Mon 24 Dec 00:27:42 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 2p1a-2.1-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2p1a-2.1-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2p1a-2.1-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p1a-2.1-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/2p1a-2.1-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p1a-2.1-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 00:27:47 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/2p1a-2.1-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p1a-2.1-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 276 and 0 Target number of residues in the AU: 276 Target solvent content: 0.5134 Checking the provided sequence file Detected sequence length: 154 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 308 Adjusted target solvent content: 0.46 Input MTZ file: 2p1a-2.1-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: 45.470 77.850 86.720 90.000 90.000 90.000 Input sequence file: 2p1a-2.1-parrot-mrncs.fasta_lf Building free atoms model in initial map for 2464 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: 29.570 2.100 Wilson plot Bfac: 26.15 18405 reflections ( 98.93 % complete ) and 0 restraints for refining 2763 atoms. Observations/parameters ratio is 1.67 ------------------------------------------------------ Starting model: R = 0.3401 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2906 (Rfree = 0.000) for 2763 atoms. Found 60 (82 requested) and removed 51 (41 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.28 2.41 NCS extension: 0 residues added, 2772 seeds are put forward Round 1: 180 peptides, 31 chains. Longest chain 17 peptides. Score 0.467 Round 2: 208 peptides, 23 chains. Longest chain 24 peptides. Score 0.706 Round 3: 220 peptides, 22 chains. Longest chain 24 peptides. Score 0.752 Round 4: 235 peptides, 19 chains. Longest chain 44 peptides. Score 0.816 Round 5: 241 peptides, 17 chains. Longest chain 40 peptides. Score 0.844 Taking the results from Round 5 Chains 17, Residues 224, Estimated correctness of the model 97.2 % 4 chains (128 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 98 A and 108 A 15 chains (230 residues) following loop building 3 chains (137 residues) in sequence following loop building ------------------------------------------------------ 18405 reflections ( 98.93 % complete ) and 3331 restraints for refining 2370 atoms. 1808 conditional restraints added. Observations/parameters ratio is 1.94 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3263 (Rfree = 0.000) for 2370 atoms. Found 49 (70 requested) and removed 45 (35 requested) atoms. Cycle 2: After refmac, R = 0.3043 (Rfree = 0.000) for 2364 atoms. Found 35 (69 requested) and removed 36 (35 requested) atoms. Cycle 3: After refmac, R = 0.2922 (Rfree = 0.000) for 2356 atoms. Found 23 (67 requested) and removed 35 (35 requested) atoms. Cycle 4: After refmac, R = 0.2810 (Rfree = 0.000) for 2339 atoms. Found 24 (65 requested) and removed 19 (34 requested) atoms. Cycle 5: After refmac, R = 0.2724 (Rfree = 0.000) for 2342 atoms. Found 18 (63 requested) and removed 18 (34 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.26 2.38 NCS extension: 38 residues added (63 deleted due to clashes), 2386 seeds are put forward Round 1: 236 peptides, 12 chains. Longest chain 66 peptides. Score 0.876 Round 2: 239 peptides, 10 chains. Longest chain 80 peptides. Score 0.894 Round 3: 238 peptides, 11 chains. Longest chain 71 peptides. Score 0.886 Round 4: 239 peptides, 11 chains. Longest chain 51 peptides. Score 0.887 Round 5: 226 peptides, 12 chains. Longest chain 51 peptides. Score 0.862 Taking the results from Round 2 Chains 10, Residues 229, Estimated correctness of the model 98.6 % 5 chains (187 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 86 A and 90 A Built loop between residues 31 B and 40 B Built loop between residues 57 B and 60 B 7 chains (242 residues) following loop building 2 chains (200 residues) in sequence following loop building ------------------------------------------------------ 18405 reflections ( 98.93 % complete ) and 2966 restraints for refining 2455 atoms. 1085 conditional restraints added. Observations/parameters ratio is 1.87 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2961 (Rfree = 0.000) for 2455 atoms. Found 44 (66 requested) and removed 39 (36 requested) atoms. Cycle 7: After refmac, R = 0.2758 (Rfree = 0.000) for 2456 atoms. Found 37 (64 requested) and removed 36 (36 requested) atoms. Cycle 8: After refmac, R = 0.2673 (Rfree = 0.000) for 2455 atoms. Found 29 (63 requested) and removed 19 (36 requested) atoms. Cycle 9: After refmac, R = 0.2615 (Rfree = 0.000) for 2463 atoms. Found 21 (61 requested) and removed 12 (36 requested) atoms. Cycle 10: After refmac, R = 0.2563 (Rfree = 0.000) for 2469 atoms. Found 19 (60 requested) and removed 8 (36 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.28 2.41 NCS extension: 25 residues added (25 deleted due to clashes), 2507 seeds are put forward Round 1: 240 peptides, 12 chains. Longest chain 51 peptides. Score 0.882 Round 2: 250 peptides, 11 chains. Longest chain 76 peptides. Score 0.900 Round 3: 249 peptides, 11 chains. Longest chain 83 peptides. Score 0.899 Round 4: 249 peptides, 7 chains. Longest chain 105 peptides. Score 0.923 Round 5: 240 peptides, 13 chains. Longest chain 49 peptides. Score 0.874 Taking the results from Round 4 Chains 7, Residues 242, Estimated correctness of the model 99.2 % 6 chains (237 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 79 A and 82 A Built loop between residues 100 A and 103 A Built loop between residues 33 B and 37 B 4 chains (249 residues) following loop building 3 chains (244 residues) in sequence following loop building ------------------------------------------------------ 18405 reflections ( 98.93 % complete ) and 2691 restraints for refining 2523 atoms. 620 conditional restraints added. Observations/parameters ratio is 1.82 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2773 (Rfree = 0.000) for 2523 atoms. Found 47 (61 requested) and removed 38 (37 requested) atoms. Cycle 12: After refmac, R = 0.2600 (Rfree = 0.000) for 2528 atoms. Found 40 (60 requested) and removed 37 (37 requested) atoms. Cycle 13: After refmac, R = 0.2480 (Rfree = 0.000) for 2527 atoms. Found 32 (58 requested) and removed 20 (37 requested) atoms. Cycle 14: After refmac, R = 0.2402 (Rfree = 0.000) for 2537 atoms. Found 28 (57 requested) and removed 13 (37 requested) atoms. Cycle 15: After refmac, R = 0.2351 (Rfree = 0.000) for 2545 atoms. Found 26 (58 requested) and removed 15 (38 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.26 2.38 NCS extension: 26 residues added (21 deleted due to clashes), 2583 seeds are put forward Round 1: 247 peptides, 11 chains. Longest chain 93 peptides. Score 0.897 Round 2: 246 peptides, 7 chains. Longest chain 101 peptides. Score 0.921 Round 3: 247 peptides, 7 chains. Longest chain 64 peptides. Score 0.922 Round 4: 244 peptides, 11 chains. Longest chain 47 peptides. Score 0.893 Round 5: 249 peptides, 9 chains. Longest chain 58 peptides. Score 0.911 Taking the results from Round 3 Chains 8, Residues 240, Estimated correctness of the model 99.2 % 7 chains (239 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 89 A and 95 A Built loop between residues 32 B and 39 B Built loop between residues 101 B and 104 B Built loop between residues 122 B and 125 B 3 chains (254 residues) following loop building 3 chains (254 residues) in sequence following loop building ------------------------------------------------------ 18405 reflections ( 98.93 % complete ) and 2637 restraints for refining 2566 atoms. 489 conditional restraints added. Observations/parameters ratio is 1.79 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2634 (Rfree = 0.000) for 2566 atoms. Found 52 (56 requested) and removed 43 (38 requested) atoms. Cycle 17: After refmac, R = 0.2467 (Rfree = 0.000) for 2575 atoms. Found 37 (55 requested) and removed 38 (38 requested) atoms. Cycle 18: After refmac, R = 0.2382 (Rfree = 0.000) for 2572 atoms. Found 47 (53 requested) and removed 28 (38 requested) atoms. Cycle 19: After refmac, R = 0.2306 (Rfree = 0.000) for 2590 atoms. Found 33 (52 requested) and removed 24 (38 requested) atoms. Cycle 20: After refmac, R = 0.2264 (Rfree = 0.000) for 2597 atoms. Found 34 (51 requested) and removed 27 (38 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.25 2.37 NCS extension: 21 residues added (18 deleted due to clashes), 2627 seeds are put forward Round 1: 245 peptides, 8 chains. Longest chain 99 peptides. Score 0.914 Round 2: 251 peptides, 8 chains. Longest chain 54 peptides. Score 0.919 Round 3: 250 peptides, 8 chains. Longest chain 103 peptides. Score 0.918 Round 4: 244 peptides, 10 chains. Longest chain 49 peptides. Score 0.900 Round 5: 250 peptides, 10 chains. Longest chain 89 peptides. Score 0.906 Taking the results from Round 2 Chains 10, Residues 243, Estimated correctness of the model 99.2 % 8 chains (239 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 79 A and 82 A Built loop between residues 100 A and 103 A Built loop between residues 32 B and 40 B Built loop between residues 66 B and 70 B Built loop between residues 122 B and 125 B 4 chains (258 residues) following loop building 3 chains (255 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 18405 reflections ( 98.93 % complete ) and 2557 restraints for refining 2555 atoms. 390 conditional restraints added. Observations/parameters ratio is 1.80 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2554 (Rfree = 0.000) for 2555 atoms. Found 49 (49 requested) and removed 39 (38 requested) atoms. Cycle 22: After refmac, R = 0.2416 (Rfree = 0.000) for 2562 atoms. Found 37 (47 requested) and removed 38 (38 requested) atoms. Cycle 23: After refmac, R = 0.2348 (Rfree = 0.000) for 2560 atoms. Found 30 (46 requested) and removed 34 (38 requested) atoms. Cycle 24: After refmac, R = 0.2310 (Rfree = 0.000) for 2554 atoms. Found 32 (44 requested) and removed 14 (38 requested) atoms. Cycle 25: After refmac, R = 0.2281 (Rfree = 0.000) for 2570 atoms. Found 32 (44 requested) and removed 12 (38 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.24 2.36 NCS extension: 20 residues added (18 deleted due to clashes), 2612 seeds are put forward Round 1: 249 peptides, 8 chains. Longest chain 61 peptides. Score 0.917 Round 2: 254 peptides, 7 chains. Longest chain 85 peptides. Score 0.927 Round 3: 249 peptides, 9 chains. Longest chain 103 peptides. Score 0.911 Round 4: 244 peptides, 9 chains. Longest chain 79 peptides. Score 0.906 Round 5: 244 peptides, 14 chains. Longest chain 51 peptides. Score 0.872 Taking the results from Round 2 Chains 9, Residues 247, Estimated correctness of the model 99.3 % 7 chains (244 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 93 A and 96 A Built loop between residues 122 A and 125 A Built loop between residues 32 B and 39 B Built loop between residues 122 B and 125 B 4 chains (258 residues) following loop building 3 chains (256 residues) in sequence following loop building ------------------------------------------------------ 18405 reflections ( 98.93 % complete ) and 2559 restraints for refining 2561 atoms. 391 conditional restraints added. Observations/parameters ratio is 1.80 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2550 (Rfree = 0.000) for 2561 atoms. Found 44 (44 requested) and removed 40 (38 requested) atoms. Cycle 27: After refmac, R = 0.2410 (Rfree = 0.000) for 2564 atoms. Found 37 (43 requested) and removed 36 (38 requested) atoms. Cycle 28: After refmac, R = 0.2348 (Rfree = 0.000) for 2561 atoms. Found 29 (41 requested) and removed 28 (38 requested) atoms. Cycle 29: After refmac, R = 0.2314 (Rfree = 0.000) for 2560 atoms. Found 40 (40 requested) and removed 15 (38 requested) atoms. Cycle 30: After refmac, R = 0.2288 (Rfree = 0.000) for 2582 atoms. Found 32 (40 requested) and removed 25 (38 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.25 2.37 NCS extension: 21 residues added (15 deleted due to clashes), 2610 seeds are put forward Round 1: 250 peptides, 7 chains. Longest chain 84 peptides. Score 0.924 Round 2: 248 peptides, 8 chains. Longest chain 103 peptides. Score 0.917 Round 3: 243 peptides, 10 chains. Longest chain 73 peptides. Score 0.899 Round 4: 245 peptides, 10 chains. Longest chain 79 peptides. Score 0.901 Round 5: 247 peptides, 11 chains. Longest chain 64 peptides. Score 0.897 Taking the results from Round 1 Chains 7, Residues 243, Estimated correctness of the model 99.3 % 6 chains (235 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 93 A and 96 A Built loop between residues 32 B and 40 B Built loop between residues 122 B and 125 B 4 chains (254 residues) following loop building 3 chains (246 residues) in sequence following loop building ------------------------------------------------------ 18405 reflections ( 98.93 % complete ) and 2692 restraints for refining 2559 atoms. 591 conditional restraints added. Observations/parameters ratio is 1.80 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2477 (Rfree = 0.000) for 2559 atoms. Found 38 (38 requested) and removed 38 (38 requested) atoms. Cycle 32: After refmac, R = 0.2352 (Rfree = 0.000) for 2555 atoms. Found 38 (38 requested) and removed 25 (38 requested) atoms. Cycle 33: After refmac, R = 0.2285 (Rfree = 0.000) for 2566 atoms. Found 32 (38 requested) and removed 24 (38 requested) atoms. Cycle 34: After refmac, R = 0.2252 (Rfree = 0.000) for 2572 atoms. Found 32 (38 requested) and removed 11 (38 requested) atoms. Cycle 35: After refmac, R = 0.2211 (Rfree = 0.000) for 2591 atoms. Found 28 (38 requested) and removed 21 (38 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.23 2.35 NCS extension: 27 residues added (24 deleted due to clashes), 2625 seeds are put forward Round 1: 248 peptides, 9 chains. Longest chain 102 peptides. Score 0.910 Round 2: 250 peptides, 6 chains. Longest chain 102 peptides. Score 0.930 Round 3: 241 peptides, 12 chains. Longest chain 63 peptides. Score 0.883 Round 4: 244 peptides, 11 chains. Longest chain 55 peptides. Score 0.893 Round 5: 245 peptides, 11 chains. Longest chain 74 peptides. Score 0.894 Taking the results from Round 2 Chains 6, Residues 244, Estimated correctness of the model 99.4 % 6 chains (244 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 78 A and 82 A Built loop between residues 100 A and 103 A Built loop between residues 32 B and 40 B 3 chains (256 residues) following loop building 3 chains (256 residues) in sequence following loop building ------------------------------------------------------ 18405 reflections ( 98.93 % complete ) and 2579 restraints for refining 2569 atoms. 419 conditional restraints added. Observations/parameters ratio is 1.79 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2487 (Rfree = 0.000) for 2569 atoms. Found 38 (38 requested) and removed 42 (38 requested) atoms. Cycle 37: After refmac, R = 0.2334 (Rfree = 0.000) for 2559 atoms. Found 38 (38 requested) and removed 36 (38 requested) atoms. Cycle 38: After refmac, R = 0.2299 (Rfree = 0.000) for 2558 atoms. Found 38 (38 requested) and removed 24 (38 requested) atoms. Cycle 39: After refmac, R = 0.2263 (Rfree = 0.000) for 2572 atoms. Found 38 (38 requested) and removed 29 (38 requested) atoms. Cycle 40: After refmac, R = 0.2235 (Rfree = 0.000) for 2581 atoms. Found 38 (38 requested) and removed 30 (38 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.25 2.37 NCS extension: 22 residues added (18 deleted due to clashes), 2611 seeds are put forward Round 1: 247 peptides, 8 chains. Longest chain 102 peptides. Score 0.916 Round 2: 250 peptides, 8 chains. Longest chain 61 peptides. Score 0.918 Round 3: 245 peptides, 10 chains. Longest chain 66 peptides. Score 0.901 Round 4: 243 peptides, 10 chains. Longest chain 42 peptides. Score 0.899 Round 5: 240 peptides, 12 chains. Longest chain 39 peptides. Score 0.882 Taking the results from Round 2 Chains 8, Residues 242, Estimated correctness of the model 99.1 % 8 chains (242 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 101 A and 104 A Built loop between residues 118 A and 124 A Built loop between residues 32 B and 37 B Built loop between residues 79 B and 82 B Built loop between residues 100 B and 103 B 3 chains (257 residues) following loop building 3 chains (257 residues) in sequence following loop building ------------------------------------------------------ 18405 reflections ( 98.93 % complete ) and 2569 restraints for refining 2593 atoms. 397 conditional restraints added. Observations/parameters ratio is 1.77 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2479 (Rfree = 0.000) for 2593 atoms. Found 38 (38 requested) and removed 46 (38 requested) atoms. Cycle 42: After refmac, R = 0.2354 (Rfree = 0.000) for 2584 atoms. Found 38 (38 requested) and removed 38 (38 requested) atoms. Cycle 43: After refmac, R = 0.2273 (Rfree = 0.000) for 2583 atoms. Found 38 (38 requested) and removed 26 (38 requested) atoms. Cycle 44: After refmac, R = 0.2243 (Rfree = 0.000) for 2594 atoms. Found 38 (38 requested) and removed 29 (38 requested) atoms. Failed to save intermediate PDB Cycle 45: After refmac, R = 0.2221 (Rfree = 0.000) for 2602 atoms. Found 38 (38 requested) and removed 30 (38 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.25 2.37 NCS extension: 22 residues added (17 deleted due to clashes), 2632 seeds are put forward Round 1: 246 peptides, 9 chains. Longest chain 59 peptides. Score 0.908 Round 2: 248 peptides, 8 chains. Longest chain 104 peptides. Score 0.917 Round 3: 246 peptides, 11 chains. Longest chain 59 peptides. Score 0.896 Round 4: 247 peptides, 10 chains. Longest chain 98 peptides. Score 0.903 Round 5: 240 peptides, 14 chains. Longest chain 39 peptides. Score 0.867 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 8, Residues 240, Estimated correctness of the model 99.1 % 7 chains (232 residues) have been docked in sequence Sequence coverage is 96 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 32 A and 43 A Built loop between residues 78 A and 81 A Built loop between residues 101 A and 104 A Built loop between residues 117 A and 120 A 4 chains (256 residues) following loop building 3 chains (248 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 18405 reflections ( 98.93 % complete ) and 2128 restraints for refining 2080 atoms. Observations/parameters ratio is 2.21 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3143 (Rfree = 0.000) for 2080 atoms. Found 10 (31 requested) and removed 0 (31 requested) atoms. Cycle 47: After refmac, R = 0.3020 (Rfree = 0.000) for 2080 atoms. Found 8 (31 requested) and removed 0 (31 requested) atoms. Cycle 48: After refmac, R = 0.2917 (Rfree = 0.000) for 2080 atoms. Found 4 (31 requested) and removed 0 (31 requested) atoms. Cycle 49: After refmac, R = 0.2843 (Rfree = 0.000) for 2080 atoms. Found 4 (31 requested) and removed 4 (31 requested) atoms. Writing output files ... TimeTaking 41.53