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 2p97-1.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2p97-1.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2p97-1.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p97-1.6-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/2p97-1.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p97-1.6-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 19:28:04 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/2p97-1.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p97-1.6-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 517 and 0 Target number of residues in the AU: 517 Target solvent content: 0.4524 Checking the provided sequence file Detected sequence length: 201 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 402 Adjusted target solvent content: 0.57 Input MTZ file: 2p97-1.6-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: 94 Cell parameters: 103.080 103.080 96.168 90.000 90.000 90.000 Input sequence file: 2p97-1.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 3216 target number of atoms Had to go as low as 0.50 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 1 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 72.889 1.600 Wilson plot Bfac: 14.91 68679 reflections ( 99.97 % complete ) and 0 restraints for refining 3570 atoms. Observations/parameters ratio is 4.81 ------------------------------------------------------ Starting model: R = 0.3344 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2706 (Rfree = 0.000) for 3570 atoms. Found 231 (231 requested) and removed 106 (115 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.64 1.49 NCS extension: 0 residues added, 3695 seeds are put forward Round 1: 372 peptides, 16 chains. Longest chain 64 peptides. Score 0.879 Round 2: 376 peptides, 11 chains. Longest chain 85 peptides. Score 0.904 Round 3: 381 peptides, 8 chains. Longest chain 126 peptides. Score 0.919 Round 4: 386 peptides, 9 chains. Longest chain 91 peptides. Score 0.918 Round 5: 382 peptides, 8 chains. Longest chain 129 peptides. Score 0.920 Taking the results from Round 5 Chains 9, Residues 374, Estimated correctness of the model 99.7 % 8 chains (373 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 14 A and 21 A Built loop between residues 67 A and 70 A Built loop between residues 16 B and 23 B Built loop between residues 32 B and 35 B Built loop between residues 48 B and 51 B Built loop between residues 70 B and 73 B 2 chains (393 residues) following loop building 2 chains (393 residues) in sequence following loop building ------------------------------------------------------ 68679 reflections ( 99.97 % complete ) and 3592 restraints for refining 3733 atoms. 423 conditional restraints added. Observations/parameters ratio is 4.60 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2632 (Rfree = 0.000) for 3733 atoms. Found 213 (241 requested) and removed 67 (120 requested) atoms. Failed to save intermediate PDB Cycle 2: After refmac, R = 0.2276 (Rfree = 0.000) for 3879 atoms. Found 184 (250 requested) and removed 42 (125 requested) atoms. Cycle 3: After refmac, R = 0.2136 (Rfree = 0.000) for 4009 atoms. Found 127 (259 requested) and removed 43 (129 requested) atoms. Failed to save intermediate PDB Cycle 4: After refmac, R = 0.2031 (Rfree = 0.000) for 4085 atoms. Found 116 (264 requested) and removed 38 (132 requested) atoms. Cycle 5: After refmac, R = 0.1975 (Rfree = 0.000) for 4156 atoms. Found 120 (268 requested) and removed 50 (134 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.62 1.47 NCS extension: 0 residues added, 4227 seeds are put forward Round 1: 377 peptides, 10 chains. Longest chain 102 peptides. Score 0.909 Round 2: 390 peptides, 6 chains. Longest chain 160 peptides. Score 0.931 Round 3: 385 peptides, 9 chains. Longest chain 108 peptides. Score 0.917 Round 4: 391 peptides, 7 chains. Longest chain 145 peptides. Score 0.928 Round 5: 392 peptides, 5 chains. Longest chain 180 peptides. Score 0.936 Taking the results from Round 5 Chains 5, Residues 387, Estimated correctness of the model 99.8 % 5 chains (387 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 18 A and 21 A Built loop between residues 16 B and 22 B Built loop between residues 129 B and 132 B 2 chains (396 residues) following loop building 2 chains (396 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 68679 reflections ( 99.97 % complete ) and 3853 restraints for refining 3970 atoms. 665 conditional restraints added. Observations/parameters ratio is 4.32 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2021 (Rfree = 0.000) for 3970 atoms. Found 200 (256 requested) and removed 45 (128 requested) atoms. Cycle 7: After refmac, R = 0.1957 (Rfree = 0.000) for 4123 atoms. Found 138 (266 requested) and removed 51 (133 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.1918 (Rfree = 0.000) for 4198 atoms. Found 121 (272 requested) and removed 74 (136 requested) atoms. Cycle 9: After refmac, R = 0.1882 (Rfree = 0.000) for 4234 atoms. Found 129 (269 requested) and removed 61 (137 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.1874 (Rfree = 0.000) for 4297 atoms. Found 125 (272 requested) and removed 81 (139 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.62 1.47 NCS extension: 0 residues added, 4343 seeds are put forward Round 1: 386 peptides, 7 chains. Longest chain 120 peptides. Score 0.926 Round 2: 389 peptides, 9 chains. Longest chain 160 peptides. Score 0.920 Round 3: 389 peptides, 8 chains. Longest chain 160 peptides. Score 0.923 Round 4: 393 peptides, 6 chains. Longest chain 163 peptides. Score 0.933 Round 5: 390 peptides, 10 chains. Longest chain 166 peptides. Score 0.916 Taking the results from Round 4 Chains 6, Residues 387, Estimated correctness of the model 99.8 % 5 chains (370 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 16 B and 22 B Built loop between residues 135 B and 138 B 4 chains (394 residues) following loop building 3 chains (377 residues) in sequence following loop building ------------------------------------------------------ 68679 reflections ( 99.97 % complete ) and 4137 restraints for refining 4031 atoms. 1044 conditional restraints added. Observations/parameters ratio is 4.26 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1990 (Rfree = 0.000) for 4031 atoms. Found 228 (250 requested) and removed 46 (130 requested) atoms. Failed to save intermediate PDB Cycle 12: After refmac, R = 0.1940 (Rfree = 0.000) for 4206 atoms. Found 130 (261 requested) and removed 67 (136 requested) atoms. Cycle 13: After refmac, R = 0.1889 (Rfree = 0.000) for 4264 atoms. Found 136 (258 requested) and removed 58 (137 requested) atoms. Failed to save intermediate PDB Cycle 14: After refmac, R = 0.1873 (Rfree = 0.000) for 4332 atoms. Found 124 (263 requested) and removed 74 (140 requested) atoms. Cycle 15: After refmac, R = 0.1865 (Rfree = 0.000) for 4374 atoms. Found 115 (260 requested) and removed 78 (141 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.63 1.48 NCS extension: 4 residues added (32 deleted due to clashes), 4415 seeds are put forward Round 1: 388 peptides, 8 chains. Longest chain 109 peptides. Score 0.923 Round 2: 389 peptides, 8 chains. Longest chain 179 peptides. Score 0.923 Round 3: 391 peptides, 7 chains. Longest chain 160 peptides. Score 0.928 Round 4: 389 peptides, 7 chains. Longest chain 90 peptides. Score 0.927 Round 5: 392 peptides, 5 chains. Longest chain 199 peptides. Score 0.936 Taking the results from Round 5 Chains 6, Residues 387, Estimated correctness of the model 99.8 % 4 chains (382 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 16 B and 23 B Built loop between residues 33 B and 41 B 2 chains (395 residues) following loop building 2 chains (395 residues) in sequence following loop building ------------------------------------------------------ 68679 reflections ( 99.97 % complete ) and 3957 restraints for refining 4056 atoms. 776 conditional restraints added. Observations/parameters ratio is 4.23 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1975 (Rfree = 0.000) for 4056 atoms. Found 219 (236 requested) and removed 56 (131 requested) atoms. Cycle 17: After refmac, R = 0.1931 (Rfree = 0.000) for 4213 atoms. Found 114 (245 requested) and removed 67 (136 requested) atoms. Cycle 18: After refmac, R = 0.1864 (Rfree = 0.000) for 4247 atoms. Found 149 (242 requested) and removed 52 (137 requested) atoms. Cycle 19: After refmac, R = 0.1853 (Rfree = 0.000) for 4333 atoms. Found 115 (246 requested) and removed 78 (140 requested) atoms. Cycle 20: After refmac, R = 0.1825 (Rfree = 0.000) for 4360 atoms. Found 154 (243 requested) and removed 69 (141 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.62 1.47 NCS extension: 64 residues added (135 deleted due to clashes), 4510 seeds are put forward Round 1: 385 peptides, 9 chains. Longest chain 107 peptides. Score 0.917 Round 2: 388 peptides, 7 chains. Longest chain 160 peptides. Score 0.927 Round 3: 389 peptides, 7 chains. Longest chain 160 peptides. Score 0.927 Round 4: 391 peptides, 7 chains. Longest chain 181 peptides. Score 0.928 Round 5: 388 peptides, 8 chains. Longest chain 107 peptides. Score 0.923 Taking the results from Round 4 Chains 8, Residues 384, Estimated correctness of the model 99.7 % 6 chains (380 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 16 A and 24 A Built loop between residues 33 A and 39 A Built loop between residues 71 A and 74 A Built loop between residues 16 B and 20 B 2 chains (397 residues) following loop building 2 chains (397 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 68679 reflections ( 99.97 % complete ) and 3941 restraints for refining 4081 atoms. 745 conditional restraints added. Observations/parameters ratio is 4.21 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1963 (Rfree = 0.000) for 4081 atoms. Found 227 (227 requested) and removed 56 (132 requested) atoms. Cycle 22: After refmac, R = 0.1937 (Rfree = 0.000) for 4238 atoms. Found 151 (236 requested) and removed 69 (137 requested) atoms. Failed to save intermediate PDB Cycle 23: After refmac, R = 0.1899 (Rfree = 0.000) for 4314 atoms. Found 136 (240 requested) and removed 66 (139 requested) atoms. Cycle 24: After refmac, R = 0.1886 (Rfree = 0.000) for 4373 atoms. Found 125 (243 requested) and removed 90 (141 requested) atoms. Cycle 25: After refmac, R = 0.1855 (Rfree = 0.000) for 4398 atoms. Found 135 (239 requested) and removed 70 (142 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.62 1.47 NCS extension: 0 residues added, 4463 seeds are put forward Round 1: 382 peptides, 8 chains. Longest chain 113 peptides. Score 0.920 Round 2: 387 peptides, 9 chains. Longest chain 160 peptides. Score 0.919 Round 3: 389 peptides, 5 chains. Longest chain 178 peptides. Score 0.934 Round 4: 391 peptides, 6 chains. Longest chain 106 peptides. Score 0.932 Round 5: 384 peptides, 11 chains. Longest chain 89 peptides. Score 0.909 Taking the results from Round 3 Chains 6, Residues 384, Estimated correctness of the model 99.8 % 5 chains (383 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 16 A and 24 A Built loop between residues 38 B and 41 B 4 chains (393 residues) following loop building 4 chains (393 residues) in sequence following loop building ------------------------------------------------------ 68679 reflections ( 99.97 % complete ) and 4157 restraints for refining 4135 atoms. 999 conditional restraints added. Observations/parameters ratio is 4.15 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1991 (Rfree = 0.000) for 4135 atoms. Found 209 (219 requested) and removed 70 (133 requested) atoms. Failed to save intermediate PDB Cycle 27: After refmac, R = 0.1946 (Rfree = 0.000) for 4267 atoms. Found 136 (226 requested) and removed 75 (138 requested) atoms. Cycle 28: After refmac, R = 0.1886 (Rfree = 0.000) for 4322 atoms. Found 144 (223 requested) and removed 72 (139 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.1871 (Rfree = 0.000) for 4383 atoms. Found 115 (227 requested) and removed 81 (142 requested) atoms. Cycle 30: After refmac, R = 0.1852 (Rfree = 0.000) for 4406 atoms. Found 133 (222 requested) and removed 68 (142 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.62 1.47 NCS extension: 0 residues added, 4473 seeds are put forward Round 1: 385 peptides, 6 chains. Longest chain 140 peptides. Score 0.929 Round 2: 389 peptides, 6 chains. Longest chain 180 peptides. Score 0.931 Round 3: 388 peptides, 8 chains. Longest chain 94 peptides. Score 0.923 Round 4: 388 peptides, 6 chains. Longest chain 199 peptides. Score 0.930 Round 5: 384 peptides, 6 chains. Longest chain 199 peptides. Score 0.928 Taking the results from Round 2 Chains 6, Residues 383, Estimated correctness of the model 99.7 % 6 chains (383 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 16 A and 24 A Built loop between residues 32 A and 35 A Built loop between residues 71 A and 74 A Built loop between residues 18 B and 21 B 2 chains (396 residues) following loop building 2 chains (396 residues) in sequence following loop building ------------------------------------------------------ 68679 reflections ( 99.97 % complete ) and 4091 restraints for refining 4132 atoms. 903 conditional restraints added. Observations/parameters ratio is 4.16 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1952 (Rfree = 0.000) for 4132 atoms. Found 203 (203 requested) and removed 50 (133 requested) atoms. Cycle 32: After refmac, R = 0.1897 (Rfree = 0.000) for 4278 atoms. Found 130 (211 requested) and removed 69 (138 requested) atoms. Cycle 33: After refmac, R = 0.1860 (Rfree = 0.000) for 4327 atoms. Found 132 (207 requested) and removed 68 (140 requested) atoms. Cycle 34: After refmac, R = 0.1843 (Rfree = 0.000) for 4382 atoms. Found 111 (204 requested) and removed 71 (141 requested) atoms. Cycle 35: After refmac, R = 0.1812 (Rfree = 0.000) for 4412 atoms. Found 130 (199 requested) and removed 67 (142 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.62 1.47 NCS extension: 48 residues added (151 deleted due to clashes), 4524 seeds are put forward Round 1: 379 peptides, 8 chains. Longest chain 117 peptides. Score 0.918 Round 2: 390 peptides, 6 chains. Longest chain 160 peptides. Score 0.931 Round 3: 387 peptides, 9 chains. Longest chain 94 peptides. Score 0.919 Round 4: 390 peptides, 5 chains. Longest chain 199 peptides. Score 0.935 Round 5: 388 peptides, 7 chains. Longest chain 135 peptides. Score 0.927 Taking the results from Round 4 Chains 5, Residues 385, Estimated correctness of the model 99.8 % 4 chains (382 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 16 B and 24 B Built loop between residues 33 B and 41 B 2 chains (396 residues) following loop building 2 chains (396 residues) in sequence following loop building ------------------------------------------------------ 68679 reflections ( 99.97 % complete ) and 4070 restraints for refining 4132 atoms. 882 conditional restraints added. Observations/parameters ratio is 4.16 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1950 (Rfree = 0.000) for 4132 atoms. Found 182 (182 requested) and removed 50 (133 requested) atoms. Cycle 37: After refmac, R = 0.1898 (Rfree = 0.000) for 4251 atoms. Found 137 (187 requested) and removed 59 (137 requested) atoms. Failed to save intermediate PDB Cycle 38: After refmac, R = 0.1851 (Rfree = 0.000) for 4326 atoms. Found 136 (190 requested) and removed 48 (139 requested) atoms. Cycle 39: After refmac, R = 0.1833 (Rfree = 0.000) for 4408 atoms. Found 102 (194 requested) and removed 75 (142 requested) atoms. Cycle 40: After refmac, R = 0.1817 (Rfree = 0.000) for 4425 atoms. Found 128 (189 requested) and removed 78 (143 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.62 1.47 NCS extension: 66 residues added (133 deleted due to clashes), 4542 seeds are put forward Round 1: 380 peptides, 10 chains. Longest chain 122 peptides. Score 0.910 Round 2: 386 peptides, 6 chains. Longest chain 160 peptides. Score 0.929 Round 3: 388 peptides, 7 chains. Longest chain 179 peptides. Score 0.927 Round 4: 387 peptides, 8 chains. Longest chain 127 peptides. Score 0.922 Round 5: 388 peptides, 7 chains. Longest chain 129 peptides. Score 0.927 Taking the results from Round 2 Chains 6, Residues 380, Estimated correctness of the model 99.7 % 6 chains (380 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 16 A and 24 A Built loop between residues 71 A and 74 A Built loop between residues 18 B and 23 B Built loop between residues 38 B and 41 B 2 chains (395 residues) following loop building 2 chains (395 residues) in sequence following loop building ------------------------------------------------------ 68679 reflections ( 99.97 % complete ) and 4054 restraints for refining 4139 atoms. 873 conditional restraints added. Observations/parameters ratio is 4.15 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1935 (Rfree = 0.000) for 4139 atoms. Found 171 (171 requested) and removed 41 (133 requested) atoms. Cycle 42: After refmac, R = 0.1890 (Rfree = 0.000) for 4261 atoms. Found 140 (177 requested) and removed 45 (138 requested) atoms. Cycle 43: After refmac, R = 0.1858 (Rfree = 0.000) for 4352 atoms. Found 122 (180 requested) and removed 63 (140 requested) atoms. Cycle 44: After refmac, R = 0.1845 (Rfree = 0.000) for 4403 atoms. Found 110 (177 requested) and removed 74 (142 requested) atoms. Failed to save intermediate PDB Cycle 45: After refmac, R = 0.1837 (Rfree = 0.000) for 4427 atoms. Found 123 (172 requested) and removed 60 (143 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.62 1.47 NCS extension: 78 residues added (121 deleted due to clashes), 4569 seeds are put forward Round 1: 382 peptides, 8 chains. Longest chain 120 peptides. Score 0.920 Round 2: 388 peptides, 6 chains. Longest chain 126 peptides. Score 0.930 Round 3: 383 peptides, 10 chains. Longest chain 160 peptides. Score 0.912 Round 4: 388 peptides, 8 chains. Longest chain 160 peptides. Score 0.923 Round 5: 392 peptides, 7 chains. Longest chain 179 peptides. Score 0.929 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 6, Residues 382, Estimated correctness of the model 99.7 % 6 chains (382 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 16 A and 24 A Built loop between residues 71 A and 74 A Built loop between residues 32 B and 35 B Built loop between residues 128 B and 131 B 2 chains (395 residues) following loop building 2 chains (395 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 68679 reflections ( 99.97 % complete ) and 3181 restraints for refining 3115 atoms. Observations/parameters ratio is 5.51 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2689 (Rfree = 0.000) for 3115 atoms. Found 121 (121 requested) and removed 0 (121 requested) atoms. Cycle 47: After refmac, R = 0.2463 (Rfree = 0.000) for 3115 atoms. Found 115 (125 requested) and removed 0 (104 requested) atoms. Cycle 48: After refmac, R = 0.2291 (Rfree = 0.000) for 3115 atoms. Found 42 (130 requested) and removed 2 (108 requested) atoms. Cycle 49: After refmac, R = 0.2182 (Rfree = 0.000) for 3115 atoms. Found 41 (131 requested) and removed 2 (109 requested) atoms. Writing output files ... Failed to save intermediate PDB TimeTaking 90.69