Sun 23 Dec 22:23:08 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 1vmf-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vmf-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vmf-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vmf-3.2-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/1vmf-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vmf-3.2-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 22:23:18 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/1vmf-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vmf-3.2-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 335 and 0 Target number of residues in the AU: 335 Target solvent content: 0.6012 Checking the provided sequence file Detected sequence length: 145 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 3 Adjusted target number of residues: 435 Adjusted target solvent content: 0.48 Input MTZ file: 1vmf-3.2-parrot-hancs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 19 Cell parameters: 57.443 58.601 135.061 90.000 90.000 90.000 Input sequence file: 1vmf-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 3480 target number of atoms Had to go as low as 0.65 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: 67.531 3.200 Wilson plot Bfac: 53.00 7960 reflections ( 99.76 % complete ) and 0 restraints for refining 3867 atoms. Observations/parameters ratio is 0.51 ------------------------------------------------------ Starting model: R = 0.2969 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2663 (Rfree = 0.000) for 3867 atoms. Found 34 (34 requested) and removed 22 (17 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.00 3.08 Search for helices and strands: 0 residues in 0 chains, 3960 seeds are put forward NCS extension: 0 residues added, 3960 seeds are put forward Round 1: 230 peptides, 37 chains. Longest chain 18 peptides. Score 0.472 Round 2: 294 peptides, 37 chains. Longest chain 16 peptides. Score 0.648 Round 3: 318 peptides, 29 chains. Longest chain 30 peptides. Score 0.767 Round 4: 331 peptides, 29 chains. Longest chain 28 peptides. Score 0.787 Round 5: 331 peptides, 29 chains. Longest chain 33 peptides. Score 0.787 Taking the results from Round 5 Chains 32, Residues 302, Estimated correctness of the model 81.4 % 8 chains (134 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 110 C and 115 C 31 chains (306 residues) following loop building 7 chains (138 residues) in sequence following loop building ------------------------------------------------------ 7960 reflections ( 99.76 % complete ) and 5329 restraints for refining 3206 atoms. 3590 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2597 (Rfree = 0.000) for 3206 atoms. Found 28 (28 requested) and removed 32 (14 requested) atoms. Cycle 2: After refmac, R = 0.2347 (Rfree = 0.000) for 3157 atoms. Found 13 (27 requested) and removed 19 (14 requested) atoms. Cycle 3: After refmac, R = 0.2301 (Rfree = 0.000) for 3129 atoms. Found 14 (27 requested) and removed 14 (14 requested) atoms. Cycle 4: After refmac, R = 0.2233 (Rfree = 0.000) for 3117 atoms. Found 6 (26 requested) and removed 15 (14 requested) atoms. Cycle 5: After refmac, R = 0.2229 (Rfree = 0.000) for 3101 atoms. Found 9 (25 requested) and removed 15 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.00 3.08 Search for helices and strands: 0 residues in 0 chains, 3176 seeds are put forward NCS extension: 33 residues added (23 deleted due to clashes), 3209 seeds are put forward Round 1: 323 peptides, 35 chains. Longest chain 24 peptides. Score 0.727 Round 2: 328 peptides, 29 chains. Longest chain 28 peptides. Score 0.783 Round 3: 334 peptides, 29 chains. Longest chain 45 peptides. Score 0.792 Round 4: 335 peptides, 26 chains. Longest chain 36 peptides. Score 0.813 Round 5: 336 peptides, 25 chains. Longest chain 57 peptides. Score 0.821 Taking the results from Round 5 Chains 29, Residues 311, Estimated correctness of the model 86.5 % 5 chains (145 residues) have been docked in sequence Building loops using Loopy2018 29 chains (311 residues) following loop building 5 chains (145 residues) in sequence following loop building ------------------------------------------------------ 7960 reflections ( 99.76 % complete ) and 5218 restraints for refining 3177 atoms. 3415 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2676 (Rfree = 0.000) for 3177 atoms. Found 25 (25 requested) and removed 31 (14 requested) atoms. Cycle 7: After refmac, R = 0.2394 (Rfree = 0.000) for 3156 atoms. Found 11 (25 requested) and removed 17 (14 requested) atoms. Cycle 8: After refmac, R = 0.2435 (Rfree = 0.000) for 3140 atoms. Found 15 (24 requested) and removed 19 (14 requested) atoms. Cycle 9: After refmac, R = 0.2341 (Rfree = 0.000) for 3131 atoms. Found 10 (24 requested) and removed 19 (14 requested) atoms. Cycle 10: After refmac, R = 0.2299 (Rfree = 0.000) for 3115 atoms. Found 4 (23 requested) and removed 15 (14 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.01 3.09 Search for helices and strands: 0 residues in 0 chains, 3203 seeds are put forward NCS extension: 74 residues added (14 deleted due to clashes), 3277 seeds are put forward Round 1: 317 peptides, 32 chains. Longest chain 34 peptides. Score 0.741 Round 2: 324 peptides, 25 chains. Longest chain 47 peptides. Score 0.805 Round 3: 316 peptides, 25 chains. Longest chain 35 peptides. Score 0.794 Round 4: 321 peptides, 28 chains. Longest chain 39 peptides. Score 0.780 Round 5: 320 peptides, 26 chains. Longest chain 36 peptides. Score 0.793 Taking the results from Round 2 Chains 29, Residues 299, Estimated correctness of the model 84.2 % 6 chains (156 residues) have been docked in sequence Building loops using Loopy2018 29 chains (299 residues) following loop building 6 chains (156 residues) in sequence following loop building ------------------------------------------------------ 7960 reflections ( 99.76 % complete ) and 5244 restraints for refining 3177 atoms. 3428 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2555 (Rfree = 0.000) for 3177 atoms. Found 19 (22 requested) and removed 33 (14 requested) atoms. Cycle 12: After refmac, R = 0.2371 (Rfree = 0.000) for 3151 atoms. Found 7 (22 requested) and removed 16 (14 requested) atoms. Cycle 13: After refmac, R = 0.2312 (Rfree = 0.000) for 3136 atoms. Found 9 (21 requested) and removed 16 (14 requested) atoms. Cycle 14: After refmac, R = 0.2282 (Rfree = 0.000) for 3124 atoms. Found 5 (21 requested) and removed 15 (14 requested) atoms. Cycle 15: After refmac, R = 0.2260 (Rfree = 0.000) for 3107 atoms. Found 6 (19 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.98 3.06 Search for helices and strands: 0 residues in 0 chains, 3181 seeds are put forward NCS extension: 38 residues added (16 deleted due to clashes), 3219 seeds are put forward Round 1: 307 peptides, 34 chains. Longest chain 33 peptides. Score 0.705 Round 2: 329 peptides, 28 chains. Longest chain 46 peptides. Score 0.791 Round 3: 325 peptides, 30 chains. Longest chain 37 peptides. Score 0.771 Round 4: 329 peptides, 34 chains. Longest chain 31 peptides. Score 0.746 Round 5: 315 peptides, 27 chains. Longest chain 32 peptides. Score 0.778 Taking the results from Round 2 Chains 30, Residues 301, Estimated correctness of the model 82.0 % 3 chains (82 residues) have been docked in sequence Building loops using Loopy2018 30 chains (301 residues) following loop building 3 chains (82 residues) in sequence following loop building ------------------------------------------------------ 7960 reflections ( 99.76 % complete ) and 6185 restraints for refining 3177 atoms. 4700 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2494 (Rfree = 0.000) for 3177 atoms. Found 15 (20 requested) and removed 25 (14 requested) atoms. Cycle 17: After refmac, R = 0.2238 (Rfree = 0.000) for 3156 atoms. Found 9 (19 requested) and removed 15 (14 requested) atoms. Cycle 18: After refmac, R = 0.2231 (Rfree = 0.000) for 3146 atoms. Found 16 (18 requested) and removed 16 (14 requested) atoms. Cycle 19: After refmac, R = 0.2109 (Rfree = 0.000) for 3143 atoms. Found 2 (18 requested) and removed 14 (14 requested) atoms. Cycle 20: After refmac, R = 0.2074 (Rfree = 0.000) for 3127 atoms. Found 7 (17 requested) and removed 15 (14 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.00 3.08 Search for helices and strands: 0 residues in 0 chains, 3209 seeds are put forward NCS extension: 35 residues added (36 deleted due to clashes), 3244 seeds are put forward Round 1: 304 peptides, 35 chains. Longest chain 46 peptides. Score 0.690 Round 2: 329 peptides, 31 chains. Longest chain 51 peptides. Score 0.769 Round 3: 320 peptides, 28 chains. Longest chain 46 peptides. Score 0.778 Round 4: 331 peptides, 25 chains. Longest chain 41 peptides. Score 0.815 Round 5: 343 peptides, 33 chains. Longest chain 29 peptides. Score 0.776 Taking the results from Round 4 Chains 28, Residues 306, Estimated correctness of the model 85.6 % 5 chains (114 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 99 B and 108 B 26 chains (311 residues) following loop building 4 chains (122 residues) in sequence following loop building ------------------------------------------------------ 7960 reflections ( 99.76 % complete ) and 5551 restraints for refining 3177 atoms. 3917 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2506 (Rfree = 0.000) for 3177 atoms. Found 17 (17 requested) and removed 25 (14 requested) atoms. Cycle 22: After refmac, R = 0.2250 (Rfree = 0.000) for 3163 atoms. Found 16 (16 requested) and removed 21 (14 requested) atoms. Cycle 23: After refmac, R = 0.2140 (Rfree = 0.000) for 3152 atoms. Found 11 (16 requested) and removed 14 (14 requested) atoms. Cycle 24: After refmac, R = 0.2135 (Rfree = 0.000) for 3145 atoms. Found 7 (15 requested) and removed 14 (14 requested) atoms. Cycle 25: After refmac, R = 0.2099 (Rfree = 0.000) for 3136 atoms. Found 7 (15 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.99 3.07 Search for helices and strands: 0 residues in 0 chains, 3222 seeds are put forward NCS extension: 46 residues added (51 deleted due to clashes), 3268 seeds are put forward Round 1: 298 peptides, 28 chains. Longest chain 26 peptides. Score 0.741 Round 2: 320 peptides, 27 chains. Longest chain 27 peptides. Score 0.785 Round 3: 310 peptides, 29 chains. Longest chain 28 peptides. Score 0.754 Round 4: 317 peptides, 24 chains. Longest chain 27 peptides. Score 0.803 Round 5: 328 peptides, 26 chains. Longest chain 31 peptides. Score 0.804 Taking the results from Round 5 Chains 29, Residues 302, Estimated correctness of the model 84.0 % 4 chains (73 residues) have been docked in sequence Building loops using Loopy2018 29 chains (302 residues) following loop building 4 chains (73 residues) in sequence following loop building ------------------------------------------------------ 7960 reflections ( 99.76 % complete ) and 6002 restraints for refining 3177 atoms. 4526 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2374 (Rfree = 0.000) for 3177 atoms. Found 14 (14 requested) and removed 41 (14 requested) atoms. Cycle 27: After refmac, R = 0.2174 (Rfree = 0.000) for 3139 atoms. Found 14 (14 requested) and removed 16 (14 requested) atoms. Cycle 28: After refmac, R = 0.2151 (Rfree = 0.000) for 3134 atoms. Found 9 (14 requested) and removed 14 (14 requested) atoms. Cycle 29: After refmac, R = 0.2073 (Rfree = 0.000) for 3127 atoms. Found 4 (14 requested) and removed 14 (14 requested) atoms. Cycle 30: After refmac, R = 0.2020 (Rfree = 0.000) for 3115 atoms. Found 9 (13 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.01 3.09 Search for helices and strands: 0 residues in 0 chains, 3212 seeds are put forward NCS extension: 26 residues added (10 deleted due to clashes), 3238 seeds are put forward Round 1: 282 peptides, 30 chains. Longest chain 24 peptides. Score 0.692 Round 2: 317 peptides, 27 chains. Longest chain 29 peptides. Score 0.781 Round 3: 310 peptides, 26 chains. Longest chain 39 peptides. Score 0.778 Round 4: 294 peptides, 27 chains. Longest chain 26 peptides. Score 0.743 Round 5: 303 peptides, 27 chains. Longest chain 41 peptides. Score 0.758 Taking the results from Round 2 Chains 30, Residues 290, Estimated correctness of the model 80.4 % 5 chains (93 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 64 A and 73 A 28 chains (290 residues) following loop building 4 chains (101 residues) in sequence following loop building ------------------------------------------------------ 7960 reflections ( 99.76 % complete ) and 5709 restraints for refining 3177 atoms. 4218 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2708 (Rfree = 0.000) for 3177 atoms. Found 14 (14 requested) and removed 26 (14 requested) atoms. Cycle 32: After refmac, R = 0.2263 (Rfree = 0.000) for 3156 atoms. Found 14 (14 requested) and removed 15 (14 requested) atoms. Cycle 33: After refmac, R = 0.2133 (Rfree = 0.000) for 3146 atoms. Found 10 (14 requested) and removed 17 (14 requested) atoms. Cycle 34: After refmac, R = 0.2101 (Rfree = 0.000) for 3137 atoms. Found 13 (14 requested) and removed 17 (14 requested) atoms. Cycle 35: After refmac, R = 0.2010 (Rfree = 0.000) for 3131 atoms. Found 9 (14 requested) and removed 16 (14 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.01 3.09 Search for helices and strands: 0 residues in 0 chains, 3220 seeds are put forward NCS extension: 31 residues added (7 deleted due to clashes), 3251 seeds are put forward Round 1: 256 peptides, 35 chains. Longest chain 17 peptides. Score 0.575 Round 2: 279 peptides, 29 chains. Longest chain 29 peptides. Score 0.696 Round 3: 281 peptides, 28 chains. Longest chain 24 peptides. Score 0.709 Round 4: 273 peptides, 26 chains. Longest chain 29 peptides. Score 0.712 Round 5: 257 peptides, 26 chains. Longest chain 21 peptides. Score 0.679 Taking the results from Round 4 Chains 27, Residues 247, Estimated correctness of the model 67.7 % 3 chains (46 residues) have been docked in sequence Building loops using Loopy2018 27 chains (247 residues) following loop building 3 chains (46 residues) in sequence following loop building ------------------------------------------------------ 7960 reflections ( 99.76 % complete ) and 6631 restraints for refining 3177 atoms. 5522 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2193 (Rfree = 0.000) for 3177 atoms. Found 14 (14 requested) and removed 19 (14 requested) atoms. Cycle 37: After refmac, R = 0.2338 (Rfree = 0.000) for 3168 atoms. Found 14 (14 requested) and removed 14 (14 requested) atoms. Cycle 38: After refmac, R = 0.2075 (Rfree = 0.000) for 3164 atoms. Found 11 (14 requested) and removed 16 (14 requested) atoms. Cycle 39: After refmac, R = 0.1910 (Rfree = 0.000) for 3159 atoms. Found 4 (14 requested) and removed 15 (14 requested) atoms. Cycle 40: After refmac, R = 0.1833 (Rfree = 0.000) for 3146 atoms. Found 3 (14 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.99 3.07 Search for helices and strands: 0 residues in 0 chains, 3215 seeds are put forward NCS extension: 36 residues added (3 deleted due to clashes), 3251 seeds are put forward Round 1: 262 peptides, 34 chains. Longest chain 23 peptides. Score 0.603 Round 2: 279 peptides, 29 chains. Longest chain 27 peptides. Score 0.696 Round 3: 285 peptides, 26 chains. Longest chain 27 peptides. Score 0.735 Round 4: 273 peptides, 27 chains. Longest chain 25 peptides. Score 0.703 Round 5: 277 peptides, 31 chains. Longest chain 23 peptides. Score 0.671 Taking the results from Round 3 Chains 28, Residues 259, Estimated correctness of the model 72.3 % 2 chains (35 residues) have been docked in sequence Building loops using Loopy2018 28 chains (259 residues) following loop building 2 chains (35 residues) in sequence following loop building ------------------------------------------------------ 7960 reflections ( 99.76 % complete ) and 6593 restraints for refining 3177 atoms. 5471 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2192 (Rfree = 0.000) for 3177 atoms. Found 13 (14 requested) and removed 16 (14 requested) atoms. Cycle 42: After refmac, R = 0.1940 (Rfree = 0.000) for 3170 atoms. Found 13 (14 requested) and removed 14 (14 requested) atoms. Cycle 43: After refmac, R = 0.1904 (Rfree = 0.000) for 3165 atoms. Found 9 (14 requested) and removed 14 (14 requested) atoms. Cycle 44: After refmac, R = 0.1757 (Rfree = 0.000) for 3158 atoms. Found 3 (14 requested) and removed 14 (14 requested) atoms. Cycle 45: After refmac, R = 0.1788 (Rfree = 0.000) for 3144 atoms. Found 1 (14 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.99 3.07 Search for helices and strands: 0 residues in 0 chains, 3213 seeds are put forward NCS extension: 20 residues added (10 deleted due to clashes), 3233 seeds are put forward Round 1: 242 peptides, 38 chains. Longest chain 15 peptides. Score 0.496 Round 2: 279 peptides, 32 chains. Longest chain 29 peptides. Score 0.666 Round 3: 269 peptides, 33 chains. Longest chain 18 peptides. Score 0.632 Round 4: 260 peptides, 31 chains. Longest chain 28 peptides. Score 0.632 Round 5: 261 peptides, 35 chains. Longest chain 18 peptides. Score 0.589 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 35, Residues 247, Estimated correctness of the model 57.6 % 3 chains (54 residues) have been docked in sequence Sequence coverage is 21 % Consider running further cycles of model building using 1vmf-3_warpNtrace.pdb as input Building loops using Loopy2018 35 chains (247 residues) following loop building 3 chains (54 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7960 reflections ( 99.76 % complete ) and 6295 restraints for refining 3177 atoms. 5080 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2164 (Rfree = 0.000) for 3177 atoms. Found 0 (14 requested) and removed 14 (14 requested) atoms. Cycle 47: After refmac, R = 0.2149 (Rfree = 0.000) for 3152 atoms. Found 0 (14 requested) and removed 14 (14 requested) atoms. Cycle 48: After refmac, R = 0.1976 (Rfree = 0.000) for 3135 atoms. Found 0 (14 requested) and removed 10 (14 requested) atoms. Cycle 49: After refmac, R = 0.1905 (Rfree = 0.000) for 3121 atoms. Found 0 (14 requested) and removed 3 (14 requested) atoms. Writing output files ... TimeTaking 56.88