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 2f4l-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2f4l-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2f4l-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2f4l-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/2f4l-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2f4l-3.2-parrot-hancs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Tue 25 Dec 19:28:04 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/2f4l-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2f4l-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 895 and 0 Target number of residues in the AU: 895 Target solvent content: 0.6248 Checking the provided sequence file Detected sequence length: 297 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1188 Adjusted target solvent content: 0.50 Input MTZ file: 2f4l-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: 19 Cell parameters: 80.030 103.980 155.130 90.000 90.000 90.000 Input sequence file: 2f4l-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 9504 target number of atoms Had to go as low as 0.65 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: 86.372 3.200 Wilson plot Bfac: 63.68 21953 reflections ( 99.76 % complete ) and 0 restraints for refining 10491 atoms. Observations/parameters ratio is 0.52 ------------------------------------------------------ Starting model: R = 0.2938 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2634 (Rfree = 0.000) for 10491 atoms. Found 84 (94 requested) and removed 113 (47 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.16 3.16 Search for helices and strands: 0 residues in 0 chains, 10590 seeds are put forward NCS extension: 0 residues added, 10590 seeds are put forward Round 1: 704 peptides, 105 chains. Longest chain 25 peptides. Score 0.528 Round 2: 819 peptides, 93 chains. Longest chain 30 peptides. Score 0.679 Round 3: 867 peptides, 83 chains. Longest chain 36 peptides. Score 0.744 Round 4: 890 peptides, 76 chains. Longest chain 38 peptides. Score 0.777 Round 5: 897 peptides, 65 chains. Longest chain 45 peptides. Score 0.809 Taking the results from Round 5 Chains 76, Residues 832, Estimated correctness of the model 84.8 % 15 chains (322 residues) have been docked in sequence Building loops using Loopy2018 76 chains (832 residues) following loop building 15 chains (322 residues) in sequence following loop building ------------------------------------------------------ 21953 reflections ( 99.76 % complete ) and 15157 restraints for refining 8673 atoms. 10703 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2628 (Rfree = 0.000) for 8673 atoms. Found 67 (77 requested) and removed 77 (38 requested) atoms. Cycle 2: After refmac, R = 0.2454 (Rfree = 0.000) for 8584 atoms. Found 35 (75 requested) and removed 62 (38 requested) atoms. Cycle 3: After refmac, R = 0.2244 (Rfree = 0.000) for 8500 atoms. Found 26 (73 requested) and removed 49 (38 requested) atoms. Cycle 4: After refmac, R = 0.2221 (Rfree = 0.000) for 8445 atoms. Found 18 (71 requested) and removed 46 (38 requested) atoms. Cycle 5: After refmac, R = 0.2190 (Rfree = 0.000) for 8406 atoms. Found 15 (69 requested) and removed 38 (37 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.17 3.17 Search for helices and strands: 0 residues in 0 chains, 8587 seeds are put forward NCS extension: 26 residues added (2 deleted due to clashes), 8613 seeds are put forward Round 1: 853 peptides, 83 chains. Longest chain 37 peptides. Score 0.735 Round 2: 904 peptides, 63 chains. Longest chain 51 peptides. Score 0.817 Round 3: 897 peptides, 65 chains. Longest chain 46 peptides. Score 0.809 Round 4: 926 peptides, 70 chains. Longest chain 37 peptides. Score 0.811 Round 5: 919 peptides, 64 chains. Longest chain 54 peptides. Score 0.822 Taking the results from Round 5 Chains 74, Residues 855, Estimated correctness of the model 86.6 % 18 chains (439 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 280 C and 283 C 72 chains (856 residues) following loop building 17 chains (441 residues) in sequence following loop building ------------------------------------------------------ 21953 reflections ( 99.76 % complete ) and 14302 restraints for refining 8675 atoms. 9260 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2614 (Rfree = 0.000) for 8675 atoms. Found 62 (69 requested) and removed 79 (38 requested) atoms. Cycle 7: After refmac, R = 0.2388 (Rfree = 0.000) for 8606 atoms. Found 28 (68 requested) and removed 48 (38 requested) atoms. Cycle 8: After refmac, R = 0.2287 (Rfree = 0.000) for 8553 atoms. Found 20 (66 requested) and removed 39 (38 requested) atoms. Cycle 9: After refmac, R = 0.2243 (Rfree = 0.000) for 8523 atoms. Found 9 (64 requested) and removed 38 (38 requested) atoms. Cycle 10: After refmac, R = 0.2207 (Rfree = 0.000) for 8480 atoms. Found 9 (62 requested) and removed 38 (38 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.19 3.19 Search for helices and strands: 0 residues in 0 chains, 8600 seeds are put forward NCS extension: 12 residues added (10 deleted due to clashes), 8612 seeds are put forward Round 1: 844 peptides, 77 chains. Longest chain 47 peptides. Score 0.748 Round 2: 889 peptides, 67 chains. Longest chain 57 peptides. Score 0.800 Round 3: 907 peptides, 75 chains. Longest chain 58 peptides. Score 0.789 Round 4: 907 peptides, 69 chains. Longest chain 58 peptides. Score 0.804 Round 5: 921 peptides, 68 chains. Longest chain 55 peptides. Score 0.813 Taking the results from Round 5 Chains 79, Residues 853, Estimated correctness of the model 85.3 % 16 chains (326 residues) have been docked in sequence Building loops using Loopy2018 79 chains (853 residues) following loop building 16 chains (326 residues) in sequence following loop building ------------------------------------------------------ 21953 reflections ( 99.76 % complete ) and 15514 restraints for refining 8676 atoms. 10885 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2572 (Rfree = 0.000) for 8676 atoms. Found 59 (62 requested) and removed 65 (38 requested) atoms. Cycle 12: After refmac, R = 0.2402 (Rfree = 0.000) for 8636 atoms. Found 24 (60 requested) and removed 45 (38 requested) atoms. Cycle 13: After refmac, R = 0.2326 (Rfree = 0.000) for 8584 atoms. Found 24 (59 requested) and removed 38 (38 requested) atoms. Cycle 14: After refmac, R = 0.2261 (Rfree = 0.000) for 8562 atoms. Found 26 (56 requested) and removed 39 (38 requested) atoms. Cycle 15: After refmac, R = 0.2176 (Rfree = 0.000) for 8540 atoms. Found 23 (55 requested) and removed 38 (38 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.18 3.18 Search for helices and strands: 0 residues in 0 chains, 8672 seeds are put forward NCS extension: 13 residues added (39 deleted due to clashes), 8685 seeds are put forward Round 1: 832 peptides, 74 chains. Longest chain 45 peptides. Score 0.749 Round 2: 872 peptides, 66 chains. Longest chain 55 peptides. Score 0.794 Round 3: 869 peptides, 72 chains. Longest chain 42 peptides. Score 0.777 Round 4: 893 peptides, 66 chains. Longest chain 57 peptides. Score 0.805 Round 5: 865 peptides, 70 chains. Longest chain 37 peptides. Score 0.780 Taking the results from Round 4 Chains 75, Residues 827, Estimated correctness of the model 84.2 % 18 chains (439 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 123 C and 131 C 74 chains (829 residues) following loop building 17 chains (446 residues) in sequence following loop building ------------------------------------------------------ 21953 reflections ( 99.76 % complete ) and 14379 restraints for refining 8675 atoms. 9477 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2573 (Rfree = 0.000) for 8675 atoms. Found 54 (54 requested) and removed 85 (38 requested) atoms. Cycle 17: After refmac, R = 0.2338 (Rfree = 0.000) for 8621 atoms. Found 38 (52 requested) and removed 44 (38 requested) atoms. Cycle 18: After refmac, R = 0.2280 (Rfree = 0.000) for 8605 atoms. Found 28 (51 requested) and removed 41 (38 requested) atoms. Cycle 19: After refmac, R = 0.2200 (Rfree = 0.000) for 8583 atoms. Found 17 (49 requested) and removed 39 (38 requested) atoms. Cycle 20: After refmac, R = 0.2387 (Rfree = 0.000) for 8550 atoms. Found 47 (47 requested) and removed 42 (38 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.12 3.12 Search for helices and strands: 0 residues in 0 chains, 8723 seeds are put forward NCS extension: 28 residues added (9 deleted due to clashes), 8751 seeds are put forward Round 1: 829 peptides, 77 chains. Longest chain 40 peptides. Score 0.738 Round 2: 884 peptides, 74 chains. Longest chain 47 peptides. Score 0.779 Round 3: 873 peptides, 79 chains. Longest chain 42 peptides. Score 0.759 Round 4: 861 peptides, 66 chains. Longest chain 47 peptides. Score 0.788 Round 5: 869 peptides, 75 chains. Longest chain 41 peptides. Score 0.768 Taking the results from Round 4 Chains 69, Residues 795, Estimated correctness of the model 81.6 % 13 chains (352 residues) have been docked in sequence Building loops using Loopy2018 69 chains (795 residues) following loop building 13 chains (352 residues) in sequence following loop building ------------------------------------------------------ 21953 reflections ( 99.76 % complete ) and 15471 restraints for refining 8676 atoms. 10995 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2501 (Rfree = 0.000) for 8676 atoms. Found 46 (46 requested) and removed 68 (38 requested) atoms. Cycle 22: After refmac, R = 0.2312 (Rfree = 0.000) for 8615 atoms. Found 24 (45 requested) and removed 43 (38 requested) atoms. Cycle 23: After refmac, R = 0.2230 (Rfree = 0.000) for 8569 atoms. Found 23 (43 requested) and removed 39 (38 requested) atoms. Cycle 24: After refmac, R = 0.2238 (Rfree = 0.000) for 8533 atoms. Found 21 (41 requested) and removed 38 (38 requested) atoms. Cycle 25: After refmac, R = 0.2191 (Rfree = 0.000) for 8505 atoms. Found 17 (40 requested) and removed 38 (38 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.17 3.17 Search for helices and strands: 0 residues in 0 chains, 8637 seeds are put forward NCS extension: 17 residues added (16 deleted due to clashes), 8654 seeds are put forward Round 1: 799 peptides, 81 chains. Longest chain 38 peptides. Score 0.705 Round 2: 835 peptides, 63 chains. Longest chain 42 peptides. Score 0.782 Round 3: 849 peptides, 74 chains. Longest chain 51 peptides. Score 0.759 Round 4: 857 peptides, 71 chains. Longest chain 44 peptides. Score 0.773 Round 5: 812 peptides, 71 chains. Longest chain 42 peptides. Score 0.746 Taking the results from Round 2 Chains 79, Residues 772, Estimated correctness of the model 80.6 % 17 chains (348 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 46 B and 50 B 77 chains (771 residues) following loop building 16 chains (351 residues) in sequence following loop building ------------------------------------------------------ 21953 reflections ( 99.76 % complete ) and 15514 restraints for refining 8676 atoms. 11141 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2546 (Rfree = 0.000) for 8676 atoms. Found 38 (38 requested) and removed 78 (38 requested) atoms. Cycle 27: After refmac, R = 0.2376 (Rfree = 0.000) for 8605 atoms. Found 32 (38 requested) and removed 43 (38 requested) atoms. Cycle 28: After refmac, R = 0.2273 (Rfree = 0.000) for 8578 atoms. Found 18 (38 requested) and removed 39 (38 requested) atoms. Cycle 29: After refmac, R = 0.2225 (Rfree = 0.000) for 8546 atoms. Found 17 (38 requested) and removed 38 (38 requested) atoms. Cycle 30: After refmac, R = 0.2224 (Rfree = 0.000) for 8516 atoms. Found 16 (38 requested) and removed 39 (38 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.18 3.18 Search for helices and strands: 0 residues in 0 chains, 8625 seeds are put forward NCS extension: 21 residues added (18 deleted due to clashes), 8646 seeds are put forward Round 1: 798 peptides, 85 chains. Longest chain 33 peptides. Score 0.691 Round 2: 836 peptides, 79 chains. Longest chain 41 peptides. Score 0.737 Round 3: 836 peptides, 74 chains. Longest chain 47 peptides. Score 0.752 Round 4: 817 peptides, 71 chains. Longest chain 56 peptides. Score 0.749 Round 5: 800 peptides, 79 chains. Longest chain 40 peptides. Score 0.712 Taking the results from Round 3 Chains 83, Residues 762, Estimated correctness of the model 75.4 % 12 chains (269 residues) have been docked in sequence Building loops using Loopy2018 83 chains (762 residues) following loop building 12 chains (269 residues) in sequence following loop building ------------------------------------------------------ 21953 reflections ( 99.76 % complete ) and 16378 restraints for refining 8675 atoms. 12343 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2486 (Rfree = 0.000) for 8675 atoms. Found 38 (38 requested) and removed 61 (38 requested) atoms. Cycle 32: After refmac, R = 0.2319 (Rfree = 0.000) for 8613 atoms. Found 24 (38 requested) and removed 44 (38 requested) atoms. Cycle 33: After refmac, R = 0.2269 (Rfree = 0.000) for 8576 atoms. Found 18 (38 requested) and removed 38 (38 requested) atoms. Cycle 34: After refmac, R = 0.2239 (Rfree = 0.000) for 8545 atoms. Found 15 (38 requested) and removed 39 (38 requested) atoms. Cycle 35: After refmac, R = 0.2209 (Rfree = 0.000) for 8505 atoms. Found 16 (38 requested) and removed 38 (38 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.17 3.17 Search for helices and strands: 0 residues in 0 chains, 8616 seeds are put forward NCS extension: 13 residues added (16 deleted due to clashes), 8629 seeds are put forward Round 1: 758 peptides, 81 chains. Longest chain 43 peptides. Score 0.675 Round 2: 817 peptides, 69 chains. Longest chain 48 peptides. Score 0.755 Round 3: 789 peptides, 72 chains. Longest chain 33 peptides. Score 0.728 Round 4: 790 peptides, 64 chains. Longest chain 62 peptides. Score 0.753 Round 5: 792 peptides, 73 chains. Longest chain 45 peptides. Score 0.727 Taking the results from Round 2 Chains 77, Residues 748, Estimated correctness of the model 76.0 % 13 chains (232 residues) have been docked in sequence Building loops using Loopy2018 77 chains (748 residues) following loop building 13 chains (232 residues) in sequence following loop building ------------------------------------------------------ 21953 reflections ( 99.76 % complete ) and 16713 restraints for refining 8675 atoms. 12899 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2817 (Rfree = 0.000) for 8675 atoms. Found 38 (38 requested) and removed 65 (38 requested) atoms. Cycle 37: After refmac, R = 0.2353 (Rfree = 0.000) for 8625 atoms. Found 21 (38 requested) and removed 44 (38 requested) atoms. Cycle 38: After refmac, R = 0.2287 (Rfree = 0.000) for 8594 atoms. Found 27 (38 requested) and removed 43 (38 requested) atoms. Cycle 39: After refmac, R = 0.2252 (Rfree = 0.000) for 8572 atoms. Found 25 (38 requested) and removed 38 (38 requested) atoms. Cycle 40: After refmac, R = 0.2420 (Rfree = 0.000) for 8550 atoms. Found 38 (38 requested) and removed 41 (38 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.18 3.18 Search for helices and strands: 0 residues in 0 chains, 8695 seeds are put forward NCS extension: 19 residues added (11 deleted due to clashes), 8714 seeds are put forward Round 1: 728 peptides, 81 chains. Longest chain 41 peptides. Score 0.650 Round 2: 789 peptides, 74 chains. Longest chain 41 peptides. Score 0.721 Round 3: 785 peptides, 69 chains. Longest chain 39 peptides. Score 0.735 Round 4: 789 peptides, 75 chains. Longest chain 48 peptides. Score 0.718 Round 5: 781 peptides, 75 chains. Longest chain 44 peptides. Score 0.712 Taking the results from Round 3 Chains 78, Residues 716, Estimated correctness of the model 72.3 % 12 chains (270 residues) have been docked in sequence Building loops using Loopy2018 78 chains (716 residues) following loop building 12 chains (270 residues) in sequence following loop building ------------------------------------------------------ 21953 reflections ( 99.76 % complete ) and 16517 restraints for refining 8676 atoms. 12685 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2453 (Rfree = 0.000) for 8676 atoms. Found 38 (38 requested) and removed 62 (38 requested) atoms. Cycle 42: After refmac, R = 0.2293 (Rfree = 0.000) for 8610 atoms. Found 36 (38 requested) and removed 42 (38 requested) atoms. Cycle 43: After refmac, R = 0.2272 (Rfree = 0.000) for 8587 atoms. Found 30 (38 requested) and removed 39 (38 requested) atoms. Cycle 44: After refmac, R = 0.2247 (Rfree = 0.000) for 8561 atoms. Found 26 (38 requested) and removed 38 (38 requested) atoms. Cycle 45: After refmac, R = 0.2203 (Rfree = 0.000) for 8535 atoms. Found 24 (38 requested) and removed 39 (38 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.19 3.19 Search for helices and strands: 0 residues in 0 chains, 8643 seeds are put forward NCS extension: 34 residues added (10 deleted due to clashes), 8677 seeds are put forward Round 1: 703 peptides, 81 chains. Longest chain 41 peptides. Score 0.629 Round 2: 754 peptides, 71 chains. Longest chain 57 peptides. Score 0.707 Round 3: 758 peptides, 79 chains. Longest chain 34 peptides. Score 0.682 Round 4: 777 peptides, 72 chains. Longest chain 41 peptides. Score 0.720 Round 5: 735 peptides, 73 chains. Longest chain 36 peptides. Score 0.686 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 80, Residues 705, Estimated correctness of the model 69.3 % 12 chains (225 residues) have been docked in sequence Sequence coverage is 31 % Consider running further cycles of model building using 2f4l-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 32 D and 46 D 78 chains (714 residues) following loop building 11 chains (238 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 21953 reflections ( 99.76 % complete ) and 16692 restraints for refining 8676 atoms. 13036 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2419 (Rfree = 0.000) for 8676 atoms. Found 0 (38 requested) and removed 38 (38 requested) atoms. Cycle 47: After refmac, R = 0.2280 (Rfree = 0.000) for 8614 atoms. Found 0 (38 requested) and removed 31 (38 requested) atoms. Cycle 48: After refmac, R = 0.2249 (Rfree = 0.000) for 8569 atoms. Found 0 (38 requested) and removed 7 (38 requested) atoms. Cycle 49: After refmac, R = 0.2238 (Rfree = 0.000) for 8561 atoms. Found 0 (38 requested) and removed 5 (38 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 21:43:57 GMT 2018 Job finished. TimeTaking 136.03 Used memory is bytes: 20649672