After refmac, R = 0.3176 (Rfree = 0.000) for 9690 atoms. Found 55 (145 requested) and removed 0 (145 requested) atoms. Cycle 48: After refmac, R = 0.3040 (Rfree = 0.000) for 9690 atoms. Found 40 (146 requested) and removed 9 (146 requested) atoms. Cycle 49: After refmac, R = 0.2965 (Rfree = 0.000) for 9690 atoms. TimeTaking 153.43