null Mon 24 Dec 01:09:31 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 2p97-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2p97-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2p97-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p97-3.2-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/2p97-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p97-3.2-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 01:09:35 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/2p97-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p97-3.2-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 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-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: 94 Cell parameters: 103.080 103.080 96.168 90.000 90.000 90.000 Input sequence file: 2p97-3.2-parrot-mrncs.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 3564 atoms. Observations/parameters ratio is 0.63 ------------------------------------------------------ Starting model: R = 0.3194 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2664 (Rfree = 0.000) for 3564 atoms. Found 31 (31 requested) and removed 20 (15 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.14 2.86 Search for helices and strands: 0 residues in 0 chains, 3651 seeds are put forward NCS extension: 0 residues added, 3651 seeds are put forward Round 1: 254 peptides, 38 chains. Longest chain 13 peptides. Score 0.504 Round 2: 303 peptides, 30 chains. Longest chain 34 peptides. Score 0.699 Round 3: 320 peptides, 26 chains. Longest chain 39 peptides. Score 0.760 Round 4: 320 peptides, 30 chains. Longest chain 27 peptides. Score 0.729 Round 5: 328 peptides, 29 chains. Longest chain 38 peptides. Score 0.750 Taking the results from Round 3 Chains 27, Residues 294, Estimated correctness of the model 76.9 % 5 chains (104 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 142 A and 146 A 26 chains (296 residues) following loop building 4 chains (107 residues) in sequence following loop building ------------------------------------------------------ 8981 reflections ( 99.80 % complete ) and 5536 restraints for refining 3156 atoms. 3987 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2851 (Rfree = 0.000) for 3156 atoms. Found 28 (28 requested) and removed 26 (14 requested) atoms. Cycle 2: After refmac, R = 0.2684 (Rfree = 0.000) for 3113 atoms. Found 26 (27 requested) and removed 15 (14 requested) atoms. Cycle 3: After refmac, R = 0.2600 (Rfree = 0.000) for 3107 atoms. Found 17 (27 requested) and removed 14 (14 requested) atoms. Cycle 4: After refmac, R = 0.2528 (Rfree = 0.000) for 3102 atoms. Found 7 (25 requested) and removed 13 (13 requested) atoms. Cycle 5: After refmac, R = 0.2510 (Rfree = 0.000) for 3087 atoms. Found 3 (25 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.13 2.85 Search for helices and strands: 0 residues in 0 chains, 3175 seeds are put forward NCS extension: 44 residues added (6 deleted due to clashes), 3219 seeds are put forward Round 1: 303 peptides, 32 chains. Longest chain 18 peptides. Score 0.681 Round 2: 311 peptides, 23 chains. Longest chain 36 peptides. Score 0.769 Round 3: 321 peptides, 21 chains. Longest chain 50 peptides. Score 0.797 Round 4: 310 peptides, 22 chains. Longest chain 36 peptides. Score 0.775 Round 5: 301 peptides, 24 chains. Longest chain 47 peptides. Score 0.745 Taking the results from Round 3 Chains 21, Residues 300, Estimated correctness of the model 83.0 % 5 chains (149 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 91 A and 94 A 20 chains (300 residues) following loop building 4 chains (151 residues) in sequence following loop building ------------------------------------------------------ 8981 reflections ( 99.80 % complete ) and 4676 restraints for refining 2971 atoms. 2935 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2978 (Rfree = 0.000) for 2971 atoms. Found 23 (23 requested) and removed 28 (13 requested) atoms. Cycle 7: After refmac, R = 0.2771 (Rfree = 0.000) for 2951 atoms. Found 20 (23 requested) and removed 15 (13 requested) atoms. Cycle 8: After refmac, R = 0.2664 (Rfree = 0.000) for 2951 atoms. Found 11 (22 requested) and removed 15 (13 requested) atoms. Cycle 9: After refmac, R = 0.2599 (Rfree = 0.000) for 2942 atoms. Found 2 (22 requested) and removed 15 (13 requested) atoms. Cycle 10: After refmac, R = 0.2592 (Rfree = 0.000) for 2928 atoms. Found 2 (21 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.15 2.87 Search for helices and strands: 0 residues in 0 chains, 3002 seeds are put forward NCS extension: 108 residues added (20 deleted due to clashes), 3110 seeds are put forward Round 1: 293 peptides, 31 chains. Longest chain 25 peptides. Score 0.671 Round 2: 305 peptides, 24 chains. Longest chain 47 peptides. Score 0.752 Round 3: 314 peptides, 28 chains. Longest chain 31 peptides. Score 0.735 Round 4: 315 peptides, 26 chains. Longest chain 37 peptides. Score 0.752 Round 5: 307 peptides, 24 chains. Longest chain 45 peptides. Score 0.755 Taking the results from Round 5 Chains 27, Residues 283, Estimated correctness of the model 76.0 % 4 chains (94 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 102 A and 110 A 26 chains (290 residues) following loop building 3 chains (101 residues) in sequence following loop building ------------------------------------------------------ 8981 reflections ( 99.80 % complete ) and 5032 restraints for refining 2935 atoms. 3506 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2866 (Rfree = 0.000) for 2935 atoms. Found 21 (21 requested) and removed 28 (13 requested) atoms. Cycle 12: After refmac, R = 0.2661 (Rfree = 0.000) for 2915 atoms. Found 8 (20 requested) and removed 15 (13 requested) atoms. Cycle 13: After refmac, R = 0.2593 (Rfree = 0.000) for 2898 atoms. Found 10 (20 requested) and removed 15 (13 requested) atoms. Cycle 14: After refmac, R = 0.2543 (Rfree = 0.000) for 2892 atoms. Found 4 (18 requested) and removed 12 (12 requested) atoms. Cycle 15: After refmac, R = 0.2545 (Rfree = 0.000) for 2879 atoms. Found 2 (18 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.13 2.85 Search for helices and strands: 0 residues in 0 chains, 2950 seeds are put forward NCS extension: 29 residues added (16 deleted due to clashes), 2979 seeds are put forward Round 1: 299 peptides, 30 chains. Longest chain 27 peptides. Score 0.691 Round 2: 298 peptides, 23 chains. Longest chain 47 peptides. Score 0.749 Round 3: 307 peptides, 23 chains. Longest chain 51 peptides. Score 0.763 Round 4: 288 peptides, 27 chains. Longest chain 36 peptides. Score 0.697 Round 5: 291 peptides, 27 chains. Longest chain 31 peptides. Score 0.703 Taking the results from Round 3 Chains 28, Residues 284, Estimated correctness of the model 77.4 % 6 chains (139 residues) have been docked in sequence Building loops using Loopy2018 28 chains (284 residues) following loop building 6 chains (139 residues) in sequence following loop building ------------------------------------------------------ 8981 reflections ( 99.80 % complete ) and 4796 restraints for refining 2936 atoms. 3154 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2811 (Rfree = 0.000) for 2936 atoms. Found 18 (18 requested) and removed 30 (13 requested) atoms. Cycle 17: After refmac, R = 0.2629 (Rfree = 0.000) for 2912 atoms. Found 10 (18 requested) and removed 14 (13 requested) atoms. Cycle 18: After refmac, R = 0.2562 (Rfree = 0.000) for 2903 atoms. Found 6 (17 requested) and removed 13 (13 requested) atoms. Cycle 19: After refmac, R = 0.2525 (Rfree = 0.000) for 2891 atoms. Found 3 (16 requested) and removed 12 (12 requested) atoms. Cycle 20: After refmac, R = 0.2511 (Rfree = 0.000) for 2880 atoms. Found 7 (15 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, 2954 seeds are put forward NCS extension: 64 residues added (13 deleted due to clashes), 3018 seeds are put forward Round 1: 270 peptides, 29 chains. Longest chain 21 peptides. Score 0.642 Round 2: 297 peptides, 25 chains. Longest chain 29 peptides. Score 0.731 Round 3: 303 peptides, 25 chains. Longest chain 39 peptides. Score 0.741 Round 4: 300 peptides, 27 chains. Longest chain 33 peptides. Score 0.719 Round 5: 296 peptides, 26 chains. Longest chain 41 peptides. Score 0.721 Taking the results from Round 3 Chains 30, Residues 278, Estimated correctness of the model 73.4 % 6 chains (115 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 88 A and 92 A Built loop between residues 127 A and 130 A 26 chains (281 residues) following loop building 4 chains (120 residues) in sequence following loop building ------------------------------------------------------ 8981 reflections ( 99.80 % complete ) and 4972 restraints for refining 2936 atoms. 3418 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2730 (Rfree = 0.000) for 2936 atoms. Found 16 (16 requested) and removed 22 (13 requested) atoms. Cycle 22: After refmac, R = 0.2549 (Rfree = 0.000) for 2920 atoms. Found 15 (15 requested) and removed 14 (13 requested) atoms. Cycle 23: After refmac, R = 0.2499 (Rfree = 0.000) for 2918 atoms. Found 14 (15 requested) and removed 15 (13 requested) atoms. Cycle 24: After refmac, R = 0.2481 (Rfree = 0.000) for 2917 atoms. Found 3 (14 requested) and removed 13 (13 requested) atoms. Cycle 25: After refmac, R = 0.2436 (Rfree = 0.000) for 2905 atoms. Found 5 (14 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.16 2.88 Search for helices and strands: 0 residues in 0 chains, 2989 seeds are put forward NCS extension: 51 residues added (51 deleted due to clashes), 3040 seeds are put forward Round 1: 272 peptides, 31 chains. Longest chain 26 peptides. Score 0.626 Round 2: 294 peptides, 26 chains. Longest chain 63 peptides. Score 0.717 Round 3: 292 peptides, 25 chains. Longest chain 35 peptides. Score 0.722 Round 4: 287 peptides, 25 chains. Longest chain 51 peptides. Score 0.713 Round 5: 302 peptides, 29 chains. Longest chain 51 peptides. Score 0.706 Taking the results from Round 3 Chains 30, Residues 267, Estimated correctness of the model 69.7 % 5 chains (90 residues) have been docked in sequence Building loops using Loopy2018 30 chains (267 residues) following loop building 5 chains (90 residues) in sequence following loop building ------------------------------------------------------ 8981 reflections ( 99.80 % complete ) and 5264 restraints for refining 2936 atoms. 3872 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2735 (Rfree = 0.000) for 2936 atoms. Found 13 (13 requested) and removed 20 (13 requested) atoms. Cycle 27: After refmac, R = 0.2585 (Rfree = 0.000) for 2925 atoms. Found 12 (13 requested) and removed 14 (13 requested) atoms. Cycle 28: After refmac, R = 0.2539 (Rfree = 0.000) for 2919 atoms. Found 7 (13 requested) and removed 13 (13 requested) atoms. Cycle 29: After refmac, R = 0.2528 (Rfree = 0.000) for 2907 atoms. Found 5 (13 requested) and removed 13 (13 requested) atoms. Cycle 30: After refmac, R = 0.2507 (Rfree = 0.000) for 2895 atoms. Found 4 (12 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.10 2.82 Search for helices and strands: 0 residues in 0 chains, 2976 seeds are put forward NCS extension: 18 residues added (9 deleted due to clashes), 2994 seeds are put forward Round 1: 268 peptides, 31 chains. Longest chain 24 peptides. Score 0.617 Round 2: 286 peptides, 23 chains. Longest chain 43 peptides. Score 0.729 Round 3: 284 peptides, 32 chains. Longest chain 31 peptides. Score 0.642 Round 4: 286 peptides, 25 chains. Longest chain 31 peptides. Score 0.711 Round 5: 274 peptides, 26 chains. Longest chain 34 peptides. Score 0.680 Taking the results from Round 2 Chains 25, Residues 263, Estimated correctness of the model 71.1 % 4 chains (96 residues) have been docked in sequence Building loops using Loopy2018 25 chains (263 residues) following loop building 4 chains (96 residues) in sequence following loop building ------------------------------------------------------ 8981 reflections ( 99.80 % complete ) and 5187 restraints for refining 2935 atoms. 3789 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2694 (Rfree = 0.000) for 2935 atoms. Found 13 (13 requested) and removed 17 (13 requested) atoms. Cycle 32: After refmac, R = 0.2529 (Rfree = 0.000) for 2920 atoms. Found 13 (13 requested) and removed 14 (13 requested) atoms. Cycle 33: After refmac, R = 0.2477 (Rfree = 0.000) for 2913 atoms. Found 4 (13 requested) and removed 13 (13 requested) atoms. Cycle 34: After refmac, R = 0.2477 (Rfree = 0.000) for 2901 atoms. Found 3 (13 requested) and removed 13 (13 requested) atoms. Cycle 35: After refmac, R = 0.2488 (Rfree = 0.000) for 2888 atoms. Found 6 (12 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.11 2.83 Search for helices and strands: 0 residues in 0 chains, 2975 seeds are put forward NCS extension: 16 residues added (9 deleted due to clashes), 2991 seeds are put forward Round 1: 264 peptides, 32 chains. Longest chain 29 peptides. Score 0.597 Round 2: 294 peptides, 26 chains. Longest chain 40 peptides. Score 0.717 Round 3: 306 peptides, 29 chains. Longest chain 37 peptides. Score 0.713 Round 4: 287 peptides, 28 chains. Longest chain 37 peptides. Score 0.686 Round 5: 302 peptides, 29 chains. Longest chain 22 peptides. Score 0.706 Taking the results from Round 2 Chains 29, Residues 268, Estimated correctness of the model 68.7 % 4 chains (92 residues) have been docked in sequence Building loops using Loopy2018 29 chains (268 residues) following loop building 4 chains (92 residues) in sequence following loop building ------------------------------------------------------ 8981 reflections ( 99.80 % complete ) and 5233 restraints for refining 2936 atoms. 3815 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2692 (Rfree = 0.000) for 2936 atoms. Found 13 (13 requested) and removed 20 (13 requested) atoms. Cycle 37: After refmac, R = 0.2577 (Rfree = 0.000) for 2924 atoms. Found 13 (13 requested) and removed 15 (13 requested) atoms. Cycle 38: After refmac, R = 0.2511 (Rfree = 0.000) for 2920 atoms. Found 3 (13 requested) and removed 14 (13 requested) atoms. Cycle 39: After refmac, R = 0.2470 (Rfree = 0.000) for 2907 atoms. Found 6 (13 requested) and removed 14 (13 requested) atoms. Cycle 40: After refmac, R = 0.2408 (Rfree = 0.000) for 2896 atoms. Found 7 (13 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.09 2.81 Search for helices and strands: 0 residues in 0 chains, 2954 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 2973 seeds are put forward Round 1: 275 peptides, 29 chains. Longest chain 30 peptides. Score 0.653 Round 2: 298 peptides, 25 chains. Longest chain 36 peptides. Score 0.732 Round 3: 283 peptides, 27 chains. Longest chain 30 peptides. Score 0.688 Round 4: 295 peptides, 24 chains. Longest chain 43 peptides. Score 0.736 Round 5: 270 peptides, 28 chains. Longest chain 26 peptides. Score 0.652 Taking the results from Round 4 Chains 27, Residues 271, Estimated correctness of the model 72.4 % 5 chains (128 residues) have been docked in sequence Building loops using Loopy2018 27 chains (271 residues) following loop building 5 chains (128 residues) in sequence following loop building ------------------------------------------------------ 8981 reflections ( 99.80 % complete ) and 4862 restraints for refining 2936 atoms. 3282 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2650 (Rfree = 0.000) for 2936 atoms. Found 13 (13 requested) and removed 22 (13 requested) atoms. Cycle 42: After refmac, R = 0.2480 (Rfree = 0.000) for 2921 atoms. Found 9 (13 requested) and removed 13 (13 requested) atoms. Cycle 43: After refmac, R = 0.2433 (Rfree = 0.000) for 2911 atoms. Found 4 (13 requested) and removed 14 (13 requested) atoms. Cycle 44: After refmac, R = 0.2396 (Rfree = 0.000) for 2900 atoms. Found 4 (13 requested) and removed 13 (13 requested) atoms. Cycle 45: After refmac, R = 0.2366 (Rfree = 0.000) for 2889 atoms. Found 3 (12 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.09 2.81 Search for helices and strands: 0 residues in 0 chains, 2964 seeds are put forward NCS extension: 14 residues added (13 deleted due to clashes), 2978 seeds are put forward Round 1: 260 peptides, 25 chains. Longest chain 31 peptides. Score 0.661 Round 2: 271 peptides, 20 chains. Longest chain 46 peptides. Score 0.728 Round 3: 281 peptides, 26 chains. Longest chain 31 peptides. Score 0.693 Round 4: 275 peptides, 27 chains. Longest chain 27 peptides. Score 0.672 Round 5: 289 peptides, 25 chains. Longest chain 31 peptides. Score 0.717 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 21, Residues 251, Estimated correctness of the model 70.9 % 5 chains (132 residues) have been docked in sequence Sequence coverage is 52 % Consider running further cycles of model building using 2p97-3_warpNtrace.pdb as input Building loops using Loopy2018 21 chains (251 residues) following loop building 5 chains (132 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8981 reflections ( 99.80 % complete ) and 4967 restraints for refining 2936 atoms. 3472 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2542 (Rfree = 0.000) for 2936 atoms. Found 0 (13 requested) and removed 3 (13 requested) atoms. Cycle 47: After refmac, R = 0.2417 (Rfree = 0.000) for 2928 atoms. Found 0 (13 requested) and removed 2 (13 requested) atoms. Cycle 48: After refmac, R = 0.2397 (Rfree = 0.000) for 2923 atoms. Found 0 (13 requested) and removed 0 (13 requested) atoms. Cycle 49: After refmac, R = 0.2380 (Rfree = 0.000) for 2922 atoms. Found 0 (13 requested) and removed 2 (13 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:47:54 GMT 2018 Job finished. TimeTaking 38.38 Used memory is bytes: 9520448