Mon 24 Dec 01:13:31 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 2o08-2.5-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2o08-2.5-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2o08-2.5-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2o08-2.5-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/2o08-2.5-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2o08-2.5-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 01:13:36 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/2o08-2.5-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2o08-2.5-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 442 and 0 Target number of residues in the AU: 442 Target solvent content: 0.5609 Checking the provided sequence file Detected sequence length: 188 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 376 Adjusted target solvent content: 0.63 Input MTZ file: 2o08-2.5-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: 20 Cell parameters: 87.690 166.470 74.630 90.000 90.000 90.000 Input sequence file: 2o08-2.5-parrot-mrncs.fasta_lf Building free atoms model in initial map for 3008 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 3 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 83.235 2.500 Wilson plot Bfac: 38.59 19066 reflections ( 98.80 % complete ) and 0 restraints for refining 3347 atoms. Observations/parameters ratio is 1.42 ------------------------------------------------------ Starting model: R = 0.3303 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2701 (Rfree = 0.000) for 3347 atoms. Found 36 (60 requested) and removed 32 (30 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.60 2.18 NCS extension: 0 residues added, 3351 seeds are put forward Round 1: 276 peptides, 38 chains. Longest chain 19 peptides. Score 0.544 Round 2: 289 peptides, 29 chains. Longest chain 19 peptides. Score 0.662 Round 3: 316 peptides, 25 chains. Longest chain 35 peptides. Score 0.742 Round 4: 324 peptides, 25 chains. Longest chain 42 peptides. Score 0.754 Round 5: 318 peptides, 22 chains. Longest chain 49 peptides. Score 0.767 Taking the results from Round 5 Chains 25, Residues 296, Estimated correctness of the model 90.0 % 9 chains (198 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 170 A and 173 A 24 chains (298 residues) following loop building 8 chains (200 residues) in sequence following loop building ------------------------------------------------------ 19066 reflections ( 98.80 % complete ) and 4624 restraints for refining 3163 atoms. 2601 conditional restraints added. Observations/parameters ratio is 1.51 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2833 (Rfree = 0.000) for 3163 atoms. Found 57 (57 requested) and removed 36 (28 requested) atoms. Cycle 2: After refmac, R = 0.2638 (Rfree = 0.000) for 3152 atoms. Found 39 (56 requested) and removed 33 (28 requested) atoms. Cycle 3: After refmac, R = 0.2480 (Rfree = 0.000) for 3139 atoms. Found 38 (55 requested) and removed 29 (28 requested) atoms. Cycle 4: After refmac, R = 0.2357 (Rfree = 0.000) for 3135 atoms. Found 34 (54 requested) and removed 29 (28 requested) atoms. Cycle 5: After refmac, R = 0.2293 (Rfree = 0.000) for 3131 atoms. Found 34 (52 requested) and removed 29 (28 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.54 2.13 NCS extension: 52 residues added (28 deleted due to clashes), 3202 seeds are put forward Round 1: 337 peptides, 15 chains. Longest chain 63 peptides. Score 0.836 Round 2: 343 peptides, 16 chains. Longest chain 54 peptides. Score 0.836 Round 3: 348 peptides, 17 chains. Longest chain 38 peptides. Score 0.836 Round 4: 344 peptides, 17 chains. Longest chain 58 peptides. Score 0.831 Round 5: 347 peptides, 14 chains. Longest chain 87 peptides. Score 0.851 Taking the results from Round 5 Chains 16, Residues 333, Estimated correctness of the model 95.6 % 8 chains (281 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 35 A and 45 A Built loop between residues 65 B and 74 B 12 chains (343 residues) following loop building 6 chains (298 residues) in sequence following loop building ------------------------------------------------------ 19066 reflections ( 98.80 % complete ) and 3688 restraints for refining 3216 atoms. 1042 conditional restraints added. Observations/parameters ratio is 1.48 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2412 (Rfree = 0.000) for 3216 atoms. Found 52 (52 requested) and removed 33 (29 requested) atoms. Cycle 7: After refmac, R = 0.2193 (Rfree = 0.000) for 3218 atoms. Found 44 (51 requested) and removed 31 (29 requested) atoms. Cycle 8: After refmac, R = 0.2070 (Rfree = 0.000) for 3221 atoms. Found 33 (50 requested) and removed 29 (29 requested) atoms. Cycle 9: After refmac, R = 0.2005 (Rfree = 0.000) for 3215 atoms. Found 31 (49 requested) and removed 31 (29 requested) atoms. Cycle 10: After refmac, R = 0.1937 (Rfree = 0.000) for 3202 atoms. Found 25 (48 requested) and removed 29 (29 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.53 2.12 NCS extension: 190 residues added (146 deleted due to clashes), 3395 seeds are put forward Round 1: 357 peptides, 12 chains. Longest chain 81 peptides. Score 0.870 Round 2: 357 peptides, 11 chains. Longest chain 70 peptides. Score 0.875 Round 3: 352 peptides, 10 chains. Longest chain 58 peptides. Score 0.876 Round 4: 355 peptides, 13 chains. Longest chain 148 peptides. Score 0.864 Round 5: 349 peptides, 15 chains. Longest chain 89 peptides. Score 0.848 Taking the results from Round 3 Chains 10, Residues 342, Estimated correctness of the model 96.8 % 7 chains (283 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 31 B and 38 B Built loop between residues 154 B and 157 B 7 chains (349 residues) following loop building 5 chains (291 residues) in sequence following loop building ------------------------------------------------------ 19066 reflections ( 98.80 % complete ) and 3722 restraints for refining 3159 atoms. 1133 conditional restraints added. Observations/parameters ratio is 1.51 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2298 (Rfree = 0.000) for 3159 atoms. Found 46 (46 requested) and removed 31 (28 requested) atoms. Cycle 12: After refmac, R = 0.2070 (Rfree = 0.000) for 3168 atoms. Found 44 (44 requested) and removed 32 (28 requested) atoms. Cycle 13: After refmac, R = 0.1987 (Rfree = 0.000) for 3177 atoms. Found 36 (43 requested) and removed 31 (28 requested) atoms. Cycle 14: After refmac, R = 0.1964 (Rfree = 0.000) for 3177 atoms. Found 31 (42 requested) and removed 28 (28 requested) atoms. Cycle 15: After refmac, R = 0.2007 (Rfree = 0.000) for 3176 atoms. Found 38 (41 requested) and removed 28 (28 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.52 2.11 NCS extension: 63 residues added (97 deleted due to clashes), 3266 seeds are put forward Round 1: 352 peptides, 11 chains. Longest chain 149 peptides. Score 0.871 Round 2: 357 peptides, 8 chains. Longest chain 82 peptides. Score 0.890 Round 3: 344 peptides, 14 chains. Longest chain 57 peptides. Score 0.848 Round 4: 352 peptides, 10 chains. Longest chain 155 peptides. Score 0.876 Round 5: 351 peptides, 13 chains. Longest chain 71 peptides. Score 0.860 Taking the results from Round 2 Chains 9, Residues 349, Estimated correctness of the model 97.5 % 7 chains (333 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 76 A and 87 A Built loop between residues 65 B and 68 B Built loop between residues 89 B and 92 B Built loop between residues 155 B and 159 B 4 chains (359 residues) following loop building 3 chains (350 residues) in sequence following loop building ------------------------------------------------------ 19066 reflections ( 98.80 % complete ) and 3425 restraints for refining 3250 atoms. 501 conditional restraints added. Observations/parameters ratio is 1.47 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2101 (Rfree = 0.000) for 3250 atoms. Found 41 (41 requested) and removed 37 (29 requested) atoms. Cycle 17: After refmac, R = 0.1925 (Rfree = 0.000) for 3247 atoms. Found 39 (39 requested) and removed 31 (29 requested) atoms. Cycle 18: After refmac, R = 0.1856 (Rfree = 0.000) for 3246 atoms. Found 39 (39 requested) and removed 29 (29 requested) atoms. Cycle 19: After refmac, R = 0.1845 (Rfree = 0.000) for 3250 atoms. Found 38 (38 requested) and removed 29 (29 requested) atoms. Cycle 20: After refmac, R = 0.1833 (Rfree = 0.000) for 3252 atoms. Found 37 (37 requested) and removed 29 (29 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.53 2.12 NCS extension: 137 residues added (247 deleted due to clashes), 3401 seeds are put forward Round 1: 357 peptides, 7 chains. Longest chain 90 peptides. Score 0.894 Round 2: 363 peptides, 7 chains. Longest chain 122 peptides. Score 0.899 Round 3: 358 peptides, 9 chains. Longest chain 154 peptides. Score 0.886 Round 4: 361 peptides, 10 chains. Longest chain 123 peptides. Score 0.883 Round 5: 358 peptides, 13 chains. Longest chain 62 peptides. Score 0.866 Taking the results from Round 2 Chains 7, Residues 356, Estimated correctness of the model 97.8 % 7 chains (356 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 15 A and 18 A Built loop between residues 73 A and 77 A Built loop between residues 95 A and 98 A Built loop between residues 135 A and 139 A Built loop between residues 61 B and 64 B 2 chains (368 residues) following loop building 2 chains (368 residues) in sequence following loop building ------------------------------------------------------ 19066 reflections ( 98.80 % complete ) and 3284 restraints for refining 3262 atoms. 249 conditional restraints added. Observations/parameters ratio is 1.46 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1895 (Rfree = 0.000) for 3262 atoms. Found 35 (35 requested) and removed 33 (29 requested) atoms. Cycle 22: After refmac, R = 0.1779 (Rfree = 0.000) for 3256 atoms. Found 34 (34 requested) and removed 32 (29 requested) atoms. Cycle 23: After refmac, R = 0.1717 (Rfree = 0.000) for 3253 atoms. Found 33 (33 requested) and removed 30 (29 requested) atoms. Cycle 24: After refmac, R = 0.1701 (Rfree = 0.000) for 3252 atoms. Found 32 (32 requested) and removed 29 (29 requested) atoms. Cycle 25: After refmac, R = 0.1655 (Rfree = 0.000) for 3250 atoms. Found 31 (31 requested) and removed 29 (29 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.51 2.10 NCS extension: 0 residues added, 3253 seeds are put forward Round 1: 361 peptides, 7 chains. Longest chain 153 peptides. Score 0.897 Round 2: 368 peptides, 4 chains. Longest chain 184 peptides. Score 0.915 Round 3: 362 peptides, 9 chains. Longest chain 154 peptides. Score 0.889 Round 4: 357 peptides, 13 chains. Longest chain 72 peptides. Score 0.865 Round 5: 357 peptides, 14 chains. Longest chain 103 peptides. Score 0.860 Taking the results from Round 2 Chains 4, Residues 364, Estimated correctness of the model 98.4 % 3 chains (350 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 142 B and 145 B 3 chains (366 residues) following loop building 2 chains (352 residues) in sequence following loop building ------------------------------------------------------ 19066 reflections ( 98.80 % complete ) and 3367 restraints for refining 3254 atoms. 406 conditional restraints added. Observations/parameters ratio is 1.46 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1831 (Rfree = 0.000) for 3254 atoms. Found 29 (29 requested) and removed 30 (29 requested) atoms. Cycle 27: After refmac, R = 0.1737 (Rfree = 0.000) for 3247 atoms. Found 29 (29 requested) and removed 31 (29 requested) atoms. Cycle 28: After refmac, R = 0.1708 (Rfree = 0.000) for 3243 atoms. Found 29 (29 requested) and removed 29 (29 requested) atoms. Cycle 29: After refmac, R = 0.1686 (Rfree = 0.000) for 3240 atoms. Found 29 (29 requested) and removed 29 (29 requested) atoms. Cycle 30: After refmac, R = 0.1678 (Rfree = 0.000) for 3240 atoms. Found 29 (29 requested) and removed 26 (29 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.51 2.10 NCS extension: 11 residues added (5 deleted due to clashes), 3255 seeds are put forward Round 1: 361 peptides, 8 chains. Longest chain 153 peptides. Score 0.893 Round 2: 366 peptides, 5 chains. Longest chain 183 peptides. Score 0.909 Round 3: 357 peptides, 11 chains. Longest chain 104 peptides. Score 0.875 Round 4: 359 peptides, 12 chains. Longest chain 111 peptides. Score 0.872 Round 5: 352 peptides, 16 chains. Longest chain 88 peptides. Score 0.845 Taking the results from Round 2 Chains 5, Residues 361, Estimated correctness of the model 98.2 % 5 chains (361 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 34 A and 37 A Built loop between residues 77 A and 80 A Built loop between residues 115 A and 118 A 2 chains (367 residues) following loop building 2 chains (367 residues) in sequence following loop building ------------------------------------------------------ 19066 reflections ( 98.80 % complete ) and 3271 restraints for refining 3262 atoms. 244 conditional restraints added. Observations/parameters ratio is 1.46 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1842 (Rfree = 0.000) for 3262 atoms. Found 29 (29 requested) and removed 31 (29 requested) atoms. Cycle 32: After refmac, R = 0.1716 (Rfree = 0.000) for 3254 atoms. Found 29 (29 requested) and removed 32 (29 requested) atoms. Failed to save intermediate PDB Cycle 33: After refmac, R = 0.1654 (Rfree = 0.000) for 3248 atoms. Found 29 (29 requested) and removed 29 (29 requested) atoms. Cycle 34: After refmac, R = 0.1653 (Rfree = 0.000) for 3242 atoms. Found 29 (29 requested) and removed 29 (29 requested) atoms. Cycle 35: After refmac, R = 0.1629 (Rfree = 0.000) for 3240 atoms. Found 29 (29 requested) and removed 29 (29 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.50 2.09 NCS extension: 0 residues added, 3240 seeds are put forward Round 1: 363 peptides, 8 chains. Longest chain 98 peptides. Score 0.894 Round 2: 366 peptides, 6 chains. Longest chain 134 peptides. Score 0.905 Round 3: 364 peptides, 7 chains. Longest chain 153 peptides. Score 0.899 Round 4: 357 peptides, 11 chains. Longest chain 68 peptides. Score 0.875 Round 5: 349 peptides, 18 chains. Longest chain 51 peptides. Score 0.831 Taking the results from Round 2 Chains 7, Residues 360, Estimated correctness of the model 98.1 % 6 chains (359 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 14 A and 17 A Built loop between residues 42 A and 45 A Built loop between residues 150 A and 153 A Built loop between residues 49 B and 52 B 2 chains (367 residues) following loop building 2 chains (367 residues) in sequence following loop building ------------------------------------------------------ 19066 reflections ( 98.80 % complete ) and 3261 restraints for refining 3254 atoms. 234 conditional restraints added. Observations/parameters ratio is 1.46 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1830 (Rfree = 0.000) for 3254 atoms. Found 29 (29 requested) and removed 30 (29 requested) atoms. Cycle 37: After refmac, R = 0.1712 (Rfree = 0.000) for 3250 atoms. Found 29 (29 requested) and removed 30 (29 requested) atoms. Cycle 38: After refmac, R = 0.1665 (Rfree = 0.000) for 3246 atoms. Found 29 (29 requested) and removed 30 (29 requested) atoms. Cycle 39: After refmac, R = 0.1644 (Rfree = 0.000) for 3242 atoms. Found 29 (29 requested) and removed 30 (29 requested) atoms. Cycle 40: After refmac, R = 0.1656 (Rfree = 0.000) for 3238 atoms. Found 29 (29 requested) and removed 30 (29 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.51 2.10 NCS extension: 0 residues added, 3240 seeds are put forward Round 1: 364 peptides, 7 chains. Longest chain 153 peptides. Score 0.899 Round 2: 367 peptides, 5 chains. Longest chain 134 peptides. Score 0.910 Round 3: 361 peptides, 10 chains. Longest chain 154 peptides. Score 0.883 Round 4: 360 peptides, 10 chains. Longest chain 78 peptides. Score 0.883 Round 5: 350 peptides, 15 chains. Longest chain 54 peptides. Score 0.849 Taking the results from Round 2 Chains 5, Residues 362, Estimated correctness of the model 98.2 % 5 chains (362 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 15 A and 18 A Built loop between residues 142 A and 145 A Built loop between residues 49 B and 52 B 2 chains (368 residues) following loop building 2 chains (368 residues) in sequence following loop building ------------------------------------------------------ 19066 reflections ( 98.80 % complete ) and 3239 restraints for refining 3251 atoms. 204 conditional restraints added. Observations/parameters ratio is 1.47 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1805 (Rfree = 0.000) for 3251 atoms. Found 29 (29 requested) and removed 29 (29 requested) atoms. Cycle 42: After refmac, R = 0.1698 (Rfree = 0.000) for 3247 atoms. Found 29 (29 requested) and removed 31 (29 requested) atoms. Cycle 43: After refmac, R = 0.1672 (Rfree = 0.000) for 3241 atoms. Found 29 (29 requested) and removed 29 (29 requested) atoms. Cycle 44: After refmac, R = 0.1670 (Rfree = 0.000) for 3238 atoms. Found 29 (29 requested) and removed 29 (29 requested) atoms. Cycle 45: After refmac, R = 0.1669 (Rfree = 0.000) for 3235 atoms. Found 29 (29 requested) and removed 27 (29 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.51 2.10 NCS extension: 0 residues added, 3237 seeds are put forward Round 1: 367 peptides, 6 chains. Longest chain 154 peptides. Score 0.906 Round 2: 367 peptides, 6 chains. Longest chain 143 peptides. Score 0.906 Round 3: 361 peptides, 8 chains. Longest chain 154 peptides. Score 0.893 Round 4: 359 peptides, 9 chains. Longest chain 103 peptides. Score 0.887 Round 5: 352 peptides, 11 chains. Longest chain 51 peptides. Score 0.871 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 7, Residues 361, Estimated correctness of the model 98.1 % 6 chains (360 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 50 A and 53 A Built loop between residues 98 A and 101 A Built loop between residues 15 B and 18 B Built loop between residues 42 B and 45 B 3 chains (369 residues) following loop building 3 chains (369 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 19066 reflections ( 98.80 % complete ) and 3038 restraints for refining 2983 atoms. Observations/parameters ratio is 1.60 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2427 (Rfree = 0.000) for 2983 atoms. Found 27 (27 requested) and removed 0 (27 requested) atoms. Cycle 47: After refmac, R = 0.2180 (Rfree = 0.000) for 2983 atoms. Found 12 (27 requested) and removed 2 (27 requested) atoms. Cycle 48: After refmac, R = 0.2107 (Rfree = 0.000) for 2983 atoms. Found 7 (27 requested) and removed 6 (27 requested) atoms. Cycle 49: After refmac, R = 0.2104 (Rfree = 0.000) for 2983 atoms. Found 6 (27 requested) and removed 4 (27 requested) atoms. Writing output files ... TimeTaking 55.1