null Mon 24 Dec 00:20:46 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 2o62-1.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2o62-1.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2o62-1.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2o62-1.8-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/2o62-1.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2o62-1.8-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 00:20:51 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/2o62-1.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2o62-1.8-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 587 and 0 Target number of residues in the AU: 587 Target solvent content: 0.4555 Checking the provided sequence file Detected sequence length: 270 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 540 Adjusted target solvent content: 0.50 Input MTZ file: 2o62-1.8-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: 19 Cell parameters: 61.210 71.880 132.610 90.000 90.000 90.000 Input sequence file: 2o62-1.8-parrot-mrncs.fasta_lf Building free atoms model in initial map for 4320 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: 66.305 1.750 Wilson plot Bfac: 15.38 56224 reflections ( 94.10 % complete ) and 0 restraints for refining 4753 atoms. Observations/parameters ratio is 2.96 ------------------------------------------------------ Starting model: R = 0.3707 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3259 (Rfree = 0.000) for 4753 atoms. Found 156 (238 requested) and removed 124 (119 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.81 1.81 NCS extension: 0 residues added, 4785 seeds are put forward Round 1: 386 peptides, 43 chains. Longest chain 31 peptides. Score 0.697 Round 2: 423 peptides, 32 chains. Longest chain 43 peptides. Score 0.813 Round 3: 448 peptides, 25 chains. Longest chain 64 peptides. Score 0.867 Round 4: 465 peptides, 22 chains. Longest chain 85 peptides. Score 0.890 Round 5: 479 peptides, 20 chains. Longest chain 89 peptides. Score 0.905 Taking the results from Round 5 Chains 25, Residues 459, Estimated correctness of the model 99.4 % 7 chains (336 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 240 B and 244 B 23 chains (461 residues) following loop building 6 chains (339 residues) in sequence following loop building ------------------------------------------------------ 56224 reflections ( 94.10 % complete ) and 5725 restraints for refining 4603 atoms. 2509 conditional restraints added. Observations/parameters ratio is 3.05 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3470 (Rfree = 0.000) for 4603 atoms. Found 177 (230 requested) and removed 123 (115 requested) atoms. Cycle 2: After refmac, R = 0.3174 (Rfree = 0.000) for 4637 atoms. Found 139 (228 requested) and removed 54 (116 requested) atoms. Cycle 3: After refmac, R = 0.2980 (Rfree = 0.000) for 4696 atoms. Found 113 (231 requested) and removed 26 (118 requested) atoms. Cycle 4: After refmac, R = 0.2832 (Rfree = 0.000) for 4762 atoms. Found 101 (234 requested) and removed 22 (119 requested) atoms. Cycle 5: After refmac, R = 0.2715 (Rfree = 0.000) for 4824 atoms. Found 90 (237 requested) and removed 18 (121 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.76 1.76 NCS extension: 73 residues added (28 deleted due to clashes), 4972 seeds are put forward Round 1: 481 peptides, 19 chains. Longest chain 96 peptides. Score 0.909 Round 2: 492 peptides, 15 chains. Longest chain 96 peptides. Score 0.927 Round 3: 496 peptides, 17 chains. Longest chain 83 peptides. Score 0.922 Round 4: 492 peptides, 15 chains. Longest chain 97 peptides. Score 0.927 Round 5: 498 peptides, 18 chains. Longest chain 84 peptides. Score 0.920 Taking the results from Round 4 Chains 16, Residues 477, Estimated correctness of the model 99.6 % 8 chains (423 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 154 A and 163 A Built loop between residues 230 A and 234 A Built loop between residues 66 B and 70 B 12 chains (490 residues) following loop building 5 chains (437 residues) in sequence following loop building ------------------------------------------------------ 56224 reflections ( 94.10 % complete ) and 5492 restraints for refining 4877 atoms. 1749 conditional restraints added. Observations/parameters ratio is 2.88 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2658 (Rfree = 0.000) for 4877 atoms. Found 172 (239 requested) and removed 103 (122 requested) atoms. Cycle 7: After refmac, R = 0.2466 (Rfree = 0.000) for 4940 atoms. Found 139 (237 requested) and removed 47 (123 requested) atoms. Cycle 8: After refmac, R = 0.2334 (Rfree = 0.000) for 5024 atoms. Found 118 (242 requested) and removed 31 (126 requested) atoms. Cycle 9: After refmac, R = 0.2237 (Rfree = 0.000) for 5107 atoms. Found 101 (246 requested) and removed 37 (128 requested) atoms. Cycle 10: After refmac, R = 0.2152 (Rfree = 0.000) for 5162 atoms. Found 93 (249 requested) and removed 32 (129 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.75 1.75 NCS extension: 88 residues added (28 deleted due to clashes), 5313 seeds are put forward Round 1: 503 peptides, 13 chains. Longest chain 94 peptides. Score 0.936 Round 2: 507 peptides, 10 chains. Longest chain 153 peptides. Score 0.945 Round 3: 508 peptides, 8 chains. Longest chain 167 peptides. Score 0.951 Round 4: 508 peptides, 10 chains. Longest chain 153 peptides. Score 0.946 Round 5: 507 peptides, 9 chains. Longest chain 145 peptides. Score 0.948 Taking the results from Round 3 Chains 9, Residues 500, Estimated correctness of the model 99.8 % 7 chains (488 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 154 A and 162 A Built loop between residues 182 A and 191 A Built loop between residues 200 A and 203 A Built loop between residues 172 B and 177 B 4 chains (520 residues) following loop building 3 chains (509 residues) in sequence following loop building ------------------------------------------------------ 56224 reflections ( 94.10 % complete ) and 5015 restraints for refining 5048 atoms. 858 conditional restraints added. Observations/parameters ratio is 2.78 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2279 (Rfree = 0.000) for 5048 atoms. Found 178 (243 requested) and removed 136 (126 requested) atoms. Cycle 12: After refmac, R = 0.2150 (Rfree = 0.000) for 5081 atoms. Found 124 (240 requested) and removed 48 (127 requested) atoms. Cycle 13: After refmac, R = 0.2055 (Rfree = 0.000) for 5151 atoms. Found 107 (243 requested) and removed 56 (129 requested) atoms. Cycle 14: After refmac, R = 0.1990 (Rfree = 0.000) for 5191 atoms. Found 111 (239 requested) and removed 61 (130 requested) atoms. Cycle 15: After refmac, R = 0.1934 (Rfree = 0.000) for 5236 atoms. Found 106 (236 requested) and removed 68 (131 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.74 1.74 NCS extension: 136 residues added (81 deleted due to clashes), 5417 seeds are put forward Round 1: 512 peptides, 12 chains. Longest chain 111 peptides. Score 0.942 Round 2: 522 peptides, 6 chains. Longest chain 268 peptides. Score 0.959 Round 3: 510 peptides, 10 chains. Longest chain 143 peptides. Score 0.946 Round 4: 520 peptides, 8 chains. Longest chain 170 peptides. Score 0.954 Round 5: 523 peptides, 6 chains. Longest chain 148 peptides. Score 0.959 Taking the results from Round 5 Chains 6, Residues 517, Estimated correctness of the model 99.9 % 6 chains (517 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 40 A and 44 A Built loop between residues 155 A and 160 A Built loop between residues 182 A and 190 A Built loop between residues 120 B and 123 B 2 chains (533 residues) following loop building 2 chains (533 residues) in sequence following loop building ------------------------------------------------------ 56224 reflections ( 94.10 % complete ) and 4820 restraints for refining 5065 atoms. 513 conditional restraints added. Observations/parameters ratio is 2.78 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2052 (Rfree = 0.000) for 5065 atoms. Found 207 (223 requested) and removed 114 (126 requested) atoms. Cycle 17: After refmac, R = 0.1964 (Rfree = 0.000) for 5154 atoms. Found 144 (222 requested) and removed 64 (129 requested) atoms. Cycle 18: After refmac, R = 0.1918 (Rfree = 0.000) for 5225 atoms. Found 129 (225 requested) and removed 82 (131 requested) atoms. Cycle 19: After refmac, R = 0.1868 (Rfree = 0.000) for 5266 atoms. Found 121 (222 requested) and removed 90 (132 requested) atoms. Cycle 20: After refmac, R = 0.1842 (Rfree = 0.000) for 5294 atoms. Found 144 (217 requested) and removed 80 (132 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.74 1.74 NCS extension: 142 residues added (125 deleted due to clashes), 5507 seeds are put forward Round 1: 518 peptides, 9 chains. Longest chain 146 peptides. Score 0.951 Round 2: 519 peptides, 9 chains. Longest chain 121 peptides. Score 0.951 Round 3: 514 peptides, 10 chains. Longest chain 146 peptides. Score 0.948 Round 4: 517 peptides, 8 chains. Longest chain 151 peptides. Score 0.953 Round 5: 521 peptides, 8 chains. Longest chain 153 peptides. Score 0.954 Taking the results from Round 5 Chains 8, Residues 513, Estimated correctness of the model 99.8 % 7 chains (505 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 155 A and 160 A Built loop between residues 183 A and 189 A Built loop between residues 241 A and 244 A Built loop between residues 66 B and 70 B 4 chains (527 residues) following loop building 3 chains (519 residues) in sequence following loop building ------------------------------------------------------ 56224 reflections ( 94.10 % complete ) and 4979 restraints for refining 5063 atoms. 753 conditional restraints added. Observations/parameters ratio is 2.78 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1978 (Rfree = 0.000) for 5063 atoms. Found 192 (202 requested) and removed 79 (126 requested) atoms. Cycle 22: After refmac, R = 0.1893 (Rfree = 0.000) for 5174 atoms. Found 113 (207 requested) and removed 63 (129 requested) atoms. Cycle 23: After refmac, R = 0.1845 (Rfree = 0.000) for 5222 atoms. Found 120 (204 requested) and removed 64 (130 requested) atoms. Cycle 24: After refmac, R = 0.1832 (Rfree = 0.000) for 5270 atoms. Found 99 (201 requested) and removed 81 (132 requested) atoms. Cycle 25: After refmac, R = 0.1793 (Rfree = 0.000) for 5284 atoms. Found 127 (196 requested) and removed 59 (132 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.75 1.75 NCS extension: 23 residues added (8 deleted due to clashes), 5377 seeds are put forward Round 1: 522 peptides, 8 chains. Longest chain 146 peptides. Score 0.955 Round 2: 520 peptides, 8 chains. Longest chain 153 peptides. Score 0.954 Round 3: 523 peptides, 8 chains. Longest chain 146 peptides. Score 0.955 Round 4: 518 peptides, 7 chains. Longest chain 151 peptides. Score 0.956 Round 5: 523 peptides, 8 chains. Longest chain 153 peptides. Score 0.955 Taking the results from Round 4 Chains 7, Residues 511, Estimated correctness of the model 99.8 % 7 chains (511 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 155 A and 160 A Built loop between residues 183 A and 189 A Built loop between residues 66 B and 70 B Built loop between residues 98 B and 101 B Built loop between residues 173 B and 176 B 2 chains (527 residues) following loop building 2 chains (527 residues) in sequence following loop building ------------------------------------------------------ 56224 reflections ( 94.10 % complete ) and 4936 restraints for refining 5049 atoms. 684 conditional restraints added. Observations/parameters ratio is 2.78 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1961 (Rfree = 0.000) for 5049 atoms. Found 187 (187 requested) and removed 76 (126 requested) atoms. Cycle 27: After refmac, R = 0.1887 (Rfree = 0.000) for 5153 atoms. Found 130 (191 requested) and removed 53 (129 requested) atoms. Cycle 28: After refmac, R = 0.1852 (Rfree = 0.000) for 5227 atoms. Found 131 (194 requested) and removed 69 (131 requested) atoms. Cycle 29: After refmac, R = 0.1832 (Rfree = 0.000) for 5279 atoms. Found 125 (191 requested) and removed 83 (132 requested) atoms. Cycle 30: After refmac, R = 0.1799 (Rfree = 0.000) for 5312 atoms. Found 133 (186 requested) and removed 78 (133 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.74 1.74 NCS extension: 220 residues added (73 deleted due to clashes), 5591 seeds are put forward Round 1: 520 peptides, 9 chains. Longest chain 146 peptides. Score 0.952 Round 2: 520 peptides, 6 chains. Longest chain 153 peptides. Score 0.959 Round 3: 518 peptides, 8 chains. Longest chain 156 peptides. Score 0.954 Round 4: 521 peptides, 6 chains. Longest chain 168 peptides. Score 0.959 Round 5: 521 peptides, 10 chains. Longest chain 148 peptides. Score 0.950 Taking the results from Round 4 Chains 6, Residues 515, Estimated correctness of the model 99.9 % 6 chains (515 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 155 A and 160 A Built loop between residues 183 A and 190 A Built loop between residues 200 A and 203 A Built loop between residues 173 B and 176 B 2 chains (529 residues) following loop building 2 chains (529 residues) in sequence following loop building ------------------------------------------------------ 56224 reflections ( 94.10 % complete ) and 4923 restraints for refining 5073 atoms. 656 conditional restraints added. Observations/parameters ratio is 2.77 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1947 (Rfree = 0.000) for 5073 atoms. Found 173 (173 requested) and removed 87 (127 requested) atoms. Cycle 32: After refmac, R = 0.1865 (Rfree = 0.000) for 5155 atoms. Found 131 (170 requested) and removed 43 (129 requested) atoms. Cycle 33: After refmac, R = 0.1818 (Rfree = 0.000) for 5238 atoms. Found 119 (173 requested) and removed 73 (131 requested) atoms. Cycle 34: After refmac, R = 0.1803 (Rfree = 0.000) for 5280 atoms. Found 124 (169 requested) and removed 84 (132 requested) atoms. Cycle 35: After refmac, R = 0.1772 (Rfree = 0.000) for 5318 atoms. Found 126 (165 requested) and removed 97 (133 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.74 1.74 NCS extension: 20 residues added (10 deleted due to clashes), 5371 seeds are put forward Round 1: 522 peptides, 8 chains. Longest chain 146 peptides. Score 0.955 Round 2: 518 peptides, 7 chains. Longest chain 151 peptides. Score 0.956 Round 3: 521 peptides, 8 chains. Longest chain 105 peptides. Score 0.954 Round 4: 518 peptides, 9 chains. Longest chain 154 peptides. Score 0.951 Round 5: 519 peptides, 8 chains. Longest chain 105 peptides. Score 0.954 Taking the results from Round 2 Chains 7, Residues 511, Estimated correctness of the model 99.8 % 7 chains (511 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 155 A and 160 A Built loop between residues 183 A and 191 A Built loop between residues 200 A and 203 A Built loop between residues 66 B and 70 B Built loop between residues 173 B and 176 B 2 chains (529 residues) following loop building 2 chains (529 residues) in sequence following loop building ------------------------------------------------------ 56224 reflections ( 94.10 % complete ) and 4879 restraints for refining 5047 atoms. 602 conditional restraints added. Observations/parameters ratio is 2.79 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1930 (Rfree = 0.000) for 5047 atoms. Found 151 (151 requested) and removed 74 (126 requested) atoms. Cycle 37: After refmac, R = 0.1838 (Rfree = 0.000) for 5120 atoms. Found 133 (154 requested) and removed 37 (128 requested) atoms. Cycle 38: After refmac, R = 0.1789 (Rfree = 0.000) for 5211 atoms. Found 119 (157 requested) and removed 73 (130 requested) atoms. Cycle 39: After refmac, R = 0.1761 (Rfree = 0.000) for 5255 atoms. Found 142 (153 requested) and removed 81 (131 requested) atoms. Cycle 40: After refmac, R = 0.1770 (Rfree = 0.000) for 5315 atoms. Found 127 (149 requested) and removed 111 (133 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.73 1.73 NCS extension: 145 residues added (120 deleted due to clashes), 5480 seeds are put forward Round 1: 516 peptides, 10 chains. Longest chain 121 peptides. Score 0.948 Round 2: 520 peptides, 7 chains. Longest chain 201 peptides. Score 0.956 Round 3: 514 peptides, 10 chains. Longest chain 111 peptides. Score 0.948 Round 4: 519 peptides, 8 chains. Longest chain 201 peptides. Score 0.954 Round 5: 521 peptides, 8 chains. Longest chain 153 peptides. Score 0.954 Taking the results from Round 2 Chains 7, Residues 513, Estimated correctness of the model 99.8 % 7 chains (513 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 53 A and 58 A Built loop between residues 155 A and 160 A Built loop between residues 182 A and 189 A Built loop between residues 16 B and 19 B Built loop between residues 66 B and 70 B 2 chains (532 residues) following loop building 2 chains (532 residues) in sequence following loop building ------------------------------------------------------ 56224 reflections ( 94.10 % complete ) and 4852 restraints for refining 5067 atoms. 554 conditional restraints added. Observations/parameters ratio is 2.77 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1910 (Rfree = 0.000) for 5067 atoms. Found 137 (137 requested) and removed 77 (126 requested) atoms. Cycle 42: After refmac, R = 0.1830 (Rfree = 0.000) for 5123 atoms. Found 133 (133 requested) and removed 42 (128 requested) atoms. Cycle 43: After refmac, R = 0.1785 (Rfree = 0.000) for 5208 atoms. Found 120 (136 requested) and removed 67 (130 requested) atoms. Cycle 44: After refmac, R = 0.1764 (Rfree = 0.000) for 5255 atoms. Found 131 (131 requested) and removed 75 (131 requested) atoms. Cycle 45: After refmac, R = 0.1767 (Rfree = 0.000) for 5303 atoms. Found 126 (133 requested) and removed 81 (133 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.74 1.74 NCS extension: 145 residues added (122 deleted due to clashes), 5497 seeds are put forward Round 1: 518 peptides, 10 chains. Longest chain 105 peptides. Score 0.949 Round 2: 522 peptides, 6 chains. Longest chain 153 peptides. Score 0.959 Round 3: 518 peptides, 9 chains. Longest chain 151 peptides. Score 0.951 Round 4: 519 peptides, 7 chains. Longest chain 146 peptides. Score 0.956 Round 5: 520 peptides, 8 chains. Longest chain 158 peptides. Score 0.954 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 6, Residues 516, Estimated correctness of the model 99.9 % 6 chains (516 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 155 A and 160 A Built loop between residues 182 A and 189 A Built loop between residues 66 B and 70 B Built loop between residues 147 B and 150 B 2 chains (531 residues) following loop building 2 chains (531 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 56224 reflections ( 94.10 % complete ) and 4292 restraints for refining 4214 atoms. Observations/parameters ratio is 3.34 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2475 (Rfree = 0.000) for 4214 atoms. Found 105 (105 requested) and removed 0 (105 requested) atoms. Cycle 47: After refmac, R = 0.2254 (Rfree = 0.000) for 4214 atoms. Found 93 (108 requested) and removed 0 (108 requested) atoms. Cycle 48: After refmac, R = 0.2104 (Rfree = 0.000) for 4214 atoms. Found 43 (110 requested) and removed 1 (110 requested) atoms. Cycle 49: After refmac, R = 0.2008 (Rfree = 0.000) for 4214 atoms. Found 27 (111 requested) and removed 3 (111 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:41:02 GMT 2018 Job finished. TimeTaking 80.27 Used memory is bytes: 15461464