null Sun 23 Dec 22:22:46 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 2i51-1.7-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2i51-1.7-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2i51-1.7-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2i51-1.7-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/2i51-1.7-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2i51-1.7-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 22:22:56 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/2i51-1.7-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2i51-1.7-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 489 and 0 Target number of residues in the AU: 489 Target solvent content: 0.4555 Checking the provided sequence file Detected sequence length: 195 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 390 Adjusted target solvent content: 0.57 Input MTZ file: 2i51-1.7-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: 19 Cell parameters: 65.591 65.955 112.360 90.000 90.000 90.000 Input sequence file: 2i51-1.7-parrot-hancs.fasta_lf Building free atoms model in initial map for 3120 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: 56.880 1.700 Wilson plot Bfac: 15.38 49462 reflections ( 90.99 % complete ) and 0 restraints for refining 3448 atoms. Observations/parameters ratio is 3.59 ------------------------------------------------------ Starting model: R = 0.3238 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2773 (Rfree = 0.000) for 3448 atoms. Found 187 (187 requested) and removed 73 (93 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.68 1.53 NCS extension: 0 residues added, 3562 seeds are put forward Round 1: 360 peptides, 16 chains. Longest chain 68 peptides. Score 0.880 Round 2: 370 peptides, 11 chains. Longest chain 68 peptides. Score 0.910 Round 3: 373 peptides, 9 chains. Longest chain 125 peptides. Score 0.920 Round 4: 371 peptides, 8 chains. Longest chain 125 peptides. Score 0.922 Round 5: 375 peptides, 7 chains. Longest chain 133 peptides. Score 0.928 Taking the results from Round 5 Chains 8, Residues 368, Estimated correctness of the model 99.7 % 7 chains (367 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 134 A and 140 A Built loop between residues 173 A and 176 A Built loop between residues 113 B and 116 B Built loop between residues 137 B and 141 B Built loop between residues 173 B and 176 B 3 chains (382 residues) following loop building 2 chains (381 residues) in sequence following loop building ------------------------------------------------------ 49462 reflections ( 90.99 % complete ) and 3705 restraints for refining 3626 atoms. 480 conditional restraints added. Observations/parameters ratio is 3.41 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2751 (Rfree = 0.000) for 3626 atoms. Found 181 (197 requested) and removed 67 (98 requested) atoms. Cycle 2: After refmac, R = 0.2285 (Rfree = 0.000) for 3736 atoms. Found 137 (203 requested) and removed 42 (101 requested) atoms. Cycle 3: After refmac, R = 0.2089 (Rfree = 0.000) for 3812 atoms. Found 132 (208 requested) and removed 17 (104 requested) atoms. Cycle 4: After refmac, R = 0.1978 (Rfree = 0.000) for 3913 atoms. Found 115 (213 requested) and removed 46 (106 requested) atoms. Cycle 5: After refmac, R = 0.1884 (Rfree = 0.000) for 3968 atoms. Found 108 (216 requested) and removed 33 (108 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.68 1.53 NCS extension: 10 residues added (184 deleted due to clashes), 4060 seeds are put forward Round 1: 380 peptides, 6 chains. Longest chain 171 peptides. Score 0.935 Round 2: 381 peptides, 5 chains. Longest chain 171 peptides. Score 0.939 Round 3: 379 peptides, 7 chains. Longest chain 116 peptides. Score 0.931 Round 4: 378 peptides, 8 chains. Longest chain 112 peptides. Score 0.926 Round 5: 380 peptides, 6 chains. Longest chain 133 peptides. Score 0.935 Taking the results from Round 2 Chains 5, Residues 376, Estimated correctness of the model 99.7 % 5 chains (376 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 172 A and 175 A Built loop between residues 134 B and 140 B Built loop between residues 172 B and 175 B 2 chains (385 residues) following loop building 2 chains (385 residues) in sequence following loop building ------------------------------------------------------ 49462 reflections ( 90.99 % complete ) and 3861 restraints for refining 3832 atoms. 609 conditional restraints added. Observations/parameters ratio is 3.23 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2022 (Rfree = 0.000) for 3832 atoms. Found 171 (208 requested) and removed 50 (104 requested) atoms. Cycle 7: After refmac, R = 0.1897 (Rfree = 0.000) for 3948 atoms. Found 107 (215 requested) and removed 32 (107 requested) atoms. Cycle 8: After refmac, R = 0.1821 (Rfree = 0.000) for 4017 atoms. Found 105 (219 requested) and removed 35 (109 requested) atoms. Cycle 9: After refmac, R = 0.1791 (Rfree = 0.000) for 4073 atoms. Found 99 (222 requested) and removed 50 (111 requested) atoms. Cycle 10: After refmac, R = 0.1753 (Rfree = 0.000) for 4113 atoms. Found 108 (220 requested) and removed 45 (112 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.68 1.53 NCS extension: 6 residues added (188 deleted due to clashes), 4184 seeds are put forward Round 1: 379 peptides, 5 chains. Longest chain 171 peptides. Score 0.938 Round 2: 378 peptides, 6 chains. Longest chain 171 peptides. Score 0.934 Round 3: 380 peptides, 7 chains. Longest chain 117 peptides. Score 0.931 Round 4: 379 peptides, 6 chains. Longest chain 133 peptides. Score 0.934 Round 5: 374 peptides, 7 chains. Longest chain 113 peptides. Score 0.928 Taking the results from Round 1 Chains 7, Residues 374, Estimated correctness of the model 99.7 % 5 chains (372 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 133 A and 140 A Built loop between residues 172 A and 176 A Built loop between residues 173 B and 176 B 3 chains (384 residues) following loop building 2 chains (383 residues) in sequence following loop building ------------------------------------------------------ 49462 reflections ( 90.99 % complete ) and 3933 restraints for refining 3891 atoms. 692 conditional restraints added. Observations/parameters ratio is 3.18 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1983 (Rfree = 0.000) for 3891 atoms. Found 176 (207 requested) and removed 69 (105 requested) atoms. Cycle 12: After refmac, R = 0.1864 (Rfree = 0.000) for 3989 atoms. Found 106 (213 requested) and removed 36 (108 requested) atoms. Cycle 13: After refmac, R = 0.1796 (Rfree = 0.000) for 4051 atoms. Found 94 (216 requested) and removed 32 (110 requested) atoms. Cycle 14: After refmac, R = 0.1760 (Rfree = 0.000) for 4106 atoms. Found 102 (219 requested) and removed 45 (111 requested) atoms. Cycle 15: After refmac, R = 0.1743 (Rfree = 0.000) for 4147 atoms. Found 83 (221 requested) and removed 46 (113 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.68 1.53 NCS extension: 8 residues added (186 deleted due to clashes), 4196 seeds are put forward Round 1: 377 peptides, 5 chains. Longest chain 168 peptides. Score 0.937 Round 2: 376 peptides, 6 chains. Longest chain 168 peptides. Score 0.933 Round 3: 376 peptides, 6 chains. Longest chain 168 peptides. Score 0.933 Round 4: 376 peptides, 6 chains. Longest chain 133 peptides. Score 0.933 Round 5: 376 peptides, 6 chains. Longest chain 168 peptides. Score 0.933 Taking the results from Round 1 Chains 6, Residues 372, Estimated correctness of the model 99.7 % 5 chains (371 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 133 A and 140 A Built loop between residues 172 A and 176 A Built loop between residues 172 B and 175 B 2 chains (382 residues) following loop building 2 chains (382 residues) in sequence following loop building ------------------------------------------------------ 49462 reflections ( 90.99 % complete ) and 3951 restraints for refining 3902 atoms. 718 conditional restraints added. Observations/parameters ratio is 3.17 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2179 (Rfree = 0.000) for 3902 atoms. Found 160 (204 requested) and removed 51 (106 requested) atoms. Cycle 17: After refmac, R = 0.1912 (Rfree = 0.000) for 4005 atoms. Found 124 (209 requested) and removed 35 (109 requested) atoms. Cycle 18: After refmac, R = 0.1808 (Rfree = 0.000) for 4085 atoms. Found 93 (213 requested) and removed 43 (111 requested) atoms. Cycle 19: After refmac, R = 0.1764 (Rfree = 0.000) for 4121 atoms. Found 121 (216 requested) and removed 37 (112 requested) atoms. Cycle 20: After refmac, R = 0.1756 (Rfree = 0.000) for 4200 atoms. Found 90 (219 requested) and removed 69 (114 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.68 1.53 NCS extension: 10 residues added (188 deleted due to clashes), 4234 seeds are put forward Round 1: 378 peptides, 5 chains. Longest chain 171 peptides. Score 0.937 Round 2: 378 peptides, 6 chains. Longest chain 171 peptides. Score 0.934 Round 3: 377 peptides, 6 chains. Longest chain 133 peptides. Score 0.933 Round 4: 377 peptides, 6 chains. Longest chain 170 peptides. Score 0.933 Round 5: 377 peptides, 6 chains. Longest chain 170 peptides. Score 0.933 Taking the results from Round 1 Chains 7, Residues 373, Estimated correctness of the model 99.7 % 5 chains (371 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 133 A and 140 A Built loop between residues 171 A and 175 A Built loop between residues 173 B and 177 B 3 chains (384 residues) following loop building 2 chains (383 residues) in sequence following loop building ------------------------------------------------------ 49462 reflections ( 90.99 % complete ) and 4006 restraints for refining 3955 atoms. 765 conditional restraints added. Observations/parameters ratio is 3.13 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1942 (Rfree = 0.000) for 3955 atoms. Found 179 (202 requested) and removed 52 (107 requested) atoms. Cycle 22: After refmac, R = 0.1847 (Rfree = 0.000) for 4069 atoms. Found 111 (209 requested) and removed 45 (111 requested) atoms. Cycle 23: After refmac, R = 0.1787 (Rfree = 0.000) for 4133 atoms. Found 100 (211 requested) and removed 40 (112 requested) atoms. Cycle 24: After refmac, R = 0.1743 (Rfree = 0.000) for 4189 atoms. Found 109 (214 requested) and removed 38 (114 requested) atoms. Cycle 25: After refmac, R = 0.1712 (Rfree = 0.000) for 4254 atoms. Found 74 (217 requested) and removed 49 (115 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.68 1.53 NCS extension: 10 residues added (209 deleted due to clashes), 4292 seeds are put forward Round 1: 378 peptides, 5 chains. Longest chain 171 peptides. Score 0.937 Round 2: 377 peptides, 6 chains. Longest chain 169 peptides. Score 0.933 Round 3: 377 peptides, 5 chains. Longest chain 169 peptides. Score 0.937 Round 4: 376 peptides, 7 chains. Longest chain 117 peptides. Score 0.929 Round 5: 375 peptides, 7 chains. Longest chain 170 peptides. Score 0.928 Taking the results from Round 3 Chains 5, Residues 372, Estimated correctness of the model 99.7 % 5 chains (372 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 172 A and 175 A Built loop between residues 133 B and 141 B Built loop between residues 173 B and 176 B 2 chains (383 residues) following loop building 2 chains (383 residues) in sequence following loop building ------------------------------------------------------ 49462 reflections ( 90.99 % complete ) and 4046 restraints for refining 3970 atoms. 808 conditional restraints added. Observations/parameters ratio is 3.11 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1951 (Rfree = 0.000) for 3970 atoms. Found 189 (199 requested) and removed 50 (108 requested) atoms. Cycle 27: After refmac, R = 0.1851 (Rfree = 0.000) for 4101 atoms. Found 125 (205 requested) and removed 52 (111 requested) atoms. Cycle 28: After refmac, R = 0.1778 (Rfree = 0.000) for 4168 atoms. Found 112 (209 requested) and removed 39 (113 requested) atoms. Cycle 29: After refmac, R = 0.1746 (Rfree = 0.000) for 4230 atoms. Found 90 (212 requested) and removed 53 (115 requested) atoms. Cycle 30: After refmac, R = 0.1716 (Rfree = 0.000) for 4257 atoms. Found 104 (209 requested) and removed 51 (116 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.68 1.53 NCS extension: 0 residues added, 4310 seeds are put forward Round 1: 378 peptides, 5 chains. Longest chain 170 peptides. Score 0.937 Round 2: 379 peptides, 6 chains. Longest chain 170 peptides. Score 0.934 Round 3: 379 peptides, 5 chains. Longest chain 170 peptides. Score 0.938 Round 4: 377 peptides, 6 chains. Longest chain 168 peptides. Score 0.933 Round 5: 379 peptides, 6 chains. Longest chain 170 peptides. Score 0.934 Taking the results from Round 3 Chains 7, Residues 374, Estimated correctness of the model 99.7 % 5 chains (372 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 134 A and 140 A Built loop between residues 172 A and 175 A Built loop between residues 173 B and 177 B 3 chains (383 residues) following loop building 2 chains (382 residues) in sequence following loop building ------------------------------------------------------ 49462 reflections ( 90.99 % complete ) and 4060 restraints for refining 3976 atoms. 827 conditional restraints added. Observations/parameters ratio is 3.11 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1945 (Rfree = 0.000) for 3976 atoms. Found 194 (194 requested) and removed 42 (108 requested) atoms. Cycle 32: After refmac, R = 0.1833 (Rfree = 0.000) for 4122 atoms. Found 122 (202 requested) and removed 50 (112 requested) atoms. Cycle 33: After refmac, R = 0.1780 (Rfree = 0.000) for 4184 atoms. Found 106 (205 requested) and removed 36 (114 requested) atoms. Cycle 34: After refmac, R = 0.1746 (Rfree = 0.000) for 4243 atoms. Found 95 (208 requested) and removed 49 (115 requested) atoms. Cycle 35: After refmac, R = 0.1736 (Rfree = 0.000) for 4276 atoms. Found 92 (205 requested) and removed 58 (116 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.68 1.53 NCS extension: 0 residues added, 4311 seeds are put forward Round 1: 378 peptides, 5 chains. Longest chain 169 peptides. Score 0.937 Round 2: 378 peptides, 6 chains. Longest chain 169 peptides. Score 0.934 Round 3: 378 peptides, 6 chains. Longest chain 134 peptides. Score 0.934 Round 4: 378 peptides, 5 chains. Longest chain 169 peptides. Score 0.937 Round 5: 379 peptides, 5 chains. Longest chain 169 peptides. Score 0.938 Taking the results from Round 5 Chains 5, Residues 374, Estimated correctness of the model 99.7 % 5 chains (374 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 172 A and 175 A Built loop between residues 134 B and 141 B Built loop between residues 172 B and 175 B 2 chains (384 residues) following loop building 2 chains (384 residues) in sequence following loop building ------------------------------------------------------ 49462 reflections ( 90.99 % complete ) and 4097 restraints for refining 3994 atoms. 851 conditional restraints added. Observations/parameters ratio is 3.10 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1922 (Rfree = 0.000) for 3994 atoms. Found 187 (187 requested) and removed 44 (108 requested) atoms. Cycle 37: After refmac, R = 0.1822 (Rfree = 0.000) for 4124 atoms. Found 93 (193 requested) and removed 28 (112 requested) atoms. Cycle 38: After refmac, R = 0.1749 (Rfree = 0.000) for 4180 atoms. Found 93 (196 requested) and removed 26 (114 requested) atoms. Cycle 39: After refmac, R = 0.1723 (Rfree = 0.000) for 4240 atoms. Found 83 (199 requested) and removed 54 (115 requested) atoms. Cycle 40: After refmac, R = 0.1697 (Rfree = 0.000) for 4256 atoms. Found 112 (195 requested) and removed 48 (116 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.68 1.53 NCS extension: 1 residues added (2 deleted due to clashes), 4322 seeds are put forward Round 1: 379 peptides, 5 chains. Longest chain 170 peptides. Score 0.938 Round 2: 379 peptides, 6 chains. Longest chain 170 peptides. Score 0.934 Round 3: 377 peptides, 5 chains. Longest chain 168 peptides. Score 0.937 Round 4: 378 peptides, 7 chains. Longest chain 114 peptides. Score 0.930 Round 5: 380 peptides, 5 chains. Longest chain 170 peptides. Score 0.938 Taking the results from Round 5 Chains 6, Residues 375, Estimated correctness of the model 99.7 % 5 chains (374 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 173 A and 176 A Built loop between residues 135 B and 141 B Built loop between residues 172 B and 175 B 3 chains (384 residues) following loop building 2 chains (383 residues) in sequence following loop building ------------------------------------------------------ 49462 reflections ( 90.99 % complete ) and 4068 restraints for refining 3993 atoms. 827 conditional restraints added. Observations/parameters ratio is 3.10 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1926 (Rfree = 0.000) for 3993 atoms. Found 182 (182 requested) and removed 41 (108 requested) atoms. Cycle 42: After refmac, R = 0.1828 (Rfree = 0.000) for 4116 atoms. Found 112 (189 requested) and removed 48 (112 requested) atoms. Cycle 43: After refmac, R = 0.1749 (Rfree = 0.000) for 4171 atoms. Found 109 (191 requested) and removed 42 (113 requested) atoms. Cycle 44: After refmac, R = 0.1717 (Rfree = 0.000) for 4233 atoms. Found 82 (193 requested) and removed 50 (115 requested) atoms. Cycle 45: After refmac, R = 0.1697 (Rfree = 0.000) for 4251 atoms. Found 98 (190 requested) and removed 42 (116 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.68 1.53 NCS extension: 6 residues added (188 deleted due to clashes), 4313 seeds are put forward Round 1: 379 peptides, 5 chains. Longest chain 170 peptides. Score 0.938 Round 2: 378 peptides, 6 chains. Longest chain 170 peptides. Score 0.934 Round 3: 378 peptides, 6 chains. Longest chain 134 peptides. Score 0.934 Round 4: 379 peptides, 5 chains. Longest chain 170 peptides. Score 0.938 Round 5: 377 peptides, 6 chains. Longest chain 170 peptides. Score 0.933 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 7, Residues 374, Estimated correctness of the model 99.7 % 5 chains (372 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 173 A and 177 A Built loop between residues 134 B and 141 B Built loop between residues 172 B and 175 B 3 chains (384 residues) following loop building 2 chains (383 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 49462 reflections ( 90.99 % complete ) and 3241 restraints for refining 3146 atoms. Observations/parameters ratio is 3.93 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2693 (Rfree = 0.000) for 3146 atoms. Found 140 (140 requested) and removed 0 (140 requested) atoms. Cycle 47: After refmac, R = 0.2385 (Rfree = 0.000) for 3146 atoms. Found 64 (146 requested) and removed 0 (89 requested) atoms. Cycle 48: After refmac, R = 0.2190 (Rfree = 0.000) for 3146 atoms. Found 30 (149 requested) and removed 1 (91 requested) atoms. Cycle 49: After refmac, R = 0.2072 (Rfree = 0.000) for 3146 atoms. Found 24 (150 requested) and removed 10 (91 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:37:14 GMT 2018 Job finished. TimeTaking 74.46 Used memory is bytes: 7535320