null Sun 23 Dec 23:49:46 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 2i5i-1.7-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2i5i-1.7-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2i5i-1.7-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2i5i-1.7-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/2i5i-1.7-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2i5i-1.7-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 ============================================================ Sun 23 Dec 23:49:50 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/2i5i-1.7-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2i5i-1.7-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 525 and 0 Target number of residues in the AU: 525 Target solvent content: 0.4948 Checking the provided sequence file Detected sequence length: 263 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 526 Adjusted target solvent content: 0.49 Input MTZ file: 2i5i-1.7-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: 146 Cell parameters: 130.530 130.530 85.760 90.000 90.000 120.000 Input sequence file: 2i5i-1.7-parrot-mrncs.fasta_lf Building free atoms model in initial map for 4208 target number of atoms Had to go as low as 0.55 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: 29.446 1.701 Wilson plot Bfac: 22.43 59787 reflections ( 99.90 % complete ) and 0 restraints for refining 4684 atoms. Observations/parameters ratio is 3.19 ------------------------------------------------------ Starting model: R = 0.3644 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3197 (Rfree = 0.000) for 4684 atoms. Found 129 (254 requested) and removed 135 (127 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.14 2.17 NCS extension: 0 residues added, 4678 seeds are put forward Round 1: 356 peptides, 47 chains. Longest chain 23 peptides. Score 0.623 Round 2: 410 peptides, 39 chains. Longest chain 33 peptides. Score 0.769 Round 3: 422 peptides, 27 chains. Longest chain 62 peptides. Score 0.847 Round 4: 445 peptides, 19 chains. Longest chain 63 peptides. Score 0.897 Round 5: 462 peptides, 17 chains. Longest chain 74 peptides. Score 0.913 Taking the results from Round 5 Chains 21, Residues 445, Estimated correctness of the model 99.5 % 10 chains (366 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 29 A and 37 A Built loop between residues 96 A and 101 A Built loop between residues 117 A and 121 A 17 chains (456 residues) following loop building 7 chains (380 residues) in sequence following loop building ------------------------------------------------------ 59787 reflections ( 99.90 % complete ) and 5502 restraints for refining 4575 atoms. 2118 conditional restraints added. Observations/parameters ratio is 3.27 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3165 (Rfree = 0.000) for 4575 atoms. Found 136 (248 requested) and removed 128 (124 requested) atoms. Cycle 2: After refmac, R = 0.2908 (Rfree = 0.000) for 4561 atoms. Found 106 (244 requested) and removed 38 (124 requested) atoms. Cycle 3: After refmac, R = 0.2741 (Rfree = 0.000) for 4610 atoms. Found 90 (246 requested) and removed 27 (125 requested) atoms. Cycle 4: After refmac, R = 0.2622 (Rfree = 0.000) for 4654 atoms. Found 83 (248 requested) and removed 27 (126 requested) atoms. Cycle 5: After refmac, R = 0.2534 (Rfree = 0.000) for 4696 atoms. Found 81 (250 requested) and removed 20 (127 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.96 1.99 NCS extension: 29 residues added (164 deleted due to clashes), 4796 seeds are put forward Round 1: 479 peptides, 13 chains. Longest chain 156 peptides. Score 0.933 Round 2: 475 peptides, 14 chains. Longest chain 130 peptides. Score 0.928 Round 3: 478 peptides, 14 chains. Longest chain 157 peptides. Score 0.930 Round 4: 480 peptides, 17 chains. Longest chain 107 peptides. Score 0.922 Round 5: 478 peptides, 17 chains. Longest chain 63 peptides. Score 0.921 Taking the results from Round 1 Chains 15, Residues 466, Estimated correctness of the model 99.7 % 7 chains (399 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 157 A and 167 A Built loop between residues 197 A and 207 A Built loop between residues 227 B and 230 B 11 chains (485 residues) following loop building 4 chains (419 residues) in sequence following loop building ------------------------------------------------------ 59787 reflections ( 99.90 % complete ) and 5197 restraints for refining 4682 atoms. 1539 conditional restraints added. Observations/parameters ratio is 3.19 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2653 (Rfree = 0.000) for 4682 atoms. Found 148 (249 requested) and removed 56 (127 requested) atoms. Cycle 7: After refmac, R = 0.2501 (Rfree = 0.000) for 4769 atoms. Found 103 (254 requested) and removed 22 (129 requested) atoms. Cycle 8: After refmac, R = 0.2397 (Rfree = 0.000) for 4844 atoms. Found 92 (258 requested) and removed 10 (131 requested) atoms. Cycle 9: After refmac, R = 0.2316 (Rfree = 0.000) for 4917 atoms. Found 80 (262 requested) and removed 14 (133 requested) atoms. Cycle 10: After refmac, R = 0.2263 (Rfree = 0.000) for 4975 atoms. Found 63 (265 requested) and removed 7 (135 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.94 1.97 NCS extension: 57 residues added (242 deleted due to clashes), 5089 seeds are put forward Round 1: 494 peptides, 14 chains. Longest chain 80 peptides. Score 0.936 Round 2: 502 peptides, 6 chains. Longest chain 197 peptides. Score 0.958 Round 3: 502 peptides, 12 chains. Longest chain 65 peptides. Score 0.944 Round 4: 505 peptides, 8 chains. Longest chain 156 peptides. Score 0.955 Round 5: 498 peptides, 13 chains. Longest chain 181 peptides. Score 0.940 Taking the results from Round 2 Chains 7, Residues 496, Estimated correctness of the model 99.9 % 5 chains (484 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 160 A and 167 A Built loop between residues 200 B and 207 B 5 chains (508 residues) following loop building 3 chains (496 residues) in sequence following loop building ------------------------------------------------------ 59787 reflections ( 99.90 % complete ) and 4946 restraints for refining 5011 atoms. 858 conditional restraints added. Observations/parameters ratio is 2.98 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2440 (Rfree = 0.000) for 5011 atoms. Found 134 (267 requested) and removed 69 (136 requested) atoms. Cycle 12: After refmac, R = 0.2317 (Rfree = 0.000) for 5068 atoms. Found 86 (264 requested) and removed 24 (137 requested) atoms. Cycle 13: After refmac, R = 0.2230 (Rfree = 0.000) for 5124 atoms. Found 78 (267 requested) and removed 15 (139 requested) atoms. Cycle 14: After refmac, R = 0.2175 (Rfree = 0.000) for 5185 atoms. Found 80 (270 requested) and removed 17 (140 requested) atoms. Cycle 15: After refmac, R = 0.2128 (Rfree = 0.000) for 5242 atoms. Found 71 (274 requested) and removed 21 (142 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.93 1.96 NCS extension: 45 residues added (228 deleted due to clashes), 5338 seeds are put forward Round 1: 504 peptides, 13 chains. Longest chain 156 peptides. Score 0.942 Round 2: 511 peptides, 8 chains. Longest chain 182 peptides. Score 0.956 Round 3: 503 peptides, 10 chains. Longest chain 134 peptides. Score 0.949 Round 4: 503 peptides, 12 chains. Longest chain 158 peptides. Score 0.944 Round 5: 508 peptides, 10 chains. Longest chain 104 peptides. Score 0.951 Taking the results from Round 2 Chains 10, Residues 503, Estimated correctness of the model 99.9 % 5 chains (462 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 161 A and 167 A 9 chains (508 residues) following loop building 4 chains (467 residues) in sequence following loop building ------------------------------------------------------ 59787 reflections ( 99.90 % complete ) and 5246 restraints for refining 5138 atoms. 1255 conditional restraints added. Observations/parameters ratio is 2.91 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2291 (Rfree = 0.000) for 5138 atoms. Found 160 (268 requested) and removed 70 (139 requested) atoms. Cycle 17: After refmac, R = 0.2200 (Rfree = 0.000) for 5223 atoms. Found 99 (273 requested) and removed 17 (142 requested) atoms. Cycle 18: After refmac, R = 0.2138 (Rfree = 0.000) for 5300 atoms. Found 82 (276 requested) and removed 12 (144 requested) atoms. Cycle 19: After refmac, R = 0.2083 (Rfree = 0.000) for 5366 atoms. Found 68 (279 requested) and removed 15 (145 requested) atoms. Cycle 20: After refmac, R = 0.2054 (Rfree = 0.000) for 5405 atoms. Found 77 (282 requested) and removed 15 (147 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.94 1.97 NCS extension: 90 residues added (21 deleted due to clashes), 5558 seeds are put forward Round 1: 504 peptides, 12 chains. Longest chain 177 peptides. Score 0.945 Round 2: 507 peptides, 10 chains. Longest chain 146 peptides. Score 0.950 Round 3: 503 peptides, 14 chains. Longest chain 103 peptides. Score 0.939 Round 4: 512 peptides, 5 chains. Longest chain 259 peptides. Score 0.963 Round 5: 505 peptides, 10 chains. Longest chain 184 peptides. Score 0.950 Taking the results from Round 4 Chains 6, Residues 507, Estimated correctness of the model 99.9 % 4 chains (497 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 161 A and 167 A 5 chains (512 residues) following loop building 3 chains (502 residues) in sequence following loop building ------------------------------------------------------ 59787 reflections ( 99.90 % complete ) and 5066 restraints for refining 5258 atoms. 934 conditional restraints added. Observations/parameters ratio is 2.84 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2256 (Rfree = 0.000) for 5258 atoms. Found 166 (274 requested) and removed 72 (142 requested) atoms. Cycle 22: After refmac, R = 0.2157 (Rfree = 0.000) for 5349 atoms. Found 85 (278 requested) and removed 13 (145 requested) atoms. Cycle 23: After refmac, R = 0.2094 (Rfree = 0.000) for 5418 atoms. Found 71 (282 requested) and removed 15 (147 requested) atoms. Cycle 24: After refmac, R = 0.2046 (Rfree = 0.000) for 5469 atoms. Found 65 (285 requested) and removed 16 (148 requested) atoms. Cycle 25: After refmac, R = 0.2022 (Rfree = 0.000) for 5507 atoms. Found 72 (287 requested) and removed 16 (149 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.93 1.96 NCS extension: 58 residues added (213 deleted due to clashes), 5621 seeds are put forward Round 1: 508 peptides, 10 chains. Longest chain 154 peptides. Score 0.951 Round 2: 513 peptides, 8 chains. Longest chain 146 peptides. Score 0.957 Round 3: 511 peptides, 10 chains. Longest chain 232 peptides. Score 0.952 Round 4: 510 peptides, 9 chains. Longest chain 137 peptides. Score 0.954 Round 5: 507 peptides, 10 chains. Longest chain 105 peptides. Score 0.950 Taking the results from Round 2 Chains 11, Residues 505, Estimated correctness of the model 99.9 % 7 chains (492 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 29 A and 32 A Built loop between residues 59 A and 68 A Built loop between residues 201 A and 207 A Built loop between residues 57 B and 60 B Built loop between residues 204 B and 207 B 4 chains (517 residues) following loop building 2 chains (511 residues) in sequence following loop building ------------------------------------------------------ 59787 reflections ( 99.90 % complete ) and 5029 restraints for refining 5340 atoms. 840 conditional restraints added. Observations/parameters ratio is 2.80 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2207 (Rfree = 0.000) for 5340 atoms. Found 196 (278 requested) and removed 62 (145 requested) atoms. Cycle 27: After refmac, R = 0.2098 (Rfree = 0.000) for 5464 atoms. Found 126 (285 requested) and removed 16 (148 requested) atoms. Cycle 28: After refmac, R = 0.2044 (Rfree = 0.000) for 5568 atoms. Found 88 (290 requested) and removed 21 (151 requested) atoms. Cycle 29: After refmac, R = 0.2005 (Rfree = 0.000) for 5628 atoms. Found 89 (293 requested) and removed 20 (152 requested) atoms. Cycle 30: After refmac, R = 0.1976 (Rfree = 0.000) for 5694 atoms. Found 86 (297 requested) and removed 23 (154 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.94 1.97 NCS extension: 0 residues added, 5757 seeds are put forward Round 1: 506 peptides, 11 chains. Longest chain 153 peptides. Score 0.948 Round 2: 511 peptides, 8 chains. Longest chain 106 peptides. Score 0.956 Round 3: 505 peptides, 11 chains. Longest chain 128 peptides. Score 0.947 Round 4: 512 peptides, 8 chains. Longest chain 130 peptides. Score 0.957 Round 5: 502 peptides, 13 chains. Longest chain 105 peptides. Score 0.941 Taking the results from Round 4 Chains 9, Residues 504, Estimated correctness of the model 99.9 % 7 chains (494 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 66 A and 69 A Built loop between residues 95 A and 98 A Built loop between residues 109 B and 112 B Built loop between residues 240 B and 243 B 5 chains (512 residues) following loop building 3 chains (502 residues) in sequence following loop building ------------------------------------------------------ 59787 reflections ( 99.90 % complete ) and 5323 restraints for refining 5454 atoms. 1191 conditional restraints added. Observations/parameters ratio is 2.74 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2202 (Rfree = 0.000) for 5454 atoms. Found 200 (284 requested) and removed 63 (148 requested) atoms. Cycle 32: After refmac, R = 0.2095 (Rfree = 0.000) for 5582 atoms. Found 137 (291 requested) and removed 27 (151 requested) atoms. Cycle 33: After refmac, R = 0.2027 (Rfree = 0.000) for 5686 atoms. Found 97 (297 requested) and removed 20 (154 requested) atoms. Cycle 34: After refmac, R = 0.1990 (Rfree = 0.000) for 5754 atoms. Found 87 (300 requested) and removed 24 (156 requested) atoms. Cycle 35: After refmac, R = 0.1949 (Rfree = 0.000) for 5809 atoms. Found 93 (302 requested) and removed 28 (157 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.93 1.96 NCS extension: 62 residues added (209 deleted due to clashes), 5937 seeds are put forward Round 1: 505 peptides, 11 chains. Longest chain 153 peptides. Score 0.947 Round 2: 514 peptides, 5 chains. Longest chain 200 peptides. Score 0.964 Round 3: 508 peptides, 10 chains. Longest chain 133 peptides. Score 0.951 Round 4: 504 peptides, 10 chains. Longest chain 107 peptides. Score 0.950 Round 5: 507 peptides, 8 chains. Longest chain 163 peptides. Score 0.955 Taking the results from Round 2 Chains 6, Residues 509, Estimated correctness of the model 99.9 % 5 chains (507 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 57 A and 60 A Built loop between residues 185 A and 188 A Built loop between residues 203 B and 208 B 3 chains (517 residues) following loop building 2 chains (515 residues) in sequence following loop building ------------------------------------------------------ 59787 reflections ( 99.90 % complete ) and 5218 restraints for refining 5555 atoms. 1014 conditional restraints added. Observations/parameters ratio is 2.69 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2139 (Rfree = 0.000) for 5555 atoms. Found 216 (289 requested) and removed 61 (150 requested) atoms. Cycle 37: After refmac, R = 0.2043 (Rfree = 0.000) for 5702 atoms. Found 137 (298 requested) and removed 21 (155 requested) atoms. Cycle 38: After refmac, R = 0.1975 (Rfree = 0.000) for 5806 atoms. Found 93 (303 requested) and removed 34 (158 requested) atoms. Cycle 39: After refmac, R = 0.1944 (Rfree = 0.000) for 5858 atoms. Found 93 (305 requested) and removed 27 (159 requested) atoms. Cycle 40: After refmac, R = 0.1919 (Rfree = 0.000) for 5910 atoms. Found 100 (308 requested) and removed 41 (160 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.93 1.96 NCS extension: 0 residues added, 5969 seeds are put forward Round 1: 507 peptides, 10 chains. Longest chain 153 peptides. Score 0.950 Round 2: 509 peptides, 8 chains. Longest chain 181 peptides. Score 0.956 Round 3: 502 peptides, 12 chains. Longest chain 128 peptides. Score 0.944 Round 4: 505 peptides, 9 chains. Longest chain 181 peptides. Score 0.952 Round 5: 508 peptides, 9 chains. Longest chain 179 peptides. Score 0.953 Taking the results from Round 2 Chains 8, Residues 501, Estimated correctness of the model 99.9 % 7 chains (494 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 68 A and 71 A Built loop between residues 96 A and 99 A Built loop between residues 119 A and 122 A Built loop between residues 184 B and 188 B 4 chains (510 residues) following loop building 3 chains (503 residues) in sequence following loop building ------------------------------------------------------ 59787 reflections ( 99.90 % complete ) and 5461 restraints for refining 5616 atoms. 1335 conditional restraints added. Observations/parameters ratio is 2.66 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2109 (Rfree = 0.000) for 5616 atoms. Found 239 (293 requested) and removed 60 (152 requested) atoms. Cycle 42: After refmac, R = 0.2018 (Rfree = 0.000) for 5792 atoms. Found 131 (301 requested) and removed 39 (157 requested) atoms. Cycle 43: After refmac, R = 0.1950 (Rfree = 0.000) for 5879 atoms. Found 113 (306 requested) and removed 23 (159 requested) atoms. Cycle 44: After refmac, R = 0.1909 (Rfree = 0.000) for 5959 atoms. Found 93 (311 requested) and removed 40 (162 requested) atoms. Cycle 45: After refmac, R = 0.1878 (Rfree = 0.000) for 6005 atoms. Found 93 (313 requested) and removed 34 (163 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.93 1.96 NCS extension: 61 residues added (210 deleted due to clashes), 6126 seeds are put forward Round 1: 510 peptides, 8 chains. Longest chain 174 peptides. Score 0.956 Round 2: 511 peptides, 7 chains. Longest chain 259 peptides. Score 0.959 Round 3: 505 peptides, 10 chains. Longest chain 182 peptides. Score 0.950 Round 4: 511 peptides, 7 chains. Longest chain 147 peptides. Score 0.959 Round 5: 509 peptides, 9 chains. Longest chain 179 peptides. Score 0.953 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 7, Residues 504, Estimated correctness of the model 99.9 % 7 chains (504 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 29 A and 32 A Built loop between residues 80 A and 83 A Built loop between residues 203 A and 208 A Built loop between residues 67 B and 70 B Built loop between residues 215 B and 218 B 2 chains (516 residues) following loop building 2 chains (516 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 59787 reflections ( 99.90 % complete ) and 4202 restraints for refining 4118 atoms. Observations/parameters ratio is 3.63 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2774 (Rfree = 0.000) for 4118 atoms. Found 62 (214 requested) and removed 0 (214 requested) atoms. Cycle 47: After refmac, R = 0.2602 (Rfree = 0.000) for 4118 atoms. Found 20 (218 requested) and removed 0 (113 requested) atoms. Cycle 48: After refmac, R = 0.2508 (Rfree = 0.000) for 4118 atoms. Found 10 (219 requested) and removed 1 (114 requested) atoms. Cycle 49: After refmac, R = 0.2462 (Rfree = 0.000) for 4118 atoms. Found 4 (219 requested) and removed 0 (114 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:02:18 GMT 2018 Job finished. TimeTaking 72.54 Used memory is bytes: 6987680