Tue 25 Dec 19:27:55 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 2pbl-1.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2pbl-1.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2pbl-1.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pbl-1.8-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/2pbl-1.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pbl-1.8-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 ============================================================ Tue 25 Dec 19:28:05 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/2pbl-1.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pbl-1.8-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 1033 and 0 Target number of residues in the AU: 1033 Target solvent content: 0.4463 Checking the provided sequence file Detected sequence length: 262 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1048 Adjusted target solvent content: 0.44 Input MTZ file: 2pbl-1.8-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: 4 Cell parameters: 77.197 74.438 95.727 90.000 113.394 90.000 Input sequence file: 2pbl-1.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 8384 target number of atoms Had to go as low as 0.40 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: 87.858 1.790 Wilson plot Bfac: 14.00 93715 reflections ( 99.87 % complete ) and 0 restraints for refining 9247 atoms. Observations/parameters ratio is 2.53 ------------------------------------------------------ Starting model: R = 0.3613 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3243 (Rfree = 0.000) for 9247 atoms. Found 434 (434 requested) and removed 236 (217 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.74 1.89 NCS extension: 0 residues added, 9445 seeds are put forward Round 1: 918 peptides, 57 chains. Longest chain 86 peptides. Score 0.892 Round 2: 993 peptides, 31 chains. Longest chain 125 peptides. Score 0.947 Round 3: 1008 peptides, 24 chains. Longest chain 158 peptides. Score 0.957 Round 4: 1017 peptides, 19 chains. Longest chain 157 peptides. Score 0.964 Round 5: 1016 peptides, 18 chains. Longest chain 158 peptides. Score 0.965 Taking the results from Round 5 Chains 23, Residues 998, Estimated correctness of the model 99.9 % 16 chains (961 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 136 A and 139 A Built loop between residues 219 A and 222 A Built loop between residues 103 C and 106 C Built loop between residues 33 B and 38 B Built loop between residues 101 B and 106 B Built loop between residues 62 D and 65 D Built loop between residues 225 D and 228 D 15 chains (1015 residues) following loop building 9 chains (979 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 93715 reflections ( 99.87 % complete ) and 9216 restraints for refining 8914 atoms. 1300 conditional restraints added. Observations/parameters ratio is 2.63 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3081 (Rfree = 0.000) for 8914 atoms. Found 415 (418 requested) and removed 240 (209 requested) atoms. Cycle 2: After refmac, R = 0.2861 (Rfree = 0.000) for 9066 atoms. Found 365 (418 requested) and removed 84 (213 requested) atoms. Cycle 3: After refmac, R = 0.2746 (Rfree = 0.000) for 9317 atoms. Found 304 (430 requested) and removed 50 (219 requested) atoms. Cycle 4: After refmac, R = 0.2638 (Rfree = 0.000) for 9549 atoms. Found 262 (440 requested) and removed 75 (224 requested) atoms. Cycle 5: After refmac, R = 0.2561 (Rfree = 0.000) for 9680 atoms. Found 265 (448 requested) and removed 75 (228 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.74 1.89 NCS extension: 1 residues added (116 deleted due to clashes), 9876 seeds are put forward Round 1: 1008 peptides, 23 chains. Longest chain 104 peptides. Score 0.958 Round 2: 1014 peptides, 19 chains. Longest chain 107 peptides. Score 0.963 Round 3: 1007 peptides, 22 chains. Longest chain 109 peptides. Score 0.959 Round 4: 1014 peptides, 20 chains. Longest chain 157 peptides. Score 0.962 Round 5: 1015 peptides, 19 chains. Longest chain 157 peptides. Score 0.964 Taking the results from Round 5 Chains 22, Residues 996, Estimated correctness of the model 99.9 % 19 chains (989 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 33 A and 37 A Built loop between residues 71 A and 74 A Built loop between residues 103 A and 106 A Built loop between residues 209 A and 213 A Built loop between residues 33 C and 38 C Built loop between residues 71 C and 74 C Built loop between residues 103 C and 106 C Built loop between residues 187 C and 190 C Built loop between residues 32 B and 37 B Built loop between residues 69 B and 73 B Built loop between residues 102 B and 106 B Built loop between residues 33 D and 38 D Built loop between residues 58 D and 62 D Built loop between residues 198 D and 201 D 6 chains (1032 residues) following loop building 5 chains (1028 residues) in sequence following loop building ------------------------------------------------------ 93715 reflections ( 99.87 % complete ) and 9267 restraints for refining 9516 atoms. 1076 conditional restraints added. Observations/parameters ratio is 2.46 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2760 (Rfree = 0.000) for 9516 atoms. Found 392 (438 requested) and removed 164 (223 requested) atoms. Cycle 7: After refmac, R = 0.2556 (Rfree = 0.000) for 9732 atoms. Found 301 (448 requested) and removed 97 (228 requested) atoms. Cycle 8: After refmac, R = 0.2472 (Rfree = 0.000) for 9892 atoms. Found 311 (457 requested) and removed 80 (233 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.2395 (Rfree = 0.000) for 10107 atoms. Found 227 (465 requested) and removed 102 (237 requested) atoms. Cycle 10: After refmac, R = 0.2354 (Rfree = 0.000) for 10197 atoms. Found 262 (470 requested) and removed 98 (240 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.74 1.89 NCS extension: 0 residues added (107 deleted due to clashes), 10365 seeds are put forward Round 1: 1017 peptides, 18 chains. Longest chain 104 peptides. Score 0.965 Round 2: 1024 peptides, 13 chains. Longest chain 225 peptides. Score 0.971 Round 3: 1022 peptides, 15 chains. Longest chain 157 peptides. Score 0.968 Round 4: 1023 peptides, 14 chains. Longest chain 225 peptides. Score 0.970 Round 5: 1024 peptides, 15 chains. Longest chain 157 peptides. Score 0.969 Taking the results from Round 2 Chains 13, Residues 1011, Estimated correctness of the model 99.9 % 13 chains (1011 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 70 A and 74 A Built loop between residues 103 A and 106 A Built loop between residues 209 A and 212 A Built loop between residues 103 C and 106 C Built loop between residues 208 C and 211 C Built loop between residues 103 B and 106 B Built loop between residues 154 B and 158 B Built loop between residues 33 D and 38 D 5 chains (1031 residues) following loop building 5 chains (1031 residues) in sequence following loop building ------------------------------------------------------ 93715 reflections ( 99.87 % complete ) and 9507 restraints for refining 9776 atoms. 1318 conditional restraints added. Observations/parameters ratio is 2.40 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2625 (Rfree = 0.000) for 9776 atoms. Found 421 (450 requested) and removed 130 (229 requested) atoms. Cycle 12: After refmac, R = 0.2441 (Rfree = 0.000) for 10046 atoms. Found 293 (464 requested) and removed 116 (236 requested) atoms. Failed to save intermediate PDB Cycle 13: After refmac, R = 0.2382 (Rfree = 0.000) for 10191 atoms. Found 279 (470 requested) and removed 99 (240 requested) atoms. Cycle 14: After refmac, R = 0.2317 (Rfree = 0.000) for 10346 atoms. Found 267 (477 requested) and removed 129 (243 requested) atoms. Cycle 15: After refmac, R = 0.2288 (Rfree = 0.000) for 10450 atoms. Found 280 (482 requested) and removed 115 (246 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.73 1.87 NCS extension: 0 residues added (88 deleted due to clashes), 10619 seeds are put forward Round 1: 1021 peptides, 19 chains. Longest chain 157 peptides. Score 0.964 Round 2: 1024 peptides, 15 chains. Longest chain 157 peptides. Score 0.969 Round 3: 1030 peptides, 10 chains. Longest chain 260 peptides. Score 0.974 Round 4: 1025 peptides, 15 chains. Longest chain 190 peptides. Score 0.969 Round 5: 1024 peptides, 15 chains. Longest chain 124 peptides. Score 0.969 Taking the results from Round 3 Chains 12, Residues 1020, Estimated correctness of the model 99.9 % 10 chains (1016 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 72 A and 75 A Built loop between residues 198 C and 201 C Built loop between residues 103 D and 106 D Built loop between residues 158 D and 161 D 8 chains (1028 residues) following loop building 6 chains (1024 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 93715 reflections ( 99.87 % complete ) and 9753 restraints for refining 9954 atoms. 1593 conditional restraints added. Observations/parameters ratio is 2.35 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2580 (Rfree = 0.000) for 9954 atoms. Found 442 (458 requested) and removed 138 (233 requested) atoms. Cycle 17: After refmac, R = 0.2391 (Rfree = 0.000) for 10236 atoms. Found 302 (472 requested) and removed 132 (241 requested) atoms. Cycle 18: After refmac, R = 0.2347 (Rfree = 0.000) for 10363 atoms. Found 281 (479 requested) and removed 111 (244 requested) atoms. Cycle 19: After refmac, R = 0.2290 (Rfree = 0.000) for 10507 atoms. Found 252 (485 requested) and removed 113 (247 requested) atoms. Cycle 20: After refmac, R = 0.2274 (Rfree = 0.000) for 10607 atoms. Found 251 (490 requested) and removed 132 (250 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.73 1.87 NCS extension: 4 residues added (98 deleted due to clashes), 10733 seeds are put forward Round 1: 1020 peptides, 16 chains. Longest chain 157 peptides. Score 0.967 Round 2: 1023 peptides, 13 chains. Longest chain 157 peptides. Score 0.971 Round 3: 1024 peptides, 14 chains. Longest chain 157 peptides. Score 0.970 Round 4: 1025 peptides, 17 chains. Longest chain 157 peptides. Score 0.967 Round 5: 1021 peptides, 19 chains. Longest chain 157 peptides. Score 0.964 Taking the results from Round 2 Chains 16, Residues 1010, Estimated correctness of the model 99.9 % 13 chains (1005 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 34 A and 38 A Built loop between residues 69 B and 74 B Built loop between residues 72 D and 75 D Built loop between residues 101 D and 106 D 12 chains (1022 residues) following loop building 9 chains (1018 residues) in sequence following loop building ------------------------------------------------------ 93715 reflections ( 99.87 % complete ) and 10160 restraints for refining 10087 atoms. 2034 conditional restraints added. Observations/parameters ratio is 2.32 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2571 (Rfree = 0.000) for 10087 atoms. Found 453 (455 requested) and removed 129 (237 requested) atoms. Cycle 22: After refmac, R = 0.2373 (Rfree = 0.000) for 10378 atoms. Found 295 (469 requested) and removed 111 (244 requested) atoms. Failed to save intermediate PDB Cycle 23: After refmac, R = 0.2316 (Rfree = 0.000) for 10524 atoms. Found 246 (476 requested) and removed 96 (248 requested) atoms. Cycle 24: After refmac, R = 0.2273 (Rfree = 0.000) for 10637 atoms. Found 238 (481 requested) and removed 104 (250 requested) atoms. Cycle 25: After refmac, R = 0.2242 (Rfree = 0.000) for 10729 atoms. Found 232 (486 requested) and removed 113 (253 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.74 1.89 NCS extension: 0 residues added, 10851 seeds are put forward Round 1: 1018 peptides, 16 chains. Longest chain 157 peptides. Score 0.967 Round 2: 1019 peptides, 14 chains. Longest chain 157 peptides. Score 0.969 Round 3: 1020 peptides, 14 chains. Longest chain 157 peptides. Score 0.969 Round 4: 1021 peptides, 20 chains. Longest chain 157 peptides. Score 0.963 Round 5: 1013 peptides, 22 chains. Longest chain 124 peptides. Score 0.960 Taking the results from Round 3 Chains 17, Residues 1006, Estimated correctness of the model 99.9 % 14 chains (1000 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 69 A and 74 A Built loop between residues 158 A and 161 A Built loop between residues 14 B and 20 B Built loop between residues 34 B and 38 B Built loop between residues 158 B and 161 B Built loop between residues 69 D and 73 D 11 chains (1025 residues) following loop building 8 chains (1019 residues) in sequence following loop building ------------------------------------------------------ 93715 reflections ( 99.87 % complete ) and 10140 restraints for refining 10139 atoms. 2013 conditional restraints added. Observations/parameters ratio is 2.31 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2534 (Rfree = 0.000) for 10139 atoms. Found 457 (457 requested) and removed 127 (238 requested) atoms. Cycle 27: After refmac, R = 0.2357 (Rfree = 0.000) for 10433 atoms. Found 328 (472 requested) and removed 105 (246 requested) atoms. Cycle 28: After refmac, R = 0.2303 (Rfree = 0.000) for 10613 atoms. Found 281 (480 requested) and removed 114 (250 requested) atoms. Cycle 29: After refmac, R = 0.2250 (Rfree = 0.000) for 10748 atoms. Found 263 (486 requested) and removed 113 (253 requested) atoms. Cycle 30: After refmac, R = 0.2217 (Rfree = 0.000) for 10859 atoms. Found 276 (492 requested) and removed 138 (256 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.73 1.87 NCS extension: 0 residues added (4 deleted due to clashes), 10998 seeds are put forward Round 1: 1020 peptides, 17 chains. Longest chain 157 peptides. Score 0.966 Round 2: 1022 peptides, 14 chains. Longest chain 157 peptides. Score 0.969 Round 3: 1025 peptides, 15 chains. Longest chain 157 peptides. Score 0.969 Round 4: 1021 peptides, 19 chains. Longest chain 157 peptides. Score 0.964 Round 5: 1019 peptides, 19 chains. Longest chain 157 peptides. Score 0.964 Taking the results from Round 3 Chains 19, Residues 1010, Estimated correctness of the model 99.9 % 14 chains (996 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 35 A and 38 A Built loop between residues 58 A and 61 A Built loop between residues 70 A and 74 A Built loop between residues 158 A and 161 A Built loop between residues 14 B and 17 B Built loop between residues 34 B and 38 B Built loop between residues 101 D and 106 D 11 chains (1026 residues) following loop building 7 chains (1014 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 93715 reflections ( 99.87 % complete ) and 10239 restraints for refining 10215 atoms. 2126 conditional restraints added. Observations/parameters ratio is 2.29 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2530 (Rfree = 0.000) for 10215 atoms. Found 461 (461 requested) and removed 131 (240 requested) atoms. Cycle 32: After refmac, R = 0.2356 (Rfree = 0.000) for 10513 atoms. Found 300 (475 requested) and removed 131 (247 requested) atoms. Failed to save intermediate PDB Cycle 33: After refmac, R = 0.2287 (Rfree = 0.000) for 10641 atoms. Found 294 (482 requested) and removed 89 (251 requested) atoms. Cycle 34: After refmac, R = 0.2229 (Rfree = 0.000) for 10814 atoms. Found 256 (489 requested) and removed 113 (254 requested) atoms. Cycle 35: After refmac, R = 0.2207 (Rfree = 0.000) for 10910 atoms. Found 257 (493 requested) and removed 131 (257 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.73 1.87 NCS extension: 3 residues added (107 deleted due to clashes), 11040 seeds are put forward Round 1: 1018 peptides, 17 chains. Longest chain 158 peptides. Score 0.966 Round 2: 1023 peptides, 14 chains. Longest chain 157 peptides. Score 0.970 Round 3: 1024 peptides, 15 chains. Longest chain 157 peptides. Score 0.969 Round 4: 1020 peptides, 17 chains. Longest chain 157 peptides. Score 0.966 Round 5: 1018 peptides, 21 chains. Longest chain 151 peptides. Score 0.962 Taking the results from Round 2 Chains 18, Residues 1009, Estimated correctness of the model 99.9 % 13 chains (897 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 11 A and 17 A Built loop between residues 70 A and 74 A Built loop between residues 14 B and 19 B Built loop between residues 58 B and 61 B Built loop between residues 102 B and 107 B Built loop between residues 154 B and 161 B Built loop between residues 101 D and 106 D 9 chains (1032 residues) following loop building 6 chains (925 residues) in sequence following loop building ------------------------------------------------------ 93715 reflections ( 99.87 % complete ) and 11284 restraints for refining 10307 atoms. 3525 conditional restraints added. Observations/parameters ratio is 2.27 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2542 (Rfree = 0.000) for 10307 atoms. Found 413 (455 requested) and removed 219 (242 requested) atoms. Cycle 37: After refmac, R = 0.2375 (Rfree = 0.000) for 10473 atoms. Found 334 (454 requested) and removed 96 (246 requested) atoms. Cycle 38: After refmac, R = 0.2291 (Rfree = 0.000) for 10673 atoms. Found 264 (463 requested) and removed 108 (251 requested) atoms. Failed to save intermediate PDB Cycle 39: After refmac, R = 0.2237 (Rfree = 0.000) for 10800 atoms. Found 254 (467 requested) and removed 110 (254 requested) atoms. Cycle 40: After refmac, R = 0.2190 (Rfree = 0.000) for 10908 atoms. Found 251 (473 requested) and removed 135 (257 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.73 1.87 NCS extension: 0 residues added (110 deleted due to clashes), 11033 seeds are put forward Round 1: 1015 peptides, 18 chains. Longest chain 157 peptides. Score 0.965 Round 2: 1022 peptides, 13 chains. Longest chain 157 peptides. Score 0.970 Round 3: 1023 peptides, 15 chains. Longest chain 157 peptides. Score 0.969 Round 4: 1024 peptides, 15 chains. Longest chain 157 peptides. Score 0.969 Round 5: 1020 peptides, 19 chains. Longest chain 157 peptides. Score 0.964 Taking the results from Round 2 Chains 14, Residues 1009, Estimated correctness of the model 99.9 % 13 chains (1007 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 69 A and 74 A Built loop between residues 103 A and 106 A Built loop between residues 208 A and 211 A Built loop between residues 103 C and 106 C Built loop between residues 102 B and 107 B Built loop between residues 154 B and 158 B Built loop between residues 16 D and 20 D Built loop between residues 34 D and 38 D Built loop between residues 103 D and 106 D 4 chains (1032 residues) following loop building 4 chains (1032 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 93715 reflections ( 99.87 % complete ) and 10107 restraints for refining 10292 atoms. 1897 conditional restraints added. Observations/parameters ratio is 2.28 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2539 (Rfree = 0.000) for 10292 atoms. Found 435 (435 requested) and removed 147 (241 requested) atoms. Cycle 42: After refmac, R = 0.2346 (Rfree = 0.000) for 10555 atoms. Found 290 (447 requested) and removed 109 (248 requested) atoms. Cycle 43: After refmac, R = 0.2283 (Rfree = 0.000) for 10685 atoms. Found 284 (454 requested) and removed 104 (252 requested) atoms. Cycle 44: After refmac, R = 0.2234 (Rfree = 0.000) for 10827 atoms. Found 261 (459 requested) and removed 141 (255 requested) atoms. Cycle 45: After refmac, R = 0.2210 (Rfree = 0.000) for 10913 atoms. Found 235 (452 requested) and removed 153 (257 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.73 1.87 NCS extension: 1 residues added (15 deleted due to clashes), 10998 seeds are put forward Round 1: 1017 peptides, 18 chains. Longest chain 157 peptides. Score 0.965 Round 2: 1022 peptides, 16 chains. Longest chain 157 peptides. Score 0.967 Round 3: 1021 peptides, 16 chains. Longest chain 157 peptides. Score 0.967 Round 4: 1020 peptides, 19 chains. Longest chain 157 peptides. Score 0.964 Round 5: 1024 peptides, 14 chains. Longest chain 157 peptides. Score 0.970 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 17, Residues 1010, Estimated correctness of the model 99.9 % 14 chains (1004 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 20 A and 23 A Built loop between residues 35 A and 38 A Built loop between residues 69 A and 73 A Built loop between residues 103 A and 106 A Built loop between residues 16 B and 20 B Built loop between residues 34 B and 38 B Built loop between residues 101 B and 106 B Built loop between residues 101 D and 107 D Built loop between residues 154 D and 157 D 6 chains (1031 residues) following loop building 5 chains (1030 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 93715 reflections ( 99.87 % complete ) and 8197 restraints for refining 7984 atoms. Observations/parameters ratio is 2.93 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3447 (Rfree = 0.000) for 7984 atoms. Found 272 (322 requested) and removed 0 (322 requested) atoms. Cycle 47: After refmac, R = 0.3009 (Rfree = 0.000) for 7984 atoms. Found 169 (334 requested) and removed 4 (194 requested) atoms. Cycle 48: After refmac, R = 0.2829 (Rfree = 0.000) for 7984 atoms. Found 89 (340 requested) and removed 7 (197 requested) atoms. Cycle 49: After refmac, R = 0.2741 (Rfree = 0.000) for 7984 atoms. Found 37 (343 requested) and removed 8 (199 requested) atoms. Writing output files ... Failed to save intermediate PDBFailed to save intermediate PDB Normal termination of warpNtrace Tue 25 Dec 22:13:50 GMT 2018 Job finished. Failed to save intermediate PDB TimeTaking 165.91