Mon 24 Dec 07:47:03 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2opk-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2opk-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2opk-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2opk-3.4-parrot-noncs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2opk-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2opk-3.4-parrot-noncs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Mon 24 Dec 07:47:08 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2opk-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2opk-3.4-parrot-noncs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 418 and 0 Target number of residues in the AU: 418 Target solvent content: 0.6018 Checking the provided sequence file Detected sequence length: 112 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 448 Adjusted target solvent content: 0.57 Input MTZ file: 2opk-3.4-parrot-noncs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 96 Cell parameters: 75.570 75.570 198.970 90.000 90.000 90.000 Input sequence file: 2opk-3.4-parrot-noncs.fasta_lf Building free atoms model in initial map for 3584 target number of atoms Had to go as low as 0.80 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: 28.177 3.400 Wilson plot Bfac: 53.33 8484 reflections ( 99.60 % complete ) and 0 restraints for refining 3952 atoms. Observations/parameters ratio is 0.54 ------------------------------------------------------ Starting model: R = 0.2963 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2415 (Rfree = 0.000) for 3952 atoms. Found 29 (29 requested) and removed 37 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.09 2.81 Search for helices and strands: 0 residues in 0 chains, 4001 seeds are put forward NCS extension: 0 residues added, 4001 seeds are put forward Round 1: 284 peptides, 45 chains. Longest chain 15 peptides. Score 0.478 Round 2: 334 peptides, 34 chains. Longest chain 24 peptides. Score 0.689 Round 3: 344 peptides, 32 chains. Longest chain 34 peptides. Score 0.721 Round 4: 361 peptides, 31 chains. Longest chain 25 peptides. Score 0.753 Round 5: 356 peptides, 26 chains. Longest chain 41 peptides. Score 0.779 Taking the results from Round 5 Chains 33, Residues 330, Estimated correctness of the model 75.9 % 7 chains (128 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 68 A and 72 A 32 chains (331 residues) following loop building 6 chains (131 residues) in sequence following loop building ------------------------------------------------------ 8484 reflections ( 99.60 % complete ) and 5291 restraints for refining 3278 atoms. 3480 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2539 (Rfree = 0.000) for 3278 atoms. Found 24 (24 requested) and removed 27 (12 requested) atoms. Cycle 2: After refmac, R = 0.2405 (Rfree = 0.000) for 3230 atoms. Found 13 (24 requested) and removed 21 (12 requested) atoms. Cycle 3: After refmac, R = 0.2437 (Rfree = 0.000) for 3197 atoms. Found 20 (23 requested) and removed 16 (12 requested) atoms. Cycle 4: After refmac, R = 0.2150 (Rfree = 0.000) for 3180 atoms. Found 12 (23 requested) and removed 21 (12 requested) atoms. Cycle 5: After refmac, R = 0.2060 (Rfree = 0.000) for 3165 atoms. Found 10 (21 requested) and removed 16 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.14 2.86 Search for helices and strands: 0 residues in 0 chains, 3250 seeds are put forward NCS extension: 82 residues added (35 deleted due to clashes), 3332 seeds are put forward Round 1: 352 peptides, 31 chains. Longest chain 38 peptides. Score 0.740 Round 2: 369 peptides, 25 chains. Longest chain 57 peptides. Score 0.801 Round 3: 378 peptides, 22 chains. Longest chain 63 peptides. Score 0.828 Round 4: 389 peptides, 21 chains. Longest chain 66 peptides. Score 0.844 Round 5: 360 peptides, 27 chains. Longest chain 28 peptides. Score 0.778 Taking the results from Round 4 Chains 25, Residues 368, Estimated correctness of the model 87.3 % 7 chains (226 residues) have been docked in sequence Building loops using Loopy2018 25 chains (368 residues) following loop building 7 chains (226 residues) in sequence following loop building ------------------------------------------------------ 8484 reflections ( 99.60 % complete ) and 4403 restraints for refining 3258 atoms. 2029 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2708 (Rfree = 0.000) for 3258 atoms. Found 22 (22 requested) and removed 43 (12 requested) atoms. Cycle 7: After refmac, R = 0.2443 (Rfree = 0.000) for 3229 atoms. Found 16 (21 requested) and removed 21 (12 requested) atoms. Cycle 8: After refmac, R = 0.2325 (Rfree = 0.000) for 3218 atoms. Found 13 (21 requested) and removed 17 (12 requested) atoms. Cycle 9: After refmac, R = 0.2253 (Rfree = 0.000) for 3207 atoms. Found 6 (20 requested) and removed 13 (12 requested) atoms. Cycle 10: After refmac, R = 0.2200 (Rfree = 0.000) for 3195 atoms. Found 6 (20 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.11 2.83 Search for helices and strands: 0 residues in 0 chains, 3255 seeds are put forward NCS extension: 18 residues added (27 deleted due to clashes), 3273 seeds are put forward Round 1: 353 peptides, 31 chains. Longest chain 29 peptides. Score 0.742 Round 2: 378 peptides, 21 chains. Longest chain 44 peptides. Score 0.833 Round 3: 386 peptides, 25 chains. Longest chain 42 peptides. Score 0.820 Round 4: 379 peptides, 32 chains. Longest chain 26 peptides. Score 0.770 Round 5: 357 peptides, 24 chains. Longest chain 46 peptides. Score 0.793 Taking the results from Round 2 Chains 24, Residues 357, Estimated correctness of the model 85.6 % 9 chains (200 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 38 A and 43 A Built loop between residues 85 A and 88 A Built loop between residues 58 C and 61 C Built loop between residues 68 C and 72 C Built loop between residues 84 B and 93 B 19 chains (376 residues) following loop building 4 chains (219 residues) in sequence following loop building ------------------------------------------------------ 8484 reflections ( 99.60 % complete ) and 4596 restraints for refining 3257 atoms. 2219 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2688 (Rfree = 0.000) for 3257 atoms. Found 19 (19 requested) and removed 46 (12 requested) atoms. Cycle 12: After refmac, R = 0.2472 (Rfree = 0.000) for 3217 atoms. Found 17 (19 requested) and removed 18 (12 requested) atoms. Cycle 13: After refmac, R = 0.2353 (Rfree = 0.000) for 3206 atoms. Found 12 (18 requested) and removed 18 (12 requested) atoms. Cycle 14: After refmac, R = 0.2274 (Rfree = 0.000) for 3192 atoms. Found 7 (18 requested) and removed 15 (12 requested) atoms. Cycle 15: After refmac, R = 0.2223 (Rfree = 0.000) for 3180 atoms. Found 8 (17 requested) and removed 14 (12 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.11 2.83 Search for helices and strands: 0 residues in 0 chains, 3215 seeds are put forward NCS extension: 61 residues added (47 deleted due to clashes), 3276 seeds are put forward Round 1: 341 peptides, 31 chains. Longest chain 28 peptides. Score 0.723 Round 2: 360 peptides, 26 chains. Longest chain 39 peptides. Score 0.784 Round 3: 373 peptides, 21 chains. Longest chain 43 peptides. Score 0.828 Round 4: 377 peptides, 20 chains. Longest chain 43 peptides. Score 0.838 Round 5: 369 peptides, 24 chains. Longest chain 43 peptides. Score 0.807 Taking the results from Round 4 Chains 26, Residues 357, Estimated correctness of the model 86.4 % 10 chains (226 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 79 A and 86 A Built loop between residues 60 C and 64 C 24 chains (362 residues) following loop building 8 chains (235 residues) in sequence following loop building ------------------------------------------------------ 8484 reflections ( 99.60 % complete ) and 4387 restraints for refining 3258 atoms. 2099 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2839 (Rfree = 0.000) for 3258 atoms. Found 17 (17 requested) and removed 56 (12 requested) atoms. Cycle 17: After refmac, R = 0.2588 (Rfree = 0.000) for 3201 atoms. Found 16 (16 requested) and removed 22 (12 requested) atoms. Cycle 18: After refmac, R = 0.2440 (Rfree = 0.000) for 3185 atoms. Found 15 (16 requested) and removed 16 (12 requested) atoms. Cycle 19: After refmac, R = 0.2351 (Rfree = 0.000) for 3177 atoms. Found 15 (15 requested) and removed 21 (12 requested) atoms. Cycle 20: After refmac, R = 0.2181 (Rfree = 0.000) for 3168 atoms. Found 11 (14 requested) and removed 19 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.12 2.84 Search for helices and strands: 0 residues in 0 chains, 3245 seeds are put forward NCS extension: 42 residues added (81 deleted due to clashes), 3287 seeds are put forward Round 1: 325 peptides, 35 chains. Longest chain 36 peptides. Score 0.665 Round 2: 351 peptides, 28 chains. Longest chain 27 peptides. Score 0.759 Round 3: 341 peptides, 28 chains. Longest chain 37 peptides. Score 0.745 Round 4: 338 peptides, 28 chains. Longest chain 29 peptides. Score 0.741 Round 5: 347 peptides, 31 chains. Longest chain 27 peptides. Score 0.733 Taking the results from Round 2 Chains 33, Residues 323, Estimated correctness of the model 71.8 % 8 chains (158 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 38 B and 47 B 31 chains (328 residues) following loop building 7 chains (166 residues) in sequence following loop building ------------------------------------------------------ 8484 reflections ( 99.60 % complete ) and 5256 restraints for refining 3258 atoms. 3310 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2519 (Rfree = 0.000) for 3258 atoms. Found 14 (14 requested) and removed 32 (12 requested) atoms. Cycle 22: After refmac, R = 0.2296 (Rfree = 0.000) for 3228 atoms. Found 14 (14 requested) and removed 21 (12 requested) atoms. Cycle 23: After refmac, R = 0.2269 (Rfree = 0.000) for 3218 atoms. Found 11 (13 requested) and removed 20 (12 requested) atoms. Cycle 24: After refmac, R = 0.2138 (Rfree = 0.000) for 3205 atoms. Found 10 (13 requested) and removed 21 (12 requested) atoms. Cycle 25: After refmac, R = 0.2126 (Rfree = 0.000) for 3192 atoms. Found 12 (12 requested) and removed 16 (12 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.12 2.84 Search for helices and strands: 0 residues in 0 chains, 3267 seeds are put forward NCS extension: 29 residues added (19 deleted due to clashes), 3296 seeds are put forward Round 1: 315 peptides, 30 chains. Longest chain 31 peptides. Score 0.689 Round 2: 331 peptides, 27 chains. Longest chain 34 peptides. Score 0.738 Round 3: 322 peptides, 32 chains. Longest chain 26 peptides. Score 0.684 Round 4: 326 peptides, 30 chains. Longest chain 26 peptides. Score 0.707 Round 5: 332 peptides, 28 chains. Longest chain 26 peptides. Score 0.732 Taking the results from Round 2 Chains 31, Residues 304, Estimated correctness of the model 67.1 % 6 chains (85 residues) have been docked in sequence Building loops using Loopy2018 31 chains (304 residues) following loop building 6 chains (85 residues) in sequence following loop building ------------------------------------------------------ 8484 reflections ( 99.60 % complete ) and 6164 restraints for refining 3258 atoms. 4682 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2527 (Rfree = 0.000) for 3258 atoms. Found 12 (12 requested) and removed 38 (12 requested) atoms. Cycle 27: After refmac, R = 0.2220 (Rfree = 0.000) for 3227 atoms. Found 12 (12 requested) and removed 17 (12 requested) atoms. Cycle 28: After refmac, R = 0.2153 (Rfree = 0.000) for 3214 atoms. Found 12 (12 requested) and removed 17 (12 requested) atoms. Cycle 29: After refmac, R = 0.2132 (Rfree = 0.000) for 3203 atoms. Found 7 (12 requested) and removed 12 (12 requested) atoms. Cycle 30: After refmac, R = 0.2131 (Rfree = 0.000) for 3196 atoms. Found 7 (12 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.13 2.85 Search for helices and strands: 0 residues in 0 chains, 3249 seeds are put forward NCS extension: 11 residues added (16 deleted due to clashes), 3260 seeds are put forward Round 1: 288 peptides, 32 chains. Longest chain 19 peptides. Score 0.620 Round 2: 319 peptides, 32 chains. Longest chain 22 peptides. Score 0.679 Round 3: 335 peptides, 30 chains. Longest chain 34 peptides. Score 0.722 Round 4: 317 peptides, 30 chains. Longest chain 25 peptides. Score 0.692 Round 5: 333 peptides, 33 chains. Longest chain 26 peptides. Score 0.695 Taking the results from Round 3 Chains 31, Residues 305, Estimated correctness of the model 63.4 % 4 chains (64 residues) have been docked in sequence Building loops using Loopy2018 31 chains (305 residues) following loop building 4 chains (64 residues) in sequence following loop building ------------------------------------------------------ 8484 reflections ( 99.60 % complete ) and 6213 restraints for refining 3257 atoms. 4760 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2288 (Rfree = 0.000) for 3257 atoms. Found 12 (12 requested) and removed 18 (12 requested) atoms. Cycle 32: After refmac, R = 0.2157 (Rfree = 0.000) for 3244 atoms. Found 12 (12 requested) and removed 14 (12 requested) atoms. Cycle 33: After refmac, R = 0.2118 (Rfree = 0.000) for 3239 atoms. Found 12 (12 requested) and removed 17 (12 requested) atoms. Cycle 34: After refmac, R = 0.2085 (Rfree = 0.000) for 3234 atoms. Found 8 (12 requested) and removed 13 (12 requested) atoms. Cycle 35: After refmac, R = 0.2066 (Rfree = 0.000) for 3229 atoms. Found 10 (12 requested) and removed 16 (12 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.12 2.84 Search for helices and strands: 0 residues in 0 chains, 3279 seeds are put forward NCS extension: 25 residues added (9 deleted due to clashes), 3304 seeds are put forward Round 1: 284 peptides, 33 chains. Longest chain 20 peptides. Score 0.602 Round 2: 326 peptides, 29 chains. Longest chain 44 peptides. Score 0.715 Round 3: 322 peptides, 27 chains. Longest chain 45 peptides. Score 0.724 Round 4: 320 peptides, 32 chains. Longest chain 46 peptides. Score 0.681 Round 5: 325 peptides, 28 chains. Longest chain 41 peptides. Score 0.721 Taking the results from Round 3 Chains 31, Residues 295, Estimated correctness of the model 63.8 % 5 chains (103 residues) have been docked in sequence Building loops using Loopy2018 31 chains (295 residues) following loop building 5 chains (103 residues) in sequence following loop building ------------------------------------------------------ 8484 reflections ( 99.60 % complete ) and 5971 restraints for refining 3258 atoms. 4405 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2391 (Rfree = 0.000) for 3258 atoms. Found 12 (12 requested) and removed 26 (12 requested) atoms. Cycle 37: After refmac, R = 0.2192 (Rfree = 0.000) for 3240 atoms. Found 12 (12 requested) and removed 18 (12 requested) atoms. Cycle 38: After refmac, R = 0.2142 (Rfree = 0.000) for 3231 atoms. Found 12 (12 requested) and removed 13 (12 requested) atoms. Cycle 39: After refmac, R = 0.2068 (Rfree = 0.000) for 3227 atoms. Found 12 (12 requested) and removed 15 (12 requested) atoms. Cycle 40: After refmac, R = 0.2068 (Rfree = 0.000) for 3223 atoms. Found 10 (12 requested) and removed 14 (12 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.12 2.84 Search for helices and strands: 0 residues in 0 chains, 3272 seeds are put forward NCS extension: 26 residues added (20 deleted due to clashes), 3298 seeds are put forward Round 1: 291 peptides, 34 chains. Longest chain 23 peptides. Score 0.607 Round 2: 315 peptides, 32 chains. Longest chain 27 peptides. Score 0.672 Round 3: 321 peptides, 27 chains. Longest chain 42 peptides. Score 0.722 Round 4: 323 peptides, 28 chains. Longest chain 49 peptides. Score 0.718 Round 5: 317 peptides, 25 chains. Longest chain 35 peptides. Score 0.732 Taking the results from Round 5 Chains 26, Residues 292, Estimated correctness of the model 65.7 % 5 chains (122 residues) have been docked in sequence Building loops using Loopy2018 26 chains (292 residues) following loop building 5 chains (122 residues) in sequence following loop building ------------------------------------------------------ 8484 reflections ( 99.60 % complete ) and 5727 restraints for refining 3258 atoms. 4096 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2383 (Rfree = 0.000) for 3258 atoms. Found 12 (12 requested) and removed 22 (12 requested) atoms. Cycle 42: After refmac, R = 0.2246 (Rfree = 0.000) for 3239 atoms. Found 12 (12 requested) and removed 20 (12 requested) atoms. Cycle 43: After refmac, R = 0.2158 (Rfree = 0.000) for 3229 atoms. Found 10 (12 requested) and removed 14 (12 requested) atoms. Cycle 44: After refmac, R = 0.2117 (Rfree = 0.000) for 3222 atoms. Found 7 (12 requested) and removed 12 (12 requested) atoms. Cycle 45: After refmac, R = 0.2090 (Rfree = 0.000) for 3217 atoms. Found 4 (12 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.18 2.90 Search for helices and strands: 0 residues in 0 chains, 3270 seeds are put forward NCS extension: 26 residues added (19 deleted due to clashes), 3296 seeds are put forward Round 1: 295 peptides, 34 chains. Longest chain 18 peptides. Score 0.616 Round 2: 318 peptides, 31 chains. Longest chain 25 peptides. Score 0.686 Round 3: 311 peptides, 27 chains. Longest chain 28 peptides. Score 0.706 Round 4: 311 peptides, 24 chains. Longest chain 44 peptides. Score 0.730 Round 5: 306 peptides, 28 chains. Longest chain 32 peptides. Score 0.690 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 28, Residues 287, Estimated correctness of the model 65.3 % 6 chains (118 residues) have been docked in sequence Sequence coverage is 40 % Consider running further cycles of model building using 2opk-3_warpNtrace.pdb as input Building loops using Loopy2018 28 chains (287 residues) following loop building 6 chains (118 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8484 reflections ( 99.60 % complete ) and 5803 restraints for refining 3258 atoms. 4220 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2394 (Rfree = 0.000) for 3258 atoms. Found 0 (12 requested) and removed 3 (12 requested) atoms. Cycle 47: After refmac, R = 0.2309 (Rfree = 0.000) for 3249 atoms. Found 0 (12 requested) and removed 6 (12 requested) atoms. Cycle 48: After refmac, R = 0.2295 (Rfree = 0.000) for 3238 atoms. Found 0 (12 requested) and removed 3 (12 requested) atoms. Cycle 49: After refmac, R = 0.2251 (Rfree = 0.000) for 3232 atoms. TimeTaking 47.57