Sun 23 Dec 22:23:10 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 2p8j-2.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2p8j-2.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2p8j-2.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p8j-2.0-parrot-hancs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p8j-2.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p8j-2.0-parrot-hancs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Sun 23 Dec 22:23:20 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/2p8j-2.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p8j-2.0-parrot-hancs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 546 and 0 Target number of residues in the AU: 546 Target solvent content: 0.5429 Checking the provided sequence file Detected sequence length: 209 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 418 Adjusted target solvent content: 0.65 Input MTZ file: 2p8j-2.0-parrot-hancs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 152 Cell parameters: 83.860 83.860 159.200 90.000 90.000 120.000 Input sequence file: 2p8j-2.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 3344 target number of atoms Had to go as low as 0.85 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: 72.625 2.001 Wilson plot Bfac: 33.59 44382 reflections ( 99.74 % complete ) and 0 restraints for refining 3714 atoms. Observations/parameters ratio is 2.99 ------------------------------------------------------ Starting model: R = 0.3297 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2764 (Rfree = 0.000) for 3714 atoms. Found 127 (127 requested) and removed 36 (63 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.26 1.84 NCS extension: 0 residues added, 3805 seeds are put forward Round 1: 341 peptides, 33 chains. Longest chain 40 peptides. Score 0.670 Round 2: 364 peptides, 23 chains. Longest chain 45 peptides. Score 0.770 Round 3: 385 peptides, 15 chains. Longest chain 54 peptides. Score 0.837 Round 4: 395 peptides, 11 chains. Longest chain 72 peptides. Score 0.864 Round 5: 396 peptides, 8 chains. Longest chain 120 peptides. Score 0.878 Taking the results from Round 5 Chains 9, Residues 388, Estimated correctness of the model 98.5 % 7 chains (379 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 114 A and 117 A Built loop between residues 22 B and 25 B Built loop between residues 143 B and 146 B Built loop between residues 187 B and 192 B 5 chains (398 residues) following loop building 3 chains (389 residues) in sequence following loop building ------------------------------------------------------ 44382 reflections ( 99.74 % complete ) and 3831 restraints for refining 3766 atoms. 568 conditional restraints added. Observations/parameters ratio is 2.95 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2647 (Rfree = 0.000) for 3766 atoms. Found 128 (128 requested) and removed 69 (64 requested) atoms. Cycle 2: After refmac, R = 0.2434 (Rfree = 0.000) for 3809 atoms. Found 127 (127 requested) and removed 52 (65 requested) atoms. Cycle 3: After refmac, R = 0.2299 (Rfree = 0.000) for 3859 atoms. Found 118 (129 requested) and removed 38 (66 requested) atoms. Cycle 4: After refmac, R = 0.2211 (Rfree = 0.000) for 3925 atoms. Found 120 (131 requested) and removed 42 (67 requested) atoms. Cycle 5: After refmac, R = 0.2140 (Rfree = 0.000) for 3993 atoms. Found 115 (133 requested) and removed 39 (68 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.21 1.80 NCS extension: 138 residues added (84 deleted due to clashes), 4208 seeds are put forward Round 1: 401 peptides, 6 chains. Longest chain 204 peptides. Score 0.890 Round 2: 400 peptides, 6 chains. Longest chain 175 peptides. Score 0.889 Round 3: 401 peptides, 6 chains. Longest chain 131 peptides. Score 0.890 Round 4: 401 peptides, 6 chains. Longest chain 137 peptides. Score 0.890 Round 5: 399 peptides, 8 chains. Longest chain 131 peptides. Score 0.880 Taking the results from Round 4 Chains 6, Residues 395, Estimated correctness of the model 98.8 % 6 chains (395 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 63 A and 66 A Built loop between residues 148 A and 156 A Built loop between residues 32 B and 35 B Built loop between residues 170 B and 173 B 2 chains (408 residues) following loop building 2 chains (408 residues) in sequence following loop building ------------------------------------------------------ 44382 reflections ( 99.74 % complete ) and 3745 restraints for refining 3910 atoms. 356 conditional restraints added. Observations/parameters ratio is 2.84 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2390 (Rfree = 0.000) for 3910 atoms. Found 130 (130 requested) and removed 70 (66 requested) atoms. Cycle 7: After refmac, R = 0.2238 (Rfree = 0.000) for 3958 atoms. Found 130 (130 requested) and removed 48 (67 requested) atoms. Cycle 8: After refmac, R = 0.2160 (Rfree = 0.000) for 4038 atoms. Found 120 (132 requested) and removed 53 (69 requested) atoms. Cycle 9: After refmac, R = 0.2115 (Rfree = 0.000) for 4100 atoms. Found 89 (134 requested) and removed 67 (70 requested) atoms. Cycle 10: After refmac, R = 0.2097 (Rfree = 0.000) for 4117 atoms. Found 91 (133 requested) and removed 60 (70 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.22 1.81 NCS extension: 0 residues added, 4150 seeds are put forward Round 1: 402 peptides, 6 chains. Longest chain 184 peptides. Score 0.890 Round 2: 404 peptides, 6 chains. Longest chain 131 peptides. Score 0.892 Round 3: 401 peptides, 6 chains. Longest chain 168 peptides. Score 0.890 Round 4: 401 peptides, 8 chains. Longest chain 131 peptides. Score 0.881 Round 5: 403 peptides, 7 chains. Longest chain 206 peptides. Score 0.887 Taking the results from Round 2 Chains 7, Residues 398, Estimated correctness of the model 98.8 % 6 chains (397 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 55 A and 58 A Built loop between residues 150 A and 155 A Built loop between residues 29 B and 34 B Built loop between residues 76 B and 79 B 3 chains (410 residues) following loop building 2 chains (409 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 44382 reflections ( 99.74 % complete ) and 3793 restraints for refining 3970 atoms. 392 conditional restraints added. Observations/parameters ratio is 2.79 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2335 (Rfree = 0.000) for 3970 atoms. Found 124 (124 requested) and removed 68 (67 requested) atoms. Cycle 12: After refmac, R = 0.2189 (Rfree = 0.000) for 4017 atoms. Found 121 (123 requested) and removed 68 (68 requested) atoms. Cycle 13: After refmac, R = 0.2119 (Rfree = 0.000) for 4060 atoms. Found 116 (122 requested) and removed 55 (69 requested) atoms. Cycle 14: After refmac, R = 0.2076 (Rfree = 0.000) for 4119 atoms. Found 96 (123 requested) and removed 68 (70 requested) atoms. Cycle 15: After refmac, R = 0.2055 (Rfree = 0.000) for 4141 atoms. Found 108 (121 requested) and removed 72 (70 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.22 1.81 NCS extension: 98 residues added (107 deleted due to clashes), 4278 seeds are put forward Round 1: 406 peptides, 7 chains. Longest chain 157 peptides. Score 0.889 Round 2: 408 peptides, 5 chains. Longest chain 131 peptides. Score 0.898 Round 3: 407 peptides, 6 chains. Longest chain 176 peptides. Score 0.893 Round 4: 406 peptides, 6 chains. Longest chain 149 peptides. Score 0.893 Round 5: 402 peptides, 9 chains. Longest chain 178 peptides. Score 0.878 Taking the results from Round 2 Chains 6, Residues 403, Estimated correctness of the model 98.9 % 5 chains (402 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 119 A and 122 A Built loop between residues 151 A and 155 A Built loop between residues 76 B and 79 B 3 chains (410 residues) following loop building 3 chains (410 residues) in sequence following loop building ------------------------------------------------------ 44382 reflections ( 99.74 % complete ) and 3765 restraints for refining 3981 atoms. 366 conditional restraints added. Observations/parameters ratio is 2.79 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2302 (Rfree = 0.000) for 3981 atoms. Found 114 (114 requested) and removed 69 (68 requested) atoms. Cycle 17: After refmac, R = 0.2171 (Rfree = 0.000) for 4016 atoms. Found 112 (112 requested) and removed 65 (68 requested) atoms. Cycle 18: After refmac, R = 0.2104 (Rfree = 0.000) for 4058 atoms. Found 104 (110 requested) and removed 50 (69 requested) atoms. Cycle 19: After refmac, R = 0.2061 (Rfree = 0.000) for 4110 atoms. Found 81 (112 requested) and removed 44 (70 requested) atoms. Cycle 20: After refmac, R = 0.2037 (Rfree = 0.000) for 4141 atoms. Found 82 (110 requested) and removed 54 (70 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.22 1.81 NCS extension: 0 residues added, 4170 seeds are put forward Round 1: 406 peptides, 5 chains. Longest chain 206 peptides. Score 0.897 Round 2: 406 peptides, 5 chains. Longest chain 141 peptides. Score 0.897 Round 3: 406 peptides, 5 chains. Longest chain 206 peptides. Score 0.897 Round 4: 404 peptides, 7 chains. Longest chain 93 peptides. Score 0.888 Round 5: 405 peptides, 4 chains. Longest chain 204 peptides. Score 0.900 Taking the results from Round 5 Chains 4, Residues 401, Estimated correctness of the model 99.0 % 4 chains (401 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 30 A and 33 A Built loop between residues 149 A and 154 A 2 chains (407 residues) following loop building 2 chains (407 residues) in sequence following loop building ------------------------------------------------------ 44382 reflections ( 99.74 % complete ) and 3829 restraints for refining 3979 atoms. 448 conditional restraints added. Observations/parameters ratio is 2.79 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2296 (Rfree = 0.000) for 3979 atoms. Found 103 (103 requested) and removed 69 (68 requested) atoms. Cycle 22: After refmac, R = 0.2167 (Rfree = 0.000) for 4007 atoms. Found 101 (101 requested) and removed 37 (68 requested) atoms. Cycle 23: After refmac, R = 0.2076 (Rfree = 0.000) for 4064 atoms. Found 84 (103 requested) and removed 48 (69 requested) atoms. Cycle 24: After refmac, R = 0.2056 (Rfree = 0.000) for 4095 atoms. Found 89 (101 requested) and removed 47 (70 requested) atoms. Cycle 25: After refmac, R = 0.2030 (Rfree = 0.000) for 4133 atoms. Found 99 (99 requested) and removed 49 (70 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.22 1.81 NCS extension: 0 residues added, 4186 seeds are put forward Round 1: 404 peptides, 7 chains. Longest chain 156 peptides. Score 0.888 Round 2: 403 peptides, 7 chains. Longest chain 110 peptides. Score 0.887 Round 3: 406 peptides, 4 chains. Longest chain 206 peptides. Score 0.901 Round 4: 403 peptides, 7 chains. Longest chain 131 peptides. Score 0.887 Round 5: 398 peptides, 11 chains. Longest chain 138 peptides. Score 0.866 Taking the results from Round 3 Chains 4, Residues 402, Estimated correctness of the model 99.0 % 4 chains (402 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 112 A and 115 A Built loop between residues 149 A and 155 A 2 chains (409 residues) following loop building 2 chains (409 residues) in sequence following loop building ------------------------------------------------------ 44382 reflections ( 99.74 % complete ) and 3840 restraints for refining 4050 atoms. 444 conditional restraints added. Observations/parameters ratio is 2.74 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2282 (Rfree = 0.000) for 4050 atoms. Found 97 (97 requested) and removed 73 (69 requested) atoms. Cycle 27: After refmac, R = 0.2155 (Rfree = 0.000) for 4066 atoms. Found 95 (95 requested) and removed 38 (69 requested) atoms. Cycle 28: After refmac, R = 0.2084 (Rfree = 0.000) for 4120 atoms. Found 85 (96 requested) and removed 44 (70 requested) atoms. Cycle 29: After refmac, R = 0.2054 (Rfree = 0.000) for 4155 atoms. Found 89 (94 requested) and removed 44 (71 requested) atoms. Cycle 30: After refmac, R = 0.2009 (Rfree = 0.000) for 4195 atoms. Found 94 (94 requested) and removed 59 (71 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.22 1.81 NCS extension: 0 residues added, 4232 seeds are put forward Round 1: 402 peptides, 8 chains. Longest chain 111 peptides. Score 0.882 Round 2: 407 peptides, 4 chains. Longest chain 206 peptides. Score 0.901 Round 3: 404 peptides, 6 chains. Longest chain 174 peptides. Score 0.892 Round 4: 398 peptides, 7 chains. Longest chain 166 peptides. Score 0.884 Round 5: 404 peptides, 7 chains. Longest chain 131 peptides. Score 0.888 Taking the results from Round 2 Chains 4, Residues 403, Estimated correctness of the model 99.0 % 4 chains (403 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 112 A and 115 A Built loop between residues 150 A and 155 A 2 chains (409 residues) following loop building 2 chains (409 residues) in sequence following loop building ------------------------------------------------------ 44382 reflections ( 99.74 % complete ) and 3791 restraints for refining 4025 atoms. 395 conditional restraints added. Observations/parameters ratio is 2.76 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2277 (Rfree = 0.000) for 4025 atoms. Found 88 (88 requested) and removed 71 (68 requested) atoms. Cycle 32: After refmac, R = 0.2133 (Rfree = 0.000) for 4035 atoms. Found 86 (86 requested) and removed 32 (69 requested) atoms. Cycle 33: After refmac, R = 0.2074 (Rfree = 0.000) for 4085 atoms. Found 86 (86 requested) and removed 31 (69 requested) atoms. Cycle 34: After refmac, R = 0.2038 (Rfree = 0.000) for 4139 atoms. Found 87 (87 requested) and removed 44 (70 requested) atoms. Cycle 35: After refmac, R = 0.2000 (Rfree = 0.000) for 4180 atoms. Found 84 (86 requested) and removed 49 (71 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.22 1.81 NCS extension: 0 residues added, 4215 seeds are put forward Round 1: 402 peptides, 7 chains. Longest chain 119 peptides. Score 0.886 Round 2: 407 peptides, 4 chains. Longest chain 206 peptides. Score 0.901 Round 3: 404 peptides, 7 chains. Longest chain 131 peptides. Score 0.888 Round 4: 403 peptides, 8 chains. Longest chain 123 peptides. Score 0.883 Round 5: 405 peptides, 6 chains. Longest chain 206 peptides. Score 0.892 Taking the results from Round 2 Chains 4, Residues 403, Estimated correctness of the model 99.0 % 4 chains (403 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 112 A and 115 A Built loop between residues 150 A and 155 A 2 chains (409 residues) following loop building 2 chains (409 residues) in sequence following loop building ------------------------------------------------------ 44382 reflections ( 99.74 % complete ) and 3813 restraints for refining 4034 atoms. 417 conditional restraints added. Observations/parameters ratio is 2.75 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2273 (Rfree = 0.000) for 4034 atoms. Found 79 (79 requested) and removed 70 (68 requested) atoms. Cycle 37: After refmac, R = 0.2135 (Rfree = 0.000) for 4036 atoms. Found 77 (77 requested) and removed 27 (69 requested) atoms. Cycle 38: After refmac, R = 0.2075 (Rfree = 0.000) for 4081 atoms. Found 78 (78 requested) and removed 30 (69 requested) atoms. Failed to save intermediate PDB Cycle 39: After refmac, R = 0.2041 (Rfree = 0.000) for 4126 atoms. Found 79 (79 requested) and removed 40 (70 requested) atoms. Cycle 40: After refmac, R = 0.2008 (Rfree = 0.000) for 4163 atoms. Found 77 (77 requested) and removed 47 (71 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.22 1.81 NCS extension: 0 residues added, 4194 seeds are put forward Round 1: 403 peptides, 6 chains. Longest chain 156 peptides. Score 0.891 Round 2: 403 peptides, 5 chains. Longest chain 204 peptides. Score 0.895 Round 3: 402 peptides, 7 chains. Longest chain 123 peptides. Score 0.886 Round 4: 400 peptides, 7 chains. Longest chain 131 peptides. Score 0.885 Round 5: 404 peptides, 5 chains. Longest chain 144 peptides. Score 0.896 Taking the results from Round 5 Chains 5, Residues 399, Estimated correctness of the model 98.9 % 5 chains (399 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 117 A and 120 A Built loop between residues 150 A and 155 A Built loop between residues 63 B and 66 B 2 chains (407 residues) following loop building 2 chains (407 residues) in sequence following loop building ------------------------------------------------------ 44382 reflections ( 99.74 % complete ) and 3818 restraints for refining 4022 atoms. 437 conditional restraints added. Observations/parameters ratio is 2.76 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2307 (Rfree = 0.000) for 4022 atoms. Found 71 (71 requested) and removed 73 (68 requested) atoms. Cycle 42: After refmac, R = 0.2148 (Rfree = 0.000) for 4013 atoms. Found 68 (68 requested) and removed 19 (68 requested) atoms. Cycle 43: After refmac, R = 0.2067 (Rfree = 0.000) for 4052 atoms. Found 69 (69 requested) and removed 32 (69 requested) atoms. Cycle 44: After refmac, R = 0.2036 (Rfree = 0.000) for 4088 atoms. Found 69 (69 requested) and removed 31 (69 requested) atoms. Cycle 45: After refmac, R = 0.2033 (Rfree = 0.000) for 4125 atoms. Found 70 (70 requested) and removed 36 (70 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.22 1.81 NCS extension: 0 residues added, 4159 seeds are put forward Round 1: 398 peptides, 7 chains. Longest chain 153 peptides. Score 0.884 Round 2: 401 peptides, 6 chains. Longest chain 144 peptides. Score 0.890 Round 3: 403 peptides, 7 chains. Longest chain 183 peptides. Score 0.887 Round 4: 401 peptides, 8 chains. Longest chain 144 peptides. Score 0.881 Round 5: 401 peptides, 7 chains. Longest chain 183 peptides. Score 0.886 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 6, Residues 395, Estimated correctness of the model 98.8 % 6 chains (395 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 29 A and 34 A Built loop between residues 63 A and 66 A Built loop between residues 112 B and 115 B Built loop between residues 149 B and 154 B 2 chains (407 residues) following loop building 2 chains (407 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 44382 reflections ( 99.74 % complete ) and 3381 restraints for refining 3323 atoms. Observations/parameters ratio is 3.34 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2697 (Rfree = 0.000) for 3323 atoms. Found 56 (56 requested) and removed 0 (56 requested) atoms. Cycle 47: After refmac, R = 0.2471 (Rfree = 0.000) for 3323 atoms. Found 54 (57 requested) and removed 0 (57 requested) atoms. Cycle 48: After refmac, R = 0.2307 (Rfree = 0.000) for 3323 atoms. Found 30 (58 requested) and removed 5 (58 requested) atoms. Cycle 49: After refmac, R = 0.2236 (Rfree = 0.000) for 3323 atoms. TimeTaking 75.25