Mon 24 Dec 00:31:30 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 2prr-1.9-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2prr-1.9-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2prr-1.9-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2prr-1.9-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/2prr-1.9-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2prr-1.9-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 00:31:35 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/2prr-1.9-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2prr-1.9-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 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-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: 1 Cell parameters: 65.105 93.953 120.898 84.262 81.638 77.734 Input sequence file: 2prr-1.9-parrot-mrncs.fasta_lf Building free atoms model in initial map for 18912 target number of atoms Had to go as low as 0.55 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 20986 atoms. Observations/parameters ratio is 2.61 ------------------------------------------------------ Starting model: R = 0.3236 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2756 (Rfree = 0.000) for 20986 atoms. Found 870 (870 requested) and removed 436 (435 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.09 1.95 NCS extension: 0 residues added, 21420 seeds are put forward Round 1: 1854 peptides, 189 chains. Longest chain 35 peptides. Score 0.718 Round 2: 2051 peptides, 106 chains. Longest chain 92 peptides. Score 0.860 Round 3: 2122 peptides, 64 chains. Longest chain 129 peptides. Score 0.904 Round 4: 2168 peptides, 55 chains. Longest chain 161 peptides. Score 0.916 Round 5: 2162 peptides, 57 chains. Longest chain 129 peptides. Score 0.914 Taking the results from Round 4 Chains 62, Residues 2113, Estimated correctness of the model 99.4 % 43 chains (1943 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 95 C and 104 C Built loop between residues 115 E and 117 E Built loop between residues 69 D and 72 D Built loop between residues 121 D and 128 D Built loop between residues 140 D and 144 D Built loop between residues 171 D and 175 D Built loop between residues 21 G and 30 G Built loop between residues 55 G and 60 G Built loop between residues 127 G and 130 G Built loop between residues 27 F and 32 F Built loop between residues 121 F and 124 F Built loop between residues 168 F and 171 F Built loop between residues 161 I and 164 I Built loop between residues 31 H and 34 H Built loop between residues 50 H and 53 H Built loop between residues 137 H and 141 H Built loop between residues 128 K and 131 K Built loop between residues 167 J and 171 J Built loop between residues 49 L and 53 L Built loop between residues 99 L and 105 L Built loop between residues 139 L and 142 L 35 chains (2172 residues) following loop building 22 chains (2012 residues) in sequence following loop building ------------------------------------------------------ 218969 reflections ( 95.87 % complete ) and 16898 restraints for refining 20056 atoms. Observations/parameters ratio is 2.73 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3019 (Rfree = 0.000) for 20056 atoms. Found 832 (832 requested) and removed 377 (416 requested) atoms. Cycle 2: After refmac, R = 0.2797 (Rfree = 0.000) for 20511 atoms. Found 729 (851 requested) and removed 154 (425 requested) atoms. Cycle 3: After refmac, R = 0.2677 (Rfree = 0.000) for 21086 atoms. Found 589 (874 requested) and removed 131 (437 requested) atoms. Cycle 4: After refmac, R = 0.2598 (Rfree = 0.000) for 21544 atoms. Found 494 (893 requested) and removed 146 (446 requested) atoms. Cycle 5: After refmac, R = 0.2540 (Rfree = 0.000) for 21892 atoms. Found 435 (908 requested) and removed 158 (454 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.02 1.89 NCS extension: 19 residues added (72 deleted due to clashes), 22221 seeds are put forward Round 1: 2180 peptides, 42 chains. Longest chain 187 peptides. Score 0.926 Round 2: 2199 peptides, 41 chains. Longest chain 187 peptides. Score 0.928 Round 3: 2191 peptides, 48 chains. Longest chain 140 peptides. Score 0.923 Round 4: 2174 peptides, 49 chains. Longest chain 172 peptides. Score 0.921 Round 5: 2175 peptides, 49 chains. Longest chain 187 peptides. Score 0.921 Taking the results from Round 2 Chains 44, Residues 2158, Estimated correctness of the model 99.5 % 34 chains (2082 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 34 C and 37 C Built loop between residues 101 C and 104 C Built loop between residues 95 B and 99 B Built loop between residues 106 E and 109 E Built loop between residues 121 E and 124 E Built loop between residues 76 D and 79 D Built loop between residues 127 D and 130 D Built loop between residues 65 G and 68 G Built loop between residues 124 G and 127 G Built loop between residues 122 F and 125 F Built loop between residues 27 I and 32 I Built loop between residues 65 I and 68 I Built loop between residues 102 H and 105 H Built loop between residues 113 H and 116 H Built loop between residues 26 J and 29 J Built loop between residues 27 L and 30 L Built loop between residues 170 L and 173 L 26 chains (2194 residues) following loop building 17 chains (2119 residues) in sequence following loop building ------------------------------------------------------ 218969 reflections ( 95.87 % complete ) and 17418 restraints for refining 21117 atoms. Observations/parameters ratio is 2.59 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2769 (Rfree = 0.000) for 21117 atoms. Found 814 (876 requested) and removed 292 (438 requested) atoms. Cycle 7: After refmac, R = 0.2633 (Rfree = 0.000) for 21639 atoms. Found 597 (897 requested) and removed 123 (448 requested) atoms. Cycle 8: After refmac, R = 0.2556 (Rfree = 0.000) for 22113 atoms. Found 431 (917 requested) and removed 116 (458 requested) atoms. Cycle 9: After refmac, R = 0.2496 (Rfree = 0.000) for 22428 atoms. Found 375 (930 requested) and removed 129 (465 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.2444 (Rfree = 0.000) for 22674 atoms. Found 315 (940 requested) and removed 159 (470 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.00 1.87 NCS extension: 18 residues added (43 deleted due to clashes), 22861 seeds are put forward Round 1: 2184 peptides, 39 chains. Longest chain 169 peptides. Score 0.928 Round 2: 2188 peptides, 37 chains. Longest chain 187 peptides. Score 0.930 Round 3: 2182 peptides, 40 chains. Longest chain 187 peptides. Score 0.927 Round 4: 2160 peptides, 53 chains. Longest chain 139 peptides. Score 0.916 Round 5: 2171 peptides, 50 chains. Longest chain 166 peptides. Score 0.920 Taking the results from Round 2 Chains 42, Residues 2151, Estimated correctness of the model 99.6 % 32 chains (2102 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 33 C and 36 C Built loop between residues 82 C and 85 C Built loop between residues 101 C and 104 C Built loop between residues 64 B and 68 B Built loop between residues 134 B and 137 B Built loop between residues 174 B and 177 B Built loop between residues 24 E and 35 E Built loop between residues 147 D and 150 D Built loop between residues 75 G and 78 G Built loop between residues 66 F and 69 F Built loop between residues 112 F and 123 F Built loop between residues 102 H and 105 H Built loop between residues 66 J and 69 J Built loop between residues 91 J and 96 J Built loop between residues 131 L and 134 L 25 chains (2189 residues) following loop building 17 chains (2151 residues) in sequence following loop building ------------------------------------------------------ 218969 reflections ( 95.87 % complete ) and 17529 restraints for refining 21738 atoms. Observations/parameters ratio is 2.52 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2702 (Rfree = 0.000) for 21738 atoms. Found 883 (883 requested) and removed 329 (450 requested) atoms. Cycle 12: After refmac, R = 0.2564 (Rfree = 0.000) for 22292 atoms. Found 516 (906 requested) and removed 106 (462 requested) atoms. Cycle 13: After refmac, R = 0.2486 (Rfree = 0.000) for 22702 atoms. Found 367 (922 requested) and removed 93 (470 requested) atoms. Cycle 14: After refmac, R = 0.2432 (Rfree = 0.000) for 22976 atoms. Found 305 (934 requested) and removed 121 (476 requested) atoms. Cycle 15: After refmac, R = 0.2391 (Rfree = 0.000) for 23160 atoms. Found 303 (941 requested) and removed 140 (480 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.00 1.87 NCS extension: 13 residues added (55 deleted due to clashes), 23348 seeds are put forward Round 1: 2189 peptides, 36 chains. Longest chain 188 peptides. Score 0.931 Round 2: 2201 peptides, 31 chains. Longest chain 187 peptides. Score 0.935 Round 3: 2196 peptides, 41 chains. Longest chain 187 peptides. Score 0.928 Round 4: 2181 peptides, 41 chains. Longest chain 188 peptides. Score 0.927 Round 5: 2188 peptides, 43 chains. Longest chain 160 peptides. Score 0.926 Taking the results from Round 2 Chains 32, Residues 2170, Estimated correctness of the model 99.6 % 24 chains (2129 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 102 A and 105 A Built loop between residues 24 C and 35 C Built loop between residues 145 B and 148 B Built loop between residues 63 E and 66 E Built loop between residues 75 G and 78 G Built loop between residues 121 I and 124 I Built loop between residues 154 I and 157 I Built loop between residues 147 H and 150 H Built loop between residues 113 K and 116 K Built loop between residues 159 L and 162 L 22 chains (2198 residues) following loop building 14 chains (2157 residues) in sequence following loop building ------------------------------------------------------ 218969 reflections ( 95.87 % complete ) and 17596 restraints for refining 22053 atoms. Observations/parameters ratio is 2.48 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2572 (Rfree = 0.000) for 22053 atoms. Found 896 (896 requested) and removed 334 (457 requested) atoms. Cycle 17: After refmac, R = 0.2501 (Rfree = 0.000) for 22615 atoms. Found 534 (919 requested) and removed 126 (469 requested) atoms. Cycle 18: After refmac, R = 0.2441 (Rfree = 0.000) for 23023 atoms. Found 380 (936 requested) and removed 139 (477 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.2395 (Rfree = 0.000) for 23264 atoms. Found 352 (946 requested) and removed 145 (482 requested) atoms. Failed to save intermediate PDB Cycle 20: After refmac, R = 0.2366 (Rfree = 0.000) for 23471 atoms. Found 299 (954 requested) and removed 168 (486 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.99 1.86 NCS extension: 11 residues added (61 deleted due to clashes), 23623 seeds are put forward Round 1: 2184 peptides, 38 chains. Longest chain 188 peptides. Score 0.929 Round 2: 2189 peptides, 39 chains. Longest chain 187 peptides. Score 0.929 Round 3: 2184 peptides, 41 chains. Longest chain 187 peptides. Score 0.927 Round 4: 2184 peptides, 44 chains. Longest chain 188 peptides. Score 0.925 Round 5: 2160 peptides, 62 chains. Longest chain 119 peptides. Score 0.910 Taking the results from Round 2 Chains 41, Residues 2150, Estimated correctness of the model 99.5 % 33 chains (2117 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 66 A and 70 A Built loop between residues 122 A and 125 A Built loop between residues 132 A and 135 A Built loop between residues 32 C and 40 C Built loop between residues 113 C and 116 C Built loop between residues 65 B and 68 B Built loop between residues 101 B and 104 B Built loop between residues 80 E and 83 E Built loop between residues 121 E and 124 E Built loop between residues 136 E and 139 E Built loop between residues 154 E and 157 E Built loop between residues 15 G and 18 G Built loop between residues 75 F and 78 F Built loop between residues 113 I and 116 I Built loop between residues 135 I and 138 I Built loop between residues 179 I and 182 I Built loop between residues 31 H and 36 H Built loop between residues 102 K and 105 K Built loop between residues 24 J and 35 J 21 chains (2200 residues) following loop building 14 chains (2171 residues) in sequence following loop building ------------------------------------------------------ 218969 reflections ( 95.87 % complete ) and 17673 restraints for refining 22400 atoms. Observations/parameters ratio is 2.44 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2558 (Rfree = 0.000) for 22400 atoms. Found 892 (892 requested) and removed 336 (464 requested) atoms. Failed to save intermediate PDB Cycle 22: After refmac, R = 0.2480 (Rfree = 0.000) for 22956 atoms. Found 530 (914 requested) and removed 144 (476 requested) atoms. Cycle 23: After refmac, R = 0.2426 (Rfree = 0.000) for 23342 atoms. Found 397 (929 requested) and removed 149 (484 requested) atoms. Cycle 24: After refmac, R = 0.2382 (Rfree = 0.000) for 23590 atoms. Found 369 (939 requested) and removed 143 (489 requested) atoms. Cycle 25: After refmac, R = 0.2354 (Rfree = 0.000) for 23816 atoms. Found 350 (948 requested) and removed 182 (494 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.99 1.86 NCS extension: 11 residues added (18 deleted due to clashes), 24005 seeds are put forward Round 1: 2178 peptides, 41 chains. Longest chain 186 peptides. Score 0.926 Round 2: 2180 peptides, 34 chains. Longest chain 187 peptides. Score 0.931 Round 3: 2179 peptides, 43 chains. Longest chain 164 peptides. Score 0.925 Round 4: 2169 peptides, 47 chains. Longest chain 164 peptides. Score 0.921 Round 5: 2163 peptides, 53 chains. Longest chain 164 peptides. Score 0.917 Taking the results from Round 2 Chains 39, Residues 2146, Estimated correctness of the model 99.6 % 28 chains (2072 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 65 E and 70 E Built loop between residues 121 E and 124 E Built loop between residues 27 G and 34 G Built loop between residues 154 F and 157 F Built loop between residues 34 I and 37 I Built loop between residues 102 H and 105 H Built loop between residues 25 J and 31 J Built loop between residues 75 J and 78 J Built loop between residues 140 J and 143 J Built loop between residues 148 L and 151 L 26 chains (2168 residues) following loop building 18 chains (2101 residues) in sequence following loop building ------------------------------------------------------ 218969 reflections ( 95.87 % complete ) and 17259 restraints for refining 22565 atoms. Observations/parameters ratio is 2.43 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2547 (Rfree = 0.000) for 22565 atoms. Found 880 (880 requested) and removed 307 (468 requested) atoms. Cycle 27: After refmac, R = 0.2460 (Rfree = 0.000) for 23138 atoms. Found 514 (902 requested) and removed 120 (480 requested) atoms. Cycle 28: After refmac, R = 0.2393 (Rfree = 0.000) for 23532 atoms. Found 379 (917 requested) and removed 142 (488 requested) atoms. Cycle 29: After refmac, R = 0.2347 (Rfree = 0.000) for 23769 atoms. Found 349 (927 requested) and removed 122 (493 requested) atoms. Cycle 30: After refmac, R = 0.2317 (Rfree = 0.000) for 23996 atoms. Found 305 (935 requested) and removed 179 (497 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.99 1.86 NCS extension: 12 residues added (24 deleted due to clashes), 24143 seeds are put forward Round 1: 2174 peptides, 39 chains. Longest chain 186 peptides. Score 0.927 Round 2: 2178 peptides, 35 chains. Longest chain 187 peptides. Score 0.930 Round 3: 2174 peptides, 43 chains. Longest chain 187 peptides. Score 0.925 Round 4: 2164 peptides, 52 chains. Longest chain 144 peptides. Score 0.918 Round 5: 2148 peptides, 61 chains. Longest chain 138 peptides. Score 0.910 Taking the results from Round 2 Chains 37, Residues 2143, Estimated correctness of the model 99.6 % 26 chains (2067 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 24 A and 35 A Built loop between residues 68 C and 71 C Built loop between residues 113 E and 116 E Built loop between residues 147 E and 150 E Built loop between residues 27 G and 30 G Built loop between residues 112 F and 123 F Built loop between residues 31 I and 36 I Built loop between residues 102 H and 109 H Built loop between residues 175 J and 181 J Built loop between residues 99 L and 102 L 26 chains (2178 residues) following loop building 16 chains (2112 residues) in sequence following loop building ------------------------------------------------------ 218969 reflections ( 95.87 % complete ) and 17312 restraints for refining 22780 atoms. Observations/parameters ratio is 2.40 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2531 (Rfree = 0.000) for 22780 atoms. Found 869 (869 requested) and removed 326 (472 requested) atoms. Cycle 32: After refmac, R = 0.2438 (Rfree = 0.000) for 23323 atoms. Found 584 (890 requested) and removed 122 (483 requested) atoms. Cycle 33: After refmac, R = 0.2372 (Rfree = 0.000) for 23785 atoms. Found 387 (907 requested) and removed 148 (493 requested) atoms. Cycle 34: After refmac, R = 0.2330 (Rfree = 0.000) for 24024 atoms. Found 361 (916 requested) and removed 161 (498 requested) atoms. Cycle 35: After refmac, R = 0.2302 (Rfree = 0.000) for 24224 atoms. Found 336 (925 requested) and removed 170 (502 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.98 1.85 NCS extension: 19 residues added (126 deleted due to clashes), 24421 seeds are put forward Round 1: 2177 peptides, 42 chains. Longest chain 170 peptides. Score 0.926 Round 2: 2175 peptides, 38 chains. Longest chain 188 peptides. Score 0.928 Round 3: 2162 peptides, 48 chains. Longest chain 162 peptides. Score 0.920 Round 4: 2148 peptides, 58 chains. Longest chain 158 peptides. Score 0.912 Round 5: 2149 peptides, 51 chains. Longest chain 158 peptides. Score 0.917 Taking the results from Round 2 Chains 41, Residues 2137, Estimated correctness of the model 99.5 % 28 chains (2063 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 101 A and 109 A Built loop between residues 24 C and 35 C Built loop between residues 136 C and 139 C Built loop between residues 66 B and 70 B Built loop between residues 101 E and 104 E Built loop between residues 25 G and 29 G Built loop between residues 75 G and 78 G Built loop between residues 140 G and 143 G Built loop between residues 66 F and 69 F Built loop between residues 106 F and 116 F Built loop between residues 155 F and 158 F Built loop between residues 146 I and 150 I Built loop between residues 26 J and 33 J Built loop between residues 101 J and 104 J Built loop between residues 47 L and 51 L 23 chains (2186 residues) following loop building 13 chains (2121 residues) in sequence following loop building ------------------------------------------------------ 218969 reflections ( 95.87 % complete ) and 17397 restraints for refining 22951 atoms. Observations/parameters ratio is 2.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2517 (Rfree = 0.000) for 22951 atoms. Found 857 (857 requested) and removed 327 (476 requested) atoms. Failed to save intermediate PDB Cycle 37: After refmac, R = 0.2430 (Rfree = 0.000) for 23481 atoms. Found 591 (877 requested) and removed 90 (487 requested) atoms. Failed to save intermediate PDB Cycle 38: After refmac, R = 0.2374 (Rfree = 0.000) for 23982 atoms. Found 378 (895 requested) and removed 158 (497 requested) atoms. Cycle 39: After refmac, R = 0.2328 (Rfree = 0.000) for 24202 atoms. Found 338 (904 requested) and removed 154 (502 requested) atoms. Cycle 40: After refmac, R = 0.2303 (Rfree = 0.000) for 24386 atoms. Found 343 (910 requested) and removed 177 (505 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.98 1.85 NCS extension: 38 residues added (48 deleted due to clashes), 24602 seeds are put forward Round 1: 2174 peptides, 40 chains. Longest chain 165 peptides. Score 0.927 Round 2: 2180 peptides, 34 chains. Longest chain 188 peptides. Score 0.931 Round 3: 2160 peptides, 49 chains. Longest chain 177 peptides. Score 0.919 Round 4: 2164 peptides, 44 chains. Longest chain 188 peptides. Score 0.923 Round 5: 2149 peptides, 59 chains. Longest chain 116 peptides. Score 0.911 Taking the results from Round 2 Chains 35, Residues 2146, Estimated correctness of the model 99.6 % 27 chains (2088 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 24 C and 35 C Built loop between residues 53 B and 56 B Built loop between residues 65 B and 68 B Built loop between residues 79 B and 82 B Built loop between residues 155 B and 158 B Built loop between residues 113 E and 116 E Built loop between residues 26 G and 32 G Built loop between residues 34 F and 37 F Built loop between residues 20 H and 24 H Built loop between residues 75 H and 78 H Built loop between residues 136 L and 139 L Built loop between residues 158 L and 161 L 22 chains (2181 residues) following loop building 15 chains (2124 residues) in sequence following loop building ------------------------------------------------------ 218969 reflections ( 95.87 % complete ) and 17380 restraints for refining 23053 atoms. Observations/parameters ratio is 2.37 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2511 (Rfree = 0.000) for 23053 atoms. Found 841 (841 requested) and removed 314 (478 requested) atoms. Cycle 42: After refmac, R = 0.2425 (Rfree = 0.000) for 23580 atoms. Found 649 (861 requested) and removed 109 (489 requested) atoms. Cycle 43: After refmac, R = 0.2372 (Rfree = 0.000) for 24120 atoms. Found 377 (880 requested) and removed 170 (500 requested) atoms. Cycle 44: After refmac, R = 0.2328 (Rfree = 0.000) for 24327 atoms. Found 382 (888 requested) and removed 160 (504 requested) atoms. Cycle 45: After refmac, R = 0.2301 (Rfree = 0.000) for 24549 atoms. Found 342 (896 requested) and removed 219 (509 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.98 1.85 NCS extension: 23 residues added (92 deleted due to clashes), 24708 seeds are put forward Round 1: 2143 peptides, 44 chains. Longest chain 185 peptides. Score 0.921 Round 2: 2158 peptides, 38 chains. Longest chain 187 peptides. Score 0.926 Round 3: 2163 peptides, 47 chains. Longest chain 165 peptides. Score 0.921 Round 4: 2155 peptides, 47 chains. Longest chain 187 peptides. Score 0.920 Round 5: 2139 peptides, 60 chains. Longest chain 172 peptides. Score 0.909 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 39, Residues 2120, Estimated correctness of the model 99.5 % 29 chains (2055 residues) have been docked in sequence Sequence coverage is 96 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 66 A and 70 A Built loop between residues 23 C and 35 C Built loop between residues 79 B and 82 B Built loop between residues 155 B and 158 B Built loop between residues 34 G and 37 G Built loop between residues 101 G and 105 G Built loop between residues 64 F and 69 F Built loop between residues 102 F and 109 F Built loop between residues 178 I and 181 I Built loop between residues 32 H and 35 H Built loop between residues 84 H and 87 H Built loop between residues 159 K and 162 K Built loop between residues 25 J and 31 J Built loop between residues 76 L and 79 L Built loop between residues 140 L and 143 L 23 chains (2169 residues) following loop building 14 chains (2105 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. Failed to save intermediate PDB 218969 reflections ( 95.87 % complete ) and 17257 restraints for refining 16887 atoms. Observations/parameters ratio is 3.24 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3126 (Rfree = 0.000) for 16887 atoms. Found 187 (602 requested) and removed 0 (602 requested) atoms. Cycle 47: After refmac, R = 0.3028 (Rfree = 0.000) for 16887 atoms. Found 77 (609 requested) and removed 0 (354 requested) atoms. Cycle 48: After refmac, R = 0.2960 (Rfree = 0.000) for 16887 atoms. Found 54 (611 requested) and removed 9 (355 requested) atoms. Cycle 49: After refmac, R = 0.2922 (Rfree = 0.000) for 16887 atoms. Found 42 (613 requested) and removed 11 (356 requested) atoms. Writing output files ... Failed to save intermediate PDB TimeTaking 350.43