Sun 23 Dec 22:23:02 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 2prr-1.9-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2prr-1.9-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2prr-1.9-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2prr-1.9-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/2prr-1.9-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2prr-1.9-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 22:23:12 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/2prr-1.9-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2prr-1.9-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 2694 and 0 Target number of residues in the AU: 2694 Target solvent content: 0.4889 Target number of residues exceeds 1700, conditional restraints are disabled Checking the provided sequence file Detected sequence length: 197 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 12 Adjusted target number of residues: 2364 Adjusted target solvent content: 0.55 Input MTZ file: 2prr-1.9-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: 1 Cell parameters: 65.105 93.953 120.898 84.262 81.638 77.734 Input sequence file: 2prr-1.9-parrot-hancs.fasta_lf Building free atoms model in initial map for 18912 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. 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: 119.307 1.870 Wilson plot Bfac: 21.26 218969 reflections ( 95.87 % complete ) and 0 restraints for refining 20816 atoms. Observations/parameters ratio is 2.63 ------------------------------------------------------ Starting model: R = 0.3232 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2757 (Rfree = 0.000) for 20816 atoms. Found 863 (863 requested) and removed 432 (431 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.08 1.95 NCS extension: 0 residues added, 21247 seeds are put forward Round 1: 1849 peptides, 182 chains. Longest chain 39 peptides. Score 0.727 Round 2: 2067 peptides, 109 chains. Longest chain 70 peptides. Score 0.860 Round 3: 2150 peptides, 69 chains. Longest chain 158 peptides. Score 0.904 Round 4: 2169 peptides, 52 chains. Longest chain 124 peptides. Score 0.918 Round 5: 2166 peptides, 56 chains. Longest chain 131 peptides. Score 0.915 Taking the results from Round 4 Chains 56, Residues 2117, Estimated correctness of the model 99.4 % 38 chains (1920 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 136 A and 139 A Built loop between residues 45 C and 48 C Built loop between residues 174 C and 177 C Built loop between residues 66 E and 69 E Built loop between residues 95 D and 99 D Built loop between residues 140 D and 143 D Built loop between residues 28 G and 37 G Built loop between residues 23 F and 27 F Built loop between residues 177 F and 180 F Built loop between residues 129 H and 132 H Built loop between residues 87 K and 90 K Built loop between residues 27 J and 30 J Built loop between residues 79 J and 82 J Built loop between residues 120 J and 125 J Built loop between residues 169 J and 175 J Built loop between residues 69 L and 72 L 39 chains (2158 residues) following loop building 22 chains (1965 residues) in sequence following loop building ------------------------------------------------------ 218969 reflections ( 95.87 % complete ) and 16622 restraints for refining 20019 atoms. Observations/parameters ratio is 2.73 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2995 (Rfree = 0.000) for 20019 atoms. Found 830 (830 requested) and removed 388 (415 requested) atoms. Cycle 2: After refmac, R = 0.2845 (Rfree = 0.000) for 20461 atoms. Found 665 (848 requested) and removed 106 (424 requested) atoms. Cycle 3: After refmac, R = 0.2753 (Rfree = 0.000) for 21020 atoms. Found 518 (872 requested) and removed 116 (436 requested) atoms. Cycle 4: After refmac, R = 0.2700 (Rfree = 0.000) for 21422 atoms. Found 430 (888 requested) and removed 91 (444 requested) atoms. Cycle 5: After refmac, R = 0.2648 (Rfree = 0.000) for 21761 atoms. Found 391 (902 requested) and removed 76 (451 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.03 1.90 NCS extension: 21 residues added (29 deleted due to clashes), 22114 seeds are put forward Round 1: 2175 peptides, 48 chains. Longest chain 188 peptides. Score 0.921 Round 2: 2191 peptides, 43 chains. Longest chain 187 peptides. Score 0.926 Round 3: 2173 peptides, 48 chains. Longest chain 123 peptides. Score 0.921 Round 4: 2178 peptides, 54 chains. Longest chain 143 peptides. Score 0.918 Round 5: 2173 peptides, 58 chains. Longest chain 146 peptides. Score 0.914 Taking the results from Round 2 Chains 48, Residues 2148, Estimated correctness of the model 99.5 % 33 chains (2043 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 34 C and 37 C Built loop between residues 52 B and 55 B Built loop between residues 123 B and 127 B Built loop between residues 154 B and 157 B Built loop between residues 94 E and 104 E Built loop between residues 112 E and 118 E Built loop between residues 155 G and 158 G Built loop between residues 32 F and 36 F Built loop between residues 98 F and 104 F Built loop between residues 65 I and 74 I Built loop between residues 152 I and 155 I Built loop between residues 96 H and 99 H Built loop between residues 136 H and 139 H Built loop between residues 158 H and 162 H Built loop between residues 141 K and 145 K Built loop between residues 31 J and 34 J 28 chains (2189 residues) following loop building 17 chains (2098 residues) in sequence following loop building ------------------------------------------------------ 218969 reflections ( 95.87 % complete ) and 17287 restraints for refining 21233 atoms. Observations/parameters ratio is 2.58 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2805 (Rfree = 0.000) for 21233 atoms. Found 697 (880 requested) and removed 317 (440 requested) atoms. Cycle 7: After refmac, R = 0.2650 (Rfree = 0.000) for 21613 atoms. Found 470 (896 requested) and removed 113 (448 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.2563 (Rfree = 0.000) for 21970 atoms. Found 360 (911 requested) and removed 104 (455 requested) atoms. Cycle 9: After refmac, R = 0.2503 (Rfree = 0.000) for 22226 atoms. Found 355 (922 requested) and removed 122 (461 requested) atoms. Cycle 10: After refmac, R = 0.2457 (Rfree = 0.000) for 22459 atoms. Found 309 (931 requested) and removed 117 (465 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.01 1.88 NCS extension: 3 residues added (49 deleted due to clashes), 22665 seeds are put forward Round 1: 2188 peptides, 36 chains. Longest chain 189 peptides. Score 0.931 Round 2: 2195 peptides, 40 chains. Longest chain 187 peptides. Score 0.929 Round 3: 2194 peptides, 39 chains. Longest chain 189 peptides. Score 0.929 Round 4: 2179 peptides, 50 chains. Longest chain 164 peptides. Score 0.920 Round 5: 2157 peptides, 58 chains. Longest chain 147 peptides. Score 0.913 Taking the results from Round 1 Chains 40, Residues 2152, Estimated correctness of the model 99.6 % 28 chains (2084 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 34 C and 37 C Built loop between residues 16 B and 20 B Built loop between residues 64 B and 67 B Built loop between residues 176 E and 180 E Built loop between residues 71 G and 74 G Built loop between residues 121 F and 124 F Built loop between residues 154 F and 157 F Built loop between residues 65 I and 69 I Built loop between residues 36 H and 41 H Built loop between residues 136 H and 139 H Built loop between residues 168 H and 173 H Built loop between residues 85 J and 89 J Built loop between residues 64 L and 68 L Built loop between residues 91 L and 95 L 24 chains (2186 residues) following loop building 14 chains (2122 residues) in sequence following loop building ------------------------------------------------------ 218969 reflections ( 95.87 % complete ) and 17378 restraints for refining 21687 atoms. Observations/parameters ratio is 2.52 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2606 (Rfree = 0.000) for 21687 atoms. Found 816 (899 requested) and removed 318 (449 requested) atoms. Cycle 12: After refmac, R = 0.2527 (Rfree = 0.000) for 22185 atoms. Found 507 (920 requested) and removed 135 (460 requested) atoms. Cycle 13: After refmac, R = 0.2466 (Rfree = 0.000) for 22557 atoms. Found 396 (935 requested) and removed 120 (467 requested) atoms. Cycle 14: After refmac, R = 0.2426 (Rfree = 0.000) for 22833 atoms. Found 372 (947 requested) and removed 148 (473 requested) atoms. Failed to save intermediate PDB Cycle 15: After refmac, R = 0.2393 (Rfree = 0.000) for 23057 atoms. Found 400 (956 requested) and removed 146 (478 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.00 1.87 NCS extension: 0 residues added (17 deleted due to clashes), 23322 seeds are put forward Round 1: 2188 peptides, 30 chains. Longest chain 188 peptides. Score 0.934 Round 2: 2192 peptides, 41 chains. Longest chain 128 peptides. Score 0.928 Round 3: 2183 peptides, 47 chains. Longest chain 188 peptides. Score 0.923 Round 4: 2183 peptides, 53 chains. Longest chain 166 peptides. Score 0.919 Round 5: 2181 peptides, 49 chains. Longest chain 188 peptides. Score 0.921 Taking the results from Round 1 Chains 31, Residues 2158, Estimated correctness of the model 99.6 % 22 chains (2105 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 65 C and 69 C Built loop between residues 38 E and 41 E Built loop between residues 136 E and 139 E Built loop between residues 123 D and 126 D Built loop between residues 64 G and 69 G Built loop between residues 94 G and 97 G Built loop between residues 141 I and 144 I Built loop between residues 176 J and 180 J 23 chains (2178 residues) following loop building 14 chains (2125 residues) in sequence following loop building ------------------------------------------------------ 218969 reflections ( 95.87 % complete ) and 17356 restraints for refining 22091 atoms. Observations/parameters ratio is 2.48 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2537 (Rfree = 0.000) for 22091 atoms. Found 916 (916 requested) and removed 291 (458 requested) atoms. Cycle 17: After refmac, R = 0.2481 (Rfree = 0.000) for 22716 atoms. Found 481 (942 requested) and removed 130 (471 requested) atoms. Cycle 18: After refmac, R = 0.2424 (Rfree = 0.000) for 23067 atoms. Found 403 (957 requested) and removed 124 (478 requested) atoms. Cycle 19: After refmac, R = 0.2385 (Rfree = 0.000) for 23346 atoms. Found 349 (968 requested) and removed 159 (484 requested) atoms. Cycle 20: After refmac, R = 0.2354 (Rfree = 0.000) for 23536 atoms. Found 362 (976 requested) and removed 177 (488 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.99 1.86 NCS extension: 28 residues added (31 deleted due to clashes), 23760 seeds are put forward Round 1: 2196 peptides, 34 chains. Longest chain 188 peptides. Score 0.933 Round 2: 2193 peptides, 37 chains. Longest chain 188 peptides. Score 0.930 Round 3: 2179 peptides, 44 chains. Longest chain 186 peptides. Score 0.924 Round 4: 2184 peptides, 46 chains. Longest chain 188 peptides. Score 0.924 Round 5: 2177 peptides, 51 chains. Longest chain 187 peptides. Score 0.920 Taking the results from Round 1 Chains 38, Residues 2162, Estimated correctness of the model 99.6 % 27 chains (2097 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 175 A and 178 A Built loop between residues 101 C and 104 C Built loop between residues 155 B and 158 B Built loop between residues 34 G and 37 G Built loop between residues 65 F and 69 F Built loop between residues 147 F and 150 F Built loop between residues 136 H and 139 H Built loop between residues 102 K and 105 K Built loop between residues 34 J and 37 J Built loop between residues 110 J and 114 J Built loop between residues 35 L and 38 L Built loop between residues 64 L and 68 L Built loop between residues 94 L and 97 L 24 chains (2189 residues) following loop building 14 chains (2126 residues) in sequence following loop building ------------------------------------------------------ 218969 reflections ( 95.87 % complete ) and 17403 restraints for refining 22436 atoms. Observations/parameters ratio is 2.44 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2514 (Rfree = 0.000) for 22436 atoms. Found 930 (930 requested) and removed 286 (465 requested) atoms. Cycle 22: After refmac, R = 0.2457 (Rfree = 0.000) for 23080 atoms. Found 520 (957 requested) and removed 143 (478 requested) atoms. Cycle 23: After refmac, R = 0.2397 (Rfree = 0.000) for 23457 atoms. Found 370 (973 requested) and removed 134 (486 requested) atoms. Failed to save intermediate PDB Cycle 24: After refmac, R = 0.2353 (Rfree = 0.000) for 23693 atoms. Found 344 (983 requested) and removed 141 (491 requested) atoms. Cycle 25: After refmac, R = 0.2322 (Rfree = 0.000) for 23896 atoms. Found 321 (991 requested) and removed 145 (495 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.99 1.86 NCS extension: 31 residues added (54 deleted due to clashes), 24108 seeds are put forward Round 1: 2195 peptides, 35 chains. Longest chain 187 peptides. Score 0.932 Round 2: 2185 peptides, 40 chains. Longest chain 163 peptides. Score 0.928 Round 3: 2179 peptides, 47 chains. Longest chain 187 peptides. Score 0.922 Round 4: 2171 peptides, 52 chains. Longest chain 171 peptides. Score 0.918 Round 5: 2169 peptides, 54 chains. Longest chain 147 peptides. Score 0.917 Taking the results from Round 1 Chains 39, Residues 2160, Estimated correctness of the model 99.6 % 27 chains (2091 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 113 A and 116 A Built loop between residues 175 B and 178 B Built loop between residues 65 E and 69 E Built loop between residues 94 E and 104 E Built loop between residues 32 G and 35 G Built loop between residues 101 G and 104 G Built loop between residues 136 H and 139 H Built loop between residues 34 K and 37 K Built loop between residues 95 K and 99 K Built loop between residues 65 J and 70 J Built loop between residues 102 J and 105 J Built loop between residues 121 J and 124 J Built loop between residues 151 J and 154 J 23 chains (2190 residues) following loop building 14 chains (2128 residues) in sequence following loop building ------------------------------------------------------ 218969 reflections ( 95.87 % complete ) and 17411 restraints for refining 22792 atoms. Observations/parameters ratio is 2.40 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2495 (Rfree = 0.000) for 22792 atoms. Found 945 (945 requested) and removed 311 (472 requested) atoms. Cycle 27: After refmac, R = 0.2433 (Rfree = 0.000) for 23426 atoms. Found 501 (971 requested) and removed 148 (485 requested) atoms. Cycle 28: After refmac, R = 0.2376 (Rfree = 0.000) for 23779 atoms. Found 425 (986 requested) and removed 141 (493 requested) atoms. Cycle 29: After refmac, R = 0.2332 (Rfree = 0.000) for 24063 atoms. Found 344 (998 requested) and removed 149 (499 requested) atoms. Cycle 30: After refmac, R = 0.2301 (Rfree = 0.000) for 24258 atoms. Found 315 (1006 requested) and removed 160 (503 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.98 1.85 NCS extension: 7 residues added (65 deleted due to clashes), 24427 seeds are put forward Round 1: 2180 peptides, 38 chains. Longest chain 187 peptides. Score 0.928 Round 2: 2177 peptides, 42 chains. Longest chain 163 peptides. Score 0.926 Round 3: 2167 peptides, 46 chains. Longest chain 166 peptides. Score 0.922 Round 4: 2167 peptides, 52 chains. Longest chain 163 peptides. Score 0.918 Round 5: 2184 peptides, 46 chains. Longest chain 175 peptides. Score 0.924 Taking the results from Round 1 Chains 46, Residues 2142, Estimated correctness of the model 99.5 % 29 chains (2073 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 112 A and 118 A Built loop between residues 93 C and 96 C Built loop between residues 65 B and 69 B Built loop between residues 122 B and 125 B Built loop between residues 173 B and 177 B Built loop between residues 175 E and 178 E Built loop between residues 37 G and 41 G Built loop between residues 136 G and 139 G Built loop between residues 126 H and 131 H Built loop between residues 26 J and 37 J Built loop between residues 101 J and 104 J Built loop between residues 64 L and 68 L Built loop between residues 94 L and 104 L 27 chains (2173 residues) following loop building 16 chains (2123 residues) in sequence following loop building ------------------------------------------------------ 218969 reflections ( 95.87 % complete ) and 17345 restraints for refining 22948 atoms. Observations/parameters ratio is 2.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2483 (Rfree = 0.000) for 22948 atoms. Found 933 (933 requested) and removed 280 (476 requested) atoms. Failed to save intermediate PDB Cycle 32: After refmac, R = 0.2416 (Rfree = 0.000) for 23601 atoms. Found 572 (959 requested) and removed 117 (489 requested) atoms. Cycle 33: After refmac, R = 0.2352 (Rfree = 0.000) for 24056 atoms. Found 398 (978 requested) and removed 149 (499 requested) atoms. Cycle 34: After refmac, R = 0.2313 (Rfree = 0.000) for 24305 atoms. Found 324 (988 requested) and removed 166 (504 requested) atoms. Cycle 35: After refmac, R = 0.2287 (Rfree = 0.000) for 24463 atoms. Found 349 (973 requested) and removed 186 (507 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.98 1.85 NCS extension: 15 residues added (63 deleted due to clashes), 24651 seeds are put forward Round 1: 2163 peptides, 40 chains. Longest chain 187 peptides. Score 0.926 Round 2: 2169 peptides, 45 chains. Longest chain 187 peptides. Score 0.923 Round 3: 2168 peptides, 47 chains. Longest chain 157 peptides. Score 0.921 Round 4: 2171 peptides, 51 chains. Longest chain 147 peptides. Score 0.919 Round 5: 2175 peptides, 46 chains. Longest chain 158 peptides. Score 0.923 Taking the results from Round 1 Chains 44, Residues 2123, Estimated correctness of the model 99.5 % 31 chains (2075 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 174 A and 177 A Built loop between residues 93 C and 96 C Built loop between residues 91 B and 96 B Built loop between residues 24 E and 32 E Built loop between residues 34 G and 37 G Built loop between residues 88 F and 91 F Built loop between residues 112 F and 119 F Built loop between residues 28 H and 32 H Built loop between residues 124 K and 127 K Built loop between residues 136 K and 140 K Built loop between residues 25 J and 35 J Built loop between residues 101 J and 104 J Built loop between residues 38 L and 41 L Built loop between residues 118 L and 123 L Built loop between residues 136 L and 140 L 25 chains (2166 residues) following loop building 16 chains (2128 residues) in sequence following loop building ------------------------------------------------------ 218969 reflections ( 95.87 % complete ) and 17355 restraints for refining 23202 atoms. Observations/parameters ratio is 2.36 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2479 (Rfree = 0.000) for 23202 atoms. Found 904 (904 requested) and removed 301 (481 requested) atoms. Cycle 37: After refmac, R = 0.2400 (Rfree = 0.000) for 23805 atoms. Found 611 (928 requested) and removed 137 (493 requested) atoms. Cycle 38: After refmac, R = 0.2342 (Rfree = 0.000) for 24279 atoms. Found 397 (947 requested) and removed 153 (503 requested) atoms. Failed to save intermediate PDB Cycle 39: After refmac, R = 0.2300 (Rfree = 0.000) for 24523 atoms. Found 370 (956 requested) and removed 162 (508 requested) atoms. Cycle 40: After refmac, R = 0.2271 (Rfree = 0.000) for 24731 atoms. Found 340 (964 requested) and removed 207 (513 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.98 1.85 NCS extension: 17 residues added (12 deleted due to clashes), 24887 seeds are put forward Round 1: 2152 peptides, 41 chains. Longest chain 186 peptides. Score 0.924 Round 2: 2165 peptides, 41 chains. Longest chain 185 peptides. Score 0.925 Round 3: 2170 peptides, 41 chains. Longest chain 186 peptides. Score 0.926 Round 4: 2159 peptides, 57 chains. Longest chain 165 peptides. Score 0.914 Round 5: 2156 peptides, 54 chains. Longest chain 160 peptides. Score 0.915 Taking the results from Round 3 Chains 43, Residues 2129, Estimated correctness of the model 99.5 % 33 chains (2071 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 147 A and 150 A Built loop between residues 65 C and 68 C Built loop between residues 22 E and 26 E Built loop between residues 66 E and 69 E Built loop between residues 53 F and 57 F Built loop between residues 65 F and 69 F Built loop between residues 121 F and 124 F Built loop between residues 145 F and 148 F Built loop between residues 35 I and 39 I Built loop between residues 101 I and 104 I Built loop between residues 168 I and 171 I Built loop between residues 130 H and 133 H Built loop between residues 124 K and 127 K Built loop between residues 31 J and 35 J Built loop between residues 101 J and 104 J Built loop between residues 102 L and 105 L 25 chains (2164 residues) following loop building 17 chains (2108 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 218969 reflections ( 95.87 % complete ) and 17261 restraints for refining 23271 atoms. Observations/parameters ratio is 2.35 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2498 (Rfree = 0.000) for 23271 atoms. Found 888 (888 requested) and removed 315 (482 requested) atoms. Cycle 42: After refmac, R = 0.2409 (Rfree = 0.000) for 23844 atoms. Found 649 (910 requested) and removed 130 (494 requested) atoms. Cycle 43: After refmac, R = 0.2344 (Rfree = 0.000) for 24363 atoms. Found 440 (929 requested) and removed 162 (505 requested) atoms. Failed to save intermediate PDB Cycle 44: After refmac, R = 0.2297 (Rfree = 0.000) for 24641 atoms. Found 410 (940 requested) and removed 161 (511 requested) atoms. Cycle 45: After refmac, R = 0.2263 (Rfree = 0.000) for 24890 atoms. Found 395 (949 requested) and removed 200 (516 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.98 1.85 NCS extension: 15 residues added (38 deleted due to clashes), 25111 seeds are put forward Round 1: 2156 peptides, 47 chains. Longest chain 168 peptides. Score 0.920 Round 2: 2170 peptides, 35 chains. Longest chain 186 peptides. Score 0.930 Round 3: 2154 peptides, 55 chains. Longest chain 140 peptides. Score 0.914 Round 4: 2161 peptides, 48 chains. Longest chain 130 peptides. Score 0.920 Round 5: 2131 peptides, 65 chains. Longest chain 185 peptides. Score 0.905 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 39, Residues 2135, Estimated correctness of the model 99.6 % 25 chains (2049 residues) have been docked in sequence Sequence coverage is 95 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 113 A and 116 A Built loop between residues 34 C and 37 C Built loop between residues 98 B and 101 B Built loop between residues 64 E and 69 E Built loop between residues 102 E and 110 E Built loop between residues 34 G and 37 G Built loop between residues 95 G and 99 G Built loop between residues 66 F and 69 F Built loop between residues 157 F and 162 F Built loop between residues 126 K and 129 K Built loop between residues 101 J and 104 J Built loop between residues 177 J and 180 J Built loop between residues 65 L and 73 L 23 chains (2170 residues) following loop building 12 chains (2090 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 218969 reflections ( 95.87 % complete ) and 17199 restraints for refining 16836 atoms. Observations/parameters ratio is 3.25 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3121 (Rfree = 0.000) for 16836 atoms. Found 171 (628 requested) and removed 0 (628 requested) atoms. Cycle 47: After refmac, R = 0.3033 (Rfree = 0.000) for 16836 atoms. Found 89 (634 requested) and removed 1 (352 requested) atoms. Cycle 48: After refmac, R = 0.2967 (Rfree = 0.000) for 16836 atoms. Found 56 (638 requested) and removed 11 (354 requested) atoms. Cycle 49: After refmac, R = 0.2929 (Rfree = 0.000) for 16836 atoms. TimeTaking 320.85