Sun 23 Dec 22:23:09 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 1vky-3.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vky-3.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vky-3.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vky-3.0-parrot-hancs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vky-3.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vky-3.0-parrot-hancs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Sun 23 Dec 22:23:18 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/1vky-3.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vky-3.0-parrot-hancs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 806 and 0 Target number of residues in the AU: 806 Target solvent content: 0.5479 Checking the provided sequence file Detected sequence length: 347 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 694 Adjusted target solvent content: 0.61 Input MTZ file: 1vky-3.0-parrot-hancs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 23 Cell parameters: 119.363 122.591 131.880 90.000 90.000 90.000 Input sequence file: 1vky-3.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 5552 target number of atoms Had to go as low as 0.75 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: 41.380 3.000 Wilson plot Bfac: 34.93 19666 reflections ( 99.68 % complete ) and 0 restraints for refining 6166 atoms. Observations/parameters ratio is 0.80 ------------------------------------------------------ Starting model: R = 0.3180 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2267 (Rfree = 0.000) for 6166 atoms. Found 48 (66 requested) and removed 67 (33 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.67 2.30 Search for helices and strands: 0 residues in 0 chains, 6238 seeds are put forward NCS extension: 0 residues added, 6238 seeds are put forward Round 1: 361 peptides, 56 chains. Longest chain 18 peptides. Score 0.427 Round 2: 406 peptides, 51 chains. Longest chain 33 peptides. Score 0.531 Round 3: 435 peptides, 44 chains. Longest chain 44 peptides. Score 0.613 Round 4: 456 peptides, 44 chains. Longest chain 38 peptides. Score 0.638 Round 5: 437 peptides, 43 chains. Longest chain 34 peptides. Score 0.621 Taking the results from Round 4 Chains 48, Residues 412, Estimated correctness of the model 59.9 % 6 chains (142 residues) have been docked in sequence ------------------------------------------------------ 19666 reflections ( 99.68 % complete ) and 8936 restraints for refining 5092 atoms. 6750 conditional restraints added. Observations/parameters ratio is 0.97 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2833 (Rfree = 0.000) for 5092 atoms. Found 54 (54 requested) and removed 49 (27 requested) atoms. Cycle 2: After refmac, R = 0.2621 (Rfree = 0.000) for 5051 atoms. Found 54 (54 requested) and removed 37 (27 requested) atoms. Cycle 3: After refmac, R = 0.2519 (Rfree = 0.000) for 5026 atoms. Found 47 (54 requested) and removed 31 (27 requested) atoms. Cycle 4: After refmac, R = 0.2462 (Rfree = 0.000) for 5030 atoms. Found 30 (54 requested) and removed 28 (27 requested) atoms. Cycle 5: After refmac, R = 0.2402 (Rfree = 0.000) for 5015 atoms. Found 37 (54 requested) and removed 29 (27 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.66 2.29 Search for helices and strands: 0 residues in 0 chains, 5135 seeds are put forward NCS extension: 24 residues added (12 deleted due to clashes), 5159 seeds are put forward Round 1: 440 peptides, 45 chains. Longest chain 45 peptides. Score 0.614 Round 2: 458 peptides, 35 chains. Longest chain 82 peptides. Score 0.689 Round 3: 461 peptides, 41 chains. Longest chain 44 peptides. Score 0.661 Round 4: 452 peptides, 40 chains. Longest chain 37 peptides. Score 0.656 Round 5: 440 peptides, 42 chains. Longest chain 24 peptides. Score 0.631 Taking the results from Round 2 Chains 41, Residues 423, Estimated correctness of the model 69.7 % 11 chains (209 residues) have been docked in sequence ------------------------------------------------------ 19666 reflections ( 99.68 % complete ) and 8113 restraints for refining 5095 atoms. 5582 conditional restraints added. Observations/parameters ratio is 0.96 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2764 (Rfree = 0.000) for 5095 atoms. Found 54 (54 requested) and removed 70 (27 requested) atoms. Cycle 7: After refmac, R = 0.2570 (Rfree = 0.000) for 5050 atoms. Found 54 (54 requested) and removed 29 (27 requested) atoms. Cycle 8: After refmac, R = 0.2460 (Rfree = 0.000) for 5055 atoms. Found 35 (54 requested) and removed 30 (27 requested) atoms. Cycle 9: After refmac, R = 0.2402 (Rfree = 0.000) for 5047 atoms. Found 37 (54 requested) and removed 29 (27 requested) atoms. Cycle 10: After refmac, R = 0.2365 (Rfree = 0.000) for 5043 atoms. Found 24 (54 requested) and removed 33 (27 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.68 2.31 Search for helices and strands: 0 residues in 0 chains, 5142 seeds are put forward NCS extension: 143 residues added (47 deleted due to clashes), 5285 seeds are put forward Round 1: 424 peptides, 43 chains. Longest chain 30 peptides. Score 0.605 Round 2: 457 peptides, 42 chains. Longest chain 36 peptides. Score 0.651 Round 3: 450 peptides, 41 chains. Longest chain 41 peptides. Score 0.648 Round 4: 452 peptides, 42 chains. Longest chain 48 peptides. Score 0.645 Round 5: 467 peptides, 48 chains. Longest chain 34 peptides. Score 0.629 Taking the results from Round 2 Chains 48, Residues 415, Estimated correctness of the model 62.5 % 9 chains (183 residues) have been docked in sequence ------------------------------------------------------ 19666 reflections ( 99.68 % complete ) and 8674 restraints for refining 5095 atoms. 6261 conditional restraints added. Observations/parameters ratio is 0.96 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2638 (Rfree = 0.000) for 5095 atoms. Found 54 (54 requested) and removed 55 (27 requested) atoms. Cycle 12: After refmac, R = 0.2474 (Rfree = 0.000) for 5078 atoms. Found 49 (54 requested) and removed 30 (27 requested) atoms. Cycle 13: After refmac, R = 0.2420 (Rfree = 0.000) for 5080 atoms. Found 27 (54 requested) and removed 28 (27 requested) atoms. Cycle 14: After refmac, R = 0.2388 (Rfree = 0.000) for 5067 atoms. Found 25 (54 requested) and removed 32 (27 requested) atoms. Cycle 15: After refmac, R = 0.2397 (Rfree = 0.000) for 5052 atoms. Found 37 (54 requested) and removed 31 (27 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.70 2.33 Search for helices and strands: 0 residues in 0 chains, 5194 seeds are put forward NCS extension: 12 residues added (9 deleted due to clashes), 5206 seeds are put forward Round 1: 431 peptides, 41 chains. Longest chain 26 peptides. Score 0.626 Round 2: 445 peptides, 35 chains. Longest chain 58 peptides. Score 0.675 Round 3: 453 peptides, 36 chains. Longest chain 47 peptides. Score 0.679 Round 4: 449 peptides, 36 chains. Longest chain 41 peptides. Score 0.674 Round 5: 459 peptides, 39 chains. Longest chain 51 peptides. Score 0.669 Taking the results from Round 3 Chains 42, Residues 417, Estimated correctness of the model 67.8 % 12 chains (240 residues) have been docked in sequence ------------------------------------------------------ 19666 reflections ( 99.68 % complete ) and 8065 restraints for refining 5095 atoms. 5398 conditional restraints added. Observations/parameters ratio is 0.96 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2650 (Rfree = 0.000) for 5095 atoms. Found 54 (54 requested) and removed 55 (27 requested) atoms. Cycle 17: After refmac, R = 0.2449 (Rfree = 0.000) for 5071 atoms. Found 29 (54 requested) and removed 31 (27 requested) atoms. Cycle 18: After refmac, R = 0.2389 (Rfree = 0.000) for 5061 atoms. Found 29 (54 requested) and removed 31 (27 requested) atoms. Cycle 19: After refmac, R = 0.2360 (Rfree = 0.000) for 5054 atoms. Found 26 (54 requested) and removed 31 (27 requested) atoms. Cycle 20: After refmac, R = 0.2252 (Rfree = 0.000) for 5042 atoms. Found 24 (54 requested) and removed 29 (27 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.72 2.34 Search for helices and strands: 0 residues in 0 chains, 5151 seeds are put forward NCS extension: 11 residues added (40 deleted due to clashes), 5162 seeds are put forward Round 1: 437 peptides, 34 chains. Longest chain 50 peptides. Score 0.672 Round 2: 440 peptides, 33 chains. Longest chain 38 peptides. Score 0.681 Round 3: 447 peptides, 37 chains. Longest chain 50 peptides. Score 0.667 Failed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDB Round 4: 439 peptides, 36 chains. Longest chain 51 peptides. Score 0.663 Round 5: 428 peptides, 37 chains. Longest chain 53 peptides. Score 0.645 Taking the results from Round 2 Chains 38, Residues 407, Estimated correctness of the model 68.2 % 8 chains (204 residues) have been docked in sequence ------------------------------------------------------ 19666 reflections ( 99.68 % complete ) and 8561 restraints for refining 5095 atoms. 6089 conditional restraints added. Observations/parameters ratio is 0.96 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2564 (Rfree = 0.000) for 5095 atoms. Found 54 (54 requested) and removed 41 (27 requested) atoms. Cycle 22: After refmac, R = 0.2384 (Rfree = 0.000) for 5090 atoms. Found 37 (55 requested) and removed 31 (27 requested) atoms. Cycle 23: After refmac, R = 0.2285 (Rfree = 0.000) for 5090 atoms. Found 21 (54 requested) and removed 27 (27 requested) atoms. Cycle 24: After refmac, R = 0.2234 (Rfree = 0.000) for 5080 atoms. Found 20 (54 requested) and removed 29 (27 requested) atoms. Cycle 25: After refmac, R = 0.2199 (Rfree = 0.000) for 5062 atoms. Found 28 (54 requested) and removed 31 (27 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.70 2.33 Search for helices and strands: 0 residues in 0 chains, 5138 seeds are put forward NCS extension: 5 residues added (17 deleted due to clashes), 5143 seeds are put forward Round 1: 424 peptides, 37 chains. Longest chain 43 peptides. Score 0.640 Round 2: 445 peptides, 33 chains. Longest chain 41 peptides. Score 0.686 Round 3: 436 peptides, 38 chains. Longest chain 51 peptides. Score 0.649 Round 4: 451 peptides, 37 chains. Longest chain 67 peptides. Score 0.671 Round 5: 455 peptides, 32 chains. Longest chain 38 peptides. Score 0.701 Taking the results from Round 5 Chains 36, Residues 423, Estimated correctness of the model 71.8 % 10 chains (223 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 279 A and 282 A Built loop between residues 303 A and 306 A 34 chains (427 residues) following loop building 8 chains (227 residues) in sequence following loop building ------------------------------------------------------ 19666 reflections ( 99.68 % complete ) and 8148 restraints for refining 5095 atoms. 5501 conditional restraints added. Observations/parameters ratio is 0.96 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2606 (Rfree = 0.000) for 5095 atoms. Found 54 (54 requested) and removed 39 (27 requested) atoms. Cycle 27: After refmac, R = 0.2421 (Rfree = 0.000) for 5090 atoms. Found 46 (54 requested) and removed 29 (27 requested) atoms. Cycle 28: After refmac, R = 0.2334 (Rfree = 0.000) for 5099 atoms. Found 33 (53 requested) and removed 31 (27 requested) atoms. Cycle 29: After refmac, R = 0.2313 (Rfree = 0.000) for 5096 atoms. Found 36 (52 requested) and removed 31 (27 requested) atoms. Cycle 30: After refmac, R = 0.2278 (Rfree = 0.000) for 5097 atoms. Found 30 (51 requested) and removed 33 (27 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.64 2.27 Search for helices and strands: 0 residues in 0 chains, 5190 seeds are put forward NCS extension: 37 residues added (78 deleted due to clashes), 5227 seeds are put forward Round 1: 442 peptides, 39 chains. Longest chain 40 peptides. Score 0.650 Round 2: 470 peptides, 30 chains. Longest chain 65 peptides. Score 0.726 Round 3: 455 peptides, 35 chains. Longest chain 37 peptides. Score 0.686 Round 4: 445 peptides, 38 chains. Longest chain 38 peptides. Score 0.659 Round 5: 459 peptides, 35 chains. Longest chain 42 peptides. Score 0.690 Taking the results from Round 2 Chains 34, Residues 440, Estimated correctness of the model 75.9 % 8 chains (240 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 250 B and 253 B 33 chains (442 residues) following loop building 7 chains (242 residues) in sequence following loop building ------------------------------------------------------ 19666 reflections ( 99.68 % complete ) and 7978 restraints for refining 5095 atoms. 5183 conditional restraints added. Observations/parameters ratio is 0.96 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2560 (Rfree = 0.000) for 5095 atoms. Found 49 (49 requested) and removed 60 (27 requested) atoms. Cycle 32: After refmac, R = 0.2394 (Rfree = 0.000) for 5074 atoms. Found 45 (48 requested) and removed 36 (27 requested) atoms. Cycle 33: After refmac, R = 0.2333 (Rfree = 0.000) for 5076 atoms. Found 28 (46 requested) and removed 32 (27 requested) atoms. Cycle 34: After refmac, R = 0.2313 (Rfree = 0.000) for 5070 atoms. Found 27 (45 requested) and removed 33 (27 requested) atoms. Cycle 35: After refmac, R = 0.2291 (Rfree = 0.000) for 5059 atoms. Found 38 (44 requested) and removed 30 (27 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.66 2.29 Search for helices and strands: 0 residues in 0 chains, 5150 seeds are put forward NCS extension: 70 residues added (9 deleted due to clashes), 5220 seeds are put forward Round 1: 428 peptides, 36 chains. Longest chain 43 peptides. Score 0.651 Round 2: 443 peptides, 33 chains. Longest chain 65 peptides. Score 0.684 Round 3: 445 peptides, 36 chains. Longest chain 70 peptides. Score 0.670 Round 4: 449 peptides, 37 chains. Longest chain 45 peptides. Score 0.669 Round 5: 444 peptides, 34 chains. Longest chain 43 peptides. Score 0.680 Taking the results from Round 2 Chains 36, Residues 410, Estimated correctness of the model 68.8 % 11 chains (259 residues) have been docked in sequence ------------------------------------------------------ 19666 reflections ( 99.68 % complete ) and 8114 restraints for refining 5094 atoms. 5410 conditional restraints added. Observations/parameters ratio is 0.97 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2435 (Rfree = 0.000) for 5094 atoms. Found 43 (43 requested) and removed 43 (27 requested) atoms. Cycle 37: After refmac, R = 0.2317 (Rfree = 0.000) for 5082 atoms. Found 39 (43 requested) and removed 34 (27 requested) atoms. Cycle 38: After refmac, R = 0.2307 (Rfree = 0.000) for 5085 atoms. Found 21 (43 requested) and removed 31 (27 requested) atoms. Cycle 39: After refmac, R = 0.2258 (Rfree = 0.000) for 5068 atoms. Found 36 (43 requested) and removed 29 (27 requested) atoms. Cycle 40: After refmac, R = 0.2270 (Rfree = 0.000) for 5072 atoms. Found 27 (43 requested) and removed 38 (27 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.63 2.27 Search for helices and strands: 0 residues in 0 chains, 5173 seeds are put forward NCS extension: 8 residues added (73 deleted due to clashes), 5181 seeds are put forward Round 1: 423 peptides, 38 chains. Longest chain 39 peptides. Score 0.634 Round 2: 454 peptides, 37 chains. Longest chain 80 peptides. Score 0.674 Round 3: 456 peptides, 42 chains. Longest chain 44 peptides. Score 0.650 Round 4: 469 peptides, 35 chains. Longest chain 42 peptides. Score 0.700 Round 5: 452 peptides, 43 chains. Longest chain 42 peptides. Score 0.639 Taking the results from Round 4 Chains 41, Residues 434, Estimated correctness of the model 71.6 % 12 chains (253 residues) have been docked in sequence ------------------------------------------------------ 19666 reflections ( 99.68 % complete ) and 7750 restraints for refining 5095 atoms. 4964 conditional restraints added. Observations/parameters ratio is 0.96 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2504 (Rfree = 0.000) for 5095 atoms. Found 43 (43 requested) and removed 45 (27 requested) atoms. Cycle 42: After refmac, R = 0.2311 (Rfree = 0.000) for 5081 atoms. Found 37 (43 requested) and removed 32 (27 requested) atoms. Cycle 43: After refmac, R = 0.2262 (Rfree = 0.000) for 5078 atoms. Found 26 (43 requested) and removed 29 (27 requested) atoms. Cycle 44: After refmac, R = 0.2223 (Rfree = 0.000) for 5071 atoms. Found 24 (43 requested) and removed 27 (27 requested) atoms. Cycle 45: After refmac, R = 0.2202 (Rfree = 0.000) for 5062 atoms. Found 18 (43 requested) and removed 29 (27 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.67 2.30 Search for helices and strands: 0 residues in 0 chains, 5169 seeds are put forward NCS extension: 38 residues added (7 deleted due to clashes), 5207 seeds are put forward Round 1: 434 peptides, 36 chains. Longest chain 72 peptides. Score 0.658 Round 2: 449 peptides, 36 chains. Longest chain 35 peptides. Score 0.674 Round 3: 438 peptides, 38 chains. Longest chain 28 peptides. Score 0.651 Round 4: 451 peptides, 41 chains. Longest chain 54 peptides. Score 0.649 Round 5: 440 peptides, 40 chains. Longest chain 50 peptides. Score 0.642 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 38, Residues 413, Estimated correctness of the model 66.9 % 13 chains (219 residues) have been docked in sequence Sequence coverage is 52 % Consider running further cycles of model building using 1vky-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 244 A and 253 A Built loop between residues 258 A and 261 A 35 chains (418 residues) following loop building 11 chains (229 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 19666 reflections ( 99.68 % complete ) and 8050 restraints for refining 5095 atoms. 5441 conditional restraints added. Observations/parameters ratio is 0.96 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2468 (Rfree = 0.000) for 5095 atoms. Found 0 (43 requested) and removed 5 (27 requested) atoms. Cycle 47: After refmac, R = 0.2384 (Rfree = 0.000) for 5075 atoms. Found 0 (43 requested) and removed 0 (27 requested) atoms. Cycle 48: After refmac, R = 0.2325 (Rfree = 0.000) for 5069 atoms. Found 0 (43 requested) and removed 3 (27 requested) atoms. Cycle 49: After refmac, R = 0.2281 (Rfree = 0.000) for 5064 atoms. TimeTaking 79.75