Sun 23 Dec 22:23:02 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 2ich-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ich-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ich-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ich-3.2-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/2ich-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ich-3.2-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 22:23:11 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/2ich-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ich-3.2-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 549 and 0 Target number of residues in the AU: 549 Target solvent content: 0.5964 Checking the provided sequence file Detected sequence length: 335 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 670 Adjusted target solvent content: 0.51 Input MTZ file: 2ich-3.2-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: 19 Cell parameters: 63.275 95.573 121.745 90.000 90.000 90.000 Input sequence file: 2ich-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 5360 target number of atoms Had to go as low as 0.65 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 3 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 29.160 3.200 Wilson plot Bfac: 51.15 12684 reflections ( 99.73 % complete ) and 0 restraints for refining 5997 atoms. Observations/parameters ratio is 0.53 ------------------------------------------------------ Starting model: R = 0.2991 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2511 (Rfree = 0.000) for 5997 atoms. Found 37 (53 requested) and removed 54 (26 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.97 2.93 Search for helices and strands: 0 residues in 0 chains, 6043 seeds are put forward NCS extension: 0 residues added, 6043 seeds are put forward Round 1: 380 peptides, 63 chains. Longest chain 20 peptides. Score 0.461 Round 2: 459 peptides, 56 chains. Longest chain 21 peptides. Score 0.649 Round 3: 478 peptides, 51 chains. Longest chain 42 peptides. Score 0.705 Round 4: 506 peptides, 45 chains. Longest chain 43 peptides. Score 0.768 Round 5: 527 peptides, 42 chains. Longest chain 47 peptides. Score 0.801 Taking the results from Round 5 Chains 50, Residues 485, Estimated correctness of the model 83.6 % 15 chains (254 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 293 B and 304 B Built loop between residues 313 B and 321 B 46 chains (485 residues) following loop building 13 chains (271 residues) in sequence following loop building ------------------------------------------------------ 12684 reflections ( 99.73 % complete ) and 7408 restraints for refining 4894 atoms. 4463 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2902 (Rfree = 0.000) for 4894 atoms. Found 43 (43 requested) and removed 76 (21 requested) atoms. Cycle 2: After refmac, R = 0.2638 (Rfree = 0.000) for 4810 atoms. Found 27 (42 requested) and removed 38 (21 requested) atoms. Cycle 3: After refmac, R = 0.2533 (Rfree = 0.000) for 4774 atoms. Found 18 (41 requested) and removed 32 (21 requested) atoms. Cycle 4: After refmac, R = 0.2438 (Rfree = 0.000) for 4751 atoms. Found 16 (39 requested) and removed 25 (21 requested) atoms. Cycle 5: After refmac, R = 0.2378 (Rfree = 0.000) for 4729 atoms. Found 14 (39 requested) and removed 24 (21 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.03 2.99 Search for helices and strands: 0 residues in 0 chains, 4854 seeds are put forward NCS extension: 67 residues added (31 deleted due to clashes), 4921 seeds are put forward Round 1: 476 peptides, 42 chains. Longest chain 45 peptides. Score 0.752 Round 2: 503 peptides, 39 chains. Longest chain 45 peptides. Score 0.793 Round 3: 488 peptides, 42 chains. Longest chain 45 peptides. Score 0.764 Round 4: 497 peptides, 42 chains. Longest chain 64 peptides. Score 0.773 Round 5: 498 peptides, 37 chains. Longest chain 38 peptides. Score 0.798 Taking the results from Round 5 Chains 48, Residues 461, Estimated correctness of the model 83.1 % 13 chains (224 residues) have been docked in sequence Building loops using Loopy2018 48 chains (461 residues) following loop building 13 chains (224 residues) in sequence following loop building ------------------------------------------------------ 12684 reflections ( 99.73 % complete ) and 8124 restraints for refining 4894 atoms. 5380 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2648 (Rfree = 0.000) for 4894 atoms. Found 34 (39 requested) and removed 41 (21 requested) atoms. Cycle 7: After refmac, R = 0.2465 (Rfree = 0.000) for 4871 atoms. Found 17 (38 requested) and removed 33 (21 requested) atoms. Cycle 8: After refmac, R = 0.2380 (Rfree = 0.000) for 4850 atoms. Found 10 (37 requested) and removed 23 (21 requested) atoms. Cycle 9: After refmac, R = 0.2308 (Rfree = 0.000) for 4831 atoms. Found 9 (36 requested) and removed 22 (21 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.2242 (Rfree = 0.000) for 4811 atoms. Found 7 (35 requested) and removed 23 (21 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.01 2.97 Search for helices and strands: 0 residues in 0 chains, 4894 seeds are put forward NCS extension: 34 residues added (10 deleted due to clashes), 4928 seeds are put forward Round 1: 487 peptides, 52 chains. Longest chain 39 peptides. Score 0.710 Round 2: 531 peptides, 45 chains. Longest chain 41 peptides. Score 0.791 Round 3: 507 peptides, 40 chains. Longest chain 71 peptides. Score 0.792 Round 4: 501 peptides, 45 chains. Longest chain 42 peptides. Score 0.763 Round 5: 519 peptides, 41 chains. Longest chain 44 peptides. Score 0.798 Taking the results from Round 5 Chains 49, Residues 478, Estimated correctness of the model 83.1 % 11 chains (242 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 128 A and 134 A 47 chains (479 residues) following loop building 10 chains (247 residues) in sequence following loop building ------------------------------------------------------ 12684 reflections ( 99.73 % complete ) and 7756 restraints for refining 4894 atoms. 4809 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2722 (Rfree = 0.000) for 4894 atoms. Found 34 (34 requested) and removed 60 (21 requested) atoms. Cycle 12: After refmac, R = 0.2517 (Rfree = 0.000) for 4844 atoms. Found 18 (34 requested) and removed 26 (21 requested) atoms. Cycle 13: After refmac, R = 0.2386 (Rfree = 0.000) for 4822 atoms. Found 14 (33 requested) and removed 23 (21 requested) atoms. Cycle 14: After refmac, R = 0.2327 (Rfree = 0.000) for 4806 atoms. Found 7 (32 requested) and removed 22 (21 requested) atoms. Cycle 15: After refmac, R = 0.2312 (Rfree = 0.000) for 4783 atoms. Found 14 (30 requested) and removed 21 (21 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.01 2.97 Search for helices and strands: 0 residues in 0 chains, 4846 seeds are put forward NCS extension: 22 residues added (18 deleted due to clashes), 4868 seeds are put forward Round 1: 486 peptides, 51 chains. Longest chain 29 peptides. Score 0.715 Round 2: 510 peptides, 41 chains. Longest chain 47 peptides. Score 0.790 Round 3: 507 peptides, 43 chains. Longest chain 43 peptides. Score 0.778 Round 4: 480 peptides, 43 chains. Longest chain 37 peptides. Score 0.751 Round 5: 476 peptides, 43 chains. Longest chain 42 peptides. Score 0.747 Taking the results from Round 2 Chains 47, Residues 469, Estimated correctness of the model 81.9 % 11 chains (230 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 37 A and 42 A 46 chains (473 residues) following loop building 10 chains (234 residues) in sequence following loop building ------------------------------------------------------ 12684 reflections ( 99.73 % complete ) and 7821 restraints for refining 4894 atoms. 4922 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2571 (Rfree = 0.000) for 4894 atoms. Found 30 (30 requested) and removed 48 (21 requested) atoms. Cycle 17: After refmac, R = 0.2362 (Rfree = 0.000) for 4865 atoms. Found 15 (29 requested) and removed 30 (21 requested) atoms. Cycle 18: After refmac, R = 0.2266 (Rfree = 0.000) for 4843 atoms. Found 18 (28 requested) and removed 23 (21 requested) atoms. Cycle 19: After refmac, R = 0.2188 (Rfree = 0.000) for 4834 atoms. Found 11 (28 requested) and removed 21 (21 requested) atoms. Cycle 20: After refmac, R = 0.2166 (Rfree = 0.000) for 4819 atoms. Found 13 (27 requested) and removed 21 (21 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.99 2.95 Search for helices and strands: 0 residues in 0 chains, 4908 seeds are put forward NCS extension: 25 residues added (36 deleted due to clashes), 4933 seeds are put forward Round 1: 444 peptides, 46 chains. Longest chain 44 peptides. Score 0.691 Round 2: 486 peptides, 42 chains. Longest chain 44 peptides. Score 0.762 Round 3: 455 peptides, 43 chains. Longest chain 44 peptides. Score 0.723 Round 4: 465 peptides, 38 chains. Longest chain 44 peptides. Score 0.761 Round 5: 440 peptides, 43 chains. Longest chain 36 peptides. Score 0.704 Taking the results from Round 2 Chains 47, Residues 444, Estimated correctness of the model 77.2 % 9 chains (164 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 38 A and 48 A 46 chains (450 residues) following loop building 8 chains (173 residues) in sequence following loop building ------------------------------------------------------ 12684 reflections ( 99.73 % complete ) and 8451 restraints for refining 4894 atoms. 5937 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2528 (Rfree = 0.000) for 4894 atoms. Found 26 (26 requested) and removed 43 (21 requested) atoms. Cycle 22: After refmac, R = 0.2353 (Rfree = 0.000) for 4854 atoms. Found 23 (25 requested) and removed 25 (21 requested) atoms. Cycle 23: After refmac, R = 0.2240 (Rfree = 0.000) for 4844 atoms. Found 13 (24 requested) and removed 23 (21 requested) atoms. Cycle 24: After refmac, R = 0.2169 (Rfree = 0.000) for 4826 atoms. Found 8 (23 requested) and removed 21 (21 requested) atoms. Cycle 25: After refmac, R = 0.2141 (Rfree = 0.000) for 4803 atoms. Found 8 (22 requested) and removed 21 (21 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.02 2.98 Search for helices and strands: 0 residues in 0 chains, 4889 seeds are put forward NCS extension: 50 residues added (20 deleted due to clashes), 4939 seeds are put forward Round 1: 419 peptides, 45 chains. Longest chain 24 peptides. Score 0.664 Round 2: 450 peptides, 44 chains. Longest chain 27 peptides. Score 0.711 Round 3: 455 peptides, 44 chains. Longest chain 33 peptides. Score 0.717 Round 4: 433 peptides, 40 chains. Longest chain 25 peptides. Score 0.713 Round 5: 426 peptides, 44 chains. Longest chain 26 peptides. Score 0.680 Taking the results from Round 3 Chains 48, Residues 411, Estimated correctness of the model 68.7 % 11 chains (172 residues) have been docked in sequence Building loops using Loopy2018 48 chains (411 residues) following loop building 11 chains (172 residues) in sequence following loop building ------------------------------------------------------ 12684 reflections ( 99.73 % complete ) and 8694 restraints for refining 4893 atoms. 6315 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2457 (Rfree = 0.000) for 4893 atoms. Found 21 (21 requested) and removed 48 (21 requested) atoms. Cycle 27: After refmac, R = 0.2303 (Rfree = 0.000) for 4846 atoms. Found 21 (21 requested) and removed 26 (21 requested) atoms. Cycle 28: After refmac, R = 0.2239 (Rfree = 0.000) for 4831 atoms. Found 17 (21 requested) and removed 25 (21 requested) atoms. Cycle 29: After refmac, R = 0.2194 (Rfree = 0.000) for 4818 atoms. Found 10 (21 requested) and removed 21 (21 requested) atoms. Cycle 30: After refmac, R = 0.2158 (Rfree = 0.000) for 4804 atoms. Found 8 (21 requested) and removed 21 (21 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.00 2.96 Search for helices and strands: 0 residues in 0 chains, 4859 seeds are put forward NCS extension: 27 residues added (10 deleted due to clashes), 4886 seeds are put forward Round 1: 398 peptides, 46 chains. Longest chain 20 peptides. Score 0.626 Round 2: 446 peptides, 51 chains. Longest chain 25 peptides. Score 0.663 Round 3: 434 peptides, 47 chains. Longest chain 23 peptides. Score 0.672 Round 4: 461 peptides, 47 chains. Longest chain 25 peptides. Score 0.707 Round 5: 449 peptides, 45 chains. Longest chain 29 peptides. Score 0.704 Taking the results from Round 4 Chains 53, Residues 414, Estimated correctness of the model 66.7 % 9 chains (114 residues) have been docked in sequence Building loops using Loopy2018 53 chains (414 residues) following loop building 9 chains (114 residues) in sequence following loop building ------------------------------------------------------ 12684 reflections ( 99.73 % complete ) and 9300 restraints for refining 4893 atoms. 7182 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2413 (Rfree = 0.000) for 4893 atoms. Found 21 (21 requested) and removed 41 (21 requested) atoms. Cycle 32: After refmac, R = 0.2268 (Rfree = 0.000) for 4859 atoms. Found 14 (21 requested) and removed 22 (21 requested) atoms. Cycle 33: After refmac, R = 0.2222 (Rfree = 0.000) for 4841 atoms. Found 13 (21 requested) and removed 22 (21 requested) atoms. Cycle 34: After refmac, R = 0.2181 (Rfree = 0.000) for 4826 atoms. Found 8 (21 requested) and removed 21 (21 requested) atoms. Cycle 35: After refmac, R = 0.2145 (Rfree = 0.000) for 4810 atoms. Found 3 (21 requested) and removed 22 (21 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.03 2.99 Search for helices and strands: 0 residues in 0 chains, 4849 seeds are put forward NCS extension: 18 residues added (5 deleted due to clashes), 4867 seeds are put forward Round 1: 406 peptides, 50 chains. Longest chain 20 peptides. Score 0.610 Round 2: 439 peptides, 44 chains. Longest chain 26 peptides. Score 0.697 Round 3: 412 peptides, 46 chains. Longest chain 21 peptides. Score 0.647 Round 4: 429 peptides, 48 chains. Longest chain 26 peptides. Score 0.658 Round 5: 422 peptides, 43 chains. Longest chain 29 peptides. Score 0.681 Taking the results from Round 2 Chains 48, Residues 395, Estimated correctness of the model 64.5 % 5 chains (56 residues) have been docked in sequence ------------------------------------------------------ 12684 reflections ( 99.73 % complete ) and 9920 restraints for refining 4894 atoms. 8141 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2325 (Rfree = 0.000) for 4894 atoms. Found 21 (21 requested) and removed 31 (21 requested) atoms. Cycle 37: After refmac, R = 0.2210 (Rfree = 0.000) for 4879 atoms. Found 16 (21 requested) and removed 22 (21 requested) atoms. Cycle 38: After refmac, R = 0.2179 (Rfree = 0.000) for 4868 atoms. Found 7 (21 requested) and removed 22 (21 requested) atoms. Cycle 39: After refmac, R = 0.2118 (Rfree = 0.000) for 4851 atoms. Found 12 (21 requested) and removed 21 (21 requested) atoms. Cycle 40: After refmac, R = 0.2065 (Rfree = 0.000) for 4839 atoms. Found 8 (21 requested) and removed 21 (21 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.02 2.98 Search for helices and strands: 0 residues in 0 chains, 4881 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 4894 seeds are put forward Round 1: 382 peptides, 56 chains. Longest chain 16 peptides. Score 0.523 Round 2: 438 peptides, 52 chains. Longest chain 20 peptides. Score 0.645 Round 3: 423 peptides, 51 chains. Longest chain 18 peptides. Score 0.629 Round 4: 388 peptides, 48 chains. Longest chain 19 peptides. Score 0.596 Round 5: 425 peptides, 50 chains. Longest chain 22 peptides. Score 0.639 Taking the results from Round 2 Chains 57, Residues 386, Estimated correctness of the model 52.6 % 9 chains (84 residues) have been docked in sequence ------------------------------------------------------ 12684 reflections ( 99.73 % complete ) and 9704 restraints for refining 4894 atoms. 7837 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2285 (Rfree = 0.000) for 4894 atoms. Found 21 (21 requested) and removed 33 (21 requested) atoms. Cycle 42: After refmac, R = 0.2163 (Rfree = 0.000) for 4874 atoms. Found 21 (21 requested) and removed 21 (21 requested) atoms. Cycle 43: After refmac, R = 0.2105 (Rfree = 0.000) for 4873 atoms. Found 10 (21 requested) and removed 22 (21 requested) atoms. Cycle 44: After refmac, R = 0.2047 (Rfree = 0.000) for 4859 atoms. Found 9 (21 requested) and removed 21 (21 requested) atoms. Failed to save intermediate PDB Cycle 45: After refmac, R = 0.2022 (Rfree = 0.000) for 4843 atoms. Found 13 (21 requested) and removed 21 (21 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.02 2.98 Search for helices and strands: 0 residues in 0 chains, 4901 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 4916 seeds are put forward Round 1: 346 peptides, 48 chains. Longest chain 16 peptides. Score 0.522 Round 2: 401 peptides, 49 chains. Longest chain 18 peptides. Score 0.609 Round 3: 408 peptides, 49 chains. Longest chain 24 peptides. Score 0.620 Round 4: 424 peptides, 52 chains. Longest chain 21 peptides. Score 0.624 Round 5: 421 peptides, 51 chains. Longest chain 23 peptides. Score 0.626 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 52, Residues 370, Estimated correctness of the model 47.9 % 8 chains (80 residues) have been docked in sequence Sequence coverage is 21 % Consider running further cycles of model building using 2ich-3_warpNtrace.pdb as input Building loops using Loopy2018 52 chains (370 residues) following loop building 8 chains (80 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 12684 reflections ( 99.73 % complete ) and 9887 restraints for refining 4893 atoms. 8095 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2359 (Rfree = 0.000) for 4893 atoms. Found 0 (21 requested) and removed 8 (21 requested) atoms. Cycle 47: After refmac, R = 0.2260 (Rfree = 0.000) for 4882 atoms. Found 0 (21 requested) and removed 5 (21 requested) atoms. Cycle 48: After refmac, R = 0.2215 (Rfree = 0.000) for 4873 atoms. Found 0 (21 requested) and removed 4 (21 requested) atoms. Cycle 49: After refmac, R = 0.2172 (Rfree = 0.000) for 4868 atoms. TimeTaking 74.68