Sun 23 Dec 22:22:41 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 1z85-2.1-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1z85-2.1-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1z85-2.1-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1z85-2.1-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/1z85-2.1-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1z85-2.1-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 22:22:50 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/1z85-2.1-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1z85-2.1-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 496 and 0 Target number of residues in the AU: 496 Target solvent content: 0.5342 Checking the provided sequence file Detected sequence length: 234 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 468 Adjusted target solvent content: 0.56 Input MTZ file: 1z85-2.1-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: 65.676 82.546 106.310 90.000 90.000 90.000 Input sequence file: 1z85-2.1-parrot-hancs.fasta_lf Building free atoms model in initial map for 3744 target number of atoms Had to go as low as 0.70 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 1 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 65.199 2.120 Wilson plot Bfac: 31.32 33464 reflections ( 99.93 % complete ) and 0 restraints for refining 4123 atoms. Observations/parameters ratio is 2.03 ------------------------------------------------------ Starting model: R = 0.3659 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3149 (Rfree = 0.000) for 4123 atoms. Found 90 (119 requested) and removed 61 (59 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.35 2.17 NCS extension: 0 residues added, 4152 seeds are put forward Round 1: 303 peptides, 38 chains. Longest chain 26 peptides. Score 0.590 Round 2: 330 peptides, 28 chains. Longest chain 28 peptides. Score 0.724 Round 3: 350 peptides, 20 chains. Longest chain 72 peptides. Score 0.805 Round 4: 348 peptides, 18 chains. Longest chain 65 peptides. Score 0.815 Round 5: 328 peptides, 19 chains. Longest chain 64 peptides. Score 0.785 Taking the results from Round 4 Chains 21, Residues 330, Estimated correctness of the model 96.1 % 8 chains (255 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 31 A and 35 A Built loop between residues 100 B and 103 B 19 chains (335 residues) following loop building 6 chains (260 residues) in sequence following loop building ------------------------------------------------------ 33464 reflections ( 99.93 % complete ) and 4757 restraints for refining 3746 atoms. 2370 conditional restraints added. Observations/parameters ratio is 2.23 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3284 (Rfree = 0.000) for 3746 atoms. Found 102 (108 requested) and removed 66 (54 requested) atoms. Cycle 2: After refmac, R = 0.2967 (Rfree = 0.000) for 3752 atoms. Found 71 (107 requested) and removed 54 (54 requested) atoms. Cycle 3: After refmac, R = 0.2778 (Rfree = 0.000) for 3745 atoms. Found 53 (105 requested) and removed 44 (54 requested) atoms. Cycle 4: After refmac, R = 0.2653 (Rfree = 0.000) for 3734 atoms. Found 41 (102 requested) and removed 27 (54 requested) atoms. Cycle 5: After refmac, R = 0.2576 (Rfree = 0.000) for 3729 atoms. Found 43 (99 requested) and removed 23 (54 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.26 2.09 NCS extension: 56 residues added (41 deleted due to clashes), 3814 seeds are put forward Round 1: 355 peptides, 15 chains. Longest chain 83 peptides. Score 0.839 Round 2: 362 peptides, 14 chains. Longest chain 84 peptides. Score 0.851 Round 3: 370 peptides, 15 chains. Longest chain 89 peptides. Score 0.853 Round 4: 373 peptides, 14 chains. Longest chain 83 peptides. Score 0.861 Round 5: 373 peptides, 13 chains. Longest chain 100 peptides. Score 0.865 Taking the results from Round 5 Chains 18, Residues 360, Estimated correctness of the model 97.8 % 6 chains (301 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 93 B and 99 B 17 chains (364 residues) following loop building 5 chains (306 residues) in sequence following loop building ------------------------------------------------------ 33464 reflections ( 99.93 % complete ) and 4058 restraints for refining 3601 atoms. 1375 conditional restraints added. Observations/parameters ratio is 2.32 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2744 (Rfree = 0.000) for 3601 atoms. Found 94 (94 requested) and removed 53 (52 requested) atoms. Cycle 7: After refmac, R = 0.2563 (Rfree = 0.000) for 3639 atoms. Found 75 (92 requested) and removed 52 (52 requested) atoms. Cycle 8: After refmac, R = 0.2435 (Rfree = 0.000) for 3655 atoms. Found 50 (91 requested) and removed 39 (53 requested) atoms. Cycle 9: After refmac, R = 0.2361 (Rfree = 0.000) for 3657 atoms. Found 50 (89 requested) and removed 19 (53 requested) atoms. Cycle 10: After refmac, R = 0.2279 (Rfree = 0.000) for 3683 atoms. Found 43 (90 requested) and removed 33 (53 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.25 2.08 NCS extension: 34 residues added (31 deleted due to clashes), 3735 seeds are put forward Round 1: 377 peptides, 14 chains. Longest chain 96 peptides. Score 0.864 Round 2: 378 peptides, 16 chains. Longest chain 80 peptides. Score 0.855 Round 3: 384 peptides, 16 chains. Longest chain 101 peptides. Score 0.860 Round 4: 389 peptides, 15 chains. Longest chain 100 peptides. Score 0.869 Round 5: 386 peptides, 14 chains. Longest chain 72 peptides. Score 0.871 Taking the results from Round 5 Chains 19, Residues 372, Estimated correctness of the model 98.0 % 10 chains (328 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 104 A and 107 A Built loop between residues 85 B and 88 B Built loop between residues 141 B and 145 B 15 chains (377 residues) following loop building 7 chains (335 residues) in sequence following loop building ------------------------------------------------------ 33464 reflections ( 99.93 % complete ) and 3932 restraints for refining 3641 atoms. 1034 conditional restraints added. Observations/parameters ratio is 2.30 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2505 (Rfree = 0.000) for 3641 atoms. Found 86 (86 requested) and removed 59 (52 requested) atoms. Cycle 12: After refmac, R = 0.2321 (Rfree = 0.000) for 3665 atoms. Found 53 (85 requested) and removed 35 (53 requested) atoms. Cycle 13: After refmac, R = 0.2226 (Rfree = 0.000) for 3679 atoms. Found 56 (83 requested) and removed 21 (53 requested) atoms. Cycle 14: After refmac, R = 0.2167 (Rfree = 0.000) for 3706 atoms. Found 39 (83 requested) and removed 23 (53 requested) atoms. Failed to save intermediate PDB Cycle 15: After refmac, R = 0.2124 (Rfree = 0.000) for 3718 atoms. Found 43 (81 requested) and removed 21 (53 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.25 2.08 NCS extension: 84 residues added (79 deleted due to clashes), 3836 seeds are put forward Round 1: 383 peptides, 12 chains. Longest chain 144 peptides. Score 0.878 Round 2: 391 peptides, 18 chains. Longest chain 70 peptides. Score 0.856 Round 3: 400 peptides, 14 chains. Longest chain 102 peptides. Score 0.882 Round 4: 398 peptides, 13 chains. Longest chain 76 peptides. Score 0.885 Round 5: 402 peptides, 15 chains. Longest chain 80 peptides. Score 0.879 Taking the results from Round 4 Chains 17, Residues 385, Estimated correctness of the model 98.4 % 10 chains (361 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 38 A and 45 A Built loop between residues 64 A and 68 A Built loop between residues 168 A and 176 A Built loop between residues 81 B and 84 B 13 chains (403 residues) following loop building 6 chains (379 residues) in sequence following loop building ------------------------------------------------------ 33464 reflections ( 99.93 % complete ) and 3989 restraints for refining 3792 atoms. 825 conditional restraints added. Observations/parameters ratio is 2.21 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2477 (Rfree = 0.000) for 3792 atoms. Found 84 (84 requested) and removed 61 (55 requested) atoms. Cycle 17: After refmac, R = 0.2278 (Rfree = 0.000) for 3804 atoms. Found 61 (81 requested) and removed 55 (55 requested) atoms. Cycle 18: After refmac, R = 0.2166 (Rfree = 0.000) for 3804 atoms. Found 53 (79 requested) and removed 34 (55 requested) atoms. Cycle 19: After refmac, R = 0.2098 (Rfree = 0.000) for 3819 atoms. Found 59 (77 requested) and removed 25 (55 requested) atoms. Cycle 20: After refmac, R = 0.2053 (Rfree = 0.000) for 3852 atoms. Found 38 (78 requested) and removed 38 (55 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.26 2.09 NCS extension: 24 residues added (39 deleted due to clashes), 3884 seeds are put forward Round 1: 406 peptides, 11 chains. Longest chain 144 peptides. Score 0.898 Round 2: 403 peptides, 11 chains. Longest chain 80 peptides. Score 0.896 Round 3: 406 peptides, 13 chains. Longest chain 108 peptides. Score 0.890 Round 4: 405 peptides, 12 chains. Longest chain 80 peptides. Score 0.893 Round 5: 406 peptides, 13 chains. Longest chain 139 peptides. Score 0.890 Taking the results from Round 1 Chains 11, Residues 395, Estimated correctness of the model 98.7 % 8 chains (363 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 63 A and 67 A Built loop between residues 207 B and 214 B 9 chains (404 residues) following loop building 6 chains (372 residues) in sequence following loop building ------------------------------------------------------ 33464 reflections ( 99.93 % complete ) and 4052 restraints for refining 3797 atoms. 900 conditional restraints added. Observations/parameters ratio is 2.20 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2369 (Rfree = 0.000) for 3797 atoms. Found 75 (75 requested) and removed 57 (55 requested) atoms. Cycle 22: After refmac, R = 0.2174 (Rfree = 0.000) for 3812 atoms. Found 69 (73 requested) and removed 46 (55 requested) atoms. Cycle 23: After refmac, R = 0.2085 (Rfree = 0.000) for 3833 atoms. Found 56 (71 requested) and removed 26 (55 requested) atoms. Cycle 24: After refmac, R = 0.2031 (Rfree = 0.000) for 3860 atoms. Found 43 (72 requested) and removed 37 (56 requested) atoms. Cycle 25: After refmac, R = 0.1991 (Rfree = 0.000) for 3859 atoms. Found 60 (69 requested) and removed 28 (56 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.25 2.08 NCS extension: 92 residues added (29 deleted due to clashes), 3985 seeds are put forward Round 1: 411 peptides, 11 chains. Longest chain 144 peptides. Score 0.901 Round 2: 413 peptides, 10 chains. Longest chain 80 peptides. Score 0.906 Round 3: 412 peptides, 11 chains. Longest chain 104 peptides. Score 0.902 Round 4: 403 peptides, 15 chains. Longest chain 66 peptides. Score 0.879 Round 5: 413 peptides, 12 chains. Longest chain 75 peptides. Score 0.898 Taking the results from Round 2 Chains 14, Residues 403, Estimated correctness of the model 98.9 % 9 chains (391 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 93 A and 97 A Built loop between residues 207 A and 215 A Built loop between residues 39 B and 44 B Built loop between residues 93 B and 96 B Built loop between residues 168 B and 172 B 8 chains (421 residues) following loop building 4 chains (410 residues) in sequence following loop building ------------------------------------------------------ 33464 reflections ( 99.93 % complete ) and 3770 restraints for refining 3872 atoms. 402 conditional restraints added. Observations/parameters ratio is 2.16 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2389 (Rfree = 0.000) for 3872 atoms. Found 69 (69 requested) and removed 59 (56 requested) atoms. Cycle 27: After refmac, R = 0.2194 (Rfree = 0.000) for 3876 atoms. Found 67 (67 requested) and removed 56 (56 requested) atoms. Cycle 28: After refmac, R = 0.2087 (Rfree = 0.000) for 3881 atoms. Found 65 (65 requested) and removed 33 (56 requested) atoms. Cycle 29: After refmac, R = 0.2014 (Rfree = 0.000) for 3911 atoms. Found 63 (63 requested) and removed 34 (56 requested) atoms. Cycle 30: After refmac, R = 0.1972 (Rfree = 0.000) for 3933 atoms. Found 57 (62 requested) and removed 35 (57 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.26 2.09 NCS extension: 126 residues added (83 deleted due to clashes), 4085 seeds are put forward Round 1: 411 peptides, 10 chains. Longest chain 144 peptides. Score 0.905 Round 2: 419 peptides, 9 chains. Longest chain 126 peptides. Score 0.913 Round 3: 414 peptides, 10 chains. Longest chain 104 peptides. Score 0.907 Round 4: 416 peptides, 12 chains. Longest chain 80 peptides. Score 0.900 Round 5: 408 peptides, 10 chains. Longest chain 145 peptides. Score 0.903 Taking the results from Round 2 Chains 13, Residues 410, Estimated correctness of the model 99.0 % 8 chains (397 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 41 A and 44 A Built loop between residues 168 A and 171 A Built loop between residues 93 B and 97 B 10 chains (417 residues) following loop building 5 chains (404 residues) in sequence following loop building ------------------------------------------------------ 33464 reflections ( 99.93 % complete ) and 3812 restraints for refining 3871 atoms. 483 conditional restraints added. Observations/parameters ratio is 2.16 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2293 (Rfree = 0.000) for 3871 atoms. Found 58 (58 requested) and removed 56 (56 requested) atoms. Failed to save intermediate PDB Cycle 32: After refmac, R = 0.2114 (Rfree = 0.000) for 3864 atoms. Found 56 (56 requested) and removed 51 (56 requested) atoms. Cycle 33: After refmac, R = 0.2019 (Rfree = 0.000) for 3867 atoms. Found 56 (56 requested) and removed 23 (56 requested) atoms. Cycle 34: After refmac, R = 0.1963 (Rfree = 0.000) for 3897 atoms. Found 46 (56 requested) and removed 27 (56 requested) atoms. Cycle 35: After refmac, R = 0.1935 (Rfree = 0.000) for 3908 atoms. Found 56 (56 requested) and removed 35 (56 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.26 2.09 NCS extension: 127 residues added (79 deleted due to clashes), 4057 seeds are put forward Round 1: 411 peptides, 10 chains. Longest chain 144 peptides. Score 0.905 Round 2: 417 peptides, 10 chains. Longest chain 81 peptides. Score 0.909 Round 3: 411 peptides, 11 chains. Longest chain 104 peptides. Score 0.901 Round 4: 413 peptides, 10 chains. Longest chain 145 peptides. Score 0.906 Round 5: 412 peptides, 12 chains. Longest chain 80 peptides. Score 0.898 Taking the results from Round 2 Chains 12, Residues 407, Estimated correctness of the model 98.9 % 8 chains (392 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 95 A and 98 A Built loop between residues 168 A and 171 A Built loop between residues 204 A and 214 A Built loop between residues 93 B and 97 B Built loop between residues 208 B and 215 B 5 chains (427 residues) following loop building 3 chains (414 residues) in sequence following loop building ------------------------------------------------------ 33464 reflections ( 99.93 % complete ) and 3852 restraints for refining 3916 atoms. 469 conditional restraints added. Observations/parameters ratio is 2.14 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2399 (Rfree = 0.000) for 3916 atoms. Found 56 (56 requested) and removed 59 (56 requested) atoms. Cycle 37: After refmac, R = 0.2178 (Rfree = 0.000) for 3907 atoms. Found 56 (56 requested) and removed 56 (56 requested) atoms. Cycle 38: After refmac, R = 0.2073 (Rfree = 0.000) for 3899 atoms. Found 56 (56 requested) and removed 28 (56 requested) atoms. Cycle 39: After refmac, R = 0.2001 (Rfree = 0.000) for 3922 atoms. Found 54 (56 requested) and removed 31 (56 requested) atoms. Cycle 40: After refmac, R = 0.1962 (Rfree = 0.000) for 3943 atoms. Found 49 (57 requested) and removed 34 (57 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.26 2.09 NCS extension: 153 residues added (80 deleted due to clashes), 4117 seeds are put forward Round 1: 414 peptides, 8 chains. Longest chain 145 peptides. Score 0.914 Round 2: 417 peptides, 10 chains. Longest chain 80 peptides. Score 0.909 Round 3: 419 peptides, 9 chains. Longest chain 145 peptides. Score 0.913 Round 4: 419 peptides, 9 chains. Longest chain 79 peptides. Score 0.913 Round 5: 411 peptides, 12 chains. Longest chain 83 peptides. Score 0.897 Taking the results from Round 1 Chains 9, Residues 406, Estimated correctness of the model 99.0 % 6 chains (391 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 206 A and 214 A Built loop between residues 205 B and 215 B 7 chains (422 residues) following loop building 4 chains (407 residues) in sequence following loop building ------------------------------------------------------ 33464 reflections ( 99.93 % complete ) and 3955 restraints for refining 3921 atoms. 599 conditional restraints added. Observations/parameters ratio is 2.13 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2343 (Rfree = 0.000) for 3921 atoms. Found 56 (56 requested) and removed 58 (56 requested) atoms. Cycle 42: After refmac, R = 0.2155 (Rfree = 0.000) for 3913 atoms. Found 56 (56 requested) and removed 51 (56 requested) atoms. Cycle 43: After refmac, R = 0.2061 (Rfree = 0.000) for 3910 atoms. Found 56 (56 requested) and removed 29 (56 requested) atoms. Cycle 44: After refmac, R = 0.1988 (Rfree = 0.000) for 3933 atoms. Found 52 (57 requested) and removed 30 (57 requested) atoms. Cycle 45: After refmac, R = 0.1949 (Rfree = 0.000) for 3951 atoms. Found 57 (57 requested) and removed 27 (57 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.25 2.08 NCS extension: 29 residues added (22 deleted due to clashes), 4012 seeds are put forward Round 1: 405 peptides, 11 chains. Longest chain 104 peptides. Score 0.897 Round 2: 417 peptides, 8 chains. Longest chain 81 peptides. Score 0.916 Round 3: 413 peptides, 12 chains. Longest chain 144 peptides. Score 0.898 Round 4: 419 peptides, 10 chains. Longest chain 80 peptides. Score 0.910 Round 5: 411 peptides, 11 chains. Longest chain 144 peptides. Score 0.901 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 10, Residues 409, Estimated correctness of the model 99.1 % 8 chains (406 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 95 A and 98 A Built loop between residues 168 A and 172 A Built loop between residues 93 B and 97 B 7 chains (417 residues) following loop building 5 chains (414 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 33464 reflections ( 99.93 % complete ) and 3365 restraints for refining 3319 atoms. Observations/parameters ratio is 2.52 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2712 (Rfree = 0.000) for 3319 atoms. Found 48 (48 requested) and removed 0 (48 requested) atoms. Cycle 47: After refmac, R = 0.2492 (Rfree = 0.000) for 3319 atoms. Found 31 (48 requested) and removed 0 (48 requested) atoms. Cycle 48: After refmac, R = 0.2337 (Rfree = 0.000) for 3319 atoms. Found 19 (49 requested) and removed 0 (49 requested) atoms. Cycle 49: After refmac, R = 0.2252 (Rfree = 0.000) for 3319 atoms. TimeTaking 68.22