Mon 24 Dec 00:42:53 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2p8j-2.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2p8j-2.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2p8j-2.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p8j-2.0-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2p8j-2.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p8j-2.0-parrot-mrncs ############### 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 00:42:58 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/mrncs/ArpWArp/wArpResults/WorkingDir/2p8j-2.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p8j-2.0-parrot-mrncs/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-mrncs.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-mrncs.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 3744 atoms. Observations/parameters ratio is 2.96 ------------------------------------------------------ Starting model: R = 0.3360 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2817 (Rfree = 0.000) for 3744 atoms. Found 128 (128 requested) and removed 47 (64 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.27 1.85 NCS extension: 0 residues added, 3825 seeds are put forward Round 1: 341 peptides, 31 chains. Longest chain 37 peptides. Score 0.685 Round 2: 353 peptides, 23 chains. Longest chain 48 peptides. Score 0.757 Round 3: 377 peptides, 15 chains. Longest chain 78 peptides. Score 0.829 Round 4: 382 peptides, 14 chains. Longest chain 58 peptides. Score 0.839 Round 5: 387 peptides, 13 chains. Longest chain 61 peptides. Score 0.848 Taking the results from Round 5 Chains 14, Residues 374, Estimated correctness of the model 97.7 % 9 chains (351 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 41 A and 52 A Built loop between residues 148 A and 158 A Built loop between residues 65 B and 75 B Built loop between residues 99 B and 102 B Built loop between residues 128 B and 131 B Built loop between residues 188 B and 192 B 5 chains (400 residues) following loop building 3 chains (386 residues) in sequence following loop building ------------------------------------------------------ 44382 reflections ( 99.74 % complete ) and 4014 restraints for refining 3863 atoms. 756 conditional restraints added. Observations/parameters ratio is 2.87 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2801 (Rfree = 0.000) for 3863 atoms. Found 132 (132 requested) and removed 79 (66 requested) atoms. Cycle 2: After refmac, R = 0.2538 (Rfree = 0.000) for 3896 atoms. Found 130 (130 requested) and removed 66 (66 requested) atoms. Cycle 3: After refmac, R = 0.2398 (Rfree = 0.000) for 3938 atoms. Found 113 (130 requested) and removed 53 (67 requested) atoms. Cycle 4: After refmac, R = 0.2304 (Rfree = 0.000) for 3980 atoms. Found 100 (131 requested) and removed 38 (68 requested) atoms. Cycle 5: After refmac, R = 0.2235 (Rfree = 0.000) for 4027 atoms. Found 89 (132 requested) and removed 41 (69 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.22 1.81 NCS extension: 48 residues added (194 deleted due to clashes), 4135 seeds are put forward Round 1: 393 peptides, 7 chains. Longest chain 137 peptides. Score 0.880 Round 2: 403 peptides, 6 chains. Longest chain 139 peptides. Score 0.891 Round 3: 395 peptides, 11 chains. Longest chain 101 peptides. Score 0.864 Round 4: 404 peptides, 6 chains. Longest chain 84 peptides. Score 0.892 Round 5: 404 peptides, 8 chains. Longest chain 138 peptides. Score 0.883 Taking the results from Round 4 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 63 A and 66 A Built loop between residues 148 A and 156 A Built loop between residues 62 B and 65 B Built loop between residues 143 B and 146 B 2 chains (410 residues) following loop building 2 chains (410 residues) in sequence following loop building ------------------------------------------------------ 44382 reflections ( 99.74 % complete ) and 3786 restraints for refining 3940 atoms. 382 conditional restraints added. Observations/parameters ratio is 2.82 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2440 (Rfree = 0.000) for 3940 atoms. Found 129 (129 requested) and removed 71 (67 requested) atoms. Cycle 7: After refmac, R = 0.2271 (Rfree = 0.000) for 3990 atoms. Found 104 (128 requested) and removed 56 (68 requested) atoms. Cycle 8: After refmac, R = 0.2180 (Rfree = 0.000) for 4032 atoms. Found 91 (127 requested) and removed 34 (69 requested) atoms. Cycle 9: After refmac, R = 0.2119 (Rfree = 0.000) for 4083 atoms. Found 86 (128 requested) and removed 33 (69 requested) atoms. Cycle 10: After refmac, R = 0.2076 (Rfree = 0.000) for 4123 atoms. Found 85 (130 requested) and removed 48 (70 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.22 1.81 NCS extension: 0 residues added, 4162 seeds are put forward Round 1: 406 peptides, 6 chains. Longest chain 178 peptides. Score 0.893 Round 2: 407 peptides, 4 chains. Longest chain 148 peptides. Score 0.901 Round 3: 401 peptides, 7 chains. Longest chain 144 peptides. Score 0.886 Round 4: 402 peptides, 5 chains. Longest chain 175 peptides. Score 0.894 Round 5: 401 peptides, 10 chains. Longest chain 93 peptides. Score 0.873 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 150 A and 156 A Built loop between residues 76 B and 79 B 2 chains (410 residues) following loop building 2 chains (410 residues) in sequence following loop building ------------------------------------------------------ 44382 reflections ( 99.74 % complete ) and 3762 restraints for refining 3983 atoms. 358 conditional restraints added. Observations/parameters ratio is 2.79 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2342 (Rfree = 0.000) for 3983 atoms. Found 122 (122 requested) and removed 69 (68 requested) atoms. Cycle 12: After refmac, R = 0.2217 (Rfree = 0.000) for 4034 atoms. Found 108 (121 requested) and removed 53 (69 requested) atoms. Cycle 13: After refmac, R = 0.2124 (Rfree = 0.000) for 4082 atoms. Found 87 (122 requested) and removed 41 (69 requested) atoms. Cycle 14: After refmac, R = 0.2080 (Rfree = 0.000) for 4121 atoms. Found 82 (124 requested) and removed 50 (70 requested) atoms. Cycle 15: After refmac, R = 0.2052 (Rfree = 0.000) for 4140 atoms. Found 86 (122 requested) and removed 41 (71 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.22 1.81 NCS extension: 0 residues added, 4186 seeds are put forward Round 1: 403 peptides, 6 chains. Longest chain 178 peptides. Score 0.891 Round 2: 404 peptides, 5 chains. Longest chain 204 peptides. Score 0.896 Round 3: 399 peptides, 9 chains. Longest chain 107 peptides. Score 0.876 Round 4: 403 peptides, 7 chains. Longest chain 131 peptides. Score 0.887 Round 5: 400 peptides, 8 chains. Longest chain 144 peptides. Score 0.881 Taking the results from Round 2 Chains 5, Residues 399, Estimated correctness of the model 98.9 % 4 chains (394 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 86 A and 89 A 4 chains (401 residues) following loop building 3 chains (396 residues) in sequence following loop building ------------------------------------------------------ 44382 reflections ( 99.74 % complete ) and 3889 restraints for refining 3970 atoms. 581 conditional restraints added. Observations/parameters ratio is 2.79 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2268 (Rfree = 0.000) for 3970 atoms. Found 116 (116 requested) and removed 67 (67 requested) atoms. Cycle 17: After refmac, R = 0.2140 (Rfree = 0.000) for 4012 atoms. Found 115 (115 requested) and removed 36 (68 requested) atoms. Cycle 18: After refmac, R = 0.2074 (Rfree = 0.000) for 4087 atoms. Found 88 (117 requested) and removed 44 (69 requested) atoms. Cycle 19: After refmac, R = 0.2023 (Rfree = 0.000) for 4127 atoms. Found 78 (118 requested) and removed 46 (70 requested) atoms. Cycle 20: After refmac, R = 0.1993 (Rfree = 0.000) for 4154 atoms. Found 78 (116 requested) and removed 50 (71 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.23 1.81 NCS extension: 104 residues added (110 deleted due to clashes), 4288 seeds are put forward Round 1: 403 peptides, 6 chains. Longest chain 178 peptides. Score 0.891 Round 2: 406 peptides, 3 chains. Longest chain 204 peptides. Score 0.905 Round 3: 402 peptides, 7 chains. Longest chain 131 peptides. Score 0.886 Round 4: 406 peptides, 2 chains. Longest chain 204 peptides. Score 0.909 Round 5: 401 peptides, 6 chains. Longest chain 93 peptides. Score 0.890 Taking the results from Round 4 Chains 5, Residues 404, Estimated correctness of the model 99.1 % 3 chains (397 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 148 B and 157 B 3 chains (407 residues) following loop building 2 chains (405 residues) in sequence following loop building ------------------------------------------------------ 44382 reflections ( 99.74 % complete ) and 3849 restraints for refining 4002 atoms. 474 conditional restraints added. Observations/parameters ratio is 2.77 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2287 (Rfree = 0.000) for 4002 atoms. Found 109 (109 requested) and removed 68 (68 requested) atoms. Cycle 22: After refmac, R = 0.2169 (Rfree = 0.000) for 4033 atoms. Found 108 (108 requested) and removed 45 (69 requested) atoms. Cycle 23: After refmac, R = 0.2098 (Rfree = 0.000) for 4092 atoms. Found 78 (109 requested) and removed 33 (70 requested) atoms. Cycle 24: After refmac, R = 0.2047 (Rfree = 0.000) for 4130 atoms. Found 72 (110 requested) and removed 38 (70 requested) atoms. Cycle 25: After refmac, R = 0.2019 (Rfree = 0.000) for 4158 atoms. Found 81 (108 requested) and removed 31 (71 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.23 1.81 NCS extension: 0 residues added, 4211 seeds are put forward Round 1: 405 peptides, 5 chains. Longest chain 178 peptides. Score 0.896 Round 2: 405 peptides, 5 chains. Longest chain 167 peptides. Score 0.896 Round 3: 402 peptides, 8 chains. Longest chain 144 peptides. Score 0.882 Round 4: 406 peptides, 5 chains. Longest chain 141 peptides. Score 0.897 Round 5: 400 peptides, 7 chains. Longest chain 174 peptides. Score 0.885 Taking the results from Round 4 Chains 7, Residues 401, Estimated correctness of the model 98.9 % 6 chains (396 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 84 A and 87 A Built loop between residues 150 A and 159 A Built loop between residues 143 B and 146 B Built loop between residues 169 B and 172 B 2 chains (410 residues) following loop building 2 chains (410 residues) in sequence following loop building ------------------------------------------------------ 44382 reflections ( 99.74 % complete ) and 3863 restraints for refining 4031 atoms. 459 conditional restraints added. Observations/parameters ratio is 2.75 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2310 (Rfree = 0.000) for 4031 atoms. Found 104 (104 requested) and removed 73 (68 requested) atoms. Cycle 27: After refmac, R = 0.2164 (Rfree = 0.000) for 4056 atoms. Found 102 (102 requested) and removed 33 (69 requested) atoms. Cycle 28: After refmac, R = 0.2094 (Rfree = 0.000) for 4117 atoms. Found 84 (104 requested) and removed 33 (70 requested) atoms. Cycle 29: After refmac, R = 0.2036 (Rfree = 0.000) for 4163 atoms. Found 93 (105 requested) and removed 32 (71 requested) atoms. Cycle 30: After refmac, R = 0.1996 (Rfree = 0.000) for 4217 atoms. Found 88 (107 requested) and removed 60 (72 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.22 1.81 NCS extension: 0 residues added, 4248 seeds are put forward Round 1: 403 peptides, 7 chains. Longest chain 157 peptides. Score 0.887 Round 2: 406 peptides, 5 chains. Longest chain 131 peptides. Score 0.897 Round 3: 403 peptides, 6 chains. Longest chain 136 peptides. Score 0.891 Round 4: 407 peptides, 4 chains. Longest chain 206 peptides. Score 0.901 Round 5: 403 peptides, 7 chains. Longest chain 120 peptides. Score 0.887 Taking the results from Round 4 Chains 6, Residues 403, Estimated correctness of the model 99.0 % 5 chains (400 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 30 A and 33 A Built loop between residues 111 A and 114 A 4 chains (407 residues) following loop building 3 chains (404 residues) in sequence following loop building ------------------------------------------------------ 44382 reflections ( 99.74 % complete ) and 3833 restraints for refining 4015 atoms. 464 conditional restraints added. Observations/parameters ratio is 2.76 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2260 (Rfree = 0.000) for 4015 atoms. Found 99 (99 requested) and removed 69 (68 requested) atoms. Cycle 32: After refmac, R = 0.2128 (Rfree = 0.000) for 4035 atoms. Found 97 (97 requested) and removed 30 (69 requested) atoms. Cycle 33: After refmac, R = 0.2065 (Rfree = 0.000) for 4096 atoms. Found 98 (98 requested) and removed 25 (70 requested) atoms. Cycle 34: After refmac, R = 0.2030 (Rfree = 0.000) for 4163 atoms. Found 88 (99 requested) and removed 43 (71 requested) atoms. Cycle 35: After refmac, R = 0.1984 (Rfree = 0.000) for 4205 atoms. Found 97 (100 requested) and removed 48 (71 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.22 1.81 NCS extension: 91 residues added (120 deleted due to clashes), 4347 seeds are put forward Round 1: 402 peptides, 9 chains. Longest chain 140 peptides. Score 0.878 Round 2: 407 peptides, 4 chains. Longest chain 206 peptides. Score 0.901 Round 3: 403 peptides, 7 chains. Longest chain 206 peptides. Score 0.887 Round 4: 402 peptides, 8 chains. Longest chain 106 peptides. Score 0.882 Round 5: 400 peptides, 8 chains. Longest chain 174 peptides. Score 0.881 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 156 A 2 chains (410 residues) following loop building 2 chains (410 residues) in sequence following loop building ------------------------------------------------------ 44382 reflections ( 99.74 % complete ) and 3834 restraints for refining 4046 atoms. 430 conditional restraints added. Observations/parameters ratio is 2.74 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2281 (Rfree = 0.000) for 4046 atoms. Found 97 (97 requested) and removed 69 (69 requested) atoms. Cycle 37: After refmac, R = 0.2159 (Rfree = 0.000) for 4062 atoms. Found 95 (95 requested) and removed 45 (69 requested) atoms. Cycle 38: After refmac, R = 0.2086 (Rfree = 0.000) for 4110 atoms. Found 95 (95 requested) and removed 37 (70 requested) atoms. Cycle 39: After refmac, R = 0.2035 (Rfree = 0.000) for 4163 atoms. Found 93 (97 requested) and removed 44 (71 requested) atoms. Cycle 40: After refmac, R = 0.2012 (Rfree = 0.000) for 4207 atoms. Found 95 (98 requested) and removed 59 (72 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.23 1.81 NCS extension: 0 residues added, 4244 seeds are put forward Round 1: 404 peptides, 7 chains. Longest chain 156 peptides. Score 0.888 Round 2: 406 peptides, 5 chains. Longest chain 131 peptides. Score 0.897 Round 3: 404 peptides, 6 chains. Longest chain 206 peptides. Score 0.892 Round 4: 401 peptides, 6 chains. Longest chain 110 peptides. Score 0.890 Round 5: 408 peptides, 3 chains. Longest chain 206 peptides. Score 0.906 Taking the results from Round 5 Chains 3, Residues 405, Estimated correctness of the model 99.1 % 3 chains (405 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 150 B and 156 B 2 chains (410 residues) following loop building 2 chains (410 residues) in sequence following loop building ------------------------------------------------------ 44382 reflections ( 99.74 % complete ) and 3804 restraints for refining 4019 atoms. 400 conditional restraints added. Observations/parameters ratio is 2.76 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2308 (Rfree = 0.000) for 4019 atoms. Found 90 (90 requested) and removed 68 (68 requested) atoms. Cycle 42: After refmac, R = 0.2175 (Rfree = 0.000) for 4031 atoms. Found 88 (88 requested) and removed 39 (69 requested) atoms. Cycle 43: After refmac, R = 0.2098 (Rfree = 0.000) for 4075 atoms. Found 89 (89 requested) and removed 32 (69 requested) atoms. Cycle 44: After refmac, R = 0.2051 (Rfree = 0.000) for 4130 atoms. Found 90 (90 requested) and removed 38 (70 requested) atoms. Cycle 45: After refmac, R = 0.2015 (Rfree = 0.000) for 4179 atoms. Found 90 (92 requested) and removed 55 (71 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.22 1.81 NCS extension: 116 residues added (90 deleted due to clashes), 4333 seeds are put forward Round 1: 403 peptides, 6 chains. Longest chain 178 peptides. Score 0.891 Round 2: 404 peptides, 7 chains. Longest chain 144 peptides. Score 0.888 Round 3: 405 peptides, 4 chains. Longest chain 204 peptides. Score 0.900 Round 4: 400 peptides, 9 chains. Longest chain 79 peptides. Score 0.876 Round 5: 404 peptides, 6 chains. Longest chain 174 peptides. Score 0.892 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 4, Residues 401, Estimated correctness of the model 99.0 % 4 chains (401 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 86 A and 90 A Built loop between residues 151 A and 156 A 2 chains (408 residues) following loop building 2 chains (408 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 44382 reflections ( 99.74 % complete ) and 3389 restraints for refining 3331 atoms. Observations/parameters ratio is 3.33 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2710 (Rfree = 0.000) for 3331 atoms. Found 67 (70 requested) and removed 0 (70 requested) atoms. Cycle 47: After refmac, R = 0.2456 (Rfree = 0.000) for 3331 atoms. Found 40 (72 requested) and removed 2 (58 requested) atoms. Cycle 48: After refmac, R = 0.2300 (Rfree = 0.000) for 3331 atoms. Found 33 (73 requested) and removed 2 (58 requested) atoms. Cycle 49: After refmac, R = 0.2218 (Rfree = 0.000) for 3331 atoms. Found 16 (73 requested) and removed 7 (59 requested) atoms. Writing output files ... TimeTaking 69.18