Mon 24 Dec 07:29:04 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2ffj-2.5-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2ffj-2.5-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2ffj-2.5-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ffj-2.5-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2ffj-2.5-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ffj-2.5-parrot-noncs ############### 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 07:29:08 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/noncs/ArpWArp/wArpResults/WorkingDir/2ffj-2.5-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ffj-2.5-parrot-noncs/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 526 and 0 Target number of residues in the AU: 526 Target solvent content: 0.5757 Checking the provided sequence file Detected sequence length: 300 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 600 Adjusted target solvent content: 0.52 Input MTZ file: 2ffj-2.5-parrot-noncs.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: 68.806 80.677 120.868 90.000 90.000 90.000 Input sequence file: 2ffj-2.5-parrot-noncs.fasta_lf Building free atoms model in initial map for 4800 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 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: 29.898 2.450 Wilson plot Bfac: 43.40 25302 reflections ( 99.61 % complete ) and 0 restraints for refining 5308 atoms. Observations/parameters ratio is 1.19 ------------------------------------------------------ Starting model: R = 0.3469 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2755 (Rfree = 0.000) for 5308 atoms. Found 44 (101 requested) and removed 68 (50 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.63 2.56 NCS extension: 0 residues added, 5284 seeds are put forward Round 1: 318 peptides, 57 chains. Longest chain 12 peptides. Score 0.401 Round 2: 378 peptides, 44 chains. Longest chain 23 peptides. Score 0.636 Round 3: 420 peptides, 40 chains. Longest chain 34 peptides. Score 0.725 Round 4: 438 peptides, 41 chains. Longest chain 27 peptides. Score 0.741 Round 5: 439 peptides, 34 chains. Longest chain 43 peptides. Score 0.781 Taking the results from Round 5 Chains 38, Residues 405, Estimated correctness of the model 91.6 % 7 chains (172 residues) have been docked in sequence Building loops using Loopy2018 38 chains (405 residues) following loop building 7 chains (172 residues) in sequence following loop building ------------------------------------------------------ 25302 reflections ( 99.61 % complete ) and 7776 restraints for refining 4509 atoms. 5518 conditional restraints added. Observations/parameters ratio is 1.40 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3085 (Rfree = 0.000) for 4509 atoms. Found 55 (86 requested) and removed 67 (43 requested) atoms. Cycle 2: After refmac, R = 0.2957 (Rfree = 0.000) for 4447 atoms. Found 45 (84 requested) and removed 58 (43 requested) atoms. Cycle 3: After refmac, R = 0.2901 (Rfree = 0.000) for 4409 atoms. Found 39 (82 requested) and removed 50 (42 requested) atoms. Cycle 4: After refmac, R = 0.2810 (Rfree = 0.000) for 4386 atoms. Found 37 (79 requested) and removed 48 (42 requested) atoms. Cycle 5: After refmac, R = 0.2729 (Rfree = 0.000) for 4358 atoms. Found 32 (77 requested) and removed 44 (42 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.64 2.57 NCS extension: 4 residues added (5 deleted due to clashes), 4364 seeds are put forward Round 1: 424 peptides, 35 chains. Longest chain 43 peptides. Score 0.759 Round 2: 424 peptides, 30 chains. Longest chain 43 peptides. Score 0.787 Round 3: 461 peptides, 30 chains. Longest chain 46 peptides. Score 0.822 Round 4: 445 peptides, 34 chains. Longest chain 40 peptides. Score 0.787 Round 5: 438 peptides, 37 chains. Longest chain 36 peptides. Score 0.764 Taking the results from Round 3 Chains 33, Residues 431, Estimated correctness of the model 94.2 % 11 chains (249 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 283 A and 289 A 31 chains (434 residues) following loop building 10 chains (254 residues) in sequence following loop building ------------------------------------------------------ 25302 reflections ( 99.61 % complete ) and 6872 restraints for refining 4510 atoms. 4194 conditional restraints added. Observations/parameters ratio is 1.40 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2730 (Rfree = 0.000) for 4510 atoms. Found 46 (77 requested) and removed 57 (43 requested) atoms. Cycle 7: After refmac, R = 0.2571 (Rfree = 0.000) for 4475 atoms. Found 33 (76 requested) and removed 44 (43 requested) atoms. Cycle 8: After refmac, R = 0.2505 (Rfree = 0.000) for 4455 atoms. Found 30 (73 requested) and removed 43 (42 requested) atoms. Cycle 9: After refmac, R = 0.2440 (Rfree = 0.000) for 4437 atoms. Found 24 (71 requested) and removed 44 (42 requested) atoms. Cycle 10: After refmac, R = 0.2414 (Rfree = 0.000) for 4404 atoms. Found 26 (69 requested) and removed 44 (42 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.61 2.54 NCS extension: 6 residues added (3 deleted due to clashes), 4400 seeds are put forward Round 1: 419 peptides, 32 chains. Longest chain 39 peptides. Score 0.770 Round 2: 441 peptides, 28 chains. Longest chain 46 peptides. Score 0.813 Round 3: 461 peptides, 31 chains. Longest chain 43 peptides. Score 0.817 Round 4: 449 peptides, 28 chains. Longest chain 44 peptides. Score 0.821 Round 5: 458 peptides, 29 chains. Longest chain 51 peptides. Score 0.824 Taking the results from Round 5 Chains 34, Residues 429, Estimated correctness of the model 94.4 % 13 chains (275 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 36 A and 39 A Built loop between residues 205 A and 209 A Built loop between residues 227 A and 230 A Built loop between residues 239 A and 242 A Built loop between residues 245 B and 251 B 27 chains (441 residues) following loop building 8 chains (289 residues) in sequence following loop building ------------------------------------------------------ 25302 reflections ( 99.61 % complete ) and 6551 restraints for refining 4510 atoms. 3694 conditional restraints added. Observations/parameters ratio is 1.40 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2650 (Rfree = 0.000) for 4510 atoms. Found 52 (69 requested) and removed 66 (43 requested) atoms. Cycle 12: After refmac, R = 0.2458 (Rfree = 0.000) for 4486 atoms. Found 38 (67 requested) and removed 47 (43 requested) atoms. Cycle 13: After refmac, R = 0.2357 (Rfree = 0.000) for 4467 atoms. Found 35 (65 requested) and removed 45 (43 requested) atoms. Cycle 14: After refmac, R = 0.2305 (Rfree = 0.000) for 4452 atoms. Found 34 (63 requested) and removed 44 (42 requested) atoms. Cycle 15: After refmac, R = 0.2259 (Rfree = 0.000) for 4434 atoms. Found 38 (61 requested) and removed 43 (42 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.60 2.53 NCS extension: 56 residues added (77 deleted due to clashes), 4491 seeds are put forward Round 1: 452 peptides, 30 chains. Longest chain 63 peptides. Score 0.814 Round 2: 474 peptides, 24 chains. Longest chain 74 peptides. Score 0.858 Round 3: 476 peptides, 28 chains. Longest chain 39 peptides. Score 0.843 Round 4: 468 peptides, 32 chains. Longest chain 46 peptides. Score 0.819 Round 5: 464 peptides, 31 chains. Longest chain 48 peptides. Score 0.820 Taking the results from Round 2 Chains 29, Residues 450, Estimated correctness of the model 96.2 % 10 chains (314 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 53 B and 60 B Built loop between residues 191 B and 194 B 25 chains (456 residues) following loop building 8 chains (322 residues) in sequence following loop building ------------------------------------------------------ 25302 reflections ( 99.61 % complete ) and 6087 restraints for refining 4510 atoms. 3026 conditional restraints added. Observations/parameters ratio is 1.40 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2462 (Rfree = 0.000) for 4510 atoms. Found 51 (60 requested) and removed 62 (43 requested) atoms. Cycle 17: After refmac, R = 0.2293 (Rfree = 0.000) for 4490 atoms. Found 24 (58 requested) and removed 43 (43 requested) atoms. Cycle 18: After refmac, R = 0.2256 (Rfree = 0.000) for 4468 atoms. Found 26 (56 requested) and removed 42 (42 requested) atoms. Cycle 19: After refmac, R = 0.2217 (Rfree = 0.000) for 4448 atoms. Found 36 (54 requested) and removed 42 (42 requested) atoms. Cycle 20: After refmac, R = 0.2199 (Rfree = 0.000) for 4442 atoms. Found 28 (53 requested) and removed 42 (42 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.60 2.53 NCS extension: 32 residues added (67 deleted due to clashes), 4470 seeds are put forward Round 1: 480 peptides, 29 chains. Longest chain 76 peptides. Score 0.842 Round 2: 493 peptides, 25 chains. Longest chain 68 peptides. Score 0.867 Round 3: 497 peptides, 27 chains. Longest chain 63 peptides. Score 0.862 Round 4: 499 peptides, 29 chains. Longest chain 48 peptides. Score 0.856 Round 5: 489 peptides, 26 chains. Longest chain 67 peptides. Score 0.860 Taking the results from Round 2 Chains 28, Residues 468, Estimated correctness of the model 96.6 % 10 chains (324 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 174 A and 177 A Built loop between residues 53 B and 61 B 26 chains (477 residues) following loop building 8 chains (333 residues) in sequence following loop building ------------------------------------------------------ 25302 reflections ( 99.61 % complete ) and 5955 restraints for refining 4510 atoms. 2753 conditional restraints added. Observations/parameters ratio is 1.40 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2381 (Rfree = 0.000) for 4510 atoms. Found 52 (52 requested) and removed 54 (43 requested) atoms. Cycle 22: After refmac, R = 0.2273 (Rfree = 0.000) for 4506 atoms. Found 44 (50 requested) and removed 44 (43 requested) atoms. Cycle 23: After refmac, R = 0.2231 (Rfree = 0.000) for 4504 atoms. Found 31 (48 requested) and removed 46 (43 requested) atoms. Cycle 24: After refmac, R = 0.2177 (Rfree = 0.000) for 4489 atoms. Found 30 (46 requested) and removed 45 (43 requested) atoms. Cycle 25: After refmac, R = 0.2174 (Rfree = 0.000) for 4473 atoms. Found 28 (44 requested) and removed 43 (42 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.60 2.53 NCS extension: 26 residues added (71 deleted due to clashes), 4493 seeds are put forward Round 1: 478 peptides, 25 chains. Longest chain 76 peptides. Score 0.857 Round 2: 494 peptides, 19 chains. Longest chain 71 peptides. Score 0.889 Round 3: 491 peptides, 22 chains. Longest chain 64 peptides. Score 0.877 Round 4: 478 peptides, 26 chains. Longest chain 55 peptides. Score 0.853 Round 5: 459 peptides, 29 chains. Longest chain 48 peptides. Score 0.825 Taking the results from Round 2 Chains 23, Residues 475, Estimated correctness of the model 97.6 % 10 chains (367 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 82 A and 85 A Built loop between residues 228 A and 232 A Built loop between residues 265 A and 270 A Built loop between residues 245 B and 248 B Built loop between residues 265 B and 272 B 17 chains (491 residues) following loop building 5 chains (384 residues) in sequence following loop building ------------------------------------------------------ 25302 reflections ( 99.61 % complete ) and 5504 restraints for refining 4510 atoms. 2103 conditional restraints added. Observations/parameters ratio is 1.40 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2418 (Rfree = 0.000) for 4510 atoms. Found 43 (43 requested) and removed 57 (43 requested) atoms. Cycle 27: After refmac, R = 0.2251 (Rfree = 0.000) for 4491 atoms. Found 43 (43 requested) and removed 44 (43 requested) atoms. Cycle 28: After refmac, R = 0.2208 (Rfree = 0.000) for 4489 atoms. Found 42 (43 requested) and removed 48 (43 requested) atoms. Cycle 29: After refmac, R = 0.2171 (Rfree = 0.000) for 4481 atoms. Found 41 (43 requested) and removed 47 (43 requested) atoms. Cycle 30: After refmac, R = 0.2158 (Rfree = 0.000) for 4474 atoms. Found 32 (42 requested) and removed 44 (42 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.59 2.52 NCS extension: 100 residues added (33 deleted due to clashes), 4573 seeds are put forward Round 1: 489 peptides, 22 chains. Longest chain 89 peptides. Score 0.875 Round 2: 501 peptides, 20 chains. Longest chain 67 peptides. Score 0.889 Round 3: 495 peptides, 26 chains. Longest chain 41 peptides. Score 0.864 Round 4: 482 peptides, 25 chains. Longest chain 81 peptides. Score 0.859 Round 5: 492 peptides, 29 chains. Longest chain 37 peptides. Score 0.851 Taking the results from Round 2 Chains 24, Residues 481, Estimated correctness of the model 97.6 % 11 chains (398 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 54 A and 60 A Built loop between residues 264 A and 270 A Built loop between residues 55 B and 61 B Built loop between residues 189 B and 192 B Built loop between residues 245 B and 248 B Built loop between residues 266 B and 271 B 15 chains (498 residues) following loop building 5 chains (421 residues) in sequence following loop building ------------------------------------------------------ 25302 reflections ( 99.61 % complete ) and 5196 restraints for refining 4510 atoms. 1638 conditional restraints added. Observations/parameters ratio is 1.40 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2412 (Rfree = 0.000) for 4510 atoms. Found 43 (43 requested) and removed 51 (43 requested) atoms. Cycle 32: After refmac, R = 0.2255 (Rfree = 0.000) for 4497 atoms. Found 43 (43 requested) and removed 43 (43 requested) atoms. Cycle 33: After refmac, R = 0.2192 (Rfree = 0.000) for 4495 atoms. Found 30 (43 requested) and removed 44 (43 requested) atoms. Cycle 34: After refmac, R = 0.2164 (Rfree = 0.000) for 4481 atoms. Found 36 (43 requested) and removed 46 (43 requested) atoms. Cycle 35: After refmac, R = 0.2126 (Rfree = 0.000) for 4468 atoms. Found 33 (42 requested) and removed 44 (42 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.59 2.52 NCS extension: 99 residues added (307 deleted due to clashes), 4576 seeds are put forward Round 1: 486 peptides, 20 chains. Longest chain 76 peptides. Score 0.881 Round 2: 499 peptides, 20 chains. Longest chain 91 peptides. Score 0.888 Round 3: 488 peptides, 22 chains. Longest chain 65 peptides. Score 0.875 Round 4: 491 peptides, 24 chains. Longest chain 69 peptides. Score 0.869 Round 5: 484 peptides, 25 chains. Longest chain 88 peptides. Score 0.861 Taking the results from Round 2 Chains 24, Residues 479, Estimated correctness of the model 97.5 % 12 chains (411 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 103 A and 112 A Built loop between residues 174 A and 177 A Built loop between residues 174 B and 177 B Built loop between residues 226 B and 231 B 19 chains (490 residues) following loop building 8 chains (427 residues) in sequence following loop building ------------------------------------------------------ 25302 reflections ( 99.61 % complete ) and 5197 restraints for refining 4510 atoms. 1647 conditional restraints added. Observations/parameters ratio is 1.40 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2271 (Rfree = 0.000) for 4510 atoms. Found 43 (43 requested) and removed 48 (43 requested) atoms. Cycle 37: After refmac, R = 0.2121 (Rfree = 0.000) for 4501 atoms. Found 43 (43 requested) and removed 46 (43 requested) atoms. Cycle 38: After refmac, R = 0.2059 (Rfree = 0.000) for 4492 atoms. Found 43 (43 requested) and removed 46 (43 requested) atoms. Cycle 39: After refmac, R = 0.2041 (Rfree = 0.000) for 4486 atoms. Found 43 (43 requested) and removed 47 (43 requested) atoms. Cycle 40: After refmac, R = 0.2016 (Rfree = 0.000) for 4482 atoms. Found 41 (43 requested) and removed 45 (43 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.59 2.52 NCS extension: 74 residues added (24 deleted due to clashes), 4562 seeds are put forward Round 1: 485 peptides, 23 chains. Longest chain 63 peptides. Score 0.869 Round 2: 498 peptides, 21 chains. Longest chain 51 peptides. Score 0.884 Round 3: 494 peptides, 18 chains. Longest chain 89 peptides. Score 0.892 Round 4: 492 peptides, 26 chains. Longest chain 59 peptides. Score 0.862 Round 5: 499 peptides, 25 chains. Longest chain 69 peptides. Score 0.871 Taking the results from Round 3 Chains 20, Residues 476, Estimated correctness of the model 97.7 % 12 chains (407 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 110 A and 113 A Built loop between residues 174 A and 179 A Built loop between residues 266 A and 272 A Built loop between residues 174 B and 177 B Built loop between residues 226 B and 231 B 15 chains (493 residues) following loop building 7 chains (424 residues) in sequence following loop building ------------------------------------------------------ 25302 reflections ( 99.61 % complete ) and 5145 restraints for refining 4510 atoms. 1565 conditional restraints added. Observations/parameters ratio is 1.40 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2216 (Rfree = 0.000) for 4510 atoms. Found 43 (43 requested) and removed 54 (43 requested) atoms. Cycle 42: After refmac, R = 0.2096 (Rfree = 0.000) for 4494 atoms. Found 39 (43 requested) and removed 44 (43 requested) atoms. Cycle 43: After refmac, R = 0.2064 (Rfree = 0.000) for 4485 atoms. Found 35 (43 requested) and removed 46 (43 requested) atoms. Cycle 44: After refmac, R = 0.2046 (Rfree = 0.000) for 4472 atoms. Found 36 (42 requested) and removed 45 (42 requested) atoms. Cycle 45: After refmac, R = 0.2029 (Rfree = 0.000) for 4462 atoms. Found 42 (42 requested) and removed 43 (42 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.58 2.51 NCS extension: 120 residues added (246 deleted due to clashes), 4588 seeds are put forward Round 1: 485 peptides, 21 chains. Longest chain 64 peptides. Score 0.876 Round 2: 499 peptides, 20 chains. Longest chain 63 peptides. Score 0.888 Round 3: 499 peptides, 20 chains. Longest chain 54 peptides. Score 0.888 Round 4: 493 peptides, 17 chains. Longest chain 123 peptides. Score 0.895 Round 5: 477 peptides, 29 chains. Longest chain 50 peptides. Score 0.840 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 20, Residues 476, Estimated correctness of the model 97.8 % 10 chains (408 residues) have been docked in sequence Sequence coverage is 85 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 264 A and 272 A Built loop between residues 189 B and 192 B Built loop between residues 215 B and 218 B Built loop between residues 280 B and 289 B 14 chains (488 residues) following loop building 6 chains (427 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 25302 reflections ( 99.61 % complete ) and 3558 restraints for refining 3535 atoms. Observations/parameters ratio is 1.79 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3079 (Rfree = 0.000) for 3535 atoms. Found 26 (33 requested) and removed 0 (33 requested) atoms. Cycle 47: After refmac, R = 0.2914 (Rfree = 0.000) for 3535 atoms. Found 14 (34 requested) and removed 1 (34 requested) atoms. Cycle 48: After refmac, R = 0.2842 (Rfree = 0.000) for 3535 atoms. Found 5 (34 requested) and removed 3 (34 requested) atoms. Cycle 49: After refmac, R = 0.2798 (Rfree = 0.000) for 3535 atoms. TimeTaking 53.33