Tue 25 Dec 19:27:57 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 2p97-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2p97-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2p97-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p97-3.2-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/2p97-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p97-3.2-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 ============================================================ Tue 25 Dec 19:28:07 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/2p97-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p97-3.2-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 363 and 0 Target number of residues in the AU: 363 Target solvent content: 0.6155 Checking the provided sequence file Detected sequence length: 201 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 402 Adjusted target solvent content: 0.57 Input MTZ file: 2p97-3.2-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: 94 Cell parameters: 103.080 103.080 96.168 90.000 90.000 90.000 Input sequence file: 2p97-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 3216 target number of atoms Had to go as low as 0.80 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: 72.889 3.200 Wilson plot Bfac: 59.30 8981 reflections ( 99.80 % complete ) and 0 restraints for refining 3555 atoms. Observations/parameters ratio is 0.63 ------------------------------------------------------ Starting model: R = 0.3197 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2646 (Rfree = 0.000) for 3555 atoms. Found 22 (31 requested) and removed 71 (15 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.12 2.84 Search for helices and strands: 0 residues in 0 chains, 3565 seeds are put forward NCS extension: 0 residues added, 3565 seeds are put forward Round 1: 215 peptides, 37 chains. Longest chain 10 peptides. Score 0.402 Round 2: 272 peptides, 37 chains. Longest chain 16 peptides. Score 0.562 Round 3: 274 peptides, 36 chains. Longest chain 18 peptides. Score 0.578 Round 4: 292 peptides, 34 chains. Longest chain 25 peptides. Score 0.640 Round 5: 297 peptides, 37 chains. Longest chain 24 peptides. Score 0.621 Taking the results from Round 4 Chains 36, Residues 258, Estimated correctness of the model 51.4 % 2 chains (28 residues) have been docked in sequence ------------------------------------------------------ 8981 reflections ( 99.80 % complete ) and 5862 restraints for refining 2936 atoms. 4760 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2967 (Rfree = 0.000) for 2936 atoms. Found 26 (26 requested) and removed 22 (13 requested) atoms. Cycle 2: After refmac, R = 0.2809 (Rfree = 0.000) for 2917 atoms. Found 18 (26 requested) and removed 18 (13 requested) atoms. Cycle 3: After refmac, R = 0.2778 (Rfree = 0.000) for 2914 atoms. Found 12 (26 requested) and removed 15 (13 requested) atoms. Failed to save intermediate PDB Cycle 4: After refmac, R = 0.2731 (Rfree = 0.000) for 2908 atoms. Found 6 (26 requested) and removed 13 (13 requested) atoms. Failed to save intermediate PDB Cycle 5: After refmac, R = 0.2786 (Rfree = 0.000) for 2897 atoms. Found 8 (26 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.10 2.82 Search for helices and strands: 0 residues in 0 chains, 2987 seeds are put forward NCS extension: 18 residues added (7 deleted due to clashes), 3005 seeds are put forward Round 1: 269 peptides, 36 chains. Longest chain 20 peptides. Score 0.566 Round 2: 276 peptides, 29 chains. Longest chain 23 peptides. Score 0.655 Round 3: 301 peptides, 30 chains. Longest chain 44 peptides. Score 0.695 Round 4: 289 peptides, 28 chains. Longest chain 25 peptides. Score 0.690 Round 5: 312 peptides, 25 chains. Longest chain 43 peptides. Score 0.755 Taking the results from Round 5 Chains 27, Residues 287, Estimated correctness of the model 76.0 % 6 chains (134 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 157 B and 165 B 25 chains (291 residues) following loop building 5 chains (141 residues) in sequence following loop building ------------------------------------------------------ 8981 reflections ( 99.80 % complete ) and 4613 restraints for refining 2936 atoms. 2925 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3171 (Rfree = 0.000) for 2936 atoms. Found 26 (26 requested) and removed 35 (13 requested) atoms. Failed to save intermediate PDB Cycle 7: After refmac, R = 0.2782 (Rfree = 0.000) for 2903 atoms. Found 25 (25 requested) and removed 22 (13 requested) atoms. Cycle 8: After refmac, R = 0.2623 (Rfree = 0.000) for 2890 atoms. Found 23 (25 requested) and removed 17 (13 requested) atoms. Cycle 9: After refmac, R = 0.2481 (Rfree = 0.000) for 2895 atoms. Found 7 (23 requested) and removed 12 (12 requested) atoms. Cycle 10: After refmac, R = 0.2414 (Rfree = 0.000) for 2887 atoms. Found 4 (23 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.08 2.80 Search for helices and strands: 0 residues in 0 chains, 2972 seeds are put forward NCS extension: 21 residues added (7 deleted due to clashes), 2993 seeds are put forward Round 1: 277 peptides, 29 chains. Longest chain 21 peptides. Score 0.657 Round 2: 307 peptides, 24 chains. Longest chain 41 peptides. Score 0.755 Round 3: 311 peptides, 30 chains. Longest chain 37 peptides. Score 0.713 Round 4: 303 peptides, 24 chains. Longest chain 28 peptides. Score 0.749 Round 5: 305 peptides, 27 chains. Longest chain 32 peptides. Score 0.728 Taking the results from Round 2 Chains 25, Residues 283, Estimated correctness of the model 76.0 % 4 chains (73 residues) have been docked in sequence Building loops using Loopy2018 25 chains (283 residues) following loop building 4 chains (73 residues) in sequence following loop building ------------------------------------------------------ 8981 reflections ( 99.80 % complete ) and 5401 restraints for refining 2935 atoms. 3976 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2610 (Rfree = 0.000) for 2935 atoms. Found 23 (23 requested) and removed 21 (13 requested) atoms. Failed to save intermediate PDB Cycle 12: After refmac, R = 0.2455 (Rfree = 0.000) for 2927 atoms. Found 8 (23 requested) and removed 15 (13 requested) atoms. Failed to save intermediate PDB Cycle 13: After refmac, R = 0.2434 (Rfree = 0.000) for 2917 atoms. Found 8 (22 requested) and removed 13 (13 requested) atoms. Failed to save intermediate PDB Cycle 14: After refmac, R = 0.2414 (Rfree = 0.000) for 2909 atoms. Found 8 (22 requested) and removed 14 (13 requested) atoms. Failed to save intermediate PDB Cycle 15: After refmac, R = 0.2394 (Rfree = 0.000) for 2896 atoms. Found 9 (21 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.10 2.82 Search for helices and strands: 0 residues in 0 chains, 2951 seeds are put forward NCS extension: 50 residues added (25 deleted due to clashes), 3001 seeds are put forward Round 1: 284 peptides, 34 chains. Longest chain 22 peptides. Score 0.622 Round 2: 314 peptides, 29 chains. Longest chain 37 peptides. Score 0.727 Round 3: 296 peptides, 32 chains. Longest chain 28 peptides. Score 0.667 Round 4: 285 peptides, 29 chains. Longest chain 35 peptides. Score 0.673 Round 5: 295 peptides, 31 chains. Longest chain 36 peptides. Score 0.675 Taking the results from Round 2 Chains 33, Residues 285, Estimated correctness of the model 70.7 % 4 chains (70 residues) have been docked in sequence Building loops using Loopy2018 33 chains (285 residues) following loop building 4 chains (70 residues) in sequence following loop building ------------------------------------------------------ 8981 reflections ( 99.80 % complete ) and 5347 restraints for refining 2936 atoms. 3956 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2678 (Rfree = 0.000) for 2936 atoms. Found 20 (21 requested) and removed 25 (13 requested) atoms. Cycle 17: After refmac, R = 0.2511 (Rfree = 0.000) for 2920 atoms. Found 16 (20 requested) and removed 14 (13 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.2410 (Rfree = 0.000) for 2915 atoms. Found 7 (20 requested) and removed 13 (13 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.2395 (Rfree = 0.000) for 2901 atoms. Found 7 (19 requested) and removed 13 (13 requested) atoms. Cycle 20: After refmac, R = 0.2347 (Rfree = 0.000) for 2893 atoms. Found 3 (18 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.12 2.84 Search for helices and strands: 0 residues in 0 chains, 2987 seeds are put forward NCS extension: 17 residues added (5 deleted due to clashes), 3004 seeds are put forward Round 1: 271 peptides, 33 chains. Longest chain 23 peptides. Score 0.603 Round 2: 285 peptides, 28 chains. Longest chain 23 peptides. Score 0.683 Round 3: 292 peptides, 29 chains. Longest chain 26 peptides. Score 0.687 Round 4: 303 peptides, 28 chains. Longest chain 34 peptides. Score 0.716 Round 5: 285 peptides, 30 chains. Longest chain 30 peptides. Score 0.664 Taking the results from Round 4 Chains 33, Residues 275, Estimated correctness of the model 68.5 % 5 chains (63 residues) have been docked in sequence Building loops using Loopy2018 33 chains (275 residues) following loop building 5 chains (63 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 8981 reflections ( 99.80 % complete ) and 5482 restraints for refining 2936 atoms. 4183 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2653 (Rfree = 0.000) for 2936 atoms. Found 18 (18 requested) and removed 15 (13 requested) atoms. Cycle 22: After refmac, R = 0.2481 (Rfree = 0.000) for 2932 atoms. Found 7 (18 requested) and removed 15 (13 requested) atoms. Failed to save intermediate PDB Cycle 23: After refmac, R = 0.2423 (Rfree = 0.000) for 2922 atoms. Found 7 (17 requested) and removed 13 (13 requested) atoms. Failed to save intermediate PDB Cycle 24: After refmac, R = 0.2398 (Rfree = 0.000) for 2914 atoms. Found 4 (17 requested) and removed 13 (13 requested) atoms. Failed to save intermediate PDB Cycle 25: After refmac, R = 0.2382 (Rfree = 0.000) for 2901 atoms. Found 6 (16 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.15 2.87 Search for helices and strands: 0 residues in 0 chains, 2994 seeds are put forward NCS extension: 26 residues added (2 deleted due to clashes), 3020 seeds are put forward Round 1: 261 peptides, 34 chains. Longest chain 21 peptides. Score 0.568 Round 2: 294 peptides, 27 chains. Longest chain 34 peptides. Score 0.708 Round 3: 294 peptides, 29 chains. Longest chain 35 peptides. Score 0.691 Round 4: 293 peptides, 26 chains. Longest chain 27 peptides. Score 0.715 Round 5: 286 peptides, 23 chains. Longest chain 36 peptides. Score 0.729 Taking the results from Round 5 Chains 30, Residues 263, Estimated correctness of the model 71.1 % 5 chains (69 residues) have been docked in sequence Building loops using Loopy2018 30 chains (263 residues) following loop building 5 chains (69 residues) in sequence following loop building ------------------------------------------------------ 8981 reflections ( 99.80 % complete ) and 5499 restraints for refining 2936 atoms. 4187 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2764 (Rfree = 0.000) for 2936 atoms. Found 16 (16 requested) and removed 24 (13 requested) atoms. Cycle 27: After refmac, R = 0.2607 (Rfree = 0.000) for 2914 atoms. Found 12 (15 requested) and removed 13 (13 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.2531 (Rfree = 0.000) for 2909 atoms. Found 10 (15 requested) and removed 14 (13 requested) atoms. Cycle 29: After refmac, R = 0.2463 (Rfree = 0.000) for 2902 atoms. Found 8 (14 requested) and removed 13 (13 requested) atoms. Failed to save intermediate PDB Cycle 30: After refmac, R = 0.2421 (Rfree = 0.000) for 2893 atoms. Found 7 (13 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.12 2.84 Search for helices and strands: 0 residues in 0 chains, 2977 seeds are put forward NCS extension: 9 residues added (4 deleted due to clashes), 2986 seeds are put forward Round 1: 258 peptides, 30 chains. Longest chain 16 peptides. Score 0.605 Round 2: 286 peptides, 28 chains. Longest chain 22 peptides. Score 0.685 Round 3: 278 peptides, 27 chains. Longest chain 23 peptides. Score 0.678 Round 4: 277 peptides, 27 chains. Longest chain 22 peptides. Score 0.676 Round 5: 281 peptides, 29 chains. Longest chain 22 peptides. Score 0.665 Taking the results from Round 2 Chains 28, Residues 258, Estimated correctness of the model 61.9 % 2 chains (29 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 8981 reflections ( 99.80 % complete ) and 5954 restraints for refining 2936 atoms. 4821 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2605 (Rfree = 0.000) for 2936 atoms. Found 13 (13 requested) and removed 16 (13 requested) atoms. Failed to save intermediate PDB Cycle 32: After refmac, R = 0.2444 (Rfree = 0.000) for 2926 atoms. Found 12 (13 requested) and removed 13 (13 requested) atoms. Cycle 33: After refmac, R = 0.2365 (Rfree = 0.000) for 2922 atoms. Found 9 (13 requested) and removed 13 (13 requested) atoms. Failed to save intermediate PDB Cycle 34: After refmac, R = 0.2317 (Rfree = 0.000) for 2916 atoms. Found 3 (13 requested) and removed 14 (13 requested) atoms. Cycle 35: After refmac, R = 0.2261 (Rfree = 0.000) for 2905 atoms. Found 6 (13 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.08 2.80 Search for helices and strands: 0 residues in 0 chains, 2987 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 3002 seeds are put forward Round 1: 265 peptides, 30 chains. Longest chain 20 peptides. Score 0.621 Round 2: 288 peptides, 30 chains. Longest chain 25 peptides. Score 0.670 Round 3: 277 peptides, 31 chains. Longest chain 18 peptides. Score 0.637 Round 4: 276 peptides, 27 chains. Longest chain 25 peptides. Score 0.674 Round 5: 287 peptides, 30 chains. Longest chain 24 peptides. Score 0.668 Taking the results from Round 4 Chains 27, Residues 249, Estimated correctness of the model 59.5 % 2 chains (34 residues) have been docked in sequence ------------------------------------------------------ 8981 reflections ( 99.80 % complete ) and 5991 restraints for refining 2936 atoms. 4859 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2624 (Rfree = 0.000) for 2936 atoms. Found 13 (13 requested) and removed 16 (13 requested) atoms. Cycle 37: After refmac, R = 0.2417 (Rfree = 0.000) for 2928 atoms. Found 13 (13 requested) and removed 13 (13 requested) atoms. Cycle 38: After refmac, R = 0.2317 (Rfree = 0.000) for 2926 atoms. Found 9 (13 requested) and removed 14 (13 requested) atoms. Cycle 39: After refmac, R = 0.2256 (Rfree = 0.000) for 2920 atoms. Found 3 (13 requested) and removed 13 (13 requested) atoms. Cycle 40: After refmac, R = 0.2221 (Rfree = 0.000) for 2906 atoms. Found 6 (13 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.14 2.86 Search for helices and strands: 0 residues in 0 chains, 2983 seeds are put forward NCS extension: 23 residues added (9 deleted due to clashes), 3006 seeds are put forward Round 1: 246 peptides, 34 chains. Longest chain 20 peptides. Score 0.530 Round 2: 267 peptides, 31 chains. Longest chain 21 peptides. Score 0.615 Round 3: 262 peptides, 33 chains. Longest chain 21 peptides. Score 0.582 Round 4: 275 peptides, 29 chains. Longest chain 21 peptides. Score 0.653 Round 5: 275 peptides, 35 chains. Longest chain 18 peptides. Score 0.591 Taking the results from Round 4 Chains 30, Residues 246, Estimated correctness of the model 54.6 % 2 chains (28 residues) have been docked in sequence ------------------------------------------------------ 8981 reflections ( 99.80 % complete ) and 6031 restraints for refining 2936 atoms. 4944 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2570 (Rfree = 0.000) for 2936 atoms. Found 13 (13 requested) and removed 18 (13 requested) atoms. Failed to save intermediate PDB Cycle 42: After refmac, R = 0.2361 (Rfree = 0.000) for 2925 atoms. Found 13 (13 requested) and removed 13 (13 requested) atoms. Cycle 43: After refmac, R = 0.2289 (Rfree = 0.000) for 2918 atoms. Found 12 (13 requested) and removed 13 (13 requested) atoms. Cycle 44: After refmac, R = 0.2254 (Rfree = 0.000) for 2914 atoms. Found 8 (13 requested) and removed 14 (13 requested) atoms. Failed to save intermediate PDB Cycle 45: After refmac, R = 0.2235 (Rfree = 0.000) for 2906 atoms. Found 8 (13 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.15 2.87 Search for helices and strands: 0 residues in 0 chains, 2965 seeds are put forward NCS extension: 19 residues added (5 deleted due to clashes), 2984 seeds are put forward Round 1: 244 peptides, 31 chains. Longest chain 23 peptides. Score 0.559 Round 2: 283 peptides, 31 chains. Longest chain 33 peptides. Score 0.650 Round 3: 282 peptides, 32 chains. Longest chain 35 peptides. Score 0.638 Round 4: 290 peptides, 30 chains. Longest chain 32 peptides. Score 0.674 Round 5: 268 peptides, 30 chains. Longest chain 29 peptides. Score 0.628 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 35, Residues 260, Estimated correctness of the model 59.5 % 3 chains (54 residues) have been docked in sequence Sequence coverage is 20 % Consider running further cycles of model building using 2p97-3_warpNtrace.pdb as input Building loops using Loopy2018 35 chains (260 residues) following loop building 3 chains (54 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8981 reflections ( 99.80 % complete ) and 5592 restraints for refining 2936 atoms. 4357 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2702 (Rfree = 0.000) for 2936 atoms. Found 0 (13 requested) and removed 10 (13 requested) atoms. Cycle 47: After refmac, R = 0.2560 (Rfree = 0.000) for 2915 atoms. Found 0 (13 requested) and removed 5 (13 requested) atoms. Cycle 48: After refmac, R = 0.2531 (Rfree = 0.000) for 2904 atoms. Found 0 (13 requested) and removed 3 (13 requested) atoms. Cycle 49: After refmac, R = 0.2524 (Rfree = 0.000) for 2898 atoms. Found 0 (13 requested) and removed 3 (13 requested) atoms. Writing output files ... TimeTaking 61.54