Mon 24 Dec 07:58:40 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 2avn-2.5-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2avn-2.5-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2avn-2.5-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2avn-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/2avn-2.5-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2avn-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 07:58:45 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/2avn-2.5-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2avn-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 763 and 0 Target number of residues in the AU: 763 Target solvent content: 0.5762 Checking the provided sequence file Detected sequence length: 260 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 520 Adjusted target solvent content: 0.71 Input MTZ file: 2avn-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: 181 Cell parameters: 133.767 133.767 188.622 90.000 90.000 120.000 Input sequence file: 2avn-2.5-parrot-noncs.fasta_lf Building free atoms model in initial map for 4160 target number of atoms Had to go as low as 1.10 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: 115.845 2.500 Wilson plot Bfac: 43.67 35104 reflections ( 99.87 % complete ) and 0 restraints for refining 4663 atoms. Observations/parameters ratio is 1.88 ------------------------------------------------------ Starting model: R = 0.3617 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3281 (Rfree = 0.000) for 4663 atoms. Found 84 (84 requested) and removed 48 (42 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.72 2.02 NCS extension: 0 residues added, 4699 seeds are put forward Round 1: 388 peptides, 46 chains. Longest chain 27 peptides. Score 0.536 Round 2: 441 peptides, 37 chains. Longest chain 31 peptides. Score 0.657 Round 3: 457 peptides, 27 chains. Longest chain 83 peptides. Score 0.725 Round 4: 457 peptides, 20 chains. Longest chain 71 peptides. Score 0.759 Round 5: 464 peptides, 19 chains. Longest chain 84 peptides. Score 0.769 Taking the results from Round 5 Chains 22, Residues 445, Estimated correctness of the model 90.1 % 10 chains (367 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 93 A and 100 A Built loop between residues 220 A and 224 A Built loop between residues 82 B and 91 B 17 chains (454 residues) following loop building 7 chains (384 residues) in sequence following loop building ------------------------------------------------------ 35104 reflections ( 99.87 % complete ) and 5454 restraints for refining 4561 atoms. 1920 conditional restraints added. Observations/parameters ratio is 1.92 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2934 (Rfree = 0.000) for 4561 atoms. Found 82 (82 requested) and removed 65 (41 requested) atoms. Cycle 2: After refmac, R = 0.2674 (Rfree = 0.000) for 4506 atoms. Found 81 (81 requested) and removed 49 (41 requested) atoms. Cycle 3: After refmac, R = 0.2458 (Rfree = 0.000) for 4505 atoms. Found 79 (79 requested) and removed 44 (41 requested) atoms. Cycle 4: After refmac, R = 0.2379 (Rfree = 0.000) for 4516 atoms. Found 77 (77 requested) and removed 44 (41 requested) atoms. Cycle 5: After refmac, R = 0.2265 (Rfree = 0.000) for 4530 atoms. Found 75 (75 requested) and removed 47 (41 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.61 1.94 NCS extension: 115 residues added (70 deleted due to clashes), 4683 seeds are put forward Round 1: 480 peptides, 10 chains. Longest chain 125 peptides. Score 0.819 Round 2: 473 peptides, 14 chains. Longest chain 135 peptides. Score 0.798 Round 3: 479 peptides, 12 chains. Longest chain 89 peptides. Score 0.810 Round 4: 477 peptides, 15 chains. Longest chain 135 peptides. Score 0.796 Round 5: 472 peptides, 15 chains. Longest chain 104 peptides. Score 0.793 Taking the results from Round 1 Chains 11, Residues 470, Estimated correctness of the model 93.7 % 7 chains (448 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 144 A and 148 A Built loop between residues 177 A and 180 A Built loop between residues 201 A and 204 A 8 chains (477 residues) following loop building 4 chains (455 residues) in sequence following loop building ------------------------------------------------------ 35104 reflections ( 99.87 % complete ) and 4855 restraints for refining 4535 atoms. 934 conditional restraints added. Observations/parameters ratio is 1.94 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2195 (Rfree = 0.000) for 4535 atoms. Found 74 (74 requested) and removed 50 (41 requested) atoms. Cycle 7: After refmac, R = 0.1979 (Rfree = 0.000) for 4539 atoms. Found 72 (72 requested) and removed 41 (41 requested) atoms. Cycle 8: After refmac, R = 0.1891 (Rfree = 0.000) for 4559 atoms. Found 71 (71 requested) and removed 43 (41 requested) atoms. Cycle 9: After refmac, R = 0.1848 (Rfree = 0.000) for 4577 atoms. Found 70 (70 requested) and removed 42 (41 requested) atoms. Cycle 10: After refmac, R = 0.1788 (Rfree = 0.000) for 4601 atoms. Found 68 (68 requested) and removed 43 (41 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.60 1.93 NCS extension: 27 residues added (311 deleted due to clashes), 4655 seeds are put forward Round 1: 485 peptides, 7 chains. Longest chain 166 peptides. Score 0.834 Round 2: 488 peptides, 7 chains. Longest chain 167 peptides. Score 0.836 Round 3: 490 peptides, 8 chains. Longest chain 177 peptides. Score 0.833 Round 4: 474 peptides, 15 chains. Longest chain 116 peptides. Score 0.794 Round 5: 469 peptides, 15 chains. Longest chain 82 peptides. Score 0.790 Taking the results from Round 2 Chains 8, Residues 481, Estimated correctness of the model 94.7 % 5 chains (463 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 52 A and 55 A Built loop between residues 179 A and 182 A Built loop between residues 176 B and 180 B 4 chains (486 residues) following loop building 2 chains (470 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 35104 reflections ( 99.87 % complete ) and 4714 restraints for refining 4504 atoms. 715 conditional restraints added. Observations/parameters ratio is 1.95 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1987 (Rfree = 0.000) for 4504 atoms. Found 65 (65 requested) and removed 50 (40 requested) atoms. Cycle 12: After refmac, R = 0.1824 (Rfree = 0.000) for 4513 atoms. Found 63 (63 requested) and removed 42 (40 requested) atoms. Cycle 13: After refmac, R = 0.1750 (Rfree = 0.000) for 4528 atoms. Found 62 (62 requested) and removed 42 (41 requested) atoms. Cycle 14: After refmac, R = 0.1717 (Rfree = 0.000) for 4543 atoms. Found 61 (61 requested) and removed 43 (41 requested) atoms. Cycle 15: After refmac, R = 0.1693 (Rfree = 0.000) for 4553 atoms. Found 59 (59 requested) and removed 41 (41 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.59 1.92 NCS extension: 0 residues added, 4573 seeds are put forward Round 1: 489 peptides, 6 chains. Longest chain 171 peptides. Score 0.840 Round 2: 489 peptides, 6 chains. Longest chain 166 peptides. Score 0.840 Round 3: 484 peptides, 9 chains. Longest chain 149 peptides. Score 0.826 Round 4: 478 peptides, 12 chains. Longest chain 123 peptides. Score 0.810 Round 5: 477 peptides, 13 chains. Longest chain 112 peptides. Score 0.805 Taking the results from Round 2 Chains 6, Residues 483, Estimated correctness of the model 95.0 % 5 chains (474 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 177 A and 180 A Built loop between residues 143 B and 146 B Built loop between residues 226 B and 229 B 3 chains (489 residues) following loop building 2 chains (480 residues) in sequence following loop building ------------------------------------------------------ 35104 reflections ( 99.87 % complete ) and 4626 restraints for refining 4495 atoms. 558 conditional restraints added. Observations/parameters ratio is 1.95 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1954 (Rfree = 0.000) for 4495 atoms. Found 57 (57 requested) and removed 59 (40 requested) atoms. Cycle 17: After refmac, R = 0.1796 (Rfree = 0.000) for 4484 atoms. Found 55 (55 requested) and removed 43 (40 requested) atoms. Cycle 18: After refmac, R = 0.1741 (Rfree = 0.000) for 4490 atoms. Found 53 (53 requested) and removed 42 (40 requested) atoms. Cycle 19: After refmac, R = 0.1730 (Rfree = 0.000) for 4492 atoms. Found 52 (52 requested) and removed 43 (40 requested) atoms. Cycle 20: After refmac, R = 0.1701 (Rfree = 0.000) for 4496 atoms. Found 50 (50 requested) and removed 43 (40 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.59 1.92 NCS extension: 0 residues added (11 deleted due to clashes), 4503 seeds are put forward Round 1: 485 peptides, 7 chains. Longest chain 171 peptides. Score 0.834 Round 2: 491 peptides, 4 chains. Longest chain 209 peptides. Score 0.849 Round 3: 482 peptides, 11 chains. Longest chain 149 peptides. Score 0.816 Round 4: 483 peptides, 8 chains. Longest chain 166 peptides. Score 0.829 Round 5: 471 peptides, 14 chains. Longest chain 149 peptides. Score 0.796 Taking the results from Round 2 Chains 4, Residues 487, Estimated correctness of the model 95.5 % 4 chains (487 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 220 A and 223 A Built loop between residues 143 B and 146 B 2 chains (491 residues) following loop building 2 chains (491 residues) in sequence following loop building ------------------------------------------------------ 35104 reflections ( 99.87 % complete ) and 4448 restraints for refining 4444 atoms. 317 conditional restraints added. Observations/parameters ratio is 1.97 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1912 (Rfree = 0.000) for 4444 atoms. Found 48 (48 requested) and removed 51 (40 requested) atoms. Cycle 22: After refmac, R = 0.1789 (Rfree = 0.000) for 4437 atoms. Found 46 (46 requested) and removed 40 (40 requested) atoms. Cycle 23: After refmac, R = 0.1746 (Rfree = 0.000) for 4438 atoms. Found 45 (45 requested) and removed 43 (40 requested) atoms. Cycle 24: After refmac, R = 0.1736 (Rfree = 0.000) for 4434 atoms. Found 43 (43 requested) and removed 42 (40 requested) atoms. Cycle 25: After refmac, R = 0.1721 (Rfree = 0.000) for 4433 atoms. Found 42 (42 requested) and removed 41 (40 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.59 1.92 NCS extension: 0 residues added, 4435 seeds are put forward Round 1: 487 peptides, 6 chains. Longest chain 172 peptides. Score 0.839 Round 2: 487 peptides, 6 chains. Longest chain 133 peptides. Score 0.839 Round 3: 485 peptides, 6 chains. Longest chain 167 peptides. Score 0.838 Round 4: 480 peptides, 11 chains. Longest chain 103 peptides. Score 0.815 Round 5: 471 peptides, 15 chains. Longest chain 94 peptides. Score 0.792 Taking the results from Round 2 Chains 6, Residues 481, Estimated correctness of the model 94.9 % 5 chains (472 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 143 A and 146 A Built loop between residues 122 B and 125 B Built loop between residues 176 B and 179 B 3 chains (487 residues) following loop building 2 chains (478 residues) in sequence following loop building ------------------------------------------------------ 35104 reflections ( 99.87 % complete ) and 4642 restraints for refining 4441 atoms. 592 conditional restraints added. Observations/parameters ratio is 1.98 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1953 (Rfree = 0.000) for 4441 atoms. Found 40 (40 requested) and removed 53 (40 requested) atoms. Cycle 27: After refmac, R = 0.1804 (Rfree = 0.000) for 4425 atoms. Found 40 (40 requested) and removed 41 (40 requested) atoms. Cycle 28: After refmac, R = 0.1771 (Rfree = 0.000) for 4421 atoms. Found 40 (40 requested) and removed 47 (40 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.1736 (Rfree = 0.000) for 4411 atoms. Found 40 (40 requested) and removed 42 (40 requested) atoms. Cycle 30: After refmac, R = 0.1709 (Rfree = 0.000) for 4407 atoms. Found 39 (39 requested) and removed 39 (39 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.60 1.93 NCS extension: 1 residues added (8 deleted due to clashes), 4409 seeds are put forward Round 1: 486 peptides, 7 chains. Longest chain 171 peptides. Score 0.835 Round 2: 490 peptides, 5 chains. Longest chain 133 peptides. Score 0.844 Round 3: 483 peptides, 11 chains. Longest chain 149 peptides. Score 0.817 Round 4: 483 peptides, 9 chains. Longest chain 106 peptides. Score 0.825 Round 5: 467 peptides, 11 chains. Longest chain 116 peptides. Score 0.806 Taking the results from Round 2 Chains 5, Residues 485, Estimated correctness of the model 95.2 % 5 chains (485 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 143 A and 146 A Built loop between residues 122 B and 125 B Built loop between residues 220 B and 223 B 2 chains (491 residues) following loop building 2 chains (491 residues) in sequence following loop building ------------------------------------------------------ 35104 reflections ( 99.87 % complete ) and 4494 restraints for refining 4442 atoms. 363 conditional restraints added. Observations/parameters ratio is 1.98 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1910 (Rfree = 0.000) for 4442 atoms. Found 40 (40 requested) and removed 50 (40 requested) atoms. Cycle 32: After refmac, R = 0.1770 (Rfree = 0.000) for 4428 atoms. Found 40 (40 requested) and removed 41 (40 requested) atoms. Cycle 33: After refmac, R = 0.1733 (Rfree = 0.000) for 4425 atoms. Found 40 (40 requested) and removed 42 (40 requested) atoms. Cycle 34: After refmac, R = 0.1721 (Rfree = 0.000) for 4422 atoms. Found 40 (40 requested) and removed 42 (40 requested) atoms. Cycle 35: After refmac, R = 0.1732 (Rfree = 0.000) for 4420 atoms. Found 40 (40 requested) and removed 42 (40 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.60 1.93 NCS extension: 0 residues added, 4419 seeds are put forward Round 1: 490 peptides, 6 chains. Longest chain 171 peptides. Score 0.841 Round 2: 491 peptides, 5 chains. Longest chain 247 peptides. Score 0.845 Round 3: 479 peptides, 9 chains. Longest chain 167 peptides. Score 0.822 Round 4: 478 peptides, 10 chains. Longest chain 131 peptides. Score 0.818 Round 5: 463 peptides, 14 chains. Longest chain 119 peptides. Score 0.790 Taking the results from Round 2 Chains 5, Residues 486, Estimated correctness of the model 95.2 % 4 chains (477 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 143 A and 146 A Built loop between residues 223 A and 226 A 3 chains (490 residues) following loop building 2 chains (481 residues) in sequence following loop building ------------------------------------------------------ 35104 reflections ( 99.87 % complete ) and 4585 restraints for refining 4444 atoms. 506 conditional restraints added. Observations/parameters ratio is 1.97 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1941 (Rfree = 0.000) for 4444 atoms. Found 40 (40 requested) and removed 53 (40 requested) atoms. Cycle 37: After refmac, R = 0.1797 (Rfree = 0.000) for 4431 atoms. Found 40 (40 requested) and removed 40 (40 requested) atoms. Cycle 38: After refmac, R = 0.1764 (Rfree = 0.000) for 4428 atoms. Found 40 (40 requested) and removed 43 (40 requested) atoms. Cycle 39: After refmac, R = 0.1752 (Rfree = 0.000) for 4422 atoms. Found 40 (40 requested) and removed 44 (40 requested) atoms. Cycle 40: After refmac, R = 0.1713 (Rfree = 0.000) for 4416 atoms. Found 40 (40 requested) and removed 41 (40 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.60 1.93 NCS extension: 1 residues added (11 deleted due to clashes), 4417 seeds are put forward Round 1: 490 peptides, 6 chains. Longest chain 171 peptides. Score 0.841 Round 2: 485 peptides, 8 chains. Longest chain 133 peptides. Score 0.830 Round 3: 491 peptides, 5 chains. Longest chain 247 peptides. Score 0.845 Round 4: 483 peptides, 13 chains. Longest chain 122 peptides. Score 0.809 Round 5: 482 peptides, 12 chains. Longest chain 88 peptides. Score 0.812 Taking the results from Round 3 Chains 5, Residues 486, Estimated correctness of the model 95.2 % 5 chains (486 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 161 A and 164 A Built loop between residues 181 A and 184 A Built loop between residues 226 A and 229 A 2 chains (492 residues) following loop building 2 chains (492 residues) in sequence following loop building ------------------------------------------------------ 35104 reflections ( 99.87 % complete ) and 4455 restraints for refining 4440 atoms. 313 conditional restraints added. Observations/parameters ratio is 1.98 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1936 (Rfree = 0.000) for 4440 atoms. Found 40 (40 requested) and removed 46 (40 requested) atoms. Cycle 42: After refmac, R = 0.1793 (Rfree = 0.000) for 4431 atoms. Found 40 (40 requested) and removed 40 (40 requested) atoms. Cycle 43: After refmac, R = 0.1751 (Rfree = 0.000) for 4427 atoms. Found 40 (40 requested) and removed 43 (40 requested) atoms. Cycle 44: After refmac, R = 0.1715 (Rfree = 0.000) for 4421 atoms. Found 40 (40 requested) and removed 44 (40 requested) atoms. Cycle 45: After refmac, R = 0.1706 (Rfree = 0.000) for 4413 atoms. Found 40 (40 requested) and removed 42 (40 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.59 1.92 NCS extension: 0 residues added, 4413 seeds are put forward Round 1: 489 peptides, 6 chains. Longest chain 171 peptides. Score 0.840 Round 2: 492 peptides, 4 chains. Longest chain 138 peptides. Score 0.849 Round 3: 477 peptides, 12 chains. Longest chain 106 peptides. Score 0.809 Round 4: 483 peptides, 11 chains. Longest chain 120 peptides. Score 0.817 Round 5: 478 peptides, 14 chains. Longest chain 119 peptides. Score 0.801 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 4, Residues 488, Estimated correctness of the model 95.5 % 4 chains (488 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 118 A and 122 A Built loop between residues 143 B and 146 B 2 chains (493 residues) following loop building 2 chains (493 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 35104 reflections ( 99.87 % complete ) and 4153 restraints for refining 4062 atoms. Observations/parameters ratio is 2.16 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2425 (Rfree = 0.000) for 4062 atoms. Found 36 (36 requested) and removed 0 (36 requested) atoms. Cycle 47: After refmac, R = 0.2218 (Rfree = 0.000) for 4062 atoms. Found 37 (37 requested) and removed 5 (37 requested) atoms. Cycle 48: After refmac, R = 0.2115 (Rfree = 0.000) for 4062 atoms. Found 37 (37 requested) and removed 12 (37 requested) atoms. Cycle 49: After refmac, R = 0.2077 (Rfree = 0.000) for 4062 atoms. TimeTaking 75.55