Sun 23 Dec 22:23:05 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 1zkg-2.3-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1zkg-2.3-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1zkg-2.3-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zkg-2.3-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/1zkg-2.3-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zkg-2.3-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 22:23:13 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/1zkg-2.3-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zkg-2.3-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 388 and 0 Target number of residues in the AU: 388 Target solvent content: 0.5689 Checking the provided sequence file Detected sequence length: 212 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 424 Adjusted target solvent content: 0.53 Input MTZ file: 1zkg-2.3-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: 4 Cell parameters: 50.537 87.114 59.148 90.000 110.732 90.000 Input sequence file: 1zkg-2.3-parrot-hancs.fasta_lf Building free atoms model in initial map for 3392 target number of atoms Had to go as low as 0.65 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 3 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: 29.148 2.300 Wilson plot Bfac: 41.24 21357 reflections ( 99.93 % complete ) and 0 restraints for refining 3772 atoms. Observations/parameters ratio is 1.42 ------------------------------------------------------ Starting model: R = 0.3301 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2388 (Rfree = 0.000) for 3772 atoms. Found 63 (86 requested) and removed 50 (43 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.51 2.41 NCS extension: 0 residues added, 3785 seeds are put forward Round 1: 247 peptides, 36 chains. Longest chain 20 peptides. Score 0.520 Round 2: 280 peptides, 30 chains. Longest chain 26 peptides. Score 0.667 Round 3: 316 peptides, 28 chains. Longest chain 38 peptides. Score 0.752 Round 4: 330 peptides, 24 chains. Longest chain 38 peptides. Score 0.802 Round 5: 337 peptides, 24 chains. Longest chain 46 peptides. Score 0.811 Taking the results from Round 5 Chains 25, Residues 313, Estimated correctness of the model 94.7 % 7 chains (196 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 33 B and 37 B 24 chains (316 residues) following loop building 6 chains (199 residues) in sequence following loop building ------------------------------------------------------ 21357 reflections ( 99.93 % complete ) and 4699 restraints for refining 3260 atoms. 2554 conditional restraints added. Observations/parameters ratio is 1.64 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2872 (Rfree = 0.000) for 3260 atoms. Found 74 (74 requested) and removed 47 (37 requested) atoms. Cycle 2: After refmac, R = 0.2631 (Rfree = 0.000) for 3263 atoms. Found 40 (73 requested) and removed 40 (37 requested) atoms. Cycle 3: After refmac, R = 0.2535 (Rfree = 0.000) for 3241 atoms. Found 31 (72 requested) and removed 40 (37 requested) atoms. Cycle 4: After refmac, R = 0.2444 (Rfree = 0.000) for 3216 atoms. Found 33 (70 requested) and removed 37 (37 requested) atoms. Cycle 5: After refmac, R = 0.2414 (Rfree = 0.000) for 3201 atoms. Found 30 (67 requested) and removed 36 (36 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.45 2.35 NCS extension: 73 residues added (17 deleted due to clashes), 3281 seeds are put forward Round 1: 327 peptides, 20 chains. Longest chain 41 peptides. Score 0.824 Round 2: 344 peptides, 14 chains. Longest chain 61 peptides. Score 0.876 Round 3: 340 peptides, 20 chains. Longest chain 45 peptides. Score 0.839 Round 4: 345 peptides, 23 chains. Longest chain 34 peptides. Score 0.827 Round 5: 355 peptides, 19 chains. Longest chain 56 peptides. Score 0.860 Taking the results from Round 2 Chains 19, Residues 330, Estimated correctness of the model 97.6 % 7 chains (238 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 29 A and 36 A Built loop between residues 47 B and 54 B Built loop between residues 76 B and 85 B 13 chains (343 residues) following loop building 4 chains (258 residues) in sequence following loop building ------------------------------------------------------ 21357 reflections ( 99.93 % complete ) and 4166 restraints for refining 3276 atoms. 1654 conditional restraints added. Observations/parameters ratio is 1.63 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2595 (Rfree = 0.000) for 3276 atoms. Found 67 (67 requested) and removed 45 (37 requested) atoms. Cycle 7: After refmac, R = 0.2400 (Rfree = 0.000) for 3289 atoms. Found 51 (66 requested) and removed 43 (37 requested) atoms. Cycle 8: After refmac, R = 0.2257 (Rfree = 0.000) for 3293 atoms. Found 32 (64 requested) and removed 39 (37 requested) atoms. Cycle 9: After refmac, R = 0.2215 (Rfree = 0.000) for 3276 atoms. Found 32 (63 requested) and removed 38 (37 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.2190 (Rfree = 0.000) for 3266 atoms. Found 32 (61 requested) and removed 37 (37 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.45 2.35 NCS extension: 136 residues added (72 deleted due to clashes), 3405 seeds are put forward Round 1: 354 peptides, 18 chains. Longest chain 63 peptides. Score 0.864 Round 2: 367 peptides, 14 chains. Longest chain 64 peptides. Score 0.894 Round 3: 375 peptides, 15 chains. Longest chain 70 peptides. Score 0.896 Round 4: 364 peptides, 20 chains. Longest chain 40 peptides. Score 0.863 Round 5: 374 peptides, 17 chains. Longest chain 72 peptides. Score 0.886 Taking the results from Round 3 Chains 18, Residues 360, Estimated correctness of the model 98.2 % 8 chains (282 residues) have been docked in sequence Building loops using Loopy2018 18 chains (360 residues) following loop building 8 chains (282 residues) in sequence following loop building ------------------------------------------------------ 21357 reflections ( 99.93 % complete ) and 4159 restraints for refining 3350 atoms. 1474 conditional restraints added. Observations/parameters ratio is 1.59 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2390 (Rfree = 0.000) for 3350 atoms. Found 62 (62 requested) and removed 53 (38 requested) atoms. Cycle 12: After refmac, R = 0.2201 (Rfree = 0.000) for 3351 atoms. Found 46 (60 requested) and removed 39 (38 requested) atoms. Cycle 13: After refmac, R = 0.2123 (Rfree = 0.000) for 3357 atoms. Found 26 (59 requested) and removed 39 (38 requested) atoms. Cycle 14: After refmac, R = 0.2092 (Rfree = 0.000) for 3339 atoms. Found 23 (56 requested) and removed 38 (38 requested) atoms. Cycle 15: After refmac, R = 0.2086 (Rfree = 0.000) for 3322 atoms. Found 25 (55 requested) and removed 38 (38 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.46 2.36 NCS extension: 125 residues added (24 deleted due to clashes), 3440 seeds are put forward Round 1: 363 peptides, 20 chains. Longest chain 51 peptides. Score 0.862 Round 2: 370 peptides, 12 chains. Longest chain 89 peptides. Score 0.905 Round 3: 379 peptides, 20 chains. Longest chain 53 peptides. Score 0.876 Round 4: 383 peptides, 13 chains. Longest chain 64 peptides. Score 0.909 Round 5: 363 peptides, 21 chains. Longest chain 48 peptides. Score 0.857 Taking the results from Round 4 Chains 13, Residues 370, Estimated correctness of the model 98.6 % 7 chains (307 residues) have been docked in sequence Building loops using Loopy2018 13 chains (370 residues) following loop building 7 chains (307 residues) in sequence following loop building ------------------------------------------------------ 21357 reflections ( 99.93 % complete ) and 4018 restraints for refining 3459 atoms. 1142 conditional restraints added. Observations/parameters ratio is 1.54 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2409 (Rfree = 0.000) for 3459 atoms. Found 55 (55 requested) and removed 55 (39 requested) atoms. Cycle 17: After refmac, R = 0.2172 (Rfree = 0.000) for 3446 atoms. Found 54 (54 requested) and removed 42 (39 requested) atoms. Cycle 18: After refmac, R = 0.2064 (Rfree = 0.000) for 3452 atoms. Found 35 (52 requested) and removed 39 (39 requested) atoms. Cycle 19: After refmac, R = 0.2020 (Rfree = 0.000) for 3448 atoms. Found 34 (51 requested) and removed 39 (39 requested) atoms. Cycle 20: After refmac, R = 0.1988 (Rfree = 0.000) for 3442 atoms. Found 27 (49 requested) and removed 40 (39 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.45 2.35 NCS extension: 115 residues added (53 deleted due to clashes), 3557 seeds are put forward Round 1: 369 peptides, 12 chains. Longest chain 64 peptides. Score 0.904 Round 2: 375 peptides, 12 chains. Longest chain 64 peptides. Score 0.908 Round 3: 373 peptides, 20 chains. Longest chain 35 peptides. Score 0.871 Round 4: 372 peptides, 12 chains. Longest chain 64 peptides. Score 0.906 Round 5: 355 peptides, 25 chains. Longest chain 45 peptides. Score 0.826 Taking the results from Round 2 Chains 16, Residues 363, Estimated correctness of the model 98.6 % 9 chains (325 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 45 A and 51 A Built loop between residues 158 A and 161 A Built loop between residues 103 B and 106 B Built loop between residues 180 B and 188 B 10 chains (375 residues) following loop building 5 chains (341 residues) in sequence following loop building ------------------------------------------------------ 21357 reflections ( 99.93 % complete ) and 3841 restraints for refining 3501 atoms. 811 conditional restraints added. Observations/parameters ratio is 1.53 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2304 (Rfree = 0.000) for 3501 atoms. Found 48 (48 requested) and removed 58 (40 requested) atoms. Cycle 22: After refmac, R = 0.2090 (Rfree = 0.000) for 3484 atoms. Found 45 (46 requested) and removed 41 (40 requested) atoms. Cycle 23: After refmac, R = 0.2001 (Rfree = 0.000) for 3487 atoms. Found 39 (45 requested) and removed 40 (40 requested) atoms. Cycle 24: After refmac, R = 0.1930 (Rfree = 0.000) for 3483 atoms. Found 33 (43 requested) and removed 44 (40 requested) atoms. Cycle 25: After refmac, R = 0.1926 (Rfree = 0.000) for 3472 atoms. Found 31 (41 requested) and removed 40 (39 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.45 2.35 NCS extension: 49 residues added (57 deleted due to clashes), 3519 seeds are put forward Round 1: 376 peptides, 19 chains. Longest chain 48 peptides. Score 0.878 Round 2: 380 peptides, 13 chains. Longest chain 90 peptides. Score 0.907 Round 3: 376 peptides, 21 chains. Longest chain 49 peptides. Score 0.869 Round 4: 372 peptides, 16 chains. Longest chain 71 peptides. Score 0.889 Round 5: 377 peptides, 18 chains. Longest chain 50 peptides. Score 0.884 Taking the results from Round 2 Chains 15, Residues 367, Estimated correctness of the model 98.6 % 8 chains (292 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 180 A and 183 A Built loop between residues 45 B and 52 B Built loop between residues 187 B and 191 B 12 chains (378 residues) following loop building 5 chains (303 residues) in sequence following loop building ------------------------------------------------------ 21357 reflections ( 99.93 % complete ) and 3952 restraints for refining 3409 atoms. 1101 conditional restraints added. Observations/parameters ratio is 1.57 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2295 (Rfree = 0.000) for 3409 atoms. Found 39 (39 requested) and removed 45 (39 requested) atoms. Cycle 27: After refmac, R = 0.2117 (Rfree = 0.000) for 3397 atoms. Found 39 (39 requested) and removed 40 (39 requested) atoms. Cycle 28: After refmac, R = 0.2040 (Rfree = 0.000) for 3394 atoms. Found 39 (39 requested) and removed 39 (39 requested) atoms. Cycle 29: After refmac, R = 0.2010 (Rfree = 0.000) for 3392 atoms. Found 36 (39 requested) and removed 42 (39 requested) atoms. Cycle 30: After refmac, R = 0.1980 (Rfree = 0.000) for 3385 atoms. Found 36 (38 requested) and removed 39 (38 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.44 2.34 NCS extension: 24 residues added (20 deleted due to clashes), 3413 seeds are put forward Round 1: 374 peptides, 18 chains. Longest chain 51 peptides. Score 0.881 Round 2: 384 peptides, 9 chains. Longest chain 100 peptides. Score 0.925 Round 3: 379 peptides, 12 chains. Longest chain 82 peptides. Score 0.911 Round 4: 376 peptides, 17 chains. Longest chain 62 peptides. Score 0.887 Round 5: 380 peptides, 15 chains. Longest chain 71 peptides. Score 0.899 Taking the results from Round 2 Chains 10, Residues 375, Estimated correctness of the model 99.0 % 8 chains (367 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 99 A and 106 A Built loop between residues 183 A and 188 A Built loop between residues 114 B and 118 B Built loop between residues 158 B and 161 B 6 chains (390 residues) following loop building 4 chains (382 residues) in sequence following loop building ------------------------------------------------------ 21357 reflections ( 99.93 % complete ) and 3640 restraints for refining 3572 atoms. 353 conditional restraints added. Observations/parameters ratio is 1.49 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2314 (Rfree = 0.000) for 3572 atoms. Found 41 (41 requested) and removed 52 (41 requested) atoms. Cycle 32: After refmac, R = 0.2075 (Rfree = 0.000) for 3550 atoms. Found 40 (40 requested) and removed 42 (40 requested) atoms. Cycle 33: After refmac, R = 0.1983 (Rfree = 0.000) for 3544 atoms. Found 40 (40 requested) and removed 41 (40 requested) atoms. Cycle 34: After refmac, R = 0.1938 (Rfree = 0.000) for 3540 atoms. Found 40 (40 requested) and removed 40 (40 requested) atoms. Cycle 35: After refmac, R = 0.1923 (Rfree = 0.000) for 3537 atoms. Found 40 (40 requested) and removed 41 (40 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.44 2.34 NCS extension: 198 residues added (89 deleted due to clashes), 3736 seeds are put forward Round 1: 385 peptides, 11 chains. Longest chain 82 peptides. Score 0.918 Round 2: 389 peptides, 9 chains. Longest chain 180 peptides. Score 0.928 Round 3: 387 peptides, 13 chains. Longest chain 53 peptides. Score 0.912 Round 4: 381 peptides, 11 chains. Longest chain 62 peptides. Score 0.916 Round 5: 370 peptides, 15 chains. Longest chain 51 peptides. Score 0.892 Taking the results from Round 2 Chains 9, Residues 380, Estimated correctness of the model 99.1 % 7 chains (361 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 27 A and 30 A Built loop between residues 45 B and 49 B Built loop between residues 73 B and 77 B Built loop between residues 181 B and 184 B 5 chains (390 residues) following loop building 3 chains (371 residues) in sequence following loop building ------------------------------------------------------ 21357 reflections ( 99.93 % complete ) and 3735 restraints for refining 3613 atoms. 479 conditional restraints added. Observations/parameters ratio is 1.48 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2383 (Rfree = 0.000) for 3613 atoms. Found 41 (41 requested) and removed 72 (41 requested) atoms. Cycle 37: After refmac, R = 0.2153 (Rfree = 0.000) for 3571 atoms. Found 41 (41 requested) and removed 47 (41 requested) atoms. Cycle 38: After refmac, R = 0.2099 (Rfree = 0.000) for 3561 atoms. Found 41 (41 requested) and removed 43 (41 requested) atoms. Cycle 39: After refmac, R = 0.1998 (Rfree = 0.000) for 3557 atoms. Found 40 (40 requested) and removed 40 (40 requested) atoms. Cycle 40: After refmac, R = 0.1996 (Rfree = 0.000) for 3555 atoms. Found 40 (40 requested) and removed 44 (40 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.46 2.36 NCS extension: 177 residues added (38 deleted due to clashes), 3729 seeds are put forward Round 1: 385 peptides, 9 chains. Longest chain 81 peptides. Score 0.926 Round 2: 388 peptides, 9 chains. Longest chain 84 peptides. Score 0.928 Round 3: 385 peptides, 12 chains. Longest chain 54 peptides. Score 0.914 Round 4: 384 peptides, 12 chains. Longest chain 67 peptides. Score 0.914 Round 5: 379 peptides, 14 chains. Longest chain 93 peptides. Score 0.903 Taking the results from Round 2 Chains 11, Residues 379, Estimated correctness of the model 99.1 % 8 chains (364 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 47 A and 51 A Built loop between residues 75 A and 78 A Built loop between residues 109 A and 113 A Built loop between residues 76 B and 79 B Built loop between residues 123 B and 127 B 4 chains (390 residues) following loop building 3 chains (377 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 21357 reflections ( 99.93 % complete ) and 3673 restraints for refining 3574 atoms. 415 conditional restraints added. Observations/parameters ratio is 1.49 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2204 (Rfree = 0.000) for 3574 atoms. Found 41 (41 requested) and removed 52 (41 requested) atoms. Cycle 42: After refmac, R = 0.2013 (Rfree = 0.000) for 3557 atoms. Found 40 (40 requested) and removed 41 (40 requested) atoms. Cycle 43: After refmac, R = 0.1933 (Rfree = 0.000) for 3555 atoms. Found 40 (40 requested) and removed 40 (40 requested) atoms. Cycle 44: After refmac, R = 0.1881 (Rfree = 0.000) for 3555 atoms. Found 40 (40 requested) and removed 42 (40 requested) atoms. Cycle 45: After refmac, R = 0.1873 (Rfree = 0.000) for 3551 atoms. Found 40 (40 requested) and removed 42 (40 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.43 2.33 NCS extension: 17 residues added (0 deleted due to clashes), 3572 seeds are put forward Round 1: 378 peptides, 10 chains. Longest chain 62 peptides. Score 0.918 Round 2: 385 peptides, 7 chains. Longest chain 106 peptides. Score 0.933 Round 3: 372 peptides, 12 chains. Longest chain 62 peptides. Score 0.906 Round 4: 373 peptides, 14 chains. Longest chain 79 peptides. Score 0.898 Round 5: 364 peptides, 20 chains. Longest chain 65 peptides. Score 0.863 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 9, Residues 378, Estimated correctness of the model 99.2 % 6 chains (304 residues) have been docked in sequence Sequence coverage is 80 % Consider running further cycles of model building using 1zkg-2_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 37 A and 42 A 8 chains (382 residues) following loop building 5 chains (308 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 21357 reflections ( 99.93 % complete ) and 3926 restraints for refining 3426 atoms. 1024 conditional restraints added. Observations/parameters ratio is 1.56 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2231 (Rfree = 0.000) for 3426 atoms. Found 0 (39 requested) and removed 6 (39 requested) atoms. Cycle 47: After refmac, R = 0.2132 (Rfree = 0.000) for 3412 atoms. Found 0 (39 requested) and removed 0 (39 requested) atoms. Cycle 48: After refmac, R = 0.2076 (Rfree = 0.000) for 3411 atoms. Found 0 (39 requested) and removed 1 (39 requested) atoms. Cycle 49: After refmac, R = 0.2058 (Rfree = 0.000) for 3408 atoms. TimeTaking 63.98