Mon 24 Dec 07:38:21 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 2afb-2.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2afb-2.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2afb-2.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2afb-2.0-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/2afb-2.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2afb-2.0-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 07:38:25 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/2afb-2.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2afb-2.0-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 656 and 0 Target number of residues in the AU: 656 Target solvent content: 0.5159 Checking the provided sequence file Detected sequence length: 351 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 702 Adjusted target solvent content: 0.48 Input MTZ file: 2afb-2.0-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: 155 Cell parameters: 120.993 120.993 260.300 90.000 90.000 120.000 Input sequence file: 2afb-2.0-parrot-noncs.fasta_lf Building free atoms model in initial map for 5616 target number of atoms Had to go as low as 0.50 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: 97.203 2.050 Wilson plot Bfac: 26.83 45456 reflections ( 98.19 % complete ) and 0 restraints for refining 6260 atoms. Observations/parameters ratio is 1.82 ------------------------------------------------------ Starting model: R = 0.3467 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2965 (Rfree = 0.000) for 6260 atoms. Found 140 (199 requested) and removed 111 (99 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.13 2.19 NCS extension: 0 residues added, 6289 seeds are put forward Round 1: 441 peptides, 59 chains. Longest chain 21 peptides. Score 0.603 Round 2: 509 peptides, 35 chains. Longest chain 40 peptides. Score 0.817 Round 3: 538 peptides, 26 chains. Longest chain 50 peptides. Score 0.871 Round 4: 549 peptides, 25 chains. Longest chain 67 peptides. Score 0.880 Round 5: 580 peptides, 16 chains. Longest chain 111 peptides. Score 0.920 Taking the results from Round 5 Chains 19, Residues 564, Estimated correctness of the model 99.2 % 11 chains (520 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 43 A and 46 A Built loop between residues 66 A and 73 A Built loop between residues 135 A and 139 A Built loop between residues 304 A and 307 A Built loop between residues 82 B and 85 B Built loop between residues 168 B and 178 B 9 chains (579 residues) following loop building 5 chains (544 residues) in sequence following loop building ------------------------------------------------------ 45456 reflections ( 98.19 % complete ) and 6080 restraints for refining 5569 atoms. 1567 conditional restraints added. Observations/parameters ratio is 2.04 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3254 (Rfree = 0.000) for 5569 atoms. Found 174 (178 requested) and removed 105 (89 requested) atoms. Cycle 2: After refmac, R = 0.2913 (Rfree = 0.000) for 5612 atoms. Found 132 (175 requested) and removed 89 (89 requested) atoms. Cycle 3: After refmac, R = 0.2708 (Rfree = 0.000) for 5590 atoms. Found 120 (173 requested) and removed 43 (90 requested) atoms. Cycle 4: After refmac, R = 0.2583 (Rfree = 0.000) for 5635 atoms. Found 91 (173 requested) and removed 42 (90 requested) atoms. Cycle 5: After refmac, R = 0.2467 (Rfree = 0.000) for 5652 atoms. Found 94 (174 requested) and removed 31 (90 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.11 2.17 NCS extension: 22 residues added (177 deleted due to clashes), 5745 seeds are put forward Round 1: 592 peptides, 12 chains. Longest chain 111 peptides. Score 0.934 Round 2: 599 peptides, 13 chains. Longest chain 121 peptides. Score 0.934 Round 3: 606 peptides, 10 chains. Longest chain 205 peptides. Score 0.942 Round 4: 603 peptides, 14 chains. Longest chain 206 peptides. Score 0.933 Round 5: 607 peptides, 12 chains. Longest chain 169 peptides. Score 0.938 Taking the results from Round 3 Chains 11, Residues 596, Estimated correctness of the model 99.6 % 7 chains (558 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 82 A and 85 A Built loop between residues 285 A and 288 A Built loop between residues 303 B and 306 B 7 chains (601 residues) following loop building 4 chains (564 residues) in sequence following loop building ------------------------------------------------------ 45456 reflections ( 98.19 % complete ) and 5828 restraints for refining 5532 atoms. 1162 conditional restraints added. Observations/parameters ratio is 2.05 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2561 (Rfree = 0.000) for 5532 atoms. Found 151 (169 requested) and removed 101 (88 requested) atoms. Cycle 7: After refmac, R = 0.2383 (Rfree = 0.000) for 5573 atoms. Found 132 (167 requested) and removed 47 (89 requested) atoms. Cycle 8: After refmac, R = 0.2292 (Rfree = 0.000) for 5643 atoms. Found 106 (169 requested) and removed 62 (90 requested) atoms. Cycle 9: After refmac, R = 0.2249 (Rfree = 0.000) for 5673 atoms. Found 104 (167 requested) and removed 54 (90 requested) atoms. Cycle 10: After refmac, R = 0.2203 (Rfree = 0.000) for 5714 atoms. Found 104 (164 requested) and removed 63 (91 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.11 2.17 NCS extension: 23 residues added (69 deleted due to clashes), 5782 seeds are put forward Round 1: 607 peptides, 12 chains. Longest chain 168 peptides. Score 0.938 Round 2: 614 peptides, 9 chains. Longest chain 172 peptides. Score 0.947 Round 3: 615 peptides, 11 chains. Longest chain 206 peptides. Score 0.943 Round 4: 618 peptides, 12 chains. Longest chain 97 peptides. Score 0.942 Round 5: 619 peptides, 9 chains. Longest chain 184 peptides. Score 0.948 Taking the results from Round 5 Chains 9, Residues 610, Estimated correctness of the model 99.7 % 7 chains (588 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 29 A and 32 A Built loop between residues 301 A and 304 A Built loop between residues 31 B and 34 B 6 chains (616 residues) following loop building 4 chains (594 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 45456 reflections ( 98.19 % complete ) and 5783 restraints for refining 5643 atoms. 936 conditional restraints added. Observations/parameters ratio is 2.01 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2372 (Rfree = 0.000) for 5643 atoms. Found 158 (158 requested) and removed 102 (90 requested) atoms. Cycle 12: After refmac, R = 0.2242 (Rfree = 0.000) for 5691 atoms. Found 117 (156 requested) and removed 85 (90 requested) atoms. Cycle 13: After refmac, R = 0.2169 (Rfree = 0.000) for 5715 atoms. Found 116 (153 requested) and removed 61 (91 requested) atoms. Cycle 14: After refmac, R = 0.2133 (Rfree = 0.000) for 5760 atoms. Found 101 (150 requested) and removed 71 (91 requested) atoms. Cycle 15: After refmac, R = 0.2078 (Rfree = 0.000) for 5785 atoms. Found 79 (147 requested) and removed 52 (92 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.10 2.16 NCS extension: 13 residues added (27 deleted due to clashes), 5826 seeds are put forward Round 1: 617 peptides, 11 chains. Longest chain 137 peptides. Score 0.943 Round 2: 624 peptides, 6 chains. Longest chain 172 peptides. Score 0.955 Round 3: 617 peptides, 7 chains. Longest chain 203 peptides. Score 0.952 Round 4: 620 peptides, 12 chains. Longest chain 172 peptides. Score 0.942 Round 5: 612 peptides, 13 chains. Longest chain 185 peptides. Score 0.938 Taking the results from Round 2 Chains 6, Residues 618, Estimated correctness of the model 99.7 % 5 chains (598 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 95 B and 98 B 5 chains (620 residues) following loop building 4 chains (600 residues) in sequence following loop building ------------------------------------------------------ 45456 reflections ( 98.19 % complete ) and 5750 restraints for refining 5690 atoms. 854 conditional restraints added. Observations/parameters ratio is 2.00 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2256 (Rfree = 0.000) for 5690 atoms. Found 141 (141 requested) and removed 98 (90 requested) atoms. Cycle 17: After refmac, R = 0.2139 (Rfree = 0.000) for 5717 atoms. Found 133 (138 requested) and removed 91 (91 requested) atoms. Cycle 18: After refmac, R = 0.2093 (Rfree = 0.000) for 5751 atoms. Found 117 (135 requested) and removed 65 (91 requested) atoms. Cycle 19: After refmac, R = 0.2055 (Rfree = 0.000) for 5798 atoms. Found 127 (133 requested) and removed 56 (92 requested) atoms. Cycle 20: After refmac, R = 0.2021 (Rfree = 0.000) for 5859 atoms. Found 104 (135 requested) and removed 81 (93 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.11 2.17 NCS extension: 12 residues added (21 deleted due to clashes), 5894 seeds are put forward Round 1: 614 peptides, 12 chains. Longest chain 131 peptides. Score 0.940 Round 2: 623 peptides, 6 chains. Longest chain 206 peptides. Score 0.955 Round 3: 621 peptides, 8 chains. Longest chain 172 peptides. Score 0.951 Round 4: 623 peptides, 10 chains. Longest chain 207 peptides. Score 0.947 Round 5: 616 peptides, 15 chains. Longest chain 155 peptides. Score 0.934 Taking the results from Round 2 Chains 6, Residues 617, Estimated correctness of the model 99.7 % 6 chains (617 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 255 A and 258 A 5 chains (619 residues) following loop building 5 chains (619 residues) in sequence following loop building ------------------------------------------------------ 45456 reflections ( 98.19 % complete ) and 5769 restraints for refining 5750 atoms. 794 conditional restraints added. Observations/parameters ratio is 1.98 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2221 (Rfree = 0.000) for 5750 atoms. Found 128 (128 requested) and removed 101 (91 requested) atoms. Cycle 22: After refmac, R = 0.2103 (Rfree = 0.000) for 5764 atoms. Found 124 (125 requested) and removed 82 (92 requested) atoms. Cycle 23: After refmac, R = 0.2053 (Rfree = 0.000) for 5803 atoms. Found 122 (122 requested) and removed 54 (92 requested) atoms. Cycle 24: After refmac, R = 0.2027 (Rfree = 0.000) for 5865 atoms. Found 104 (123 requested) and removed 67 (93 requested) atoms. Cycle 25: After refmac, R = 0.2004 (Rfree = 0.000) for 5897 atoms. Found 120 (120 requested) and removed 60 (94 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.10 2.16 NCS extension: 6 residues added (26 deleted due to clashes), 5963 seeds are put forward Round 1: 617 peptides, 11 chains. Longest chain 137 peptides. Score 0.943 Round 2: 622 peptides, 8 chains. Longest chain 166 peptides. Score 0.951 Round 3: 622 peptides, 12 chains. Longest chain 133 peptides. Score 0.943 Round 4: 626 peptides, 9 chains. Longest chain 167 peptides. Score 0.950 Round 5: 623 peptides, 9 chains. Longest chain 172 peptides. Score 0.949 Taking the results from Round 2 Chains 9, Residues 614, Estimated correctness of the model 99.7 % 7 chains (609 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 253 A and 256 A Built loop between residues 95 B and 98 B 7 chains (618 residues) following loop building 5 chains (613 residues) in sequence following loop building ------------------------------------------------------ 45456 reflections ( 98.19 % complete ) and 5736 restraints for refining 5757 atoms. 806 conditional restraints added. Observations/parameters ratio is 1.97 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2178 (Rfree = 0.000) for 5757 atoms. Found 117 (117 requested) and removed 96 (91 requested) atoms. Cycle 27: After refmac, R = 0.2081 (Rfree = 0.000) for 5770 atoms. Found 114 (114 requested) and removed 53 (92 requested) atoms. Cycle 28: After refmac, R = 0.2028 (Rfree = 0.000) for 5826 atoms. Found 115 (115 requested) and removed 68 (92 requested) atoms. Cycle 29: After refmac, R = 0.2010 (Rfree = 0.000) for 5868 atoms. Found 97 (112 requested) and removed 74 (93 requested) atoms. Cycle 30: After refmac, R = 0.1978 (Rfree = 0.000) for 5888 atoms. Found 108 (108 requested) and removed 59 (93 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.10 2.16 NCS extension: 10 residues added (29 deleted due to clashes), 5948 seeds are put forward Round 1: 622 peptides, 8 chains. Longest chain 172 peptides. Score 0.951 Round 2: 626 peptides, 6 chains. Longest chain 172 peptides. Score 0.956 Round 3: 630 peptides, 7 chains. Longest chain 172 peptides. Score 0.955 Round 4: 623 peptides, 11 chains. Longest chain 161 peptides. Score 0.945 Round 5: 622 peptides, 10 chains. Longest chain 155 peptides. Score 0.947 Taking the results from Round 2 Chains 6, Residues 620, Estimated correctness of the model 99.7 % 6 chains (620 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 95 B and 98 B 5 chains (622 residues) following loop building 5 chains (622 residues) in sequence following loop building ------------------------------------------------------ 45456 reflections ( 98.19 % complete ) and 5673 restraints for refining 5748 atoms. 677 conditional restraints added. Observations/parameters ratio is 1.98 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2155 (Rfree = 0.000) for 5748 atoms. Found 102 (102 requested) and removed 99 (91 requested) atoms. Cycle 32: After refmac, R = 0.2052 (Rfree = 0.000) for 5742 atoms. Found 99 (99 requested) and removed 64 (91 requested) atoms. Cycle 33: After refmac, R = 0.2010 (Rfree = 0.000) for 5773 atoms. Found 96 (96 requested) and removed 59 (92 requested) atoms. Cycle 34: After refmac, R = 0.1998 (Rfree = 0.000) for 5808 atoms. Found 92 (92 requested) and removed 56 (92 requested) atoms. Cycle 35: After refmac, R = 0.1971 (Rfree = 0.000) for 5839 atoms. Found 93 (93 requested) and removed 61 (93 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.10 2.16 NCS extension: 7 residues added (26 deleted due to clashes), 5879 seeds are put forward Round 1: 622 peptides, 8 chains. Longest chain 172 peptides. Score 0.951 Round 2: 626 peptides, 6 chains. Longest chain 208 peptides. Score 0.956 Round 3: 621 peptides, 10 chains. Longest chain 173 peptides. Score 0.947 Round 4: 622 peptides, 11 chains. Longest chain 153 peptides. Score 0.945 Round 5: 624 peptides, 10 chains. Longest chain 149 peptides. Score 0.947 Taking the results from Round 2 Chains 6, Residues 620, Estimated correctness of the model 99.7 % 6 chains (620 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 253 A and 256 A 5 chains (622 residues) following loop building 5 chains (622 residues) in sequence following loop building ------------------------------------------------------ 45456 reflections ( 98.19 % complete ) and 5677 restraints for refining 5739 atoms. 687 conditional restraints added. Observations/parameters ratio is 1.98 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2152 (Rfree = 0.000) for 5739 atoms. Found 91 (91 requested) and removed 94 (91 requested) atoms. Cycle 37: After refmac, R = 0.2051 (Rfree = 0.000) for 5718 atoms. Found 91 (91 requested) and removed 50 (91 requested) atoms. Cycle 38: After refmac, R = 0.1991 (Rfree = 0.000) for 5756 atoms. Found 91 (91 requested) and removed 47 (91 requested) atoms. Cycle 39: After refmac, R = 0.1977 (Rfree = 0.000) for 5793 atoms. Found 92 (92 requested) and removed 73 (92 requested) atoms. Cycle 40: After refmac, R = 0.1962 (Rfree = 0.000) for 5809 atoms. Found 92 (92 requested) and removed 65 (92 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.10 2.16 NCS extension: 8 residues added (26 deleted due to clashes), 5846 seeds are put forward Round 1: 625 peptides, 7 chains. Longest chain 172 peptides. Score 0.954 Round 2: 623 peptides, 7 chains. Longest chain 208 peptides. Score 0.953 Round 3: 622 peptides, 11 chains. Longest chain 148 peptides. Score 0.945 Round 4: 629 peptides, 8 chains. Longest chain 208 peptides. Score 0.953 Round 5: 623 peptides, 13 chains. Longest chain 155 peptides. Score 0.941 Taking the results from Round 1 Chains 7, Residues 618, Estimated correctness of the model 99.7 % 7 chains (618 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 281 A and 284 A Built loop between residues 44 B and 48 B 5 chains (623 residues) following loop building 5 chains (623 residues) in sequence following loop building ------------------------------------------------------ 45456 reflections ( 98.19 % complete ) and 5686 restraints for refining 5737 atoms. 681 conditional restraints added. Observations/parameters ratio is 1.98 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2136 (Rfree = 0.000) for 5737 atoms. Found 91 (91 requested) and removed 97 (91 requested) atoms. Cycle 42: After refmac, R = 0.2037 (Rfree = 0.000) for 5719 atoms. Found 91 (91 requested) and removed 52 (91 requested) atoms. Cycle 43: After refmac, R = 0.1988 (Rfree = 0.000) for 5755 atoms. Found 91 (91 requested) and removed 46 (91 requested) atoms. Cycle 44: After refmac, R = 0.1972 (Rfree = 0.000) for 5795 atoms. Found 92 (92 requested) and removed 62 (92 requested) atoms. Cycle 45: After refmac, R = 0.1961 (Rfree = 0.000) for 5823 atoms. Found 92 (92 requested) and removed 63 (92 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.10 2.16 NCS extension: 8 residues added (29 deleted due to clashes), 5861 seeds are put forward Round 1: 624 peptides, 7 chains. Longest chain 172 peptides. Score 0.953 Round 2: 626 peptides, 6 chains. Longest chain 208 peptides. Score 0.956 Round 3: 621 peptides, 11 chains. Longest chain 173 peptides. Score 0.944 Round 4: 623 peptides, 9 chains. Longest chain 184 peptides. Score 0.949 Round 5: 623 peptides, 9 chains. Longest chain 167 peptides. Score 0.949 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 6, Residues 620, Estimated correctness of the model 99.7 % 6 chains (620 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 183 A and 197 A Built loop between residues 216 A and 228 A Built loop between residues 279 A and 282 A Built loop between residues 217 B and 231 B 2 chains (659 residues) following loop building 2 chains (659 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 45456 reflections ( 98.19 % complete ) and 5291 restraints for refining 5179 atoms. Observations/parameters ratio is 2.19 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2790 (Rfree = 0.000) for 5179 atoms. Found 62 (82 requested) and removed 0 (82 requested) atoms. Cycle 47: After refmac, R = 0.2557 (Rfree = 0.000) for 5179 atoms. Found 35 (83 requested) and removed 1 (83 requested) atoms. Cycle 48: After refmac, R = 0.2464 (Rfree = 0.000) for 5179 atoms. Found 20 (84 requested) and removed 4 (84 requested) atoms. Cycle 49: After refmac, R = 0.2415 (Rfree = 0.000) for 5179 atoms. Found 8 (84 requested) and removed 7 (84 requested) atoms. Writing output files ... TimeTaking 89.47