Mon 24 Dec 00:00:11 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 1z85-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1z85-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1z85-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1z85-3.2-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/1z85-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1z85-3.2-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 ============================================================ Mon 24 Dec 00:00:15 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/1z85-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1z85-3.2-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 399 and 0 Target number of residues in the AU: 399 Target solvent content: 0.6253 Checking the provided sequence file Detected sequence length: 234 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 468 Adjusted target solvent content: 0.56 Input MTZ file: 1z85-3.2-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: 19 Cell parameters: 65.676 82.546 106.310 90.000 90.000 90.000 Input sequence file: 1z85-3.2-parrot-mrncs.fasta_lf Building free atoms model in initial map for 3744 target number of atoms Had to go as low as 0.70 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: 65.199 3.200 Wilson plot Bfac: 63.89 9974 reflections ( 99.81 % complete ) and 0 restraints for refining 4177 atoms. Observations/parameters ratio is 0.60 ------------------------------------------------------ Starting model: R = 0.3200 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3349 (Rfree = 0.000) for 4177 atoms. Found 37 (37 requested) and removed 38 (18 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.34 3.08 Search for helices and strands: 0 residues in 0 chains, 4235 seeds are put forward NCS extension: 0 residues added, 4235 seeds are put forward Round 1: 246 peptides, 39 chains. Longest chain 20 peptides. Score 0.443 Round 2: 303 peptides, 34 chains. Longest chain 32 peptides. Score 0.627 Round 3: 308 peptides, 29 chains. Longest chain 27 peptides. Score 0.680 Round 4: 324 peptides, 32 chains. Longest chain 49 peptides. Score 0.683 Round 5: 317 peptides, 27 chains. Longest chain 45 peptides. Score 0.712 Taking the results from Round 5 Chains 27, Residues 290, Estimated correctness of the model 67.7 % 5 chains (125 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 128 A and 136 A Built loop between residues 119 B and 123 B 25 chains (300 residues) following loop building 3 chains (135 residues) in sequence following loop building ------------------------------------------------------ 9974 reflections ( 99.81 % complete ) and 5753 restraints for refining 3417 atoms. 3975 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2950 (Rfree = 0.000) for 3417 atoms. Found 30 (30 requested) and removed 39 (15 requested) atoms. Cycle 2: After refmac, R = 0.2801 (Rfree = 0.000) for 3312 atoms. Found 17 (29 requested) and removed 27 (15 requested) atoms. Cycle 3: After refmac, R = 0.2721 (Rfree = 0.000) for 3262 atoms. Found 17 (28 requested) and removed 23 (14 requested) atoms. Cycle 4: After refmac, R = 0.2705 (Rfree = 0.000) for 3224 atoms. Found 16 (27 requested) and removed 21 (14 requested) atoms. Cycle 5: After refmac, R = 0.2664 (Rfree = 0.000) for 3206 atoms. Found 14 (26 requested) and removed 26 (14 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.28 3.03 Search for helices and strands: 0 residues in 0 chains, 3297 seeds are put forward NCS extension: 61 residues added (35 deleted due to clashes), 3358 seeds are put forward Round 1: 302 peptides, 32 chains. Longest chain 25 peptides. Score 0.644 Round 2: 325 peptides, 28 chains. Longest chain 28 peptides. Score 0.717 Round 3: 343 peptides, 25 chains. Longest chain 50 peptides. Score 0.764 Round 4: 339 peptides, 26 chains. Longest chain 50 peptides. Score 0.752 Round 5: 333 peptides, 31 chains. Longest chain 29 peptides. Score 0.706 Taking the results from Round 3 Chains 27, Residues 318, Estimated correctness of the model 77.6 % 7 chains (178 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 116 A and 119 A Built loop between residues 94 B and 104 B Built loop between residues 128 B and 138 B 24 chains (337 residues) following loop building 4 chains (198 residues) in sequence following loop building ------------------------------------------------------ 9974 reflections ( 99.81 % complete ) and 4862 restraints for refining 3418 atoms. 2719 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2962 (Rfree = 0.000) for 3418 atoms. Found 27 (27 requested) and removed 45 (15 requested) atoms. Cycle 7: After refmac, R = 0.2756 (Rfree = 0.000) for 3356 atoms. Found 22 (26 requested) and removed 30 (15 requested) atoms. Cycle 8: After refmac, R = 0.2676 (Rfree = 0.000) for 3327 atoms. Found 14 (26 requested) and removed 19 (15 requested) atoms. Cycle 9: After refmac, R = 0.2615 (Rfree = 0.000) for 3312 atoms. Found 9 (24 requested) and removed 21 (14 requested) atoms. Cycle 10: After refmac, R = 0.2571 (Rfree = 0.000) for 3286 atoms. Found 17 (24 requested) and removed 17 (14 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.20 2.95 Search for helices and strands: 0 residues in 0 chains, 3373 seeds are put forward NCS extension: 119 residues added (24 deleted due to clashes), 3492 seeds are put forward Round 1: 309 peptides, 29 chains. Longest chain 31 peptides. Score 0.682 Round 2: 328 peptides, 28 chains. Longest chain 41 peptides. Score 0.721 Round 3: 334 peptides, 33 chains. Longest chain 30 peptides. Score 0.692 Round 4: 331 peptides, 28 chains. Longest chain 32 peptides. Score 0.726 Round 5: 321 peptides, 28 chains. Longest chain 29 peptides. Score 0.710 Taking the results from Round 4 Chains 30, Residues 303, Estimated correctness of the model 70.5 % 5 chains (111 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 127 B and 136 B 28 chains (308 residues) following loop building 4 chains (119 residues) in sequence following loop building ------------------------------------------------------ 9974 reflections ( 99.81 % complete ) and 5930 restraints for refining 3417 atoms. 4210 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2827 (Rfree = 0.000) for 3417 atoms. Found 24 (24 requested) and removed 34 (15 requested) atoms. Cycle 12: After refmac, R = 0.2772 (Rfree = 0.000) for 3387 atoms. Found 14 (23 requested) and removed 21 (15 requested) atoms. Cycle 13: After refmac, R = 0.2915 (Rfree = 0.000) for 3369 atoms. Found 20 (23 requested) and removed 26 (15 requested) atoms. Cycle 14: After refmac, R = 0.2589 (Rfree = 0.000) for 3351 atoms. Found 9 (22 requested) and removed 21 (15 requested) atoms. Cycle 15: After refmac, R = 0.2543 (Rfree = 0.000) for 3331 atoms. Found 10 (21 requested) and removed 20 (14 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.20 2.95 Search for helices and strands: 0 residues in 0 chains, 3412 seeds are put forward NCS extension: 70 residues added (20 deleted due to clashes), 3482 seeds are put forward Round 1: 302 peptides, 34 chains. Longest chain 30 peptides. Score 0.625 Round 2: 324 peptides, 27 chains. Longest chain 38 peptides. Score 0.723 Round 3: 314 peptides, 30 chains. Longest chain 31 peptides. Score 0.682 Round 4: 331 peptides, 32 chains. Longest chain 30 peptides. Score 0.695 Round 5: 317 peptides, 27 chains. Longest chain 32 peptides. Score 0.712 Taking the results from Round 2 Chains 29, Residues 297, Estimated correctness of the model 69.9 % 4 chains (83 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 96 A and 100 A 28 chains (298 residues) following loop building 3 chains (86 residues) in sequence following loop building ------------------------------------------------------ 9974 reflections ( 99.81 % complete ) and 6195 restraints for refining 3418 atoms. 4663 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2693 (Rfree = 0.000) for 3418 atoms. Found 21 (21 requested) and removed 32 (15 requested) atoms. Cycle 17: After refmac, R = 0.2649 (Rfree = 0.000) for 3398 atoms. Found 16 (20 requested) and removed 29 (15 requested) atoms. Cycle 18: After refmac, R = 0.2582 (Rfree = 0.000) for 3375 atoms. Found 15 (20 requested) and removed 19 (15 requested) atoms. Cycle 19: After refmac, R = 0.2547 (Rfree = 0.000) for 3364 atoms. Found 17 (19 requested) and removed 24 (15 requested) atoms. Cycle 20: After refmac, R = 0.2555 (Rfree = 0.000) for 3349 atoms. Found 16 (19 requested) and removed 19 (15 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.18 2.93 Search for helices and strands: 0 residues in 0 chains, 3432 seeds are put forward NCS extension: 48 residues added (33 deleted due to clashes), 3480 seeds are put forward Round 1: 288 peptides, 35 chains. Longest chain 28 peptides. Score 0.587 Round 2: 306 peptides, 27 chains. Longest chain 40 peptides. Score 0.693 Round 3: 313 peptides, 30 chains. Longest chain 45 peptides. Score 0.681 Round 4: 310 peptides, 24 chains. Longest chain 50 peptides. Score 0.724 Round 5: 315 peptides, 28 chains. Longest chain 32 peptides. Score 0.700 Taking the results from Round 4 Chains 24, Residues 286, Estimated correctness of the model 70.1 % 4 chains (116 residues) have been docked in sequence Building loops using Loopy2018 24 chains (286 residues) following loop building 4 chains (116 residues) in sequence following loop building ------------------------------------------------------ 9974 reflections ( 99.81 % complete ) and 5931 restraints for refining 3418 atoms. 4287 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2625 (Rfree = 0.000) for 3418 atoms. Found 18 (18 requested) and removed 26 (15 requested) atoms. Cycle 22: After refmac, R = 0.2626 (Rfree = 0.000) for 3388 atoms. Found 17 (17 requested) and removed 22 (15 requested) atoms. Cycle 23: After refmac, R = 0.2852 (Rfree = 0.000) for 3375 atoms. Found 17 (17 requested) and removed 24 (15 requested) atoms. Cycle 24: After refmac, R = 0.2497 (Rfree = 0.000) for 3348 atoms. Found 16 (16 requested) and removed 19 (15 requested) atoms. Cycle 25: After refmac, R = 0.2783 (Rfree = 0.000) for 3340 atoms. Found 16 (16 requested) and removed 16 (15 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.22 2.97 Search for helices and strands: 0 residues in 0 chains, 3412 seeds are put forward NCS extension: 31 residues added (9 deleted due to clashes), 3443 seeds are put forward Round 1: 303 peptides, 30 chains. Longest chain 39 peptides. Score 0.663 Round 2: 314 peptides, 29 chains. Longest chain 49 peptides. Score 0.691 Round 3: 303 peptides, 32 chains. Longest chain 26 peptides. Score 0.645 Round 4: 322 peptides, 27 chains. Longest chain 84 peptides. Score 0.720 Round 5: 317 peptides, 30 chains. Longest chain 31 peptides. Score 0.688 Taking the results from Round 4 Chains 29, Residues 295, Estimated correctness of the model 69.3 % 3 chains (137 residues) have been docked in sequence Building loops using Loopy2018 29 chains (295 residues) following loop building 3 chains (137 residues) in sequence following loop building ------------------------------------------------------ 9974 reflections ( 99.81 % complete ) and 5671 restraints for refining 3418 atoms. 3888 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2754 (Rfree = 0.000) for 3418 atoms. Found 15 (15 requested) and removed 63 (15 requested) atoms. Cycle 27: After refmac, R = 0.2850 (Rfree = 0.000) for 3360 atoms. Found 15 (15 requested) and removed 21 (15 requested) atoms. Cycle 28: After refmac, R = 0.2614 (Rfree = 0.000) for 3333 atoms. Found 12 (15 requested) and removed 19 (15 requested) atoms. Cycle 29: After refmac, R = 0.2761 (Rfree = 0.000) for 3313 atoms. Found 14 (14 requested) and removed 21 (14 requested) atoms. Cycle 30: After refmac, R = 0.2498 (Rfree = 0.000) for 3300 atoms. Found 14 (14 requested) and removed 16 (14 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.26 3.01 Search for helices and strands: 0 residues in 0 chains, 3373 seeds are put forward NCS extension: 55 residues added (53 deleted due to clashes), 3428 seeds are put forward Round 1: 290 peptides, 34 chains. Longest chain 46 peptides. Score 0.601 Round 2: 303 peptides, 27 chains. Longest chain 38 peptides. Score 0.688 Round 3: 320 peptides, 26 chains. Longest chain 44 peptides. Score 0.724 Round 4: 332 peptides, 34 chains. Longest chain 39 peptides. Score 0.681 Round 5: 321 peptides, 32 chains. Longest chain 37 peptides. Score 0.678 Taking the results from Round 3 Chains 27, Residues 294, Estimated correctness of the model 70.1 % 5 chains (128 residues) have been docked in sequence Building loops using Loopy2018 27 chains (294 residues) following loop building 5 chains (128 residues) in sequence following loop building ------------------------------------------------------ 9974 reflections ( 99.81 % complete ) and 5685 restraints for refining 3418 atoms. 3931 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2698 (Rfree = 0.000) for 3418 atoms. Found 12 (15 requested) and removed 34 (15 requested) atoms. Cycle 32: After refmac, R = 0.2644 (Rfree = 0.000) for 3375 atoms. Found 9 (15 requested) and removed 22 (15 requested) atoms. Cycle 33: After refmac, R = 0.2836 (Rfree = 0.000) for 3347 atoms. Found 15 (15 requested) and removed 27 (15 requested) atoms. Cycle 34: After refmac, R = 0.2538 (Rfree = 0.000) for 3319 atoms. Found 14 (14 requested) and removed 17 (14 requested) atoms. Cycle 35: After refmac, R = 0.2504 (Rfree = 0.000) for 3302 atoms. Found 13 (14 requested) and removed 20 (14 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.24 2.99 Search for helices and strands: 0 residues in 0 chains, 3354 seeds are put forward NCS extension: 13 residues added (27 deleted due to clashes), 3367 seeds are put forward Round 1: 291 peptides, 35 chains. Longest chain 26 peptides. Score 0.594 Round 2: 327 peptides, 26 chains. Longest chain 34 peptides. Score 0.735 Round 3: 311 peptides, 30 chains. Longest chain 29 peptides. Score 0.677 Round 4: 337 peptides, 26 chains. Longest chain 37 peptides. Score 0.749 Round 5: 315 peptides, 32 chains. Longest chain 27 peptides. Score 0.668 Taking the results from Round 4 Chains 26, Residues 311, Estimated correctness of the model 74.9 % 3 chains (87 residues) have been docked in sequence Building loops using Loopy2018 26 chains (311 residues) following loop building 3 chains (87 residues) in sequence following loop building ------------------------------------------------------ 9974 reflections ( 99.81 % complete ) and 6045 restraints for refining 3418 atoms. 4418 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2630 (Rfree = 0.000) for 3418 atoms. Found 15 (15 requested) and removed 26 (15 requested) atoms. Cycle 37: After refmac, R = 0.2520 (Rfree = 0.000) for 3398 atoms. Found 8 (15 requested) and removed 17 (15 requested) atoms. Cycle 38: After refmac, R = 0.2781 (Rfree = 0.000) for 3382 atoms. Found 15 (15 requested) and removed 26 (15 requested) atoms. Cycle 39: After refmac, R = 0.2489 (Rfree = 0.000) for 3364 atoms. Found 13 (15 requested) and removed 21 (15 requested) atoms. Cycle 40: After refmac, R = 0.2429 (Rfree = 0.000) for 3346 atoms. Found 13 (15 requested) and removed 20 (15 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.20 2.95 Search for helices and strands: 0 residues in 0 chains, 3430 seeds are put forward NCS extension: 24 residues added (9 deleted due to clashes), 3454 seeds are put forward Round 1: 280 peptides, 36 chains. Longest chain 23 peptides. Score 0.560 Round 2: 304 peptides, 28 chains. Longest chain 51 peptides. Score 0.682 Round 3: 312 peptides, 31 chains. Longest chain 55 peptides. Score 0.671 Round 4: 312 peptides, 29 chains. Longest chain 28 peptides. Score 0.687 Round 5: 313 peptides, 32 chains. Longest chain 29 peptides. Score 0.664 Taking the results from Round 4 Chains 30, Residues 283, Estimated correctness of the model 62.4 % 3 chains (61 residues) have been docked in sequence ------------------------------------------------------ 9974 reflections ( 99.81 % complete ) and 6465 restraints for refining 3418 atoms. 5081 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2584 (Rfree = 0.000) for 3418 atoms. Found 15 (15 requested) and removed 24 (15 requested) atoms. Cycle 42: After refmac, R = 0.2512 (Rfree = 0.000) for 3404 atoms. Found 15 (15 requested) and removed 16 (15 requested) atoms. Cycle 43: After refmac, R = 0.2485 (Rfree = 0.000) for 3399 atoms. Found 10 (15 requested) and removed 15 (15 requested) atoms. Cycle 44: After refmac, R = 0.2433 (Rfree = 0.000) for 3388 atoms. Found 14 (15 requested) and removed 15 (15 requested) atoms. Cycle 45: After refmac, R = 0.2427 (Rfree = 0.000) for 3377 atoms. Found 7 (15 requested) and removed 15 (15 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.23 2.98 Search for helices and strands: 0 residues in 0 chains, 3451 seeds are put forward NCS extension: 23 residues added (4 deleted due to clashes), 3474 seeds are put forward Round 1: 277 peptides, 29 chains. Longest chain 37 peptides. Score 0.622 Round 2: 306 peptides, 31 chains. Longest chain 33 peptides. Score 0.660 Round 3: 318 peptides, 32 chains. Longest chain 32 peptides. Score 0.673 Round 4: 321 peptides, 29 chains. Longest chain 41 peptides. Score 0.702 Round 5: 313 peptides, 30 chains. Longest chain 51 peptides. Score 0.681 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 33, Residues 292, Estimated correctness of the model 65.6 % 5 chains (123 residues) have been docked in sequence Sequence coverage is 41 % Consider running further cycles of model building using 1z85-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 34 A and 47 A Built loop between residues 83 A and 95 A 29 chains (309 residues) following loop building 3 chains (146 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 9974 reflections ( 99.81 % complete ) and 5547 restraints for refining 3418 atoms. 3716 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2722 (Rfree = 0.000) for 3418 atoms. Found 0 (15 requested) and removed 12 (15 requested) atoms. Cycle 47: After refmac, R = 0.2615 (Rfree = 0.000) for 3390 atoms. Found 0 (15 requested) and removed 11 (15 requested) atoms. Cycle 48: After refmac, R = 0.2610 (Rfree = 0.000) for 3365 atoms. Found 0 (15 requested) and removed 9 (15 requested) atoms. Cycle 49: After refmac, R = 0.2548 (Rfree = 0.000) for 3347 atoms. TimeTaking 45.85