null 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 2fno-1.9-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2fno-1.9-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2fno-1.9-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fno-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/2fno-1.9-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fno-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/2fno-1.9-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fno-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 529 and 0 Target number of residues in the AU: 529 Target solvent content: 0.5124 Checking the provided sequence file Detected sequence length: 248 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 496 Adjusted target solvent content: 0.54 Input MTZ file: 2fno-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: 5 Cell parameters: 110.204 50.261 117.660 90.000 115.716 90.000 Input sequence file: 2fno-1.9-parrot-hancs.fasta_lf Building free atoms model in initial map for 3968 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: 106.006 1.904 Wilson plot Bfac: 26.04 38894 reflections ( 85.02 % complete ) and 0 restraints for refining 4409 atoms. Observations/parameters ratio is 2.21 ------------------------------------------------------ Starting model: R = 0.3394 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2799 (Rfree = 0.000) for 4409 atoms. Found 173 (173 requested) and removed 90 (86 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.10 1.99 NCS extension: 0 residues added, 4492 seeds are put forward Round 1: 351 peptides, 43 chains. Longest chain 23 peptides. Score 0.635 Round 2: 395 peptides, 31 chains. Longest chain 33 peptides. Score 0.787 Round 3: 419 peptides, 24 chains. Longest chain 51 peptides. Score 0.847 Round 4: 437 peptides, 17 chains. Longest chain 45 peptides. Score 0.890 Round 5: 440 peptides, 14 chains. Longest chain 93 peptides. Score 0.903 Taking the results from Round 5 Chains 16, Residues 426, Estimated correctness of the model 99.2 % 11 chains (406 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 40 A and 43 A Built loop between residues 70 A and 73 A Built loop between residues 164 A and 167 A Built loop between residues 212 A and 215 A Built loop between residues 75 B and 84 B Built loop between residues 100 B and 108 B Built loop between residues 127 B and 132 B Built loop between residues 225 B and 229 B 7 chains (453 residues) following loop building 3 chains (436 residues) in sequence following loop building ------------------------------------------------------ 38894 reflections ( 85.02 % complete ) and 4331 restraints for refining 4170 atoms. 811 conditional restraints added. Observations/parameters ratio is 2.33 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3196 (Rfree = 0.000) for 4170 atoms. Found 164 (164 requested) and removed 91 (82 requested) atoms. Cycle 2: After refmac, R = 0.2795 (Rfree = 0.000) for 4235 atoms. Found 135 (164 requested) and removed 71 (83 requested) atoms. Cycle 3: After refmac, R = 0.2598 (Rfree = 0.000) for 4259 atoms. Found 131 (162 requested) and removed 41 (84 requested) atoms. Cycle 4: After refmac, R = 0.2526 (Rfree = 0.000) for 4324 atoms. Found 91 (164 requested) and removed 47 (85 requested) atoms. Cycle 5: After refmac, R = 0.2434 (Rfree = 0.000) for 4352 atoms. Found 103 (161 requested) and removed 39 (85 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.06 1.95 NCS extension: 5 residues added (150 deleted due to clashes), 4430 seeds are put forward Round 1: 452 peptides, 9 chains. Longest chain 177 peptides. Score 0.926 Round 2: 454 peptides, 8 chains. Longest chain 192 peptides. Score 0.930 Round 3: 453 peptides, 12 chains. Longest chain 124 peptides. Score 0.917 Round 4: 454 peptides, 9 chains. Longest chain 92 peptides. Score 0.927 Round 5: 460 peptides, 9 chains. Longest chain 133 peptides. Score 0.930 Taking the results from Round 5 Chains 11, Residues 451, Estimated correctness of the model 99.5 % 7 chains (388 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 199 A and 203 A Built loop between residues 203 B and 206 B 8 chains (454 residues) following loop building 5 chains (393 residues) in sequence following loop building ------------------------------------------------------ 38894 reflections ( 85.02 % complete ) and 4618 restraints for refining 4201 atoms. 1260 conditional restraints added. Observations/parameters ratio is 2.31 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2510 (Rfree = 0.000) for 4201 atoms. Found 155 (155 requested) and removed 88 (82 requested) atoms. Cycle 7: After refmac, R = 0.2373 (Rfree = 0.000) for 4263 atoms. Found 117 (154 requested) and removed 50 (83 requested) atoms. Cycle 8: After refmac, R = 0.2281 (Rfree = 0.000) for 4328 atoms. Found 98 (156 requested) and removed 63 (85 requested) atoms. Cycle 9: After refmac, R = 0.2229 (Rfree = 0.000) for 4358 atoms. Found 106 (154 requested) and removed 68 (85 requested) atoms. Cycle 10: After refmac, R = 0.2190 (Rfree = 0.000) for 4391 atoms. Found 106 (151 requested) and removed 67 (86 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.05 1.94 NCS extension: 7 residues added (34 deleted due to clashes), 4442 seeds are put forward Round 1: 456 peptides, 10 chains. Longest chain 175 peptides. Score 0.925 Round 2: 461 peptides, 7 chains. Longest chain 177 peptides. Score 0.936 Round 3: 460 peptides, 8 chains. Longest chain 176 peptides. Score 0.933 Round 4: 459 peptides, 7 chains. Longest chain 227 peptides. Score 0.935 Round 5: 458 peptides, 8 chains. Longest chain 130 peptides. Score 0.932 Taking the results from Round 2 Chains 8, Residues 454, Estimated correctness of the model 99.6 % 6 chains (444 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 71 A and 74 A Built loop between residues 105 A and 108 A Built loop between residues 51 B and 54 B Built loop between residues 70 B and 73 B 4 chains (462 residues) following loop building 2 chains (452 residues) in sequence following loop building ------------------------------------------------------ 38894 reflections ( 85.02 % complete ) and 4213 restraints for refining 4288 atoms. 607 conditional restraints added. Observations/parameters ratio is 2.27 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2368 (Rfree = 0.000) for 4288 atoms. Found 145 (145 requested) and removed 88 (84 requested) atoms. Cycle 12: After refmac, R = 0.2248 (Rfree = 0.000) for 4340 atoms. Found 100 (143 requested) and removed 57 (85 requested) atoms. Cycle 13: After refmac, R = 0.2151 (Rfree = 0.000) for 4380 atoms. Found 103 (141 requested) and removed 43 (86 requested) atoms. Cycle 14: After refmac, R = 0.2146 (Rfree = 0.000) for 4434 atoms. Found 102 (143 requested) and removed 82 (87 requested) atoms. Cycle 15: After refmac, R = 0.2089 (Rfree = 0.000) for 4450 atoms. Found 106 (140 requested) and removed 72 (87 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.04 1.93 NCS extension: 6 residues added (11 deleted due to clashes), 4493 seeds are put forward Round 1: 459 peptides, 6 chains. Longest chain 176 peptides. Score 0.938 Round 2: 456 peptides, 9 chains. Longest chain 141 peptides. Score 0.928 Round 3: 460 peptides, 7 chains. Longest chain 143 peptides. Score 0.936 Round 4: 460 peptides, 9 chains. Longest chain 136 peptides. Score 0.930 Round 5: 454 peptides, 10 chains. Longest chain 96 peptides. Score 0.924 Taking the results from Round 1 Chains 7, Residues 453, Estimated correctness of the model 99.6 % 6 chains (452 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 27 A and 30 A Built loop between residues 69 A and 72 A Built loop between residues 70 B and 73 B 4 chains (459 residues) following loop building 4 chains (459 residues) in sequence following loop building ------------------------------------------------------ 38894 reflections ( 85.02 % complete ) and 4153 restraints for refining 4297 atoms. 517 conditional restraints added. Observations/parameters ratio is 2.26 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2246 (Rfree = 0.000) for 4297 atoms. Found 132 (132 requested) and removed 69 (84 requested) atoms. Cycle 17: After refmac, R = 0.2199 (Rfree = 0.000) for 4355 atoms. Found 122 (130 requested) and removed 60 (85 requested) atoms. Cycle 18: After refmac, R = 0.2112 (Rfree = 0.000) for 4416 atoms. Found 117 (131 requested) and removed 75 (86 requested) atoms. Cycle 19: After refmac, R = 0.2105 (Rfree = 0.000) for 4455 atoms. Found 111 (129 requested) and removed 92 (87 requested) atoms. Cycle 20: After refmac, R = 0.2065 (Rfree = 0.000) for 4469 atoms. Found 121 (127 requested) and removed 85 (88 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.03 1.92 NCS extension: 5 residues added (29 deleted due to clashes), 4514 seeds are put forward Round 1: 458 peptides, 7 chains. Longest chain 156 peptides. Score 0.935 Round 2: 458 peptides, 7 chains. Longest chain 121 peptides. Score 0.935 Round 3: 458 peptides, 9 chains. Longest chain 164 peptides. Score 0.929 Round 4: 457 peptides, 7 chains. Longest chain 141 peptides. Score 0.935 Round 5: 454 peptides, 14 chains. Longest chain 110 peptides. Score 0.911 Taking the results from Round 4 Chains 10, Residues 450, Estimated correctness of the model 99.6 % 8 chains (446 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 69 A and 74 A Built loop between residues 104 A and 108 A Built loop between residues 70 B and 73 B Built loop between residues 172 B and 177 B Built loop between residues 202 B and 205 B 3 chains (461 residues) following loop building 3 chains (461 residues) in sequence following loop building ------------------------------------------------------ 38894 reflections ( 85.02 % complete ) and 4112 restraints for refining 4300 atoms. 455 conditional restraints added. Observations/parameters ratio is 2.26 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2299 (Rfree = 0.000) for 4300 atoms. Found 118 (118 requested) and removed 66 (84 requested) atoms. Cycle 22: After refmac, R = 0.2208 (Rfree = 0.000) for 4350 atoms. Found 116 (116 requested) and removed 50 (85 requested) atoms. Cycle 23: After refmac, R = 0.2132 (Rfree = 0.000) for 4414 atoms. Found 118 (118 requested) and removed 61 (86 requested) atoms. Cycle 24: After refmac, R = 0.2094 (Rfree = 0.000) for 4466 atoms. Found 104 (115 requested) and removed 80 (87 requested) atoms. Cycle 25: After refmac, R = 0.2063 (Rfree = 0.000) for 4487 atoms. Found 113 (113 requested) and removed 81 (88 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.04 1.93 NCS extension: 6 residues added (32 deleted due to clashes), 4528 seeds are put forward Round 1: 459 peptides, 8 chains. Longest chain 117 peptides. Score 0.932 Round 2: 459 peptides, 8 chains. Longest chain 129 peptides. Score 0.932 Round 3: 455 peptides, 8 chains. Longest chain 118 peptides. Score 0.931 Round 4: 452 peptides, 10 chains. Longest chain 118 peptides. Score 0.923 Round 5: 452 peptides, 11 chains. Longest chain 117 peptides. Score 0.920 Taking the results from Round 2 Chains 8, Residues 451, Estimated correctness of the model 99.6 % 7 chains (441 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 71 A and 74 A Built loop between residues 104 A and 108 A Built loop between residues 128 A and 131 A Built loop between residues 71 B and 75 B Built loop between residues 202 B and 205 B 3 chains (463 residues) following loop building 2 chains (453 residues) in sequence following loop building ------------------------------------------------------ 38894 reflections ( 85.02 % complete ) and 4247 restraints for refining 4324 atoms. 635 conditional restraints added. Observations/parameters ratio is 2.25 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2254 (Rfree = 0.000) for 4324 atoms. Found 105 (105 requested) and removed 71 (85 requested) atoms. Cycle 27: After refmac, R = 0.2149 (Rfree = 0.000) for 4353 atoms. Found 103 (103 requested) and removed 39 (85 requested) atoms. Cycle 28: After refmac, R = 0.2074 (Rfree = 0.000) for 4412 atoms. Found 104 (104 requested) and removed 51 (86 requested) atoms. Cycle 29: After refmac, R = 0.2032 (Rfree = 0.000) for 4464 atoms. Found 105 (105 requested) and removed 69 (87 requested) atoms. Cycle 30: After refmac, R = 0.2013 (Rfree = 0.000) for 4498 atoms. Found 103 (103 requested) and removed 64 (88 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.05 1.94 NCS extension: 4 residues added (41 deleted due to clashes), 4548 seeds are put forward Round 1: 458 peptides, 8 chains. Longest chain 143 peptides. Score 0.932 Round 2: 458 peptides, 6 chains. Longest chain 141 peptides. Score 0.938 Round 3: 458 peptides, 9 chains. Longest chain 141 peptides. Score 0.929 Round 4: 459 peptides, 9 chains. Longest chain 136 peptides. Score 0.929 Round 5: 460 peptides, 8 chains. Longest chain 141 peptides. Score 0.933 Taking the results from Round 2 Chains 6, Residues 452, Estimated correctness of the model 99.6 % 6 chains (452 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 71 A and 74 A Built loop between residues 103 A and 108 A Built loop between residues 71 B and 75 B Built loop between residues 127 B and 131 B 2 chains (464 residues) following loop building 2 chains (464 residues) in sequence following loop building ------------------------------------------------------ 38894 reflections ( 85.02 % complete ) and 4129 restraints for refining 4358 atoms. 444 conditional restraints added. Observations/parameters ratio is 2.23 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2264 (Rfree = 0.000) for 4358 atoms. Found 96 (96 requested) and removed 75 (85 requested) atoms. Cycle 32: After refmac, R = 0.2134 (Rfree = 0.000) for 4376 atoms. Found 93 (93 requested) and removed 29 (86 requested) atoms. Cycle 33: After refmac, R = 0.2058 (Rfree = 0.000) for 4435 atoms. Found 94 (94 requested) and removed 49 (87 requested) atoms. Cycle 34: After refmac, R = 0.2032 (Rfree = 0.000) for 4475 atoms. Found 92 (92 requested) and removed 64 (88 requested) atoms. Cycle 35: After refmac, R = 0.2016 (Rfree = 0.000) for 4497 atoms. Found 88 (88 requested) and removed 65 (88 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.05 1.94 NCS extension: 20 residues added (250 deleted due to clashes), 4545 seeds are put forward Round 1: 458 peptides, 8 chains. Longest chain 176 peptides. Score 0.932 Round 2: 459 peptides, 5 chains. Longest chain 141 peptides. Score 0.941 Round 3: 456 peptides, 9 chains. Longest chain 144 peptides. Score 0.928 Round 4: 460 peptides, 8 chains. Longest chain 118 peptides. Score 0.933 Round 5: 450 peptides, 9 chains. Longest chain 114 peptides. Score 0.925 Taking the results from Round 2 Chains 5, Residues 454, Estimated correctness of the model 99.7 % 5 chains (454 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 71 A and 75 A Built loop between residues 127 A and 131 A Built loop between residues 103 B and 108 B 2 chains (464 residues) following loop building 2 chains (464 residues) in sequence following loop building ------------------------------------------------------ 38894 reflections ( 85.02 % complete ) and 4157 restraints for refining 4354 atoms. 472 conditional restraints added. Observations/parameters ratio is 2.23 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2231 (Rfree = 0.000) for 4354 atoms. Found 85 (85 requested) and removed 61 (85 requested) atoms. Cycle 37: After refmac, R = 0.2118 (Rfree = 0.000) for 4374 atoms. Found 86 (86 requested) and removed 26 (86 requested) atoms. Cycle 38: After refmac, R = 0.2053 (Rfree = 0.000) for 4430 atoms. Found 87 (87 requested) and removed 52 (87 requested) atoms. Cycle 39: After refmac, R = 0.2002 (Rfree = 0.000) for 4464 atoms. Found 87 (87 requested) and removed 59 (87 requested) atoms. Cycle 40: After refmac, R = 0.1977 (Rfree = 0.000) for 4489 atoms. Found 88 (88 requested) and removed 64 (88 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.05 1.94 NCS extension: 5 residues added (29 deleted due to clashes), 4523 seeds are put forward Round 1: 460 peptides, 7 chains. Longest chain 176 peptides. Score 0.936 Round 2: 461 peptides, 6 chains. Longest chain 144 peptides. Score 0.939 Round 3: 455 peptides, 11 chains. Longest chain 93 peptides. Score 0.921 Round 4: 461 peptides, 6 chains. Longest chain 144 peptides. Score 0.939 Round 5: 452 peptides, 7 chains. Longest chain 136 peptides. Score 0.933 Taking the results from Round 4 Chains 6, Residues 455, Estimated correctness of the model 99.6 % 5 chains (445 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 102 A and 105 A Built loop between residues 127 B and 131 B 4 chains (460 residues) following loop building 3 chains (450 residues) in sequence following loop building ------------------------------------------------------ 38894 reflections ( 85.02 % complete ) and 4253 restraints for refining 4317 atoms. 648 conditional restraints added. Observations/parameters ratio is 2.25 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2255 (Rfree = 0.000) for 4317 atoms. Found 85 (85 requested) and removed 78 (85 requested) atoms. Cycle 42: After refmac, R = 0.2139 (Rfree = 0.000) for 4316 atoms. Found 85 (85 requested) and removed 32 (85 requested) atoms. Cycle 43: After refmac, R = 0.2077 (Rfree = 0.000) for 4367 atoms. Found 85 (85 requested) and removed 44 (85 requested) atoms. Cycle 44: After refmac, R = 0.2033 (Rfree = 0.000) for 4405 atoms. Found 86 (86 requested) and removed 62 (86 requested) atoms. Cycle 45: After refmac, R = 0.2016 (Rfree = 0.000) for 4425 atoms. Found 87 (87 requested) and removed 62 (87 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.05 1.94 NCS extension: 17 residues added (283 deleted due to clashes), 4469 seeds are put forward Round 1: 457 peptides, 8 chains. Longest chain 118 peptides. Score 0.932 Round 2: 462 peptides, 5 chains. Longest chain 176 peptides. Score 0.942 Round 3: 459 peptides, 7 chains. Longest chain 141 peptides. Score 0.935 Round 4: 461 peptides, 7 chains. Longest chain 219 peptides. Score 0.936 Round 5: 455 peptides, 12 chains. Longest chain 74 peptides. Score 0.918 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 5, Residues 457, Estimated correctness of the model 99.7 % 5 chains (457 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 71 A and 74 A Built loop between residues 127 A and 131 A Built loop between residues 69 B and 73 B 2 chains (465 residues) following loop building 2 chains (465 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 38894 reflections ( 85.02 % complete ) and 3693 restraints for refining 3611 atoms. Observations/parameters ratio is 2.69 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2844 (Rfree = 0.000) for 3611 atoms. Found 60 (71 requested) and removed 0 (71 requested) atoms. Cycle 47: After refmac, R = 0.2647 (Rfree = 0.000) for 3611 atoms. Found 31 (72 requested) and removed 1 (72 requested) atoms. Cycle 48: After refmac, R = 0.2515 (Rfree = 0.000) for 3611 atoms. Found 17 (72 requested) and removed 4 (72 requested) atoms. Cycle 49: After refmac, R = 0.2449 (Rfree = 0.000) for 3611 atoms. Found 27 (73 requested) and removed 2 (73 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:40:07 GMT 2018 Job finished. TimeTaking 77.08 Used memory is bytes: 15962544