Sun 23 Dec 23:54:14 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 2fea-2.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2fea-2.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2fea-2.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fea-2.0-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/2fea-2.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fea-2.0-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 23:54:18 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/2fea-2.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fea-2.0-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 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-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: 4 Cell parameters: 59.005 43.112 109.575 90.000 98.912 90.000 Input sequence file: 2fea-2.0-parrot-mrncs.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 4155 atoms. Observations/parameters ratio is 2.19 ------------------------------------------------------ Starting model: R = 0.3600 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3079 (Rfree = 0.000) for 4155 atoms. Found 113 (142 requested) and removed 83 (71 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.18 2.07 NCS extension: 0 residues added, 4185 seeds are put forward Round 1: 328 peptides, 45 chains. Longest chain 15 peptides. Score 0.589 Round 2: 356 peptides, 28 chains. Longest chain 35 peptides. Score 0.775 Round 3: 381 peptides, 18 chains. Longest chain 84 peptides. Score 0.859 Round 4: 384 peptides, 16 chains. Longest chain 50 peptides. Score 0.871 Round 5: 390 peptides, 13 chains. Longest chain 68 peptides. Score 0.889 Taking the results from Round 5 Chains 17, Residues 377, Estimated correctness of the model 98.7 % 10 chains (333 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 39 A and 43 A Built loop between residues 168 A and 171 A Built loop between residues 48 B and 57 B Built loop between residues 99 B and 105 B Built loop between residues 144 B and 151 B Built loop between residues 171 B and 180 B 9 chains (404 residues) following loop building 4 chains (365 residues) in sequence following loop building ------------------------------------------------------ 36466 reflections ( 97.75 % complete ) and 4400 restraints for refining 3923 atoms. 1244 conditional restraints added. Observations/parameters ratio is 2.32 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3108 (Rfree = 0.000) for 3923 atoms. Found 134 (134 requested) and removed 79 (67 requested) atoms. Cycle 2: After refmac, R = 0.2779 (Rfree = 0.000) for 3947 atoms. Found 118 (133 requested) and removed 68 (68 requested) atoms. Cycle 3: After refmac, R = 0.2608 (Rfree = 0.000) for 3973 atoms. Found 89 (131 requested) and removed 43 (68 requested) atoms. Cycle 4: After refmac, R = 0.2487 (Rfree = 0.000) for 4005 atoms. Found 90 (132 requested) and removed 30 (68 requested) atoms. Cycle 5: After refmac, R = 0.2412 (Rfree = 0.000) for 4056 atoms. Found 89 (133 requested) and removed 41 (69 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.10 1.99 NCS extension: 172 residues added (68 deleted due to clashes), 4279 seeds are put forward Round 1: 410 peptides, 12 chains. Longest chain 93 peptides. Score 0.906 Round 2: 419 peptides, 8 chains. Longest chain 94 peptides. Score 0.925 Round 3: 422 peptides, 11 chains. Longest chain 81 peptides. Score 0.917 Round 4: 425 peptides, 8 chains. Longest chain 104 peptides. Score 0.928 Round 5: 429 peptides, 7 chains. Longest chain 113 peptides. Score 0.933 Taking the results from Round 5 Chains 8, Residues 422, Estimated correctness of the model 99.5 % 6 chains (411 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 32 A and 37 A Built loop between residues 148 A and 151 A Built loop between residues 81 B and 84 B Built loop between residues 148 B and 151 B 3 chains (430 residues) following loop building 2 chains (421 residues) in sequence following loop building ------------------------------------------------------ 36466 reflections ( 97.75 % complete ) and 3981 restraints for refining 4036 atoms. 479 conditional restraints added. Observations/parameters ratio is 2.26 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2456 (Rfree = 0.000) for 4036 atoms. Found 126 (132 requested) and removed 76 (69 requested) atoms. Cycle 7: After refmac, R = 0.2303 (Rfree = 0.000) for 4076 atoms. Found 102 (131 requested) and removed 70 (69 requested) atoms. Cycle 8: After refmac, R = 0.2198 (Rfree = 0.000) for 4099 atoms. Found 85 (129 requested) and removed 50 (70 requested) atoms. Cycle 9: After refmac, R = 0.2118 (Rfree = 0.000) for 4133 atoms. Found 82 (127 requested) and removed 45 (70 requested) atoms. Cycle 10: After refmac, R = 0.2069 (Rfree = 0.000) for 4159 atoms. Found 82 (125 requested) and removed 65 (71 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.10 1.99 NCS extension: 5 residues added (4 deleted due to clashes), 4182 seeds are put forward Round 1: 431 peptides, 4 chains. Longest chain 145 peptides. Score 0.944 Round 2: 433 peptides, 5 chains. Longest chain 166 peptides. Score 0.941 Round 3: 429 peptides, 7 chains. Longest chain 124 peptides. Score 0.933 Round 4: 433 peptides, 6 chains. Longest chain 147 peptides. Score 0.938 Round 5: 430 peptides, 6 chains. Longest chain 145 peptides. Score 0.937 Taking the results from Round 1 Chains 4, Residues 427, Estimated correctness of the model 99.6 % 4 chains (427 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 148 A and 151 A Built loop between residues 148 B and 151 B 2 chains (431 residues) following loop building 2 chains (431 residues) in sequence following loop building ------------------------------------------------------ 36466 reflections ( 97.75 % complete ) and 3906 restraints for refining 4045 atoms. 349 conditional restraints added. Observations/parameters ratio is 2.25 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2178 (Rfree = 0.000) for 4045 atoms. Found 119 (119 requested) and removed 63 (69 requested) atoms. Cycle 12: After refmac, R = 0.2087 (Rfree = 0.000) for 4097 atoms. Found 82 (118 requested) and removed 50 (70 requested) atoms. Cycle 13: After refmac, R = 0.2015 (Rfree = 0.000) for 4124 atoms. Found 110 (116 requested) and removed 61 (70 requested) atoms. Cycle 14: After refmac, R = 0.1990 (Rfree = 0.000) for 4170 atoms. Found 97 (114 requested) and removed 65 (71 requested) atoms. Cycle 15: After refmac, R = 0.1961 (Rfree = 0.000) for 4199 atoms. Found 109 (112 requested) and removed 71 (71 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.09 1.98 NCS extension: 2 residues added (1 deleted due to clashes), 4240 seeds are put forward Round 1: 432 peptides, 5 chains. Longest chain 145 peptides. Score 0.941 Round 2: 433 peptides, 5 chains. Longest chain 147 peptides. Score 0.941 Round 3: 431 peptides, 8 chains. Longest chain 100 peptides. Score 0.931 Round 4: 426 peptides, 9 chains. Longest chain 126 peptides. Score 0.925 Round 5: 431 peptides, 7 chains. Longest chain 145 peptides. Score 0.934 Taking the results from Round 2 Chains 6, Residues 428, Estimated correctness of the model 99.6 % 5 chains (427 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 3 chains (434 residues) following loop building 2 chains (433 residues) in sequence following loop building ------------------------------------------------------ 36466 reflections ( 97.75 % complete ) and 3872 restraints for refining 4057 atoms. 294 conditional restraints added. Observations/parameters ratio is 2.25 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2110 (Rfree = 0.000) for 4057 atoms. Found 105 (105 requested) and removed 59 (69 requested) atoms. Cycle 17: After refmac, R = 0.2015 (Rfree = 0.000) for 4103 atoms. Found 91 (104 requested) and removed 45 (70 requested) atoms. Cycle 18: After refmac, R = 0.1958 (Rfree = 0.000) for 4147 atoms. Found 78 (105 requested) and removed 54 (71 requested) atoms. Cycle 19: After refmac, R = 0.1925 (Rfree = 0.000) for 4166 atoms. Found 81 (102 requested) and removed 54 (71 requested) atoms. Cycle 20: After refmac, R = 0.1897 (Rfree = 0.000) for 4193 atoms. Found 94 (100 requested) and removed 50 (71 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.10 1.99 NCS extension: 0 residues added, 4237 seeds are put forward Round 1: 434 peptides, 5 chains. Longest chain 144 peptides. Score 0.942 Round 2: 431 peptides, 5 chains. Longest chain 145 peptides. Score 0.941 Round 3: 434 peptides, 6 chains. Longest chain 145 peptides. Score 0.939 Round 4: 432 peptides, 6 chains. Longest chain 174 peptides. Score 0.938 Round 5: 435 peptides, 5 chains. Longest chain 145 peptides. Score 0.942 Taking the results from Round 5 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 47 A and 50 A Built loop between residues 148 A and 151 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 3875 restraints for refining 4068 atoms. 275 conditional restraints added. Observations/parameters ratio is 2.24 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2105 (Rfree = 0.000) for 4068 atoms. Found 95 (95 requested) and removed 60 (69 requested) atoms. Cycle 22: After refmac, R = 0.1995 (Rfree = 0.000) for 4100 atoms. Found 92 (92 requested) and removed 35 (70 requested) atoms. Cycle 23: After refmac, R = 0.1947 (Rfree = 0.000) for 4153 atoms. Found 87 (94 requested) and removed 52 (71 requested) atoms. Cycle 24: After refmac, R = 0.1902 (Rfree = 0.000) for 4188 atoms. Found 92 (92 requested) and removed 63 (71 requested) atoms. Cycle 25: After refmac, R = 0.1895 (Rfree = 0.000) for 4209 atoms. Found 89 (89 requested) and removed 73 (72 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.10 1.99 NCS extension: 0 residues added, 4225 seeds are put forward Round 1: 437 peptides, 5 chains. Longest chain 145 peptides. Score 0.943 Round 2: 432 peptides, 6 chains. Longest chain 147 peptides. Score 0.938 Round 3: 431 peptides, 6 chains. Longest chain 142 peptides. Score 0.937 Round 4: 433 peptides, 5 chains. Longest chain 147 peptides. Score 0.941 Round 5: 431 peptides, 6 chains. Longest chain 145 peptides. Score 0.937 Taking the results from Round 1 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 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 (438 residues) following loop building 2 chains (438 residues) in sequence following loop building ------------------------------------------------------ 36466 reflections ( 97.75 % complete ) and 3894 restraints for refining 4094 atoms. 271 conditional restraints added. Observations/parameters ratio is 2.23 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2067 (Rfree = 0.000) for 4094 atoms. Found 84 (84 requested) and removed 61 (70 requested) atoms. Cycle 27: After refmac, R = 0.1962 (Rfree = 0.000) for 4115 atoms. Found 82 (82 requested) and removed 39 (70 requested) atoms. Cycle 28: After refmac, R = 0.1913 (Rfree = 0.000) for 4155 atoms. Found 82 (82 requested) and removed 49 (71 requested) atoms. Cycle 29: After refmac, R = 0.1884 (Rfree = 0.000) for 4188 atoms. Found 80 (80 requested) and removed 51 (71 requested) atoms. Cycle 30: After refmac, R = 0.1857 (Rfree = 0.000) for 4215 atoms. Found 78 (78 requested) and removed 68 (72 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.09 1.98 NCS extension: 0 residues added, 4225 seeds are put forward Round 1: 436 peptides, 6 chains. Longest chain 144 peptides. Score 0.940 Round 2: 435 peptides, 6 chains. Longest chain 166 peptides. Score 0.939 Round 3: 436 peptides, 5 chains. Longest chain 162 peptides. Score 0.943 Round 4: 433 peptides, 9 chains. Longest chain 121 peptides. Score 0.929 Round 5: 434 peptides, 6 chains. Longest chain 145 peptides. Score 0.939 Taking the results from Round 3 Chains 7, Residues 431, Estimated correctness of the model 99.6 % 5 chains (428 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 164 A and 172 A Built loop between residues 148 B and 151 B Built loop between residues 200 B and 204 B 2 chains (440 residues) following loop building 2 chains (440 residues) in sequence following loop building ------------------------------------------------------ 36466 reflections ( 97.75 % complete ) and 3872 restraints for refining 4104 atoms. 224 conditional restraints added. Observations/parameters ratio is 2.22 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2075 (Rfree = 0.000) for 4104 atoms. Found 73 (73 requested) and removed 70 (70 requested) atoms. Cycle 32: After refmac, R = 0.1976 (Rfree = 0.000) for 4103 atoms. Found 70 (70 requested) and removed 33 (70 requested) atoms. Cycle 33: After refmac, R = 0.1920 (Rfree = 0.000) for 4138 atoms. Found 70 (70 requested) and removed 32 (70 requested) atoms. Cycle 34: After refmac, R = 0.1884 (Rfree = 0.000) for 4172 atoms. Found 71 (71 requested) and removed 47 (71 requested) atoms. Cycle 35: After refmac, R = 0.1879 (Rfree = 0.000) for 4192 atoms. Found 71 (71 requested) and removed 63 (71 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.09 1.98 NCS extension: 0 residues added, 4200 seeds are put forward Round 1: 438 peptides, 6 chains. Longest chain 144 peptides. Score 0.940 Round 2: 437 peptides, 5 chains. Longest chain 147 peptides. Score 0.943 Round 3: 436 peptides, 8 chains. Longest chain 143 peptides. Score 0.933 Round 4: 442 peptides, 3 chains. Longest chain 221 peptides. Score 0.951 Round 5: 425 peptides, 9 chains. Longest chain 100 peptides. Score 0.925 Taking the results from Round 4 Chains 3, Residues 439, Estimated correctness of the model 99.7 % 3 chains (439 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 150 B and 153 B 2 chains (441 residues) following loop building 2 chains (441 residues) in sequence following loop building ------------------------------------------------------ 36466 reflections ( 97.75 % complete ) and 3839 restraints for refining 4092 atoms. 180 conditional restraints added. Observations/parameters ratio is 2.23 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2086 (Rfree = 0.000) for 4092 atoms. Found 70 (70 requested) and removed 63 (70 requested) atoms. Cycle 37: After refmac, R = 0.1970 (Rfree = 0.000) for 4097 atoms. Found 70 (70 requested) and removed 22 (70 requested) atoms. Cycle 38: After refmac, R = 0.1913 (Rfree = 0.000) for 4143 atoms. Found 70 (70 requested) and removed 34 (70 requested) atoms. Cycle 39: After refmac, R = 0.1875 (Rfree = 0.000) for 4173 atoms. Found 71 (71 requested) and removed 48 (71 requested) atoms. Cycle 40: After refmac, R = 0.1854 (Rfree = 0.000) for 4193 atoms. Found 71 (71 requested) and removed 57 (71 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.10 1.99 NCS extension: 0 residues added, 4207 seeds are put forward Round 1: 439 peptides, 6 chains. Longest chain 145 peptides. Score 0.941 Round 2: 436 peptides, 6 chains. Longest chain 145 peptides. Score 0.940 Round 3: 441 peptides, 4 chains. Longest chain 197 peptides. Score 0.947 Round 4: 435 peptides, 7 chains. Longest chain 102 peptides. Score 0.936 Round 5: 431 peptides, 9 chains. Longest chain 85 peptides. Score 0.928 Taking the results from Round 3 Chains 5, Residues 437, Estimated correctness of the model 99.7 % 4 chains (436 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 148 A and 151 A Built loop between residues 200 B and 204 B 2 chains (441 residues) following loop building 2 chains (441 residues) in sequence following loop building ------------------------------------------------------ 36466 reflections ( 97.75 % complete ) and 3851 restraints for refining 4105 atoms. 192 conditional restraints added. Observations/parameters ratio is 2.22 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2059 (Rfree = 0.000) for 4105 atoms. Found 70 (70 requested) and removed 59 (70 requested) atoms. Cycle 42: After refmac, R = 0.1948 (Rfree = 0.000) for 4113 atoms. Found 70 (70 requested) and removed 33 (70 requested) atoms. Cycle 43: After refmac, R = 0.1898 (Rfree = 0.000) for 4148 atoms. Found 71 (71 requested) and removed 42 (71 requested) atoms. Cycle 44: After refmac, R = 0.1860 (Rfree = 0.000) for 4175 atoms. Found 71 (71 requested) and removed 51 (71 requested) atoms. Cycle 45: After refmac, R = 0.1858 (Rfree = 0.000) for 4192 atoms. Found 71 (71 requested) and removed 60 (71 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.10 1.99 NCS extension: 0 residues added, 4203 seeds are put forward Round 1: 439 peptides, 6 chains. Longest chain 145 peptides. Score 0.941 Round 2: 438 peptides, 4 chains. Longest chain 222 peptides. Score 0.946 Round 3: 439 peptides, 6 chains. Longest chain 145 peptides. Score 0.941 Round 4: 432 peptides, 8 chains. Longest chain 100 peptides. Score 0.932 Round 5: 434 peptides, 9 chains. Longest chain 100 peptides. Score 0.929 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 4, Residues 434, Estimated correctness of the model 99.7 % 4 chains (434 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 47 A and 50 A Built loop between residues 148 A and 151 A 2 chains (438 residues) following loop building 2 chains (438 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 36466 reflections ( 97.75 % complete ) and 3632 restraints for refining 3545 atoms. Observations/parameters ratio is 2.57 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2598 (Rfree = 0.000) for 3545 atoms. Found 60 (60 requested) and removed 0 (60 requested) atoms. Cycle 47: After refmac, R = 0.2400 (Rfree = 0.000) for 3545 atoms. Found 29 (61 requested) and removed 0 (61 requested) atoms. Cycle 48: After refmac, R = 0.2285 (Rfree = 0.000) for 3545 atoms. Found 14 (62 requested) and removed 3 (62 requested) atoms. Cycle 49: After refmac, R = 0.2230 (Rfree = 0.000) for 3545 atoms. Found 10 (62 requested) and removed 3 (62 requested) atoms. Writing output files ... TimeTaking 50.9