null Tue 25 Dec 19:27:55 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 1vlm-2.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vlm-2.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vlm-2.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vlm-2.2-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/1vlm-2.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vlm-2.2-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 19:28:05 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/1vlm-2.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vlm-2.2-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 380 and 0 Target number of residues in the AU: 380 Target solvent content: 0.5284 Checking the provided sequence file Detected sequence length: 219 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 438 Adjusted target solvent content: 0.46 Input MTZ file: 1vlm-2.2-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: 18 Cell parameters: 65.648 70.734 93.922 90.000 90.000 90.000 Input sequence file: 1vlm-2.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 3504 target number of atoms Had to go as low as 0.50 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 1 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: 93.922 2.200 Wilson plot Bfac: 29.78 22604 reflections ( 98.93 % complete ) and 0 restraints for refining 3891 atoms. Observations/parameters ratio is 1.45 ------------------------------------------------------ Starting model: R = 0.3441 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2909 (Rfree = 0.000) for 3891 atoms. Found 76 (101 requested) and removed 52 (50 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.30 2.43 NCS extension: 0 residues added, 3915 seeds are put forward Round 1: 244 peptides, 36 chains. Longest chain 15 peptides. Score 0.539 Round 2: 306 peptides, 35 chains. Longest chain 30 peptides. Score 0.706 Round 3: 310 peptides, 25 chains. Longest chain 51 peptides. Score 0.797 Round 4: 314 peptides, 30 chains. Longest chain 47 peptides. Score 0.764 Round 5: 325 peptides, 22 chains. Longest chain 60 peptides. Score 0.837 Taking the results from Round 5 Chains 24, Residues 303, Estimated correctness of the model 96.5 % 7 chains (210 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 48 B and 52 B Built loop between residues 69 B and 72 B Built loop between residues 130 B and 134 B 20 chains (309 residues) following loop building 4 chains (218 residues) in sequence following loop building ------------------------------------------------------ 22604 reflections ( 98.93 % complete ) and 4528 restraints for refining 3344 atoms. 2415 conditional restraints added. Observations/parameters ratio is 1.69 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3286 (Rfree = 0.000) for 3344 atoms. Found 87 (87 requested) and removed 49 (43 requested) atoms. Cycle 2: After refmac, R = 0.3042 (Rfree = 0.000) for 3352 atoms. Found 58 (86 requested) and removed 44 (44 requested) atoms. Cycle 3: After refmac, R = 0.2865 (Rfree = 0.000) for 3350 atoms. Found 46 (84 requested) and removed 43 (43 requested) atoms. Cycle 4: After refmac, R = 0.2776 (Rfree = 0.000) for 3344 atoms. Found 41 (82 requested) and removed 25 (43 requested) atoms. Cycle 5: After refmac, R = 0.2685 (Rfree = 0.000) for 3353 atoms. Found 36 (80 requested) and removed 15 (43 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.28 2.41 NCS extension: 138 residues added (104 deleted due to clashes), 3524 seeds are put forward Round 1: 337 peptides, 18 chains. Longest chain 121 peptides. Score 0.873 Round 2: 358 peptides, 14 chains. Longest chain 122 peptides. Score 0.909 Round 3: 347 peptides, 19 chains. Longest chain 70 peptides. Score 0.877 Round 4: 361 peptides, 16 chains. Longest chain 114 peptides. Score 0.903 Round 5: 352 peptides, 15 chains. Longest chain 92 peptides. Score 0.901 Taking the results from Round 2 Chains 18, Residues 344, Estimated correctness of the model 98.8 % 7 chains (276 residues) have been docked in sequence Building loops using Loopy2018 18 chains (344 residues) following loop building 7 chains (276 residues) in sequence following loop building ------------------------------------------------------ 22604 reflections ( 98.93 % complete ) and 4075 restraints for refining 3403 atoms. 1590 conditional restraints added. Observations/parameters ratio is 1.66 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2878 (Rfree = 0.000) for 3403 atoms. Found 59 (81 requested) and removed 49 (44 requested) atoms. Cycle 7: After refmac, R = 0.2702 (Rfree = 0.000) for 3403 atoms. Found 42 (80 requested) and removed 44 (44 requested) atoms. Cycle 8: After refmac, R = 0.2597 (Rfree = 0.000) for 3391 atoms. Found 40 (77 requested) and removed 31 (44 requested) atoms. Cycle 9: After refmac, R = 0.2522 (Rfree = 0.000) for 3398 atoms. Found 33 (76 requested) and removed 17 (44 requested) atoms. Cycle 10: After refmac, R = 0.2459 (Rfree = 0.000) for 3413 atoms. Found 31 (75 requested) and removed 17 (44 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.28 2.41 NCS extension: 184 residues added (257 deleted due to clashes), 3615 seeds are put forward Round 1: 368 peptides, 13 chains. Longest chain 99 peptides. Score 0.920 Round 2: 368 peptides, 9 chains. Longest chain 131 peptides. Score 0.935 Round 3: 365 peptides, 12 chains. Longest chain 142 peptides. Score 0.922 Round 4: 372 peptides, 13 chains. Longest chain 133 peptides. Score 0.922 Round 5: 370 peptides, 11 chains. Longest chain 133 peptides. Score 0.929 Taking the results from Round 2 Chains 11, Residues 359, Estimated correctness of the model 99.4 % 6 chains (335 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 175 A and 183 A 10 chains (366 residues) following loop building 5 chains (342 residues) in sequence following loop building ------------------------------------------------------ 22604 reflections ( 98.93 % complete ) and 3761 restraints for refining 3551 atoms. 841 conditional restraints added. Observations/parameters ratio is 1.59 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2718 (Rfree = 0.000) for 3551 atoms. Found 75 (75 requested) and removed 50 (46 requested) atoms. Cycle 12: After refmac, R = 0.2597 (Rfree = 0.000) for 3565 atoms. Found 67 (74 requested) and removed 46 (46 requested) atoms. Cycle 13: After refmac, R = 0.2474 (Rfree = 0.000) for 3581 atoms. Found 53 (73 requested) and removed 47 (46 requested) atoms. Cycle 14: After refmac, R = 0.2397 (Rfree = 0.000) for 3581 atoms. Found 48 (71 requested) and removed 45 (46 requested) atoms. Cycle 15: After refmac, R = 0.2358 (Rfree = 0.000) for 3583 atoms. Found 45 (69 requested) and removed 29 (46 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.29 2.42 NCS extension: 61 residues added (154 deleted due to clashes), 3660 seeds are put forward Round 1: 371 peptides, 11 chains. Longest chain 141 peptides. Score 0.929 Round 2: 377 peptides, 10 chains. Longest chain 131 peptides. Score 0.936 Round 3: 370 peptides, 11 chains. Longest chain 141 peptides. Score 0.929 Round 4: 369 peptides, 11 chains. Longest chain 133 peptides. Score 0.928 Round 5: 371 peptides, 12 chains. Longest chain 141 peptides. Score 0.925 Taking the results from Round 2 Chains 12, Residues 367, Estimated correctness of the model 99.4 % 7 chains (342 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 56 A and 60 A Built loop between residues 127 A and 137 A Built loop between residues 176 A and 180 A 7 chains (379 residues) following loop building 4 chains (357 residues) in sequence following loop building ------------------------------------------------------ 22604 reflections ( 98.93 % complete ) and 3739 restraints for refining 3633 atoms. 687 conditional restraints added. Observations/parameters ratio is 1.56 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2625 (Rfree = 0.000) for 3633 atoms. Found 68 (68 requested) and removed 52 (47 requested) atoms. Cycle 17: After refmac, R = 0.2462 (Rfree = 0.000) for 3643 atoms. Found 63 (66 requested) and removed 47 (47 requested) atoms. Cycle 18: After refmac, R = 0.2362 (Rfree = 0.000) for 3657 atoms. Found 30 (65 requested) and removed 41 (47 requested) atoms. Cycle 19: After refmac, R = 0.2307 (Rfree = 0.000) for 3641 atoms. Found 27 (63 requested) and removed 30 (47 requested) atoms. Cycle 20: After refmac, R = 0.2267 (Rfree = 0.000) for 3636 atoms. Found 31 (60 requested) and removed 24 (47 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.29 2.42 NCS extension: 80 residues added (219 deleted due to clashes), 3725 seeds are put forward Round 1: 375 peptides, 12 chains. Longest chain 99 peptides. Score 0.928 Round 2: 379 peptides, 7 chains. Longest chain 142 peptides. Score 0.947 Round 3: 376 peptides, 13 chains. Longest chain 99 peptides. Score 0.924 Round 4: 381 peptides, 10 chains. Longest chain 142 peptides. Score 0.938 Round 5: 377 peptides, 13 chains. Longest chain 90 peptides. Score 0.925 Taking the results from Round 2 Chains 8, Residues 372, Estimated correctness of the model 99.6 % 6 chains (359 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 123 A and 134 A Built loop between residues 175 A and 180 A Built loop between residues 153 B and 159 B 4 chains (389 residues) following loop building 3 chains (378 residues) in sequence following loop building ------------------------------------------------------ 22604 reflections ( 98.93 % complete ) and 3650 restraints for refining 3688 atoms. 462 conditional restraints added. Observations/parameters ratio is 1.53 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2617 (Rfree = 0.000) for 3688 atoms. Found 60 (60 requested) and removed 57 (48 requested) atoms. Cycle 22: After refmac, R = 0.2434 (Rfree = 0.000) for 3682 atoms. Found 53 (58 requested) and removed 48 (48 requested) atoms. Cycle 23: After refmac, R = 0.2340 (Rfree = 0.000) for 3685 atoms. Found 46 (56 requested) and removed 48 (48 requested) atoms. Cycle 24: After refmac, R = 0.2269 (Rfree = 0.000) for 3679 atoms. Found 45 (54 requested) and removed 46 (48 requested) atoms. Cycle 25: After refmac, R = 0.2213 (Rfree = 0.000) for 3677 atoms. Found 40 (52 requested) and removed 37 (48 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.28 2.41 NCS extension: 52 residues added (187 deleted due to clashes), 3735 seeds are put forward Round 1: 372 peptides, 9 chains. Longest chain 141 peptides. Score 0.937 Round 2: 377 peptides, 8 chains. Longest chain 99 peptides. Score 0.943 Round 3: 373 peptides, 12 chains. Longest chain 135 peptides. Score 0.926 Round 4: 376 peptides, 10 chains. Longest chain 79 peptides. Score 0.935 Round 5: 377 peptides, 11 chains. Longest chain 141 peptides. Score 0.932 Taking the results from Round 2 Chains 12, Residues 369, Estimated correctness of the model 99.5 % 8 chains (363 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 97 A and 103 A Built loop between residues 127 A and 136 A Built loop between residues 175 A and 180 A Built loop between residues 110 B and 114 B Built loop between residues 152 B and 159 B 4 chains (390 residues) following loop building 3 chains (389 residues) in sequence following loop building ------------------------------------------------------ 22604 reflections ( 98.93 % complete ) and 3666 restraints for refining 3708 atoms. 431 conditional restraints added. Observations/parameters ratio is 1.52 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2549 (Rfree = 0.000) for 3708 atoms. Found 50 (50 requested) and removed 53 (48 requested) atoms. Cycle 27: After refmac, R = 0.2412 (Rfree = 0.000) for 3694 atoms. Found 48 (48 requested) and removed 48 (48 requested) atoms. Cycle 28: After refmac, R = 0.2324 (Rfree = 0.000) for 3689 atoms. Found 33 (48 requested) and removed 48 (48 requested) atoms. Cycle 29: After refmac, R = 0.2250 (Rfree = 0.000) for 3670 atoms. Found 42 (47 requested) and removed 47 (47 requested) atoms. Cycle 30: After refmac, R = 0.2209 (Rfree = 0.000) for 3662 atoms. Found 46 (47 requested) and removed 37 (47 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.28 2.41 NCS extension: 44 residues added (180 deleted due to clashes), 3718 seeds are put forward Round 1: 386 peptides, 9 chains. Longest chain 141 peptides. Score 0.943 Round 2: 377 peptides, 9 chains. Longest chain 125 peptides. Score 0.939 Round 3: 382 peptides, 9 chains. Longest chain 89 peptides. Score 0.942 Round 4: 379 peptides, 12 chains. Longest chain 130 peptides. Score 0.930 Round 5: 375 peptides, 11 chains. Longest chain 70 peptides. Score 0.931 Taking the results from Round 1 Chains 9, Residues 377, Estimated correctness of the model 99.5 % 7 chains (364 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 54 A and 57 A Built loop between residues 162 A and 165 A Built loop between residues 176 A and 180 A Built loop between residues 152 B and 159 B 5 chains (390 residues) following loop building 3 chains (377 residues) in sequence following loop building ------------------------------------------------------ 22604 reflections ( 98.93 % complete ) and 3658 restraints for refining 3645 atoms. 472 conditional restraints added. Observations/parameters ratio is 1.55 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2424 (Rfree = 0.000) for 3645 atoms. Found 47 (47 requested) and removed 52 (47 requested) atoms. Cycle 32: After refmac, R = 0.2296 (Rfree = 0.000) for 3630 atoms. Found 47 (47 requested) and removed 47 (47 requested) atoms. Cycle 33: After refmac, R = 0.2201 (Rfree = 0.000) for 3627 atoms. Found 47 (47 requested) and removed 44 (47 requested) atoms. Cycle 34: After refmac, R = 0.2160 (Rfree = 0.000) for 3624 atoms. Found 47 (47 requested) and removed 43 (47 requested) atoms. Cycle 35: After refmac, R = 0.2128 (Rfree = 0.000) for 3626 atoms. Found 47 (47 requested) and removed 39 (47 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.29 2.42 NCS extension: 47 residues added (191 deleted due to clashes), 3682 seeds are put forward Round 1: 388 peptides, 7 chains. Longest chain 140 peptides. Score 0.951 Round 2: 381 peptides, 11 chains. Longest chain 80 peptides. Score 0.934 Round 3: 389 peptides, 8 chains. Longest chain 136 peptides. Score 0.948 Round 4: 389 peptides, 10 chains. Longest chain 136 peptides. Score 0.941 Round 5: 393 peptides, 10 chains. Longest chain 79 peptides. Score 0.943 Taking the results from Round 1 Chains 7, Residues 381, Estimated correctness of the model 99.6 % 7 chains (381 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 54 A and 57 A Built loop between residues 99 A and 102 A Built loop between residues 176 A and 179 A Built loop between residues 151 B and 159 B 3 chains (394 residues) following loop building 3 chains (394 residues) in sequence following loop building ------------------------------------------------------ 22604 reflections ( 98.93 % complete ) and 3622 restraints for refining 3655 atoms. 356 conditional restraints added. Observations/parameters ratio is 1.55 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2428 (Rfree = 0.000) for 3655 atoms. Found 47 (47 requested) and removed 52 (47 requested) atoms. Cycle 37: After refmac, R = 0.2299 (Rfree = 0.000) for 3641 atoms. Found 47 (47 requested) and removed 48 (47 requested) atoms. Cycle 38: After refmac, R = 0.2233 (Rfree = 0.000) for 3640 atoms. Found 47 (47 requested) and removed 47 (47 requested) atoms. Cycle 39: After refmac, R = 0.2188 (Rfree = 0.000) for 3639 atoms. Found 47 (47 requested) and removed 47 (47 requested) atoms. Cycle 40: After refmac, R = 0.2166 (Rfree = 0.000) for 3635 atoms. Found 47 (47 requested) and removed 38 (47 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.29 2.42 NCS extension: 47 residues added (230 deleted due to clashes), 3694 seeds are put forward Round 1: 393 peptides, 7 chains. Longest chain 141 peptides. Score 0.953 Round 2: 393 peptides, 10 chains. Longest chain 125 peptides. Score 0.943 Round 3: 390 peptides, 9 chains. Longest chain 99 peptides. Score 0.945 Round 4: 385 peptides, 9 chains. Longest chain 79 peptides. Score 0.943 Round 5: 387 peptides, 9 chains. Longest chain 138 peptides. Score 0.944 Taking the results from Round 1 Chains 7, Residues 386, Estimated correctness of the model 99.6 % 6 chains (383 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 54 A and 57 A Built loop between residues 73 A and 84 A Built loop between residues 152 B and 159 B Built loop between residues 188 B and 191 B 2 chains (403 residues) following loop building 2 chains (403 residues) in sequence following loop building ------------------------------------------------------ 22604 reflections ( 98.93 % complete ) and 3623 restraints for refining 3711 atoms. 277 conditional restraints added. Observations/parameters ratio is 1.52 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2453 (Rfree = 0.000) for 3711 atoms. Found 48 (48 requested) and removed 55 (48 requested) atoms. Cycle 42: After refmac, R = 0.2317 (Rfree = 0.000) for 3693 atoms. Found 48 (48 requested) and removed 48 (48 requested) atoms. Cycle 43: After refmac, R = 0.2247 (Rfree = 0.000) for 3689 atoms. Found 40 (48 requested) and removed 48 (48 requested) atoms. Cycle 44: After refmac, R = 0.2185 (Rfree = 0.000) for 3679 atoms. Found 46 (48 requested) and removed 48 (48 requested) atoms. Cycle 45: After refmac, R = 0.2159 (Rfree = 0.000) for 3673 atoms. Found 39 (47 requested) and removed 48 (47 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.29 2.42 NCS extension: 5 residues added (4 deleted due to clashes), 3673 seeds are put forward Round 1: 389 peptides, 9 chains. Longest chain 141 peptides. Score 0.945 Round 2: 396 peptides, 6 chains. Longest chain 130 peptides. Score 0.957 Round 3: 392 peptides, 9 chains. Longest chain 98 peptides. Score 0.946 Round 4: 385 peptides, 10 chains. Longest chain 91 peptides. Score 0.940 Round 5: 383 peptides, 9 chains. Longest chain 121 peptides. Score 0.942 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 6, Residues 390, Estimated correctness of the model 99.7 % 5 chains (383 residues) have been docked in sequence Sequence coverage is 97 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 73 A and 78 A Built loop between residues 173 A and 176 A 4 chains (396 residues) following loop building 3 chains (389 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 22604 reflections ( 98.93 % complete ) and 3245 restraints for refining 3179 atoms. Observations/parameters ratio is 1.78 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2809 (Rfree = 0.000) for 3179 atoms. Found 20 (41 requested) and removed 0 (41 requested) atoms. Cycle 47: After refmac, R = 0.2636 (Rfree = 0.000) for 3179 atoms. Found 14 (41 requested) and removed 0 (41 requested) atoms. Cycle 48: After refmac, R = 0.2526 (Rfree = 0.000) for 3179 atoms. Found 7 (41 requested) and removed 0 (41 requested) atoms. Cycle 49: After refmac, R = 0.2452 (Rfree = 0.000) for 3179 atoms. Found 7 (42 requested) and removed 3 (42 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:35:46 GMT 2018 Job finished. TimeTaking 67.84 Used memory is bytes: 2091536