null 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 2itb-2.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2itb-2.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2itb-2.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2itb-2.0-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/2itb-2.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2itb-2.0-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 19:28:06 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/2itb-2.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2itb-2.0-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 326 and 0 Target number of residues in the AU: 326 Target solvent content: 0.5125 Checking the provided sequence file Detected sequence length: 206 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 412 Adjusted target solvent content: 0.38 Input MTZ file: 2itb-2.0-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: 19 Cell parameters: 61.232 70.168 84.235 90.000 90.000 90.000 Input sequence file: 2itb-2.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 3296 target number of atoms Had to go as low as 0.45 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: 53.913 2.050 Wilson plot Bfac: 26.09 23366 reflections ( 99.87 % complete ) and 0 restraints for refining 3670 atoms. Observations/parameters ratio is 1.59 ------------------------------------------------------ Starting model: R = 0.3350 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2792 (Rfree = 0.000) for 3670 atoms. Found 60 (117 requested) and removed 63 (58 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.17 2.55 NCS extension: 0 residues added, 3667 seeds are put forward Round 1: 244 peptides, 40 chains. Longest chain 19 peptides. Score 0.531 Round 2: 311 peptides, 23 chains. Longest chain 51 peptides. Score 0.858 Round 3: 334 peptides, 17 chains. Longest chain 76 peptides. Score 0.912 Round 4: 344 peptides, 16 chains. Longest chain 70 peptides. Score 0.923 Round 5: 354 peptides, 12 chains. Longest chain 69 peptides. Score 0.943 Taking the results from Round 5 Chains 14, Residues 342, Estimated correctness of the model 99.6 % 9 chains (310 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 131 A and 140 A Built loop between residues 16 B and 27 B Built loop between residues 75 B and 78 B Built loop between residues 107 B and 111 B Built loop between residues 131 B and 137 B 7 chains (365 residues) following loop building 4 chains (338 residues) in sequence following loop building ------------------------------------------------------ 23366 reflections ( 99.87 % complete ) and 3741 restraints for refining 3419 atoms. 893 conditional restraints added. Observations/parameters ratio is 1.71 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3038 (Rfree = 0.000) for 3419 atoms. Found 62 (109 requested) and removed 61 (54 requested) atoms. Cycle 2: After refmac, R = 0.2734 (Rfree = 0.000) for 3396 atoms. Found 53 (107 requested) and removed 55 (54 requested) atoms. Cycle 3: After refmac, R = 0.2553 (Rfree = 0.000) for 3378 atoms. Found 36 (104 requested) and removed 54 (54 requested) atoms. Cycle 4: After refmac, R = 0.2411 (Rfree = 0.000) for 3352 atoms. Found 35 (101 requested) and removed 40 (53 requested) atoms. Cycle 5: After refmac, R = 0.2308 (Rfree = 0.000) for 3335 atoms. Found 23 (98 requested) and removed 20 (53 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.13 2.51 NCS extension: 55 residues added (172 deleted due to clashes), 3406 seeds are put forward Round 1: 374 peptides, 11 chains. Longest chain 80 peptides. Score 0.954 Round 2: 385 peptides, 5 chains. Longest chain 103 peptides. Score 0.974 Round 3: 383 peptides, 9 chains. Longest chain 103 peptides. Score 0.963 Round 4: 379 peptides, 10 chains. Longest chain 103 peptides. Score 0.959 Round 5: 384 peptides, 8 chains. Longest chain 103 peptides. Score 0.966 Taking the results from Round 2 Chains 5, Residues 380, Estimated correctness of the model 99.9 % 5 chains (380 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 108 A and 111 A Built loop between residues 83 B and 87 B Built loop between residues 107 B and 110 B 2 chains (387 residues) following loop building 2 chains (387 residues) in sequence following loop building ------------------------------------------------------ 23366 reflections ( 99.87 % complete ) and 3406 restraints for refining 3426 atoms. 270 conditional restraints added. Observations/parameters ratio is 1.71 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2379 (Rfree = 0.000) for 3426 atoms. Found 69 (98 requested) and removed 56 (54 requested) atoms. Cycle 7: After refmac, R = 0.2202 (Rfree = 0.000) for 3431 atoms. Found 44 (96 requested) and removed 54 (54 requested) atoms. Cycle 8: After refmac, R = 0.2091 (Rfree = 0.000) for 3417 atoms. Found 42 (94 requested) and removed 32 (54 requested) atoms. Cycle 9: After refmac, R = 0.2021 (Rfree = 0.000) for 3423 atoms. Found 44 (92 requested) and removed 24 (54 requested) atoms. Cycle 10: After refmac, R = 0.1975 (Rfree = 0.000) for 3437 atoms. Found 40 (89 requested) and removed 38 (54 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.12 2.50 NCS extension: 0 residues added, 3441 seeds are put forward Round 1: 386 peptides, 5 chains. Longest chain 102 peptides. Score 0.974 Round 2: 386 peptides, 6 chains. Longest chain 102 peptides. Score 0.972 Round 3: 384 peptides, 7 chains. Longest chain 103 peptides. Score 0.969 Round 4: 387 peptides, 5 chains. Longest chain 103 peptides. Score 0.975 Round 5: 381 peptides, 10 chains. Longest chain 103 peptides. Score 0.960 Taking the results from Round 4 Chains 6, Residues 382, Estimated correctness of the model 99.9 % 5 chains (379 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 105 A and 111 A Built loop between residues 107 B and 110 B Built loop between residues 132 B and 135 B 2 chains (388 residues) following loop building 2 chains (388 residues) in sequence following loop building ------------------------------------------------------ 23366 reflections ( 99.87 % complete ) and 3420 restraints for refining 3445 atoms. 276 conditional restraints added. Observations/parameters ratio is 1.70 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2196 (Rfree = 0.000) for 3445 atoms. Found 63 (87 requested) and removed 58 (54 requested) atoms. Cycle 12: After refmac, R = 0.2085 (Rfree = 0.000) for 3446 atoms. Found 41 (86 requested) and removed 54 (55 requested) atoms. Cycle 13: After refmac, R = 0.1998 (Rfree = 0.000) for 3431 atoms. Found 53 (83 requested) and removed 27 (54 requested) atoms. Cycle 14: After refmac, R = 0.1928 (Rfree = 0.000) for 3456 atoms. Found 35 (81 requested) and removed 35 (55 requested) atoms. Cycle 15: After refmac, R = 0.1902 (Rfree = 0.000) for 3454 atoms. Found 47 (79 requested) and removed 31 (55 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.10 2.47 NCS extension: 0 residues added, 3472 seeds are put forward Round 1: 387 peptides, 5 chains. Longest chain 102 peptides. Score 0.975 Round 2: 386 peptides, 6 chains. Longest chain 103 peptides. Score 0.972 Round 3: 385 peptides, 7 chains. Longest chain 103 peptides. Score 0.969 Round 4: 377 peptides, 12 chains. Longest chain 74 peptides. Score 0.952 Round 5: 384 peptides, 9 chains. Longest chain 103 peptides. Score 0.963 Taking the results from Round 1 Chains 5, Residues 382, Estimated correctness of the model 99.9 % 5 chains (382 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 107 A and 110 A Built loop between residues 71 B and 74 B Built loop between residues 107 B and 110 B 2 chains (388 residues) following loop building 2 chains (388 residues) in sequence following loop building ------------------------------------------------------ 23366 reflections ( 99.87 % complete ) and 3401 restraints for refining 3445 atoms. 257 conditional restraints added. Observations/parameters ratio is 1.70 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2077 (Rfree = 0.000) for 3445 atoms. Found 60 (76 requested) and removed 57 (54 requested) atoms. Cycle 17: After refmac, R = 0.1952 (Rfree = 0.000) for 3448 atoms. Found 37 (75 requested) and removed 53 (55 requested) atoms. Cycle 18: After refmac, R = 0.1903 (Rfree = 0.000) for 3430 atoms. Found 48 (72 requested) and removed 44 (54 requested) atoms. Cycle 19: After refmac, R = 0.1882 (Rfree = 0.000) for 3432 atoms. Found 57 (70 requested) and removed 42 (54 requested) atoms. Cycle 20: After refmac, R = 0.1842 (Rfree = 0.000) for 3446 atoms. Found 64 (68 requested) and removed 37 (55 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.09 2.46 NCS extension: 0 residues added, 3475 seeds are put forward Round 1: 387 peptides, 5 chains. Longest chain 102 peptides. Score 0.975 Round 2: 387 peptides, 5 chains. Longest chain 102 peptides. Score 0.975 Round 3: 384 peptides, 7 chains. Longest chain 92 peptides. Score 0.969 Round 4: 385 peptides, 7 chains. Longest chain 104 peptides. Score 0.969 Round 5: 386 peptides, 8 chains. Longest chain 92 peptides. Score 0.967 Taking the results from Round 2 Chains 5, Residues 382, Estimated correctness of the model 99.9 % 5 chains (382 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 107 A and 110 A Built loop between residues 87 B and 90 B Built loop between residues 128 B and 131 B 2 chains (388 residues) following loop building 2 chains (388 residues) in sequence following loop building ------------------------------------------------------ 23366 reflections ( 99.87 % complete ) and 3402 restraints for refining 3439 atoms. 258 conditional restraints added. Observations/parameters ratio is 1.70 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2031 (Rfree = 0.000) for 3439 atoms. Found 65 (65 requested) and removed 55 (54 requested) atoms. Cycle 22: After refmac, R = 0.1917 (Rfree = 0.000) for 3448 atoms. Found 47 (64 requested) and removed 51 (55 requested) atoms. Cycle 23: After refmac, R = 0.1889 (Rfree = 0.000) for 3439 atoms. Found 46 (61 requested) and removed 39 (54 requested) atoms. Cycle 24: After refmac, R = 0.1858 (Rfree = 0.000) for 3444 atoms. Found 54 (59 requested) and removed 44 (55 requested) atoms. Cycle 25: After refmac, R = 0.1840 (Rfree = 0.000) for 3453 atoms. Found 53 (57 requested) and removed 44 (55 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.10 2.47 NCS extension: 0 residues added, 3462 seeds are put forward Round 1: 387 peptides, 6 chains. Longest chain 102 peptides. Score 0.972 Round 2: 384 peptides, 6 chains. Longest chain 102 peptides. Score 0.971 Round 3: 387 peptides, 5 chains. Longest chain 130 peptides. Score 0.975 Round 4: 384 peptides, 7 chains. Longest chain 103 peptides. Score 0.969 Round 5: 385 peptides, 8 chains. Longest chain 92 peptides. Score 0.966 Taking the results from Round 3 Chains 5, Residues 382, Estimated correctness of the model 99.9 % 5 chains (382 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 47 A and 50 A Built loop between residues 68 A and 72 A Built loop between residues 107 B and 110 B 2 chains (389 residues) following loop building 2 chains (389 residues) in sequence following loop building ------------------------------------------------------ 23366 reflections ( 99.87 % complete ) and 3383 restraints for refining 3437 atoms. 231 conditional restraints added. Observations/parameters ratio is 1.70 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2022 (Rfree = 0.000) for 3437 atoms. Found 54 (54 requested) and removed 56 (54 requested) atoms. Cycle 27: After refmac, R = 0.1921 (Rfree = 0.000) for 3433 atoms. Found 45 (54 requested) and removed 35 (54 requested) atoms. Cycle 28: After refmac, R = 0.1875 (Rfree = 0.000) for 3441 atoms. Found 40 (54 requested) and removed 27 (54 requested) atoms. Cycle 29: After refmac, R = 0.1838 (Rfree = 0.000) for 3451 atoms. Found 47 (55 requested) and removed 26 (55 requested) atoms. Cycle 30: After refmac, R = 0.1823 (Rfree = 0.000) for 3471 atoms. Found 45 (55 requested) and removed 24 (55 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.10 2.47 NCS extension: 0 residues added, 3492 seeds are put forward Round 1: 382 peptides, 7 chains. Longest chain 92 peptides. Score 0.968 Round 2: 387 peptides, 6 chains. Longest chain 102 peptides. Score 0.972 Round 3: 386 peptides, 7 chains. Longest chain 103 peptides. Score 0.969 Round 4: 386 peptides, 8 chains. Longest chain 102 peptides. Score 0.967 Round 5: 385 peptides, 8 chains. Longest chain 92 peptides. Score 0.966 Taking the results from Round 2 Chains 6, Residues 381, Estimated correctness of the model 99.9 % 6 chains (381 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 87 A and 90 A Built loop between residues 128 A and 131 A Built loop between residues 107 B and 110 B 3 chains (387 residues) following loop building 3 chains (387 residues) in sequence following loop building ------------------------------------------------------ 23366 reflections ( 99.87 % complete ) and 3408 restraints for refining 3443 atoms. 274 conditional restraints added. Observations/parameters ratio is 1.70 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2013 (Rfree = 0.000) for 3443 atoms. Found 54 (54 requested) and removed 58 (54 requested) atoms. Cycle 32: After refmac, R = 0.1905 (Rfree = 0.000) for 3436 atoms. Found 51 (54 requested) and removed 24 (54 requested) atoms. Cycle 33: After refmac, R = 0.1838 (Rfree = 0.000) for 3462 atoms. Found 43 (55 requested) and removed 23 (55 requested) atoms. Cycle 34: After refmac, R = 0.1805 (Rfree = 0.000) for 3480 atoms. Found 37 (55 requested) and removed 26 (55 requested) atoms. Cycle 35: After refmac, R = 0.1775 (Rfree = 0.000) for 3489 atoms. Found 42 (55 requested) and removed 28 (55 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.11 2.48 NCS extension: 18 residues added (178 deleted due to clashes), 3522 seeds are put forward Round 1: 388 peptides, 6 chains. Longest chain 102 peptides. Score 0.972 Round 2: 388 peptides, 5 chains. Longest chain 102 peptides. Score 0.975 Round 3: 385 peptides, 8 chains. Longest chain 103 peptides. Score 0.966 Round 4: 383 peptides, 8 chains. Longest chain 90 peptides. Score 0.966 Round 5: 384 peptides, 8 chains. Longest chain 90 peptides. Score 0.966 Taking the results from Round 2 Chains 5, Residues 383, Estimated correctness of the model 99.9 % 5 chains (383 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 107 A and 110 A Built loop between residues 83 B and 86 B Built loop between residues 107 B and 110 B 2 chains (389 residues) following loop building 2 chains (389 residues) in sequence following loop building ------------------------------------------------------ 23366 reflections ( 99.87 % complete ) and 3382 restraints for refining 3460 atoms. 230 conditional restraints added. Observations/parameters ratio is 1.69 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2021 (Rfree = 0.000) for 3460 atoms. Found 55 (55 requested) and removed 56 (55 requested) atoms. Cycle 37: After refmac, R = 0.1887 (Rfree = 0.000) for 3455 atoms. Found 50 (55 requested) and removed 32 (55 requested) atoms. Cycle 38: After refmac, R = 0.1830 (Rfree = 0.000) for 3471 atoms. Found 37 (55 requested) and removed 15 (55 requested) atoms. Cycle 39: After refmac, R = 0.1797 (Rfree = 0.000) for 3490 atoms. Found 32 (55 requested) and removed 21 (55 requested) atoms. Cycle 40: After refmac, R = 0.1779 (Rfree = 0.000) for 3495 atoms. Found 38 (55 requested) and removed 19 (55 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.11 2.48 NCS extension: 0 residues added, 3516 seeds are put forward Round 1: 387 peptides, 6 chains. Longest chain 102 peptides. Score 0.972 Round 2: 384 peptides, 5 chains. Longest chain 102 peptides. Score 0.974 Round 3: 380 peptides, 8 chains. Longest chain 103 peptides. Score 0.965 Round 4: 385 peptides, 7 chains. Longest chain 92 peptides. Score 0.969 Round 5: 376 peptides, 10 chains. Longest chain 92 peptides. Score 0.958 Taking the results from Round 2 Chains 5, Residues 379, Estimated correctness of the model 99.9 % 5 chains (379 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 107 A and 110 A Built loop between residues 78 B and 84 B Built loop between residues 107 B and 110 B 2 chains (388 residues) following loop building 2 chains (388 residues) in sequence following loop building ------------------------------------------------------ 23366 reflections ( 99.87 % complete ) and 3409 restraints for refining 3482 atoms. 265 conditional restraints added. Observations/parameters ratio is 1.68 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2011 (Rfree = 0.000) for 3482 atoms. Found 55 (55 requested) and removed 58 (55 requested) atoms. Cycle 42: After refmac, R = 0.1902 (Rfree = 0.000) for 3473 atoms. Found 42 (55 requested) and removed 26 (55 requested) atoms. Cycle 43: After refmac, R = 0.1855 (Rfree = 0.000) for 3488 atoms. Found 44 (55 requested) and removed 28 (55 requested) atoms. Cycle 44: After refmac, R = 0.1824 (Rfree = 0.000) for 3501 atoms. Found 37 (55 requested) and removed 32 (55 requested) atoms. Cycle 45: After refmac, R = 0.1798 (Rfree = 0.000) for 3503 atoms. Found 50 (55 requested) and removed 23 (55 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.10 2.47 NCS extension: 0 residues added, 3530 seeds are put forward Round 1: 383 peptides, 6 chains. Longest chain 92 peptides. Score 0.971 Round 2: 384 peptides, 6 chains. Longest chain 102 peptides. Score 0.971 Round 3: 381 peptides, 8 chains. Longest chain 92 peptides. Score 0.965 Round 4: 380 peptides, 9 chains. Longest chain 92 peptides. Score 0.962 Round 5: 382 peptides, 8 chains. Longest chain 92 peptides. Score 0.965 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 6, Residues 378, Estimated correctness of the model 99.9 % 6 chains (378 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 47 A and 50 A Built loop between residues 87 A and 90 A Built loop between residues 107 A and 112 A Built loop between residues 107 B and 110 B 2 chains (388 residues) following loop building 2 chains (388 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 23366 reflections ( 99.87 % complete ) and 3144 restraints for refining 3084 atoms. Observations/parameters ratio is 1.89 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2563 (Rfree = 0.000) for 3084 atoms. Found 32 (49 requested) and removed 0 (49 requested) atoms. Cycle 47: After refmac, R = 0.2393 (Rfree = 0.000) for 3084 atoms. Found 14 (49 requested) and removed 0 (49 requested) atoms. Cycle 48: After refmac, R = 0.2293 (Rfree = 0.000) for 3084 atoms. Found 11 (49 requested) and removed 3 (49 requested) atoms. Cycle 49: After refmac, R = 0.2264 (Rfree = 0.000) for 3084 atoms. Found 5 (50 requested) and removed 0 (50 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:32:46 GMT 2018 Job finished. TimeTaking 64.83 Used memory is bytes: 23918712