null Sun 23 Dec 22:22:49 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 1vpm-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vpm-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vpm-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vpm-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/1vpm-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vpm-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 ============================================================ Sun 23 Dec 22:22:58 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/1vpm-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vpm-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 358 and 0 Target number of residues in the AU: 358 Target solvent content: 0.6349 Checking the provided sequence file Detected sequence length: 169 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 3 Adjusted target number of residues: 507 Adjusted target solvent content: 0.48 Input MTZ file: 1vpm-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: 24 Cell parameters: 82.941 106.484 120.177 90.000 90.000 90.000 Input sequence file: 1vpm-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 4056 target number of atoms Had to go as low as 0.55 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: 79.699 3.200 Wilson plot Bfac: 68.98 8944 reflections ( 98.32 % complete ) and 0 restraints for refining 4518 atoms. Observations/parameters ratio is 0.49 ------------------------------------------------------ Starting model: R = 0.3055 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2877 (Rfree = 0.000) for 4518 atoms. Found 40 (40 requested) and removed 95 (20 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.22 3.31 Search for helices and strands: 0 residues in 0 chains, 4554 seeds are put forward NCS extension: 0 residues added, 4554 seeds are put forward Round 1: 261 peptides, 41 chains. Longest chain 20 peptides. Score 0.478 Round 2: 308 peptides, 37 chains. Longest chain 21 peptides. Score 0.633 Round 3: 336 peptides, 33 chains. Longest chain 35 peptides. Score 0.720 Round 4: 336 peptides, 32 chains. Longest chain 35 peptides. Score 0.728 Round 5: 346 peptides, 27 chains. Longest chain 50 peptides. Score 0.779 Taking the results from Round 5 Chains 33, Residues 319, Estimated correctness of the model 80.1 % 8 chains (132 residues) have been docked in sequence Building loops using Loopy2018 33 chains (319 residues) following loop building 8 chains (132 residues) in sequence following loop building ------------------------------------------------------ 8944 reflections ( 98.32 % complete ) and 6670 restraints for refining 3700 atoms. 4939 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2699 (Rfree = 0.000) for 3700 atoms. Found 32 (33 requested) and removed 47 (16 requested) atoms. Cycle 2: After refmac, R = 0.2541 (Rfree = 0.000) for 3609 atoms. Found 20 (32 requested) and removed 26 (16 requested) atoms. Cycle 3: After refmac, R = 0.2469 (Rfree = 0.000) for 3573 atoms. Found 19 (31 requested) and removed 27 (16 requested) atoms. Cycle 4: After refmac, R = 0.2340 (Rfree = 0.000) for 3531 atoms. Found 9 (29 requested) and removed 20 (15 requested) atoms. Cycle 5: After refmac, R = 0.2259 (Rfree = 0.000) for 3500 atoms. Found 15 (29 requested) and removed 21 (15 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.20 3.29 Search for helices and strands: 0 residues in 0 chains, 3605 seeds are put forward NCS extension: 23 residues added (20 deleted due to clashes), 3628 seeds are put forward Round 1: 322 peptides, 32 chains. Longest chain 23 peptides. Score 0.704 Round 2: 340 peptides, 31 chains. Longest chain 31 peptides. Score 0.742 Round 3: 357 peptides, 30 chains. Longest chain 36 peptides. Score 0.773 Round 4: 348 peptides, 30 chains. Longest chain 34 peptides. Score 0.761 Round 5: 359 peptides, 28 chains. Longest chain 34 peptides. Score 0.789 Taking the results from Round 5 Chains 32, Residues 331, Estimated correctness of the model 81.7 % 9 chains (147 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 109 A and 115 A 30 chains (335 residues) following loop building 8 chains (152 residues) in sequence following loop building ------------------------------------------------------ 8944 reflections ( 98.32 % complete ) and 6364 restraints for refining 3672 atoms. 4473 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3213 (Rfree = 0.000) for 3672 atoms. Found 29 (29 requested) and removed 76 (16 requested) atoms. Cycle 7: After refmac, R = 0.2778 (Rfree = 0.000) for 3596 atoms. Found 28 (28 requested) and removed 51 (16 requested) atoms. Cycle 8: After refmac, R = 0.2638 (Rfree = 0.000) for 3550 atoms. Found 28 (28 requested) and removed 37 (16 requested) atoms. Cycle 9: After refmac, R = 0.2529 (Rfree = 0.000) for 3527 atoms. Found 18 (26 requested) and removed 28 (15 requested) atoms. Cycle 10: After refmac, R = 0.2324 (Rfree = 0.000) for 3509 atoms. Found 24 (25 requested) and removed 24 (15 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.18 3.27 Search for helices and strands: 0 residues in 0 chains, 3621 seeds are put forward NCS extension: 43 residues added (22 deleted due to clashes), 3664 seeds are put forward Round 1: 328 peptides, 34 chains. Longest chain 29 peptides. Score 0.698 Round 2: 360 peptides, 32 chains. Longest chain 50 peptides. Score 0.764 Round 3: 354 peptides, 29 chains. Longest chain 57 peptides. Score 0.776 Round 4: 358 peptides, 32 chains. Longest chain 33 peptides. Score 0.761 Round 5: 344 peptides, 31 chains. Longest chain 36 peptides. Score 0.748 Taking the results from Round 3 Chains 31, Residues 325, Estimated correctness of the model 79.6 % 4 chains (132 residues) have been docked in sequence Building loops using Loopy2018 31 chains (325 residues) following loop building 4 chains (132 residues) in sequence following loop building ------------------------------------------------------ 8944 reflections ( 98.32 % complete ) and 6569 restraints for refining 3676 atoms. 4811 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2328 (Rfree = 0.000) for 3676 atoms. Found 21 (26 requested) and removed 41 (16 requested) atoms. Cycle 12: After refmac, R = 0.2535 (Rfree = 0.000) for 3634 atoms. Found 25 (25 requested) and removed 26 (16 requested) atoms. Cycle 13: After refmac, R = 0.2445 (Rfree = 0.000) for 3607 atoms. Found 24 (24 requested) and removed 28 (16 requested) atoms. Cycle 14: After refmac, R = 0.2305 (Rfree = 0.000) for 3587 atoms. Found 23 (24 requested) and removed 21 (16 requested) atoms. Cycle 15: After refmac, R = 0.2361 (Rfree = 0.000) for 3580 atoms. Found 23 (23 requested) and removed 34 (16 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.23 3.32 Search for helices and strands: 0 residues in 0 chains, 3686 seeds are put forward NCS extension: 57 residues added (29 deleted due to clashes), 3743 seeds are put forward Round 1: 326 peptides, 33 chains. Longest chain 33 peptides. Score 0.703 Round 2: 342 peptides, 34 chains. Longest chain 34 peptides. Score 0.722 Round 3: 360 peptides, 31 chains. Longest chain 47 peptides. Score 0.771 Round 4: 344 peptides, 29 chains. Longest chain 72 peptides. Score 0.762 Round 5: 344 peptides, 32 chains. Longest chain 43 peptides. Score 0.740 Taking the results from Round 3 Chains 33, Residues 329, Estimated correctness of the model 78.8 % 6 chains (149 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 89 A and 92 A 32 chains (330 residues) following loop building 5 chains (151 residues) in sequence following loop building ------------------------------------------------------ 8944 reflections ( 98.32 % complete ) and 6356 restraints for refining 3703 atoms. 4515 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2652 (Rfree = 0.000) for 3703 atoms. Found 23 (23 requested) and removed 49 (16 requested) atoms. Cycle 17: After refmac, R = 0.2403 (Rfree = 0.000) for 3656 atoms. Found 22 (22 requested) and removed 40 (16 requested) atoms. Cycle 18: After refmac, R = 0.2320 (Rfree = 0.000) for 3614 atoms. Found 21 (21 requested) and removed 30 (16 requested) atoms. Cycle 19: After refmac, R = 0.2291 (Rfree = 0.000) for 3593 atoms. Found 20 (20 requested) and removed 28 (16 requested) atoms. Cycle 20: After refmac, R = 0.2202 (Rfree = 0.000) for 3573 atoms. Found 20 (20 requested) and removed 22 (16 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.18 3.27 Search for helices and strands: 0 residues in 0 chains, 3690 seeds are put forward NCS extension: 29 residues added (27 deleted due to clashes), 3719 seeds are put forward Round 1: 336 peptides, 34 chains. Longest chain 29 peptides. Score 0.712 Round 2: 354 peptides, 26 chains. Longest chain 54 peptides. Score 0.795 Round 3: 347 peptides, 28 chains. Longest chain 50 peptides. Score 0.773 Round 4: 366 peptides, 25 chains. Longest chain 58 peptides. Score 0.816 Round 5: 350 peptides, 32 chains. Longest chain 51 peptides. Score 0.749 Taking the results from Round 4 Chains 26, Residues 341, Estimated correctness of the model 85.8 % 6 chains (161 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 93 C and 99 C 26 chains (344 residues) following loop building 5 chains (166 residues) in sequence following loop building ------------------------------------------------------ 8944 reflections ( 98.32 % complete ) and 6064 restraints for refining 3703 atoms. 4107 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2564 (Rfree = 0.000) for 3703 atoms. Found 20 (20 requested) and removed 35 (16 requested) atoms. Cycle 22: After refmac, R = 0.2338 (Rfree = 0.000) for 3663 atoms. Found 19 (19 requested) and removed 35 (16 requested) atoms. Cycle 23: After refmac, R = 0.2278 (Rfree = 0.000) for 3633 atoms. Found 18 (18 requested) and removed 29 (16 requested) atoms. Cycle 24: After refmac, R = 0.1885 (Rfree = 0.000) for 3607 atoms. Found 14 (17 requested) and removed 23 (16 requested) atoms. Cycle 25: After refmac, R = 0.1845 (Rfree = 0.000) for 3591 atoms. Found 10 (17 requested) and removed 22 (16 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.17 3.26 Search for helices and strands: 0 residues in 0 chains, 3680 seeds are put forward NCS extension: 47 residues added (57 deleted due to clashes), 3727 seeds are put forward Round 1: 334 peptides, 31 chains. Longest chain 54 peptides. Score 0.732 Round 2: 366 peptides, 34 chains. Longest chain 54 peptides. Score 0.759 Round 3: 373 peptides, 31 chains. Longest chain 54 peptides. Score 0.788 Round 4: 364 peptides, 27 chains. Longest chain 63 peptides. Score 0.802 Round 5: 354 peptides, 30 chains. Longest chain 50 peptides. Score 0.769 Taking the results from Round 4 Chains 28, Residues 337, Estimated correctness of the model 83.7 % 5 chains (173 residues) have been docked in sequence Building loops using Loopy2018 28 chains (337 residues) following loop building 5 chains (173 residues) in sequence following loop building ------------------------------------------------------ 8944 reflections ( 98.32 % complete ) and 6054 restraints for refining 3703 atoms. 4108 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2464 (Rfree = 0.000) for 3703 atoms. Found 16 (16 requested) and removed 30 (16 requested) atoms. Cycle 27: After refmac, R = 0.2120 (Rfree = 0.000) for 3670 atoms. Found 16 (16 requested) and removed 25 (16 requested) atoms. Cycle 28: After refmac, R = 0.1999 (Rfree = 0.000) for 3645 atoms. Found 11 (16 requested) and removed 23 (16 requested) atoms. Cycle 29: After refmac, R = 0.2313 (Rfree = 0.000) for 3625 atoms. Found 16 (16 requested) and removed 21 (16 requested) atoms. Cycle 30: After refmac, R = 0.2261 (Rfree = 0.000) for 3612 atoms. Found 16 (16 requested) and removed 25 (16 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.21 3.30 Search for helices and strands: 0 residues in 0 chains, 3695 seeds are put forward NCS extension: 37 residues added (19 deleted due to clashes), 3732 seeds are put forward Round 1: 296 peptides, 36 chains. Longest chain 39 peptides. Score 0.618 Round 2: 313 peptides, 28 chains. Longest chain 49 peptides. Score 0.721 Round 3: 316 peptides, 33 chains. Longest chain 36 peptides. Score 0.685 Round 4: 327 peptides, 29 chains. Longest chain 57 peptides. Score 0.736 Round 5: 320 peptides, 28 chains. Longest chain 41 peptides. Score 0.733 Taking the results from Round 4 Chains 29, Residues 298, Estimated correctness of the model 72.4 % 4 chains (141 residues) have been docked in sequence Building loops using Loopy2018 29 chains (298 residues) following loop building 4 chains (141 residues) in sequence following loop building ------------------------------------------------------ 8944 reflections ( 98.32 % complete ) and 6588 restraints for refining 3703 atoms. 4915 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2268 (Rfree = 0.000) for 3703 atoms. Found 16 (16 requested) and removed 29 (16 requested) atoms. Cycle 32: After refmac, R = 0.1981 (Rfree = 0.000) for 3679 atoms. Found 16 (16 requested) and removed 25 (16 requested) atoms. Cycle 33: After refmac, R = 0.1928 (Rfree = 0.000) for 3660 atoms. Found 8 (16 requested) and removed 21 (16 requested) atoms. Cycle 34: After refmac, R = 0.2280 (Rfree = 0.000) for 3645 atoms. Found 16 (16 requested) and removed 35 (16 requested) atoms. Cycle 35: After refmac, R = 0.2205 (Rfree = 0.000) for 3620 atoms. Found 16 (16 requested) and removed 25 (16 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.24 3.33 Search for helices and strands: 0 residues in 0 chains, 3674 seeds are put forward NCS extension: 16 residues added (5 deleted due to clashes), 3690 seeds are put forward Round 1: 297 peptides, 39 chains. Longest chain 34 peptides. Score 0.590 Round 2: 323 peptides, 27 chains. Longest chain 51 peptides. Score 0.745 Round 3: 311 peptides, 35 chains. Longest chain 34 peptides. Score 0.658 Round 4: 304 peptides, 28 chains. Longest chain 49 peptides. Score 0.706 Round 5: 302 peptides, 29 chains. Longest chain 36 peptides. Score 0.694 Taking the results from Round 2 Chains 29, Residues 296, Estimated correctness of the model 74.1 % 4 chains (116 residues) have been docked in sequence Building loops using Loopy2018 29 chains (296 residues) following loop building 4 chains (116 residues) in sequence following loop building ------------------------------------------------------ 8944 reflections ( 98.32 % complete ) and 6731 restraints for refining 3702 atoms. 5136 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2496 (Rfree = 0.000) for 3702 atoms. Found 16 (16 requested) and removed 39 (16 requested) atoms. Cycle 37: After refmac, R = 0.2332 (Rfree = 0.000) for 3670 atoms. Found 16 (16 requested) and removed 33 (16 requested) atoms. Cycle 38: After refmac, R = 0.1797 (Rfree = 0.000) for 3639 atoms. Found 8 (16 requested) and removed 19 (16 requested) atoms. Cycle 39: After refmac, R = 0.1823 (Rfree = 0.000) for 3625 atoms. Found 8 (16 requested) and removed 22 (16 requested) atoms. Cycle 40: After refmac, R = 0.1840 (Rfree = 0.000) for 3609 atoms. Found 13 (16 requested) and removed 23 (16 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.22 3.31 Search for helices and strands: 0 residues in 0 chains, 3687 seeds are put forward NCS extension: 21 residues added (40 deleted due to clashes), 3708 seeds are put forward Round 1: 292 peptides, 33 chains. Longest chain 39 peptides. Score 0.638 Round 2: 312 peptides, 27 chains. Longest chain 59 peptides. Score 0.728 Round 3: 317 peptides, 27 chains. Longest chain 57 peptides. Score 0.736 Round 4: 323 peptides, 25 chains. Longest chain 70 peptides. Score 0.760 Round 5: 305 peptides, 29 chains. Longest chain 38 peptides. Score 0.699 Taking the results from Round 4 Chains 25, Residues 298, Estimated correctness of the model 76.9 % 4 chains (146 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 95 A and 99 A 24 chains (301 residues) following loop building 3 chains (149 residues) in sequence following loop building ------------------------------------------------------ 8944 reflections ( 98.32 % complete ) and 6274 restraints for refining 3703 atoms. 4525 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2202 (Rfree = 0.000) for 3703 atoms. Found 16 (16 requested) and removed 35 (16 requested) atoms. Cycle 42: After refmac, R = 0.2018 (Rfree = 0.000) for 3679 atoms. Found 6 (16 requested) and removed 17 (16 requested) atoms. Cycle 43: After refmac, R = 0.1962 (Rfree = 0.000) for 3666 atoms. Found 11 (16 requested) and removed 18 (16 requested) atoms. Cycle 44: After refmac, R = 0.1878 (Rfree = 0.000) for 3655 atoms. Found 7 (16 requested) and removed 17 (16 requested) atoms. Cycle 45: After refmac, R = 0.1851 (Rfree = 0.000) for 3641 atoms. Found 2 (16 requested) and removed 16 (16 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.20 3.29 Search for helices and strands: 0 residues in 0 chains, 3723 seeds are put forward NCS extension: 64 residues added (30 deleted due to clashes), 3787 seeds are put forward Round 1: 291 peptides, 29 chains. Longest chain 39 peptides. Score 0.673 Round 2: 306 peptides, 28 chains. Longest chain 51 peptides. Score 0.710 Round 3: 303 peptides, 32 chains. Longest chain 31 peptides. Score 0.669 Round 4: 307 peptides, 29 chains. Longest chain 46 peptides. Score 0.703 Round 5: 298 peptides, 29 chains. Longest chain 34 peptides. Score 0.687 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 28, Residues 278, Estimated correctness of the model 67.3 % 3 chains (120 residues) have been docked in sequence Sequence coverage is 43 % Consider running further cycles of model building using 1vpm-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 105 A and 118 A 26 chains (287 residues) following loop building 2 chains (132 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8944 reflections ( 98.32 % complete ) and 6502 restraints for refining 3703 atoms. 4885 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2292 (Rfree = 0.000) for 3703 atoms. Found 0 (16 requested) and removed 12 (16 requested) atoms. Cycle 47: After refmac, R = 0.2085 (Rfree = 0.000) for 3678 atoms. Found 0 (16 requested) and removed 9 (16 requested) atoms. Cycle 48: After refmac, R = 0.2090 (Rfree = 0.000) for 3660 atoms. Found 0 (16 requested) and removed 8 (16 requested) atoms. Cycle 49: After refmac, R = 0.2012 (Rfree = 0.000) for 3649 atoms. Found 0 (16 requested) and removed 9 (16 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:28:24 GMT 2018 Job finished. TimeTaking 65.58 Used memory is bytes: 14279272