Tue 25 Dec 19:27:57 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 1vjv-2.7-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vjv-2.7-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vjv-2.7-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjv-2.7-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/1vjv-2.7-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjv-2.7-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 19:28:06 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/1vjv-2.7-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjv-2.7-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 379 and 0 Target number of residues in the AU: 379 Target solvent content: 0.5272 Checking the provided sequence file Detected sequence length: 415 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 415 Adjusted target solvent content: 0.48 Input MTZ file: 1vjv-2.7-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: 49.299 81.862 107.491 90.000 90.000 90.000 Input sequence file: 1vjv-2.7-parrot-hancs.fasta_lf Building free atoms model in initial map for 3320 target number of atoms Had to go as low as 0.45 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 Loops will be built when appropriate and at the last cycle Resolution range: 65.126 2.653 Wilson plot Bfac: 29.49 12831 reflections ( 97.62 % complete ) and 0 restraints for refining 3683 atoms. Observations/parameters ratio is 0.87 ------------------------------------------------------ Starting model: R = 0.2939 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2017 (Rfree = 0.000) for 3683 atoms. Found 41 (56 requested) and removed 53 (28 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.41 2.48 Round 1: 232 peptides, 34 chains. Longest chain 13 peptides. Score 0.531 Round 2: 276 peptides, 27 chains. Longest chain 41 peptides. Score 0.723 Round 3: 299 peptides, 19 chains. Longest chain 46 peptides. Score 0.826 Round 4: 305 peptides, 17 chains. Longest chain 43 peptides. Score 0.847 Round 5: 317 peptides, 16 chains. Longest chain 68 peptides. Score 0.866 Taking the results from Round 5 Chains 20, Residues 301, Estimated correctness of the model 95.6 % 8 chains (232 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 88 A and 94 A Built loop between residues 112 A and 121 A Built loop between residues 370 A and 374 A 16 chains (316 residues) following loop building 5 chains (248 residues) in sequence following loop building ------------------------------------------------------ 12831 reflections ( 97.62 % complete ) and 3830 restraints for refining 3152 atoms. 1501 conditional restraints added. Observations/parameters ratio is 1.02 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2601 (Rfree = 0.000) for 3152 atoms. Found 48 (48 requested) and removed 39 (24 requested) atoms. Cycle 2: After refmac, R = 0.2438 (Rfree = 0.000) for 3102 atoms. Found 44 (47 requested) and removed 32 (24 requested) atoms. Cycle 3: After refmac, R = 0.2322 (Rfree = 0.000) for 3082 atoms. Found 43 (45 requested) and removed 27 (23 requested) atoms. Failed to save intermediate PDB Cycle 4: After refmac, R = 0.2248 (Rfree = 0.000) for 3081 atoms. Found 39 (44 requested) and removed 27 (23 requested) atoms. Failed to save intermediate PDB Cycle 5: After refmac, R = 0.2134 (Rfree = 0.000) for 3084 atoms. Found 19 (43 requested) and removed 26 (23 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.39 2.45 Round 1: 312 peptides, 14 chains. Longest chain 41 peptides. Score 0.873 Round 2: 326 peptides, 12 chains. Longest chain 95 peptides. Score 0.896 Round 3: 321 peptides, 14 chains. Longest chain 55 peptides. Score 0.881 Round 4: 317 peptides, 15 chains. Longest chain 51 peptides. Score 0.872 Round 5: 326 peptides, 14 chains. Longest chain 95 peptides. Score 0.886 Taking the results from Round 2 Chains 12, Residues 314, Estimated correctness of the model 97.2 % 9 chains (281 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 45 A and 49 A Built loop between residues 88 A and 94 A Built loop between residues 114 A and 120 A 9 chains (327 residues) following loop building 6 chains (294 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 12831 reflections ( 97.62 % complete ) and 3419 restraints for refining 3087 atoms. 837 conditional restraints added. Observations/parameters ratio is 1.04 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2249 (Rfree = 0.000) for 3087 atoms. Found 42 (42 requested) and removed 33 (23 requested) atoms. Cycle 7: After refmac, R = 0.2100 (Rfree = 0.000) for 3079 atoms. Found 34 (41 requested) and removed 24 (23 requested) atoms. Cycle 8: After refmac, R = 0.1963 (Rfree = 0.000) for 3080 atoms. Found 30 (40 requested) and removed 26 (23 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.1930 (Rfree = 0.000) for 3077 atoms. Found 28 (39 requested) and removed 25 (23 requested) atoms. Cycle 10: After refmac, R = 0.1862 (Rfree = 0.000) for 3073 atoms. Found 20 (39 requested) and removed 25 (23 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.41 2.48 Round 1: 324 peptides, 12 chains. Longest chain 95 peptides. Score 0.894 Round 2: 332 peptides, 9 chains. Longest chain 96 peptides. Score 0.915 Round 3: 334 peptides, 10 chains. Longest chain 97 peptides. Score 0.912 Round 4: 336 peptides, 8 chains. Longest chain 96 peptides. Score 0.922 Round 5: 326 peptides, 15 chains. Longest chain 58 peptides. Score 0.881 Taking the results from Round 4 Chains 9, Residues 328, Estimated correctness of the model 98.4 % 7 chains (311 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 66 A and 70 A Built loop between residues 88 A and 94 A Built loop between residues 114 A and 119 A Built loop between residues 234 A and 241 A 5 chains (346 residues) following loop building 3 chains (329 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 12831 reflections ( 97.62 % complete ) and 3163 restraints for refining 3109 atoms. 346 conditional restraints added. Observations/parameters ratio is 1.03 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2261 (Rfree = 0.000) for 3109 atoms. Found 38 (38 requested) and removed 40 (23 requested) atoms. Cycle 12: After refmac, R = 0.2051 (Rfree = 0.000) for 3094 atoms. Found 37 (37 requested) and removed 25 (23 requested) atoms. Cycle 13: After refmac, R = 0.1944 (Rfree = 0.000) for 3101 atoms. Found 24 (36 requested) and removed 25 (23 requested) atoms. Cycle 14: After refmac, R = 0.1874 (Rfree = 0.000) for 3097 atoms. Found 27 (35 requested) and removed 23 (23 requested) atoms. Cycle 15: After refmac, R = 0.1841 (Rfree = 0.000) for 3095 atoms. Found 24 (34 requested) and removed 24 (23 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.39 2.45 Round 1: 331 peptides, 12 chains. Longest chain 79 peptides. Score 0.900 Round 2: 335 peptides, 9 chains. Longest chain 97 peptides. Score 0.917 Round 3: 333 peptides, 13 chains. Longest chain 79 peptides. Score 0.897 Round 4: 330 peptides, 10 chains. Longest chain 96 peptides. Score 0.909 Round 5: 332 peptides, 14 chains. Longest chain 70 peptides. Score 0.891 Taking the results from Round 2 Chains 10, Residues 326, Estimated correctness of the model 98.2 % 8 chains (315 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 29 A and 32 A Built loop between residues 64 A and 70 A Built loop between residues 88 A and 94 A Built loop between residues 114 A and 120 A Built loop between residues 157 A and 167 A 4 chains (350 residues) following loop building 3 chains (341 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 12831 reflections ( 97.62 % complete ) and 3220 restraints for refining 3140 atoms. 345 conditional restraints added. Observations/parameters ratio is 1.02 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2410 (Rfree = 0.000) for 3140 atoms. Found 34 (34 requested) and removed 39 (24 requested) atoms. Failed to save intermediate PDB Cycle 17: After refmac, R = 0.2020 (Rfree = 0.000) for 3124 atoms. Found 33 (33 requested) and removed 27 (24 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.1886 (Rfree = 0.000) for 3121 atoms. Found 24 (31 requested) and removed 26 (23 requested) atoms. Cycle 19: After refmac, R = 0.1815 (Rfree = 0.000) for 3115 atoms. Found 26 (30 requested) and removed 27 (23 requested) atoms. Cycle 20: After refmac, R = 0.1763 (Rfree = 0.000) for 3113 atoms. Found 17 (29 requested) and removed 25 (23 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.43 2.50 Round 1: 337 peptides, 10 chains. Longest chain 96 peptides. Score 0.914 Round 2: 340 peptides, 11 chains. Longest chain 58 peptides. Score 0.911 Round 3: 339 peptides, 11 chains. Longest chain 58 peptides. Score 0.911 Round 4: 335 peptides, 14 chains. Longest chain 57 peptides. Score 0.893 Round 5: 333 peptides, 15 chains. Longest chain 51 peptides. Score 0.887 Taking the results from Round 1 Chains 11, Residues 327, Estimated correctness of the model 98.0 % 8 chains (311 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 59 A and 68 A Built loop between residues 88 A and 94 A Built loop between residues 114 A and 120 A Built loop between residues 398 A and 404 A 6 chains (347 residues) following loop building 4 chains (334 residues) in sequence following loop building ------------------------------------------------------ 12831 reflections ( 97.62 % complete ) and 3192 restraints for refining 3087 atoms. 379 conditional restraints added. Observations/parameters ratio is 1.04 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2083 (Rfree = 0.000) for 3087 atoms. Found 28 (28 requested) and removed 40 (23 requested) atoms. Failed to save intermediate PDB Cycle 22: After refmac, R = 0.1888 (Rfree = 0.000) for 3068 atoms. Found 27 (27 requested) and removed 23 (23 requested) atoms. Failed to save intermediate PDB Cycle 23: After refmac, R = 0.1802 (Rfree = 0.000) for 3064 atoms. Found 24 (26 requested) and removed 24 (23 requested) atoms. Failed to save intermediate PDB Cycle 24: After refmac, R = 0.1765 (Rfree = 0.000) for 3060 atoms. Found 18 (25 requested) and removed 31 (23 requested) atoms. Cycle 25: After refmac, R = 0.1766 (Rfree = 0.000) for 3045 atoms. Found 21 (24 requested) and removed 24 (23 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.42 2.49 Round 1: 336 peptides, 12 chains. Longest chain 46 peptides. Score 0.904 Round 2: 335 peptides, 14 chains. Longest chain 97 peptides. Score 0.893 Round 3: 337 peptides, 12 chains. Longest chain 79 peptides. Score 0.905 Round 4: 334 peptides, 17 chains. Longest chain 73 peptides. Score 0.877 Round 5: 343 peptides, 9 chains. Longest chain 79 peptides. Score 0.922 Taking the results from Round 5 Chains 12, Residues 334, Estimated correctness of the model 98.4 % 8 chains (315 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 87 A and 97 A Built loop between residues 114 A and 120 A Built loop between residues 235 A and 239 A Built loop between residues 381 A and 386 A 6 chains (350 residues) following loop building 4 chains (336 residues) in sequence following loop building ------------------------------------------------------ 12831 reflections ( 97.62 % complete ) and 3196 restraints for refining 3087 atoms. 356 conditional restraints added. Observations/parameters ratio is 1.04 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2130 (Rfree = 0.000) for 3087 atoms. Found 23 (23 requested) and removed 33 (23 requested) atoms. Cycle 27: After refmac, R = 0.1931 (Rfree = 0.000) for 3074 atoms. Found 23 (23 requested) and removed 23 (23 requested) atoms. Cycle 28: After refmac, R = 0.1820 (Rfree = 0.000) for 3073 atoms. Found 20 (23 requested) and removed 23 (23 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.1764 (Rfree = 0.000) for 3068 atoms. Found 23 (23 requested) and removed 24 (23 requested) atoms. Cycle 30: After refmac, R = 0.1760 (Rfree = 0.000) for 3067 atoms. Found 17 (23 requested) and removed 24 (23 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.43 2.50 Round 1: 336 peptides, 13 chains. Longest chain 78 peptides. Score 0.899 Round 2: 339 peptides, 11 chains. Longest chain 98 peptides. Score 0.911 Round 3: 340 peptides, 11 chains. Longest chain 78 peptides. Score 0.911 Round 4: 341 peptides, 10 chains. Longest chain 112 peptides. Score 0.916 Round 5: 331 peptides, 16 chains. Longest chain 79 peptides. Score 0.880 Taking the results from Round 4 Chains 13, Residues 331, Estimated correctness of the model 98.1 % 7 chains (298 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 128 A and 131 A Built loop between residues 157 A and 165 A Built loop between residues 236 A and 240 A 10 chains (343 residues) following loop building 4 chains (310 residues) in sequence following loop building ------------------------------------------------------ 12831 reflections ( 97.62 % complete ) and 3370 restraints for refining 3087 atoms. 666 conditional restraints added. Observations/parameters ratio is 1.04 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2045 (Rfree = 0.000) for 3087 atoms. Found 23 (23 requested) and removed 29 (23 requested) atoms. Failed to save intermediate PDB Cycle 32: After refmac, R = 0.1871 (Rfree = 0.000) for 3077 atoms. Found 23 (23 requested) and removed 26 (23 requested) atoms. Failed to save intermediate PDB Cycle 33: After refmac, R = 0.1783 (Rfree = 0.000) for 3070 atoms. Found 23 (23 requested) and removed 24 (23 requested) atoms. Cycle 34: After refmac, R = 0.1715 (Rfree = 0.000) for 3069 atoms. Found 23 (23 requested) and removed 25 (23 requested) atoms. Cycle 35: After refmac, R = 0.1676 (Rfree = 0.000) for 3066 atoms. Found 20 (23 requested) and removed 25 (23 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.43 2.50 Round 1: 337 peptides, 13 chains. Longest chain 95 peptides. Score 0.900 Round 2: 343 peptides, 10 chains. Longest chain 113 peptides. Score 0.918 Round 3: 339 peptides, 13 chains. Longest chain 79 peptides. Score 0.901 Round 4: 336 peptides, 13 chains. Longest chain 55 peptides. Score 0.899 Round 5: 335 peptides, 11 chains. Longest chain 87 peptides. Score 0.908 Taking the results from Round 2 Chains 11, Residues 333, Estimated correctness of the model 98.2 % 8 chains (309 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 69 A and 72 A Built loop between residues 89 A and 94 A Built loop between residues 157 A and 166 A 8 chains (347 residues) following loop building 5 chains (323 residues) in sequence following loop building ------------------------------------------------------ 12831 reflections ( 97.62 % complete ) and 3338 restraints for refining 3087 atoms. 567 conditional restraints added. Observations/parameters ratio is 1.04 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2001 (Rfree = 0.000) for 3087 atoms. Found 23 (23 requested) and removed 34 (23 requested) atoms. Cycle 37: After refmac, R = 0.1768 (Rfree = 0.000) for 3073 atoms. Found 23 (23 requested) and removed 23 (23 requested) atoms. Cycle 38: After refmac, R = 0.1679 (Rfree = 0.000) for 3072 atoms. Found 22 (23 requested) and removed 23 (23 requested) atoms. Cycle 39: After refmac, R = 0.1629 (Rfree = 0.000) for 3071 atoms. Found 11 (23 requested) and removed 23 (23 requested) atoms. Cycle 40: After refmac, R = 0.1622 (Rfree = 0.000) for 3059 atoms. Found 14 (23 requested) and removed 25 (23 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.44 2.51 Round 1: 331 peptides, 15 chains. Longest chain 79 peptides. Score 0.885 Round 2: 342 peptides, 9 chains. Longest chain 96 peptides. Score 0.921 Round 3: 336 peptides, 13 chains. Longest chain 59 peptides. Score 0.899 Round 4: 336 peptides, 13 chains. Longest chain 79 peptides. Score 0.899 Round 5: 338 peptides, 13 chains. Longest chain 47 peptides. Score 0.901 Taking the results from Round 2 Chains 11, Residues 333, Estimated correctness of the model 98.3 % 9 chains (331 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 89 A and 94 A Built loop between residues 115 A and 120 A Built loop between residues 143 A and 146 A Built loop between residues 157 A and 166 A Built loop between residues 235 A and 238 A Built loop between residues 398 A and 403 A 4 chains (356 residues) following loop building 3 chains (355 residues) in sequence following loop building ------------------------------------------------------ 12831 reflections ( 97.62 % complete ) and 3101 restraints for refining 3100 atoms. 156 conditional restraints added. Observations/parameters ratio is 1.03 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2096 (Rfree = 0.000) for 3100 atoms. Found 23 (23 requested) and removed 37 (23 requested) atoms. Cycle 42: After refmac, R = 0.1848 (Rfree = 0.000) for 3082 atoms. Found 23 (23 requested) and removed 23 (23 requested) atoms. Cycle 43: After refmac, R = 0.1730 (Rfree = 0.000) for 3080 atoms. Found 23 (23 requested) and removed 23 (23 requested) atoms. Cycle 44: After refmac, R = 0.1688 (Rfree = 0.000) for 3079 atoms. Found 23 (23 requested) and removed 24 (23 requested) atoms. Cycle 45: After refmac, R = 0.1652 (Rfree = 0.000) for 3078 atoms. Found 23 (23 requested) and removed 24 (23 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.43 2.50 Round 1: 337 peptides, 11 chains. Longest chain 96 peptides. Score 0.909 Round 2: 342 peptides, 10 chains. Longest chain 113 peptides. Score 0.917 Round 3: 340 peptides, 12 chains. Longest chain 55 peptides. Score 0.907 Round 4: 339 peptides, 13 chains. Longest chain 87 peptides. Score 0.901 Round 5: 342 peptides, 10 chains. Longest chain 83 peptides. Score 0.917 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 13, Residues 332, Estimated correctness of the model 98.2 % 10 chains (324 residues) have been docked in sequence Sequence coverage is 97 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 28 A and 32 A Built loop between residues 70 A and 72 A Built loop between residues 88 A and 95 A Built loop between residues 114 A and 120 A Built loop between residues 158 A and 166 A Built loop between residues 236 A and 239 A Built loop between residues 331 A and 338 A 4 chains (357 residues) following loop building 3 chains (354 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 12831 reflections ( 97.62 % complete ) and 2949 restraints for refining 2896 atoms. Observations/parameters ratio is 1.11 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2541 (Rfree = 0.000) for 2896 atoms. Found 15 (22 requested) and removed 0 (22 requested) atoms. Cycle 47: After refmac, R = 0.2223 (Rfree = 0.000) for 2896 atoms. Found 2 (22 requested) and removed 1 (22 requested) atoms. Cycle 48: After refmac, R = 0.2111 (Rfree = 0.000) for 2896 atoms. Found 4 (22 requested) and removed 2 (22 requested) atoms. Cycle 49: After refmac, R = 0.2059 (Rfree = 0.000) for 2896 atoms. Found 5 (22 requested) and removed 0 (22 requested) atoms. Writing output files ... Failed to save intermediate PDB TimeTaking 63.28