Mon 24 Dec 00:38:15 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2f4l-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2f4l-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2f4l-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2f4l-3.2-parrot-mrncs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2f4l-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2f4l-3.2-parrot-mrncs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Mon 24 Dec 00:38:24 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2f4l-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2f4l-3.2-parrot-mrncs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 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-mrncs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 19 Cell parameters: 80.030 103.980 155.130 90.000 90.000 90.000 Input sequence file: 2f4l-3.2-parrot-mrncs.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 10616 atoms. Observations/parameters ratio is 0.52 ------------------------------------------------------ Starting model: R = 0.2926 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2513 (Rfree = 0.000) for 10616 atoms. Found 57 (95 requested) and removed 119 (47 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.13 3.13 Search for helices and strands: 0 residues in 0 chains, 10693 seeds are put forward NCS extension: 0 residues added, 10693 seeds are put forward Round 1: 723 peptides, 100 chains. Longest chain 22 peptides. Score 0.569 Round 2: 819 peptides, 85 chains. Longest chain 31 peptides. Score 0.706 Round 3: 854 peptides, 81 chains. Longest chain 47 peptides. Score 0.742 Round 4: 905 peptides, 69 chains. Longest chain 51 peptides. Score 0.803 Round 5: 937 peptides, 65 chains. Longest chain 51 peptides. Score 0.827 Taking the results from Round 5 Chains 70, Residues 872, Estimated correctness of the model 87.3 % 21 chains (501 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 155 B and 162 B 69 chains (875 residues) following loop building 20 chains (507 residues) in sequence following loop building ------------------------------------------------------ 21953 reflections ( 99.76 % complete ) and 13138 restraints for refining 8673 atoms. 7914 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2766 (Rfree = 0.000) for 8673 atoms. Found 77 (77 requested) and removed 119 (38 requested) atoms. Cycle 2: After refmac, R = 0.2583 (Rfree = 0.000) for 8550 atoms. Found 50 (75 requested) and removed 63 (38 requested) atoms. Cycle 3: After refmac, R = 0.2531 (Rfree = 0.000) for 8491 atoms. Found 37 (73 requested) and removed 56 (38 requested) atoms. Cycle 4: After refmac, R = 0.2443 (Rfree = 0.000) for 8449 atoms. Found 22 (71 requested) and removed 44 (38 requested) atoms. Cycle 5: After refmac, R = 0.2368 (Rfree = 0.000) for 8402 atoms. Found 30 (69 requested) and removed 46 (37 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.15 3.15 Search for helices and strands: 0 residues in 0 chains, 8585 seeds are put forward NCS extension: 17 residues added (19 deleted due to clashes), 8602 seeds are put forward Round 1: 835 peptides, 81 chains. Longest chain 36 peptides. Score 0.730 Round 2: 864 peptides, 68 chains. Longest chain 47 peptides. Score 0.785 Round 3: 862 peptides, 74 chains. Longest chain 35 peptides. Score 0.767 Round 4: 868 peptides, 73 chains. Longest chain 37 peptides. Score 0.773 Round 5: 902 peptides, 67 chains. Longest chain 38 peptides. Score 0.806 Taking the results from Round 5 Chains 75, Residues 835, Estimated correctness of the model 84.3 % 17 chains (386 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 91 C and 95 C Built loop between residues 49 B and 58 B 71 chains (843 residues) following loop building 15 chains (397 residues) in sequence following loop building ------------------------------------------------------ 21953 reflections ( 99.76 % complete ) and 14883 restraints for refining 8676 atoms. 10093 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2678 (Rfree = 0.000) for 8676 atoms. Found 46 (69 requested) and removed 86 (38 requested) atoms. Cycle 7: After refmac, R = 0.2497 (Rfree = 0.000) for 8587 atoms. Found 24 (68 requested) and removed 55 (38 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.2400 (Rfree = 0.000) for 8532 atoms. Found 19 (65 requested) and removed 46 (38 requested) atoms. Cycle 9: After refmac, R = 0.2345 (Rfree = 0.000) for 8493 atoms. Found 9 (64 requested) and removed 39 (38 requested) atoms. Cycle 10: After refmac, R = 0.2314 (Rfree = 0.000) for 8450 atoms. Found 12 (61 requested) and removed 39 (37 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.17 3.17 Search for helices and strands: 0 residues in 0 chains, 8566 seeds are put forward NCS extension: 52 residues added (4 deleted due to clashes), 8618 seeds are put forward Round 1: 824 peptides, 84 chains. Longest chain 35 peptides. Score 0.713 Round 2: 872 peptides, 68 chains. Longest chain 40 peptides. Score 0.789 Round 3: 875 peptides, 74 chains. Longest chain 49 peptides. Score 0.774 Round 4: 882 peptides, 64 chains. Longest chain 40 peptides. Score 0.804 Round 5: 871 peptides, 67 chains. Longest chain 51 peptides. Score 0.791 Taking the results from Round 4 Chains 74, Residues 818, Estimated correctness of the model 84.0 % 21 chains (424 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 277 C and 281 C 73 chains (814 residues) following loop building 20 chains (427 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 21953 reflections ( 99.76 % complete ) and 14711 restraints for refining 8676 atoms. 9973 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2631 (Rfree = 0.000) for 8676 atoms. Found 62 (62 requested) and removed 78 (38 requested) atoms. Cycle 12: After refmac, R = 0.2439 (Rfree = 0.000) for 8623 atoms. Found 23 (60 requested) and removed 43 (38 requested) atoms. Cycle 13: After refmac, R = 0.2341 (Rfree = 0.000) for 8574 atoms. Found 14 (59 requested) and removed 41 (38 requested) atoms. Cycle 14: After refmac, R = 0.2295 (Rfree = 0.000) for 8533 atoms. Found 14 (56 requested) and removed 40 (38 requested) atoms. Cycle 15: After refmac, R = 0.2309 (Rfree = 0.000) for 8502 atoms. Found 19 (55 requested) and removed 39 (38 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.16 3.16 Search for helices and strands: 0 residues in 0 chains, 8653 seeds are put forward NCS extension: 15 residues added (8 deleted due to clashes), 8668 seeds are put forward Round 1: 812 peptides, 76 chains. Longest chain 45 peptides. Score 0.730 Round 2: 852 peptides, 74 chains. Longest chain 41 peptides. Score 0.761 Round 3: 858 peptides, 68 chains. Longest chain 42 peptides. Score 0.781 Round 4: 864 peptides, 76 chains. Longest chain 49 peptides. Score 0.763 Round 5: 862 peptides, 73 chains. Longest chain 51 peptides. Score 0.770 Taking the results from Round 3 Chains 74, Residues 790, Estimated correctness of the model 80.4 % 13 chains (279 residues) have been docked in sequence Building loops using Loopy2018 74 chains (790 residues) following loop building 13 chains (279 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 21953 reflections ( 99.76 % complete ) and 16267 restraints for refining 8676 atoms. 12127 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2416 (Rfree = 0.000) for 8676 atoms. Found 40 (54 requested) and removed 61 (38 requested) atoms. Cycle 17: After refmac, R = 0.2301 (Rfree = 0.000) for 8627 atoms. Found 22 (52 requested) and removed 47 (38 requested) atoms. Cycle 18: After refmac, R = 0.2243 (Rfree = 0.000) for 8572 atoms. Found 29 (51 requested) and removed 39 (38 requested) atoms. Cycle 19: After refmac, R = 0.2515 (Rfree = 0.000) for 8542 atoms. Found 49 (49 requested) and removed 42 (38 requested) atoms. Cycle 20: After refmac, R = 0.2127 (Rfree = 0.000) for 8526 atoms. Found 23 (47 requested) and removed 44 (38 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.18 3.18 Search for helices and strands: 0 residues in 0 chains, 8681 seeds are put forward NCS extension: 27 residues added (24 deleted due to clashes), 8708 seeds are put forward Round 1: 799 peptides, 77 chains. Longest chain 37 peptides. Score 0.718 Round 2: 843 peptides, 68 chains. Longest chain 48 peptides. Score 0.773 Round 3: 845 peptides, 70 chains. Longest chain 46 peptides. Score 0.769 Round 4: 860 peptides, 74 chains. Longest chain 41 peptides. Score 0.766 Round 5: 856 peptides, 68 chains. Longest chain 41 peptides. Score 0.780 Taking the results from Round 5 Chains 82, Residues 788, Estimated correctness of the model 80.3 % 15 chains (302 residues) have been docked in sequence Building loops using Loopy2018 82 chains (788 residues) following loop building 15 chains (302 residues) in sequence following loop building ------------------------------------------------------ 21953 reflections ( 99.76 % complete ) and 15796 restraints for refining 8676 atoms. 11618 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2472 (Rfree = 0.000) for 8676 atoms. Found 46 (46 requested) and removed 63 (38 requested) atoms. Cycle 22: After refmac, R = 0.2297 (Rfree = 0.000) for 8609 atoms. Found 40 (45 requested) and removed 42 (38 requested) atoms. Cycle 23: After refmac, R = 0.2241 (Rfree = 0.000) for 8581 atoms. Found 27 (43 requested) and removed 44 (38 requested) atoms. Cycle 24: After refmac, R = 0.2589 (Rfree = 0.000) for 8553 atoms. Found 41 (41 requested) and removed 45 (38 requested) atoms. Cycle 25: After refmac, R = 0.2340 (Rfree = 0.000) for 8535 atoms. Found 40 (40 requested) and removed 41 (38 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.18 3.18 Search for helices and strands: 0 residues in 0 chains, 8698 seeds are put forward NCS extension: 28 residues added (19 deleted due to clashes), 8726 seeds are put forward Round 1: 730 peptides, 82 chains. Longest chain 34 peptides. Score 0.648 Round 2: 814 peptides, 70 chains. Longest chain 51 peptides. Score 0.750 Round 3: 812 peptides, 70 chains. Longest chain 49 peptides. Score 0.749 Round 4: 813 peptides, 73 chains. Longest chain 40 peptides. Score 0.740 Round 5: 804 peptides, 78 chains. Longest chain 36 peptides. Score 0.718 Taking the results from Round 2 Chains 83, Residues 744, Estimated correctness of the model 75.1 % 12 chains (272 residues) have been docked in sequence Building loops using Loopy2018 83 chains (744 residues) following loop building 12 chains (272 residues) in sequence following loop building ------------------------------------------------------ 21953 reflections ( 99.76 % complete ) and 16366 restraints for refining 8674 atoms. 12420 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2409 (Rfree = 0.000) for 8674 atoms. Found 38 (38 requested) and removed 64 (38 requested) atoms. Cycle 27: After refmac, R = 0.2308 (Rfree = 0.000) for 8628 atoms. Found 27 (38 requested) and removed 41 (38 requested) atoms. Cycle 28: After refmac, R = 0.2536 (Rfree = 0.000) for 8601 atoms. Found 38 (38 requested) and removed 46 (38 requested) atoms. Cycle 29: After refmac, R = 0.2251 (Rfree = 0.000) for 8577 atoms. Found 25 (38 requested) and removed 40 (38 requested) atoms. Cycle 30: After refmac, R = 0.2537 (Rfree = 0.000) for 8546 atoms. Found 38 (38 requested) and removed 49 (38 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.15 3.15 Search for helices and strands: 0 residues in 0 chains, 8682 seeds are put forward NCS extension: 21 residues added (15 deleted due to clashes), 8703 seeds are put forward Round 1: 755 peptides, 82 chains. Longest chain 30 peptides. Score 0.668 Round 2: 792 peptides, 72 chains. Longest chain 43 peptides. Score 0.730 Round 3: 807 peptides, 73 chains. Longest chain 37 peptides. Score 0.736 Round 4: 800 peptides, 70 chains. Longest chain 36 peptides. Score 0.741 Round 5: 794 peptides, 67 chains. Longest chain 42 peptides. Score 0.747 Taking the results from Round 5 Chains 73, Residues 727, Estimated correctness of the model 74.5 % 11 chains (229 residues) have been docked in sequence Building loops using Loopy2018 73 chains (727 residues) following loop building 11 chains (229 residues) in sequence following loop building ------------------------------------------------------ 21953 reflections ( 99.76 % complete ) and 16870 restraints for refining 8676 atoms. 13152 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2525 (Rfree = 0.000) for 8676 atoms. Found 38 (38 requested) and removed 52 (38 requested) atoms. Cycle 32: After refmac, R = 0.2378 (Rfree = 0.000) for 8625 atoms. Found 23 (38 requested) and removed 42 (38 requested) atoms. Cycle 33: After refmac, R = 0.2337 (Rfree = 0.000) for 8594 atoms. Found 32 (38 requested) and removed 43 (38 requested) atoms. Cycle 34: After refmac, R = 0.2283 (Rfree = 0.000) for 8576 atoms. Found 14 (38 requested) and removed 40 (38 requested) atoms. Cycle 35: After refmac, R = 0.2508 (Rfree = 0.000) for 8536 atoms. Found 38 (38 requested) and removed 45 (38 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.16 3.16 Search for helices and strands: 0 residues in 0 chains, 8696 seeds are put forward NCS extension: 31 residues added (4 deleted due to clashes), 8727 seeds are put forward Round 1: 725 peptides, 82 chains. Longest chain 29 peptides. Score 0.644 Round 2: 799 peptides, 75 chains. Longest chain 30 peptides. Score 0.725 Round 3: 800 peptides, 73 chains. Longest chain 34 peptides. Score 0.732 Round 4: 782 peptides, 74 chains. Longest chain 34 peptides. Score 0.716 Round 5: 802 peptides, 75 chains. Longest chain 50 peptides. Score 0.727 Taking the results from Round 3 Chains 78, Residues 727, Estimated correctness of the model 71.7 % 11 chains (194 residues) have been docked in sequence Building loops using Loopy2018 78 chains (727 residues) following loop building 11 chains (194 residues) in sequence following loop building ------------------------------------------------------ 21953 reflections ( 99.76 % complete ) and 17162 restraints for refining 8674 atoms. 13561 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2507 (Rfree = 0.000) for 8674 atoms. Found 37 (38 requested) and removed 51 (38 requested) atoms. Cycle 37: After refmac, R = 0.2689 (Rfree = 0.000) for 8626 atoms. Found 38 (38 requested) and removed 52 (38 requested) atoms. Cycle 38: After refmac, R = 0.2329 (Rfree = 0.000) for 8586 atoms. Found 31 (38 requested) and removed 46 (38 requested) atoms. Cycle 39: After refmac, R = 0.2278 (Rfree = 0.000) for 8546 atoms. Found 27 (38 requested) and removed 45 (38 requested) atoms. Cycle 40: After refmac, R = 0.2285 (Rfree = 0.000) for 8513 atoms. Found 34 (38 requested) and removed 41 (38 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.17 3.17 Search for helices and strands: 0 residues in 0 chains, 8640 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 8658 seeds are put forward Round 1: 703 peptides, 84 chains. Longest chain 28 peptides. Score 0.617 Round 2: 761 peptides, 73 chains. Longest chain 34 peptides. Score 0.705 Round 3: 753 peptides, 74 chains. Longest chain 46 peptides. Score 0.696 Round 4: 780 peptides, 75 chains. Longest chain 37 peptides. Score 0.712 Round 5: 782 peptides, 81 chains. Longest chain 33 peptides. Score 0.693 Taking the results from Round 4 Chains 82, Residues 705, Estimated correctness of the model 67.7 % 8 chains (133 residues) have been docked in sequence Building loops using Loopy2018 82 chains (705 residues) following loop building 8 chains (133 residues) in sequence following loop building ------------------------------------------------------ 21953 reflections ( 99.76 % complete ) and 17688 restraints for refining 8676 atoms. 14433 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2450 (Rfree = 0.000) for 8676 atoms. Found 38 (38 requested) and removed 56 (38 requested) atoms. Failed to save intermediate PDB Cycle 42: After refmac, R = 0.2342 (Rfree = 0.000) for 8643 atoms. Found 27 (38 requested) and removed 42 (38 requested) atoms. Cycle 43: After refmac, R = 0.2595 (Rfree = 0.000) for 8619 atoms. Found 38 (38 requested) and removed 45 (38 requested) atoms. Failed to save intermediate PDB Cycle 44: After refmac, R = 0.2286 (Rfree = 0.000) for 8603 atoms. Found 27 (38 requested) and removed 42 (38 requested) atoms. Cycle 45: After refmac, R = 0.2241 (Rfree = 0.000) for 8570 atoms. Found 27 (38 requested) and removed 39 (38 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.17 3.17 Search for helices and strands: 0 residues in 0 chains, 8691 seeds are put forward NCS extension: 23 residues added (14 deleted due to clashes), 8714 seeds are put forward Round 1: 709 peptides, 89 chains. Longest chain 29 peptides. Score 0.602 Round 2: 755 peptides, 78 chains. Longest chain 32 peptides. Score 0.683 Round 3: 767 peptides, 79 chains. Longest chain 33 peptides. Score 0.689 Round 4: 770 peptides, 86 chains. Longest chain 31 peptides. Score 0.666 Round 5: 803 peptides, 79 chains. Longest chain 43 peptides. Score 0.714 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 90, Residues 724, Estimated correctness of the model 68.1 % 11 chains (214 residues) have been docked in sequence Sequence coverage is 29 % Consider running further cycles of model building using 2f4l-3_warpNtrace.pdb as input Building loops using Loopy2018 90 chains (724 residues) following loop building 11 chains (214 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 21953 reflections ( 99.76 % complete ) and 16745 restraints for refining 8674 atoms. 13091 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2515 (Rfree = 0.000) for 8674 atoms. Found 0 (38 requested) and removed 38 (38 requested) atoms. Cycle 47: After refmac, R = 0.2448 (Rfree = 0.000) for 8610 atoms. Found 0 (38 requested) and removed 38 (38 requested) atoms. Cycle 48: After refmac, R = 0.2436 (Rfree = 0.000) for 8558 atoms. Found 0 (38 requested) and removed 32 (38 requested) atoms. Cycle 49: After refmac, R = 0.2352 (Rfree = 0.000) for 8518 atoms. Found 0 (38 requested) and removed 38 (38 requested) atoms. Writing output files ... TimeTaking 122.47