Tue 25 Dec 19:27:55 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 2opk-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2opk-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2opk-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2opk-3.4-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/2opk-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2opk-3.4-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 ============================================================ Tue 25 Dec 19:28:05 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/2opk-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2opk-3.4-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 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-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: 96 Cell parameters: 75.570 75.570 198.970 90.000 90.000 90.000 Input sequence file: 2opk-3.4-parrot-hancs.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 3981 atoms. Observations/parameters ratio is 0.53 ------------------------------------------------------ Starting model: R = 0.2885 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2470 (Rfree = 0.000) for 3981 atoms. Found 30 (30 requested) and removed 35 (15 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.09 2.81 Search for helices and strands: 0 residues in 0 chains, 4022 seeds are put forward NCS extension: 0 residues added, 4022 seeds are put forward Round 1: 298 peptides, 45 chains. Longest chain 13 peptides. Score 0.512 Round 2: 340 peptides, 37 chains. Longest chain 28 peptides. Score 0.675 Round 3: 352 peptides, 29 chains. Longest chain 34 peptides. Score 0.754 Round 4: 357 peptides, 29 chains. Longest chain 48 peptides. Score 0.761 Round 5: 367 peptides, 25 chains. Longest chain 36 peptides. Score 0.799 Taking the results from Round 5 Chains 31, Residues 342, Estimated correctness of the model 79.8 % 7 chains (137 residues) have been docked in sequence Building loops using Loopy2018 31 chains (342 residues) following loop building 7 chains (137 residues) in sequence following loop building ------------------------------------------------------ 8484 reflections ( 99.60 % complete ) and 5143 restraints for refining 3269 atoms. 3217 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2616 (Rfree = 0.000) for 3269 atoms. Found 24 (24 requested) and removed 34 (12 requested) atoms. Cycle 2: After refmac, R = 0.2432 (Rfree = 0.000) for 3220 atoms. Found 20 (24 requested) and removed 25 (12 requested) atoms. Cycle 3: After refmac, R = 0.2300 (Rfree = 0.000) for 3196 atoms. Found 8 (23 requested) and removed 19 (12 requested) atoms. Cycle 4: After refmac, R = 0.2191 (Rfree = 0.000) for 3182 atoms. Found 5 (23 requested) and removed 17 (12 requested) atoms. Cycle 5: After refmac, R = 0.2145 (Rfree = 0.000) for 3166 atoms. Found 12 (21 requested) and removed 14 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.16 2.88 Search for helices and strands: 0 residues in 0 chains, 3224 seeds are put forward NCS extension: 21 residues added (23 deleted due to clashes), 3245 seeds are put forward Round 1: 355 peptides, 33 chains. Longest chain 32 peptides. Score 0.730 Round 2: 384 peptides, 24 chains. Longest chain 46 peptides. Score 0.823 Round 3: 370 peptides, 28 chains. Longest chain 34 peptides. Score 0.784 Round 4: 375 peptides, 22 chains. Longest chain 56 peptides. Score 0.825 Round 5: 369 peptides, 30 chains. Longest chain 31 peptides. Score 0.770 Taking the results from Round 4 Chains 27, Residues 353, Estimated correctness of the model 84.3 % 7 chains (161 residues) have been docked in sequence Building loops using Loopy2018 27 chains (353 residues) following loop building 7 chains (161 residues) in sequence following loop building ------------------------------------------------------ 8484 reflections ( 99.60 % complete ) and 5096 restraints for refining 3258 atoms. 3074 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2858 (Rfree = 0.000) for 3258 atoms. Found 22 (22 requested) and removed 48 (12 requested) atoms. Cycle 7: After refmac, R = 0.2487 (Rfree = 0.000) for 3214 atoms. Found 17 (21 requested) and removed 29 (12 requested) atoms. Cycle 8: After refmac, R = 0.2339 (Rfree = 0.000) for 3196 atoms. Found 7 (21 requested) and removed 19 (12 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.2229 (Rfree = 0.000) for 3180 atoms. Found 10 (20 requested) and removed 16 (12 requested) atoms. Cycle 10: After refmac, R = 0.2156 (Rfree = 0.000) for 3169 atoms. Found 9 (19 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.06 2.79 Search for helices and strands: 0 residues in 0 chains, 3243 seeds are put forward NCS extension: 38 residues added (57 deleted due to clashes), 3281 seeds are put forward Round 1: 355 peptides, 30 chains. Longest chain 39 peptides. Score 0.751 Round 2: 373 peptides, 23 chains. Longest chain 39 peptides. Score 0.817 Round 3: 389 peptides, 22 chains. Longest chain 70 peptides. Score 0.839 Round 4: 381 peptides, 23 chains. Longest chain 54 peptides. Score 0.825 Round 5: 353 peptides, 25 chains. Longest chain 40 peptides. Score 0.782 Taking the results from Round 3 Chains 28, Residues 367, Estimated correctness of the model 86.5 % 7 chains (163 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 37 C and 43 C 27 chains (372 residues) following loop building 6 chains (168 residues) in sequence following loop building ------------------------------------------------------ 8484 reflections ( 99.60 % complete ) and 4996 restraints for refining 3258 atoms. 2865 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2571 (Rfree = 0.000) for 3258 atoms. Found 19 (19 requested) and removed 36 (12 requested) atoms. Cycle 12: After refmac, R = 0.2316 (Rfree = 0.000) for 3235 atoms. Found 19 (19 requested) and removed 19 (12 requested) atoms. Cycle 13: After refmac, R = 0.2165 (Rfree = 0.000) for 3226 atoms. Found 13 (18 requested) and removed 16 (12 requested) atoms. Cycle 14: After refmac, R = 0.2102 (Rfree = 0.000) for 3219 atoms. Found 10 (18 requested) and removed 15 (12 requested) atoms. Failed to save intermediate PDB Cycle 15: After refmac, R = 0.2034 (Rfree = 0.000) for 3210 atoms. Found 6 (17 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.13 2.85 Search for helices and strands: 0 residues in 0 chains, 3249 seeds are put forward NCS extension: 68 residues added (95 deleted due to clashes), 3317 seeds are put forward Round 1: 337 peptides, 31 chains. Longest chain 33 peptides. Score 0.717 Round 2: 357 peptides, 29 chains. Longest chain 36 peptides. Score 0.761 Round 3: 340 peptides, 30 chains. Longest chain 37 peptides. Score 0.729 Round 4: 356 peptides, 27 chains. Longest chain 36 peptides. Score 0.773 Round 5: 350 peptides, 28 chains. Longest chain 35 peptides. Score 0.758 Taking the results from Round 4 Chains 32, Residues 329, Estimated correctness of the model 74.7 % 7 chains (140 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 39 B and 43 B Built loop between residues 77 B and 87 B 29 chains (337 residues) following loop building 5 chains (152 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 8484 reflections ( 99.60 % complete ) and 5203 restraints for refining 3258 atoms. 3279 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2573 (Rfree = 0.000) for 3258 atoms. Found 17 (17 requested) and removed 38 (12 requested) atoms. Cycle 17: After refmac, R = 0.2291 (Rfree = 0.000) for 3222 atoms. Found 16 (16 requested) and removed 22 (12 requested) atoms. Cycle 18: After refmac, R = 0.2190 (Rfree = 0.000) for 3209 atoms. Found 9 (16 requested) and removed 13 (12 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.2139 (Rfree = 0.000) for 3202 atoms. Found 7 (15 requested) and removed 13 (12 requested) atoms. Cycle 20: After refmac, R = 0.2084 (Rfree = 0.000) for 3190 atoms. Found 2 (15 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.11 2.83 Search for helices and strands: 0 residues in 0 chains, 3251 seeds are put forward NCS extension: 87 residues added (66 deleted due to clashes), 3338 seeds are put forward Round 1: 339 peptides, 34 chains. Longest chain 26 peptides. Score 0.697 Round 2: 357 peptides, 26 chains. Longest chain 33 peptides. Score 0.780 Round 3: 349 peptides, 30 chains. Longest chain 39 peptides. Score 0.743 Round 4: 345 peptides, 26 chains. Longest chain 39 peptides. Score 0.765 Round 5: 342 peptides, 29 chains. Longest chain 40 peptides. Score 0.740 Taking the results from Round 2 Chains 31, Residues 331, Estimated correctness of the model 76.1 % 7 chains (138 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 36 B and 45 B Built loop between residues 76 B and 84 B 28 chains (340 residues) following loop building 5 chains (153 residues) in sequence following loop building ------------------------------------------------------ 8484 reflections ( 99.60 % complete ) and 5211 restraints for refining 3258 atoms. 3329 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2487 (Rfree = 0.000) for 3258 atoms. Found 14 (14 requested) and removed 49 (12 requested) atoms. Failed to save intermediate PDB Cycle 22: After refmac, R = 0.2276 (Rfree = 0.000) for 3213 atoms. Found 12 (14 requested) and removed 19 (12 requested) atoms. Cycle 23: After refmac, R = 0.2180 (Rfree = 0.000) for 3201 atoms. Found 2 (13 requested) and removed 18 (12 requested) atoms. Failed to save intermediate PDB Cycle 24: After refmac, R = 0.2126 (Rfree = 0.000) for 3180 atoms. Found 7 (13 requested) and removed 13 (12 requested) atoms. Failed to save intermediate PDB Cycle 25: After refmac, R = 0.2078 (Rfree = 0.000) for 3173 atoms. Found 3 (12 requested) and removed 16 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.11 2.83 Search for helices and strands: 0 residues in 0 chains, 3222 seeds are put forward NCS extension: 67 residues added (74 deleted due to clashes), 3289 seeds are put forward Round 1: 334 peptides, 42 chains. Longest chain 31 peptides. Score 0.621 Round 2: 347 peptides, 31 chains. Longest chain 36 peptides. Score 0.733 Round 3: 347 peptides, 33 chains. Longest chain 30 peptides. Score 0.718 Round 4: 334 peptides, 29 chains. Longest chain 36 peptides. Score 0.728 Round 5: 347 peptides, 32 chains. Longest chain 30 peptides. Score 0.725 Taking the results from Round 2 Chains 37, Residues 316, Estimated correctness of the model 66.0 % 5 chains (88 residues) have been docked in sequence Building loops using Loopy2018 37 chains (316 residues) following loop building 5 chains (88 residues) in sequence following loop building ------------------------------------------------------ 8484 reflections ( 99.60 % complete ) and 6017 restraints for refining 3258 atoms. 4441 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2378 (Rfree = 0.000) for 3258 atoms. Found 12 (12 requested) and removed 22 (12 requested) atoms. Cycle 27: After refmac, R = 0.2261 (Rfree = 0.000) for 3235 atoms. Found 12 (12 requested) and removed 14 (12 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.2222 (Rfree = 0.000) for 3230 atoms. Found 7 (12 requested) and removed 12 (12 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.2196 (Rfree = 0.000) for 3224 atoms. Found 4 (12 requested) and removed 15 (12 requested) atoms. Cycle 30: After refmac, R = 0.2190 (Rfree = 0.000) for 3212 atoms. Found 5 (12 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.11 2.83 Search for helices and strands: 0 residues in 0 chains, 3247 seeds are put forward NCS extension: 24 residues added (8 deleted due to clashes), 3271 seeds are put forward Round 1: 311 peptides, 29 chains. Longest chain 35 peptides. Score 0.690 Round 2: 315 peptides, 25 chains. Longest chain 45 peptides. Score 0.728 Round 3: 322 peptides, 29 chains. Longest chain 27 peptides. Score 0.709 Round 4: 325 peptides, 26 chains. Longest chain 37 peptides. Score 0.736 Round 5: 332 peptides, 27 chains. Longest chain 44 peptides. Score 0.739 Taking the results from Round 5 Chains 29, Residues 305, Estimated correctness of the model 67.3 % 5 chains (58 residues) have been docked in sequence Building loops using Loopy2018 29 chains (305 residues) following loop building 5 chains (58 residues) in sequence following loop building ------------------------------------------------------ 8484 reflections ( 99.60 % complete ) and 6426 restraints for refining 3258 atoms. 5041 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2386 (Rfree = 0.000) for 3258 atoms. Found 12 (12 requested) and removed 20 (12 requested) atoms. Failed to save intermediate PDB Cycle 32: After refmac, R = 0.2253 (Rfree = 0.000) for 3246 atoms. Found 12 (12 requested) and removed 13 (12 requested) atoms. Failed to save intermediate PDB Cycle 33: After refmac, R = 0.2201 (Rfree = 0.000) for 3244 atoms. Found 4 (12 requested) and removed 13 (12 requested) atoms. Cycle 34: After refmac, R = 0.2181 (Rfree = 0.000) for 3235 atoms. Found 4 (12 requested) and removed 12 (12 requested) atoms. Cycle 35: After refmac, R = 0.2167 (Rfree = 0.000) for 3227 atoms. Found 8 (12 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.13 2.85 Search for helices and strands: 0 residues in 0 chains, 3257 seeds are put forward NCS extension: 21 residues added (9 deleted due to clashes), 3278 seeds are put forward Round 1: 288 peptides, 34 chains. Longest chain 26 peptides. Score 0.601 Round 2: 325 peptides, 30 chains. Longest chain 55 peptides. Score 0.706 Round 3: 317 peptides, 29 chains. Longest chain 36 peptides. Score 0.700 Round 4: 329 peptides, 29 chains. Longest chain 35 peptides. Score 0.720 Round 5: 315 peptides, 26 chains. Longest chain 34 peptides. Score 0.721 Taking the results from Round 5 Chains 26, Residues 289, Estimated correctness of the model 63.1 % 2 chains (27 residues) have been docked in sequence Building loops using Loopy2018 26 chains (289 residues) following loop building 2 chains (27 residues) in sequence following loop building ------------------------------------------------------ 8484 reflections ( 99.60 % complete ) and 6748 restraints for refining 3257 atoms. 5529 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2390 (Rfree = 0.000) for 3257 atoms. Found 12 (12 requested) and removed 20 (12 requested) atoms. Cycle 37: After refmac, R = 0.2218 (Rfree = 0.000) for 3239 atoms. Found 9 (12 requested) and removed 15 (12 requested) atoms. Failed to save intermediate PDB Cycle 38: After refmac, R = 0.2143 (Rfree = 0.000) for 3226 atoms. Found 8 (12 requested) and removed 12 (12 requested) atoms. Cycle 39: After refmac, R = 0.2114 (Rfree = 0.000) for 3218 atoms. Found 7 (12 requested) and removed 12 (12 requested) atoms. Cycle 40: After refmac, R = 0.2086 (Rfree = 0.000) for 3212 atoms. Found 1 (12 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.14 2.86 Search for helices and strands: 0 residues in 0 chains, 3242 seeds are put forward NCS extension: 16 residues added (13 deleted due to clashes), 3258 seeds are put forward Round 1: 298 peptides, 37 chains. Longest chain 26 peptides. Score 0.593 Round 2: 316 peptides, 33 chains. Longest chain 33 peptides. Score 0.665 Round 3: 311 peptides, 29 chains. Longest chain 34 peptides. Score 0.690 Round 4: 298 peptides, 32 chains. Longest chain 29 peptides. Score 0.640 Round 5: 315 peptides, 31 chains. Longest chain 34 peptides. Score 0.680 Taking the results from Round 3 Chains 34, Residues 282, Estimated correctness of the model 55.3 % 4 chains (56 residues) have been docked in sequence ------------------------------------------------------ 8484 reflections ( 99.60 % complete ) and 6399 restraints for refining 3258 atoms. 5091 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2412 (Rfree = 0.000) for 3258 atoms. Found 12 (12 requested) and removed 21 (12 requested) atoms. Cycle 42: After refmac, R = 0.2286 (Rfree = 0.000) for 3247 atoms. Found 11 (12 requested) and removed 15 (12 requested) atoms. Cycle 43: After refmac, R = 0.2269 (Rfree = 0.000) for 3240 atoms. Found 5 (12 requested) and removed 13 (12 requested) atoms. Cycle 44: After refmac, R = 0.2241 (Rfree = 0.000) for 3232 atoms. Found 7 (12 requested) and removed 14 (12 requested) atoms. Cycle 45: After refmac, R = 0.2239 (Rfree = 0.000) for 3223 atoms. Found 6 (12 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.15 2.87 Search for helices and strands: 0 residues in 0 chains, 3264 seeds are put forward NCS extension: 26 residues added (9 deleted due to clashes), 3290 seeds are put forward Round 1: 281 peptides, 36 chains. Longest chain 19 peptides. Score 0.566 Round 2: 311 peptides, 35 chains. Longest chain 29 peptides. Score 0.638 Round 3: 318 peptides, 31 chains. Longest chain 23 peptides. Score 0.686 Round 4: 322 peptides, 29 chains. Longest chain 28 peptides. Score 0.709 Round 5: 327 peptides, 30 chains. Longest chain 26 peptides. Score 0.709 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 33, Residues 297, Estimated correctness of the model 60.2 % 4 chains (74 residues) have been docked in sequence Sequence coverage is 24 % Consider running further cycles of model building using 2opk-3_warpNtrace.pdb as input Building loops using Loopy2018 33 chains (297 residues) following loop building 4 chains (74 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8484 reflections ( 99.60 % complete ) and 6128 restraints for refining 3257 atoms. 4694 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2488 (Rfree = 0.000) for 3257 atoms. Found 0 (12 requested) and removed 12 (12 requested) atoms. Cycle 47: After refmac, R = 0.2435 (Rfree = 0.000) for 3235 atoms. Found 0 (12 requested) and removed 9 (12 requested) atoms. Cycle 48: After refmac, R = 0.2340 (Rfree = 0.000) for 3224 atoms. Found 0 (12 requested) and removed 4 (12 requested) atoms. Cycle 49: After refmac, R = 0.2291 (Rfree = 0.000) for 3218 atoms. Found 0 (12 requested) and removed 3 (12 requested) atoms. Writing output files ... Failed to save intermediate PDB TimeTaking 65.46