Mon 24 Dec 07:36:55 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2fea-2.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2fea-2.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2fea-2.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2fea-2.0-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2fea-2.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2fea-2.0-parrot-noncs ############### 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 07:36:59 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/noncs/ArpWArp/wArpResults/WorkingDir/2fea-2.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2fea-2.0-parrot-noncs/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 494 and 0 Target number of residues in the AU: 494 Target solvent content: 0.5146 Checking the provided sequence file Detected sequence length: 236 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 472 Adjusted target solvent content: 0.54 Input MTZ file: 2fea-2.0-parrot-noncs.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: 4 Cell parameters: 59.005 43.112 109.575 90.000 98.912 90.000 Input sequence file: 2fea-2.0-parrot-noncs.fasta_lf Building free atoms model in initial map for 3776 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: 22.949 2.000 Wilson plot Bfac: 26.42 36466 reflections ( 97.75 % complete ) and 0 restraints for refining 4210 atoms. Observations/parameters ratio is 2.17 ------------------------------------------------------ Starting model: R = 0.3578 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3078 (Rfree = 0.000) for 4210 atoms. Found 111 (144 requested) and removed 77 (72 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.18 2.07 NCS extension: 0 residues added, 4244 seeds are put forward Round 1: 305 peptides, 45 chains. Longest chain 15 peptides. Score 0.537 Round 2: 359 peptides, 27 chains. Longest chain 51 peptides. Score 0.785 Round 3: 380 peptides, 21 chains. Longest chain 59 peptides. Score 0.843 Round 4: 379 peptides, 19 chains. Longest chain 48 peptides. Score 0.852 Round 5: 392 peptides, 13 chains. Longest chain 59 peptides. Score 0.890 Taking the results from Round 5 Chains 13, Residues 379, Estimated correctness of the model 98.8 % 9 chains (343 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 40 A and 49 A Built loop between residues 106 A and 109 A Built loop between residues 198 A and 205 A Built loop between residues 43 B and 49 B Built loop between residues 86 B and 93 B 8 chains (406 residues) following loop building 4 chains (370 residues) in sequence following loop building ------------------------------------------------------ 36466 reflections ( 97.75 % complete ) and 4549 restraints for refining 4057 atoms. 1326 conditional restraints added. Observations/parameters ratio is 2.25 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3201 (Rfree = 0.000) for 4057 atoms. Found 139 (139 requested) and removed 84 (69 requested) atoms. Cycle 2: After refmac, R = 0.2884 (Rfree = 0.000) for 4081 atoms. Found 114 (137 requested) and removed 70 (70 requested) atoms. Cycle 3: After refmac, R = 0.2704 (Rfree = 0.000) for 4092 atoms. Found 85 (135 requested) and removed 71 (70 requested) atoms. Cycle 4: After refmac, R = 0.2560 (Rfree = 0.000) for 4091 atoms. Found 84 (132 requested) and removed 59 (70 requested) atoms. Cycle 5: After refmac, R = 0.2466 (Rfree = 0.000) for 4097 atoms. Found 60 (130 requested) and removed 49 (70 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.11 2.00 NCS extension: 29 residues added (15 deleted due to clashes), 4145 seeds are put forward Round 1: 401 peptides, 15 chains. Longest chain 99 peptides. Score 0.888 Round 2: 412 peptides, 10 chains. Longest chain 141 peptides. Score 0.915 Round 3: 418 peptides, 8 chains. Longest chain 141 peptides. Score 0.925 Round 4: 424 peptides, 8 chains. Longest chain 141 peptides. Score 0.928 Round 5: 418 peptides, 11 chains. Longest chain 141 peptides. Score 0.914 Taking the results from Round 4 Chains 9, Residues 416, Estimated correctness of the model 99.4 % 6 chains (392 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 38 A and 42 A Built loop between residues 144 B and 151 B Built loop between residues 162 B and 166 B 5 chains (427 residues) following loop building 3 chains (404 residues) in sequence following loop building ------------------------------------------------------ 36466 reflections ( 97.75 % complete ) and 4131 restraints for refining 4058 atoms. 726 conditional restraints added. Observations/parameters ratio is 2.25 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2534 (Rfree = 0.000) for 4058 atoms. Found 114 (125 requested) and removed 71 (69 requested) atoms. Cycle 7: After refmac, R = 0.2327 (Rfree = 0.000) for 4089 atoms. Found 83 (123 requested) and removed 45 (70 requested) atoms. Cycle 8: After refmac, R = 0.2221 (Rfree = 0.000) for 4116 atoms. Found 79 (121 requested) and removed 42 (70 requested) atoms. Cycle 9: After refmac, R = 0.2143 (Rfree = 0.000) for 4142 atoms. Found 81 (119 requested) and removed 51 (71 requested) atoms. Cycle 10: After refmac, R = 0.2100 (Rfree = 0.000) for 4168 atoms. Found 81 (116 requested) and removed 38 (71 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.11 2.00 NCS extension: 15 residues added (11 deleted due to clashes), 4234 seeds are put forward Round 1: 425 peptides, 6 chains. Longest chain 144 peptides. Score 0.935 Round 2: 425 peptides, 7 chains. Longest chain 142 peptides. Score 0.932 Round 3: 429 peptides, 6 chains. Longest chain 142 peptides. Score 0.937 Round 4: 424 peptides, 8 chains. Longest chain 138 peptides. Score 0.928 Round 5: 420 peptides, 7 chains. Longest chain 138 peptides. Score 0.929 Taking the results from Round 3 Chains 6, Residues 423, Estimated correctness of the model 99.6 % 5 chains (419 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 148 A and 151 A Built loop between residues 47 B and 50 B Built loop between residues 144 B and 151 B 3 chains (433 residues) following loop building 2 chains (429 residues) in sequence following loop building ------------------------------------------------------ 36466 reflections ( 97.75 % complete ) and 4011 restraints for refining 4126 atoms. 463 conditional restraints added. Observations/parameters ratio is 2.21 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2274 (Rfree = 0.000) for 4126 atoms. Found 116 (116 requested) and removed 72 (70 requested) atoms. Cycle 12: After refmac, R = 0.2150 (Rfree = 0.000) for 4162 atoms. Found 97 (114 requested) and removed 47 (71 requested) atoms. Cycle 13: After refmac, R = 0.2053 (Rfree = 0.000) for 4211 atoms. Found 104 (115 requested) and removed 46 (72 requested) atoms. Cycle 14: After refmac, R = 0.2016 (Rfree = 0.000) for 4264 atoms. Found 90 (117 requested) and removed 71 (73 requested) atoms. Cycle 15: After refmac, R = 0.1988 (Rfree = 0.000) for 4275 atoms. Found 104 (114 requested) and removed 72 (73 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.10 1.99 NCS extension: 147 residues added (70 deleted due to clashes), 4455 seeds are put forward Round 1: 428 peptides, 9 chains. Longest chain 73 peptides. Score 0.926 Round 2: 423 peptides, 9 chains. Longest chain 138 peptides. Score 0.924 Round 3: 427 peptides, 5 chains. Longest chain 138 peptides. Score 0.939 Round 4: 422 peptides, 9 chains. Longest chain 96 peptides. Score 0.924 Round 5: 425 peptides, 9 chains. Longest chain 82 peptides. Score 0.925 Taking the results from Round 3 Chains 5, Residues 422, Estimated correctness of the model 99.6 % 5 chains (422 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 44 A and 50 A Built loop between residues 149 A and 152 A Built loop between residues 144 B and 151 B 2 chains (435 residues) following loop building 2 chains (435 residues) in sequence following loop building ------------------------------------------------------ 36466 reflections ( 97.75 % complete ) and 3977 restraints for refining 4135 atoms. 380 conditional restraints added. Observations/parameters ratio is 2.20 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2161 (Rfree = 0.000) for 4135 atoms. Found 107 (107 requested) and removed 71 (70 requested) atoms. Cycle 17: After refmac, R = 0.2069 (Rfree = 0.000) for 4167 atoms. Found 100 (105 requested) and removed 42 (71 requested) atoms. Cycle 18: After refmac, R = 0.1995 (Rfree = 0.000) for 4219 atoms. Found 94 (107 requested) and removed 46 (72 requested) atoms. Cycle 19: After refmac, R = 0.1948 (Rfree = 0.000) for 4266 atoms. Found 98 (108 requested) and removed 52 (73 requested) atoms. Cycle 20: After refmac, R = 0.1915 (Rfree = 0.000) for 4305 atoms. Found 87 (106 requested) and removed 74 (73 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.10 1.99 NCS extension: 3 residues added (0 deleted due to clashes), 4321 seeds are put forward Round 1: 436 peptides, 6 chains. Longest chain 145 peptides. Score 0.940 Round 2: 437 peptides, 5 chains. Longest chain 147 peptides. Score 0.943 Round 3: 434 peptides, 5 chains. Longest chain 147 peptides. Score 0.942 Round 4: 429 peptides, 7 chains. Longest chain 108 peptides. Score 0.933 Round 5: 432 peptides, 6 chains. Longest chain 165 peptides. Score 0.938 Taking the results from Round 2 Chains 5, Residues 432, Estimated correctness of the model 99.6 % 5 chains (432 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 150 A and 153 A Built loop between residues 148 B and 151 B Built loop between residues 169 B and 172 B 2 chains (438 residues) following loop building 2 chains (438 residues) in sequence following loop building ------------------------------------------------------ 36466 reflections ( 97.75 % complete ) and 3959 restraints for refining 4153 atoms. 336 conditional restraints added. Observations/parameters ratio is 2.20 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2097 (Rfree = 0.000) for 4153 atoms. Found 99 (99 requested) and removed 75 (71 requested) atoms. Cycle 22: After refmac, R = 0.2024 (Rfree = 0.000) for 4173 atoms. Found 95 (97 requested) and removed 48 (71 requested) atoms. Cycle 23: After refmac, R = 0.1969 (Rfree = 0.000) for 4216 atoms. Found 95 (95 requested) and removed 54 (72 requested) atoms. Cycle 24: After refmac, R = 0.1937 (Rfree = 0.000) for 4255 atoms. Found 93 (93 requested) and removed 56 (72 requested) atoms. Cycle 25: After refmac, R = 0.1909 (Rfree = 0.000) for 4287 atoms. Found 91 (91 requested) and removed 66 (73 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.10 1.99 NCS extension: 2 residues added (1 deleted due to clashes), 4314 seeds are put forward Round 1: 433 peptides, 7 chains. Longest chain 145 peptides. Score 0.935 Round 2: 437 peptides, 5 chains. Longest chain 148 peptides. Score 0.943 Round 3: 426 peptides, 10 chains. Longest chain 142 peptides. Score 0.922 Round 4: 429 peptides, 6 chains. Longest chain 176 peptides. Score 0.937 Round 5: 432 peptides, 5 chains. Longest chain 142 peptides. Score 0.941 Taking the results from Round 2 Chains 5, Residues 432, Estimated correctness of the model 99.6 % 5 chains (432 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 150 A and 153 A Built loop between residues 150 B and 153 B Built loop between residues 162 B and 165 B 2 chains (438 residues) following loop building 2 chains (438 residues) in sequence following loop building ------------------------------------------------------ 36466 reflections ( 97.75 % complete ) and 3988 restraints for refining 4150 atoms. 372 conditional restraints added. Observations/parameters ratio is 2.20 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2109 (Rfree = 0.000) for 4150 atoms. Found 85 (85 requested) and removed 72 (71 requested) atoms. Cycle 27: After refmac, R = 0.2013 (Rfree = 0.000) for 4161 atoms. Found 82 (82 requested) and removed 33 (71 requested) atoms. Cycle 28: After refmac, R = 0.1948 (Rfree = 0.000) for 4209 atoms. Found 84 (84 requested) and removed 40 (72 requested) atoms. Cycle 29: After refmac, R = 0.1908 (Rfree = 0.000) for 4250 atoms. Found 84 (84 requested) and removed 50 (72 requested) atoms. Cycle 30: After refmac, R = 0.1907 (Rfree = 0.000) for 4274 atoms. Found 82 (82 requested) and removed 53 (73 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.10 1.99 NCS extension: 0 residues added, 4303 seeds are put forward Round 1: 437 peptides, 6 chains. Longest chain 146 peptides. Score 0.940 Round 2: 438 peptides, 5 chains. Longest chain 148 peptides. Score 0.943 Round 3: 427 peptides, 6 chains. Longest chain 102 peptides. Score 0.936 Round 4: 430 peptides, 6 chains. Longest chain 142 peptides. Score 0.937 Round 5: 433 peptides, 7 chains. Longest chain 108 peptides. Score 0.935 Taking the results from Round 2 Chains 5, Residues 433, Estimated correctness of the model 99.6 % 5 chains (433 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 148 A and 151 A Built loop between residues 150 B and 153 B 3 chains (437 residues) following loop building 3 chains (437 residues) in sequence following loop building ------------------------------------------------------ 36466 reflections ( 97.75 % complete ) and 3985 restraints for refining 4156 atoms. 371 conditional restraints added. Observations/parameters ratio is 2.19 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2078 (Rfree = 0.000) for 4156 atoms. Found 77 (77 requested) and removed 71 (71 requested) atoms. Cycle 32: After refmac, R = 0.1991 (Rfree = 0.000) for 4161 atoms. Found 74 (74 requested) and removed 24 (71 requested) atoms. Cycle 33: After refmac, R = 0.1949 (Rfree = 0.000) for 4211 atoms. Found 75 (75 requested) and removed 44 (72 requested) atoms. Cycle 34: After refmac, R = 0.1918 (Rfree = 0.000) for 4240 atoms. Found 72 (72 requested) and removed 38 (72 requested) atoms. Cycle 35: After refmac, R = 0.1903 (Rfree = 0.000) for 4272 atoms. Found 73 (73 requested) and removed 54 (73 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.10 1.99 NCS extension: 149 residues added (73 deleted due to clashes), 4440 seeds are put forward Round 1: 438 peptides, 5 chains. Longest chain 146 peptides. Score 0.943 Round 2: 439 peptides, 4 chains. Longest chain 220 peptides. Score 0.947 Round 3: 427 peptides, 9 chains. Longest chain 100 peptides. Score 0.926 Round 4: 435 peptides, 4 chains. Longest chain 219 peptides. Score 0.945 Round 5: 430 peptides, 7 chains. Longest chain 145 peptides. Score 0.934 Taking the results from Round 2 Chains 4, Residues 435, Estimated correctness of the model 99.7 % 4 chains (435 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 151 A and 154 A Built loop between residues 208 A and 211 A 2 chains (439 residues) following loop building 2 chains (439 residues) in sequence following loop building ------------------------------------------------------ 36466 reflections ( 97.75 % complete ) and 3952 restraints for refining 4158 atoms. 320 conditional restraints added. Observations/parameters ratio is 2.19 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2089 (Rfree = 0.000) for 4158 atoms. Found 71 (71 requested) and removed 65 (71 requested) atoms. Cycle 37: After refmac, R = 0.1988 (Rfree = 0.000) for 4161 atoms. Found 71 (71 requested) and removed 22 (71 requested) atoms. Cycle 38: After refmac, R = 0.1931 (Rfree = 0.000) for 4207 atoms. Found 72 (72 requested) and removed 36 (72 requested) atoms. Cycle 39: After refmac, R = 0.1901 (Rfree = 0.000) for 4243 atoms. Found 72 (72 requested) and removed 54 (72 requested) atoms. Cycle 40: After refmac, R = 0.1891 (Rfree = 0.000) for 4259 atoms. Found 72 (72 requested) and removed 54 (72 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.10 1.99 NCS extension: 0 residues added, 4278 seeds are put forward Round 1: 435 peptides, 5 chains. Longest chain 145 peptides. Score 0.942 Round 2: 432 peptides, 7 chains. Longest chain 147 peptides. Score 0.935 Round 3: 429 peptides, 8 chains. Longest chain 143 peptides. Score 0.930 Round 4: 438 peptides, 8 chains. Longest chain 163 peptides. Score 0.934 Round 5: 432 peptides, 8 chains. Longest chain 101 peptides. Score 0.932 Taking the results from Round 1 Chains 5, Residues 430, Estimated correctness of the model 99.6 % 5 chains (430 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 148 A and 151 A Built loop between residues 208 A and 211 A Built loop between residues 148 B and 151 B 2 chains (436 residues) following loop building 2 chains (436 residues) in sequence following loop building ------------------------------------------------------ 36466 reflections ( 97.75 % complete ) and 3977 restraints for refining 4143 atoms. 372 conditional restraints added. Observations/parameters ratio is 2.20 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2067 (Rfree = 0.000) for 4143 atoms. Found 70 (70 requested) and removed 61 (70 requested) atoms. Cycle 42: After refmac, R = 0.1958 (Rfree = 0.000) for 4151 atoms. Found 71 (71 requested) and removed 19 (71 requested) atoms. Cycle 43: After refmac, R = 0.1911 (Rfree = 0.000) for 4202 atoms. Found 71 (71 requested) and removed 39 (71 requested) atoms. Cycle 44: After refmac, R = 0.1887 (Rfree = 0.000) for 4232 atoms. Found 72 (72 requested) and removed 43 (72 requested) atoms. Cycle 45: After refmac, R = 0.1865 (Rfree = 0.000) for 4258 atoms. Found 72 (72 requested) and removed 48 (72 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.09 1.98 NCS extension: 2 residues added (1 deleted due to clashes), 4284 seeds are put forward Round 1: 435 peptides, 5 chains. Longest chain 144 peptides. Score 0.942 Round 2: 435 peptides, 6 chains. Longest chain 146 peptides. Score 0.939 Round 3: 433 peptides, 7 chains. Longest chain 146 peptides. Score 0.935 Round 4: 436 peptides, 6 chains. Longest chain 147 peptides. Score 0.940 Round 5: 429 peptides, 9 chains. Longest chain 102 peptides. Score 0.927 Taking the results from Round 1 Last building cycle: Chain fragments will be rearranged Chains 5, Residues 430, Estimated correctness of the model 99.6 % 5 chains (430 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 148 A and 151 A Built loop between residues 208 A and 211 A Built loop between residues 148 B and 151 B 2 chains (436 residues) following loop building 2 chains (436 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 36466 reflections ( 97.75 % complete ) and 3604 restraints for refining 3519 atoms. Observations/parameters ratio is 2.59 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2623 (Rfree = 0.000) for 3519 atoms. Found 57 (60 requested) and removed 0 (60 requested) atoms. Cycle 47: After refmac, R = 0.2430 (Rfree = 0.000) for 3519 atoms. Found 30 (61 requested) and removed 0 (61 requested) atoms. Cycle 48: After refmac, R = 0.2318 (Rfree = 0.000) for 3519 atoms. Found 22 (61 requested) and removed 3 (61 requested) atoms. Cycle 49: After refmac, R = 0.2256 (Rfree = 0.000) for 3519 atoms. Found 13 (62 requested) and removed 1 (62 requested) atoms. Writing output files ... TimeTaking 51.97