Sun 23 Dec 22:22:40 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 1vlc-2.5-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vlc-2.5-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vlc-2.5-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vlc-2.5-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/1vlc-2.5-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vlc-2.5-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 22:22:49 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/1vlc-2.5-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vlc-2.5-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 409 and 0 Target number of residues in the AU: 409 Target solvent content: 0.5295 Checking the provided sequence file Detected sequence length: 366 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 366 Adjusted target solvent content: 0.58 Input MTZ file: 1vlc-2.5-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: 150 Cell parameters: 119.541 119.541 57.022 90.000 90.000 120.000 Input sequence file: 1vlc-2.5-parrot-hancs.fasta_lf Building free atoms model in initial map for 2928 target number of atoms Had to go as low as 0.75 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: 103.526 2.460 Wilson plot Bfac: 30.16 16512 reflections ( 95.21 % complete ) and 0 restraints for refining 3264 atoms. Observations/parameters ratio is 1.26 ------------------------------------------------------ Starting model: R = 0.3195 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2629 (Rfree = 0.000) for 3264 atoms. Found 35 (61 requested) and removed 33 (30 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.40 2.16 Round 1: 255 peptides, 34 chains. Longest chain 25 peptides. Score 0.575 Round 2: 296 peptides, 22 chains. Longest chain 41 peptides. Score 0.777 Round 3: 318 peptides, 19 chains. Longest chain 57 peptides. Score 0.828 Round 4: 323 peptides, 16 chains. Longest chain 51 peptides. Score 0.853 Round 5: 335 peptides, 16 chains. Longest chain 55 peptides. Score 0.865 Taking the results from Round 5 Chains 20, Residues 319, Estimated correctness of the model 96.5 % 8 chains (235 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 54 A and 57 A Built loop between residues 187 A and 197 A Built loop between residues 232 A and 242 A 13 chains (329 residues) following loop building 5 chains (255 residues) in sequence following loop building ------------------------------------------------------ 16512 reflections ( 95.21 % complete ) and 3619 restraints for refining 3003 atoms. 1292 conditional restraints added. Observations/parameters ratio is 1.37 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2973 (Rfree = 0.000) for 3003 atoms. Found 57 (57 requested) and removed 49 (28 requested) atoms. Cycle 2: After refmac, R = 0.2707 (Rfree = 0.000) for 2977 atoms. Found 35 (56 requested) and removed 39 (28 requested) atoms. Cycle 3: After refmac, R = 0.2576 (Rfree = 0.000) for 2961 atoms. Found 27 (54 requested) and removed 28 (28 requested) atoms. Cycle 4: After refmac, R = 0.2570 (Rfree = 0.000) for 2947 atoms. Found 32 (53 requested) and removed 28 (28 requested) atoms. Cycle 5: After refmac, R = 0.2451 (Rfree = 0.000) for 2941 atoms. Found 24 (52 requested) and removed 31 (28 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.45 2.20 Round 1: 327 peptides, 14 chains. Longest chain 88 peptides. Score 0.868 Round 2: 335 peptides, 11 chains. Longest chain 55 peptides. Score 0.891 Round 3: 338 peptides, 10 chains. Longest chain 78 peptides. Score 0.898 Round 4: 342 peptides, 10 chains. Longest chain 97 peptides. Score 0.901 Round 5: 340 peptides, 10 chains. Longest chain 88 peptides. Score 0.900 Taking the results from Round 4 Chains 13, Residues 332, Estimated correctness of the model 98.0 % 8 chains (289 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 99 A and 106 A Built loop between residues 150 A and 156 A Built loop between residues 187 A and 190 A Built loop between residues 209 A and 212 A Built loop between residues 287 A and 290 A 7 chains (347 residues) following loop building 3 chains (306 residues) in sequence following loop building ------------------------------------------------------ 16512 reflections ( 95.21 % complete ) and 3205 restraints for refining 2967 atoms. 602 conditional restraints added. Observations/parameters ratio is 1.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2500 (Rfree = 0.000) for 2967 atoms. Found 50 (50 requested) and removed 38 (28 requested) atoms. Cycle 7: After refmac, R = 0.2322 (Rfree = 0.000) for 2971 atoms. Found 42 (49 requested) and removed 29 (28 requested) atoms. Cycle 8: After refmac, R = 0.2237 (Rfree = 0.000) for 2977 atoms. Found 27 (48 requested) and removed 28 (28 requested) atoms. Cycle 9: After refmac, R = 0.2188 (Rfree = 0.000) for 2973 atoms. Found 45 (47 requested) and removed 33 (28 requested) atoms. Cycle 10: After refmac, R = 0.2145 (Rfree = 0.000) for 2980 atoms. Found 34 (46 requested) and removed 36 (28 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.40 2.16 Round 1: 340 peptides, 10 chains. Longest chain 84 peptides. Score 0.900 Round 2: 340 peptides, 11 chains. Longest chain 60 peptides. Score 0.895 Round 3: 345 peptides, 11 chains. Longest chain 61 peptides. Score 0.899 Round 4: 336 peptides, 12 chains. Longest chain 93 peptides. Score 0.887 Round 5: 343 peptides, 12 chains. Longest chain 83 peptides. Score 0.892 Taking the results from Round 1 Chains 10, Residues 330, Estimated correctness of the model 98.0 % 8 chains (319 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 124 A and 127 A Built loop between residues 149 A and 160 A Built loop between residues 239 A and 242 A Built loop between residues 277 A and 280 A Built loop between residues 314 A and 318 A Built loop between residues 342 A and 349 A 3 chains (352 residues) following loop building 2 chains (344 residues) in sequence following loop building ------------------------------------------------------ 16512 reflections ( 95.21 % complete ) and 3057 restraints for refining 3016 atoms. 292 conditional restraints added. Observations/parameters ratio is 1.37 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2175 (Rfree = 0.000) for 3016 atoms. Found 46 (46 requested) and removed 31 (28 requested) atoms. Cycle 12: After refmac, R = 0.2051 (Rfree = 0.000) for 3021 atoms. Found 44 (44 requested) and removed 30 (28 requested) atoms. Cycle 13: After refmac, R = 0.2005 (Rfree = 0.000) for 3030 atoms. Found 40 (43 requested) and removed 28 (28 requested) atoms. Cycle 14: After refmac, R = 0.1972 (Rfree = 0.000) for 3038 atoms. Found 42 (42 requested) and removed 32 (28 requested) atoms. Cycle 15: After refmac, R = 0.1903 (Rfree = 0.000) for 3045 atoms. Found 41 (41 requested) and removed 33 (28 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.42 2.17 Round 1: 345 peptides, 9 chains. Longest chain 86 peptides. Score 0.908 Round 2: 350 peptides, 8 chains. Longest chain 122 peptides. Score 0.916 Round 3: 352 peptides, 7 chains. Longest chain 176 peptides. Score 0.921 Round 4: 344 peptides, 11 chains. Longest chain 79 peptides. Score 0.898 Round 5: 348 peptides, 10 chains. Longest chain 117 peptides. Score 0.905 Taking the results from Round 3 Chains 7, Residues 345, Estimated correctness of the model 98.7 % 5 chains (333 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 66 A and 69 A Built loop between residues 149 A and 158 A Built loop between residues 332 A and 338 A 3 chains (356 residues) following loop building 2 chains (348 residues) in sequence following loop building ------------------------------------------------------ 16512 reflections ( 95.21 % complete ) and 2984 restraints for refining 2987 atoms. 187 conditional restraints added. Observations/parameters ratio is 1.38 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2008 (Rfree = 0.000) for 2987 atoms. Found 39 (39 requested) and removed 28 (28 requested) atoms. Cycle 17: After refmac, R = 0.1915 (Rfree = 0.000) for 2994 atoms. Found 38 (38 requested) and removed 28 (28 requested) atoms. Cycle 18: After refmac, R = 0.1886 (Rfree = 0.000) for 3001 atoms. Found 38 (38 requested) and removed 30 (28 requested) atoms. Cycle 19: After refmac, R = 0.1859 (Rfree = 0.000) for 3007 atoms. Found 36 (36 requested) and removed 29 (28 requested) atoms. Cycle 20: After refmac, R = 0.1850 (Rfree = 0.000) for 3011 atoms. Found 35 (35 requested) and removed 29 (28 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.44 2.19 Round 1: 343 peptides, 9 chains. Longest chain 86 peptides. Score 0.906 Round 2: 347 peptides, 10 chains. Longest chain 112 peptides. Score 0.905 Round 3: 348 peptides, 9 chains. Longest chain 75 peptides. Score 0.910 Round 4: 347 peptides, 10 chains. Longest chain 119 peptides. Score 0.905 Round 5: 347 peptides, 9 chains. Longest chain 89 peptides. Score 0.909 Taking the results from Round 3 Chains 9, Residues 339, Estimated correctness of the model 98.3 % 7 chains (330 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 21 A and 24 A Built loop between residues 125 A and 128 A Built loop between residues 149 A and 160 A Built loop between residues 233 A and 237 A Built loop between residues 290 A and 293 A 3 chains (355 residues) following loop building 2 chains (349 residues) in sequence following loop building ------------------------------------------------------ 16512 reflections ( 95.21 % complete ) and 3003 restraints for refining 2978 atoms. 206 conditional restraints added. Observations/parameters ratio is 1.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1985 (Rfree = 0.000) for 2978 atoms. Found 34 (34 requested) and removed 31 (28 requested) atoms. Cycle 22: After refmac, R = 0.1894 (Rfree = 0.000) for 2978 atoms. Found 32 (32 requested) and removed 30 (28 requested) atoms. Cycle 23: After refmac, R = 0.1889 (Rfree = 0.000) for 2978 atoms. Found 31 (31 requested) and removed 31 (28 requested) atoms. Cycle 24: After refmac, R = 0.1856 (Rfree = 0.000) for 2977 atoms. Found 30 (30 requested) and removed 29 (28 requested) atoms. Cycle 25: After refmac, R = 0.1845 (Rfree = 0.000) for 2976 atoms. Found 29 (29 requested) and removed 31 (28 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.39 2.15 Round 1: 351 peptides, 9 chains. Longest chain 87 peptides. Score 0.912 Round 2: 356 peptides, 6 chains. Longest chain 178 peptides. Score 0.927 Round 3: 350 peptides, 9 chains. Longest chain 99 peptides. Score 0.911 Round 4: 353 peptides, 8 chains. Longest chain 111 peptides. Score 0.917 Round 5: 342 peptides, 15 chains. Longest chain 64 peptides. Score 0.876 Taking the results from Round 2 Chains 6, Residues 350, Estimated correctness of the model 98.9 % 5 chains (345 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 21 A and 24 A Built loop between residues 85 A and 95 A Built loop between residues 155 A and 158 A Built loop between residues 334 A and 337 A 1 chains (360 residues) following loop building 1 chains (360 residues) in sequence following loop building ------------------------------------------------------ 16512 reflections ( 95.21 % complete ) and 2936 restraints for refining 3007 atoms. 75 conditional restraints added. Observations/parameters ratio is 1.37 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1949 (Rfree = 0.000) for 3007 atoms. Found 28 (28 requested) and removed 29 (28 requested) atoms. Cycle 27: After refmac, R = 0.1867 (Rfree = 0.000) for 3000 atoms. Found 28 (28 requested) and removed 28 (28 requested) atoms. Cycle 28: After refmac, R = 0.1842 (Rfree = 0.000) for 2996 atoms. Found 28 (28 requested) and removed 29 (28 requested) atoms. Cycle 29: After refmac, R = 0.1837 (Rfree = 0.000) for 2994 atoms. Found 28 (28 requested) and removed 29 (28 requested) atoms. Cycle 30: After refmac, R = 0.1809 (Rfree = 0.000) for 2989 atoms. Found 28 (28 requested) and removed 29 (28 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.40 2.16 Round 1: 352 peptides, 9 chains. Longest chain 88 peptides. Score 0.912 Round 2: 355 peptides, 6 chains. Longest chain 98 peptides. Score 0.927 Round 3: 355 peptides, 8 chains. Longest chain 88 peptides. Score 0.919 Round 4: 350 peptides, 12 chains. Longest chain 78 peptides. Score 0.898 Round 5: 350 peptides, 9 chains. Longest chain 88 peptides. Score 0.911 Taking the results from Round 2 Chains 7, Residues 349, Estimated correctness of the model 98.9 % 5 chains (343 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 89 A and 95 A Built loop between residues 149 A and 158 A Built loop between residues 188 A and 191 A Built loop between residues 266 A and 269 A 1 chains (360 residues) following loop building 1 chains (360 residues) in sequence following loop building ------------------------------------------------------ 16512 reflections ( 95.21 % complete ) and 2958 restraints for refining 3010 atoms. 97 conditional restraints added. Observations/parameters ratio is 1.37 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1959 (Rfree = 0.000) for 3010 atoms. Found 28 (28 requested) and removed 31 (28 requested) atoms. Cycle 32: After refmac, R = 0.1862 (Rfree = 0.000) for 3005 atoms. Found 28 (28 requested) and removed 28 (28 requested) atoms. Cycle 33: After refmac, R = 0.1832 (Rfree = 0.000) for 3003 atoms. Found 28 (28 requested) and removed 33 (28 requested) atoms. Cycle 34: After refmac, R = 0.1834 (Rfree = 0.000) for 2995 atoms. Found 28 (28 requested) and removed 28 (28 requested) atoms. Cycle 35: After refmac, R = 0.1809 (Rfree = 0.000) for 2994 atoms. Found 28 (28 requested) and removed 33 (28 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.40 2.16 Round 1: 339 peptides, 10 chains. Longest chain 86 peptides. Score 0.899 Round 2: 348 peptides, 6 chains. Longest chain 89 peptides. Score 0.923 Round 3: 352 peptides, 9 chains. Longest chain 68 peptides. Score 0.912 Round 4: 353 peptides, 7 chains. Longest chain 88 peptides. Score 0.922 Round 5: 353 peptides, 9 chains. Longest chain 118 peptides. Score 0.913 Taking the results from Round 2 Chains 6, Residues 342, Estimated correctness of the model 98.7 % 6 chains (342 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 93 A and 96 A Built loop between residues 149 A and 159 A Built loop between residues 189 A and 193 A Built loop between residues 267 A and 270 A Built loop between residues 338 A and 341 A 1 chains (360 residues) following loop building 1 chains (360 residues) in sequence following loop building ------------------------------------------------------ 16512 reflections ( 95.21 % complete ) and 2935 restraints for refining 3000 atoms. 74 conditional restraints added. Observations/parameters ratio is 1.38 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1899 (Rfree = 0.000) for 3000 atoms. Found 28 (28 requested) and removed 29 (28 requested) atoms. Cycle 37: After refmac, R = 0.1798 (Rfree = 0.000) for 2991 atoms. Found 28 (28 requested) and removed 28 (28 requested) atoms. Cycle 38: After refmac, R = 0.1782 (Rfree = 0.000) for 2990 atoms. Found 28 (28 requested) and removed 30 (28 requested) atoms. Cycle 39: After refmac, R = 0.1778 (Rfree = 0.000) for 2988 atoms. Found 28 (28 requested) and removed 32 (28 requested) atoms. Cycle 40: After refmac, R = 0.1785 (Rfree = 0.000) for 2982 atoms. Found 28 (28 requested) and removed 31 (28 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.43 2.18 Round 1: 348 peptides, 8 chains. Longest chain 87 peptides. Score 0.914 Round 2: 351 peptides, 8 chains. Longest chain 87 peptides. Score 0.916 Round 3: 356 peptides, 5 chains. Longest chain 145 peptides. Score 0.931 Round 4: 351 peptides, 10 chains. Longest chain 67 peptides. Score 0.907 Round 5: 352 peptides, 8 chains. Longest chain 86 peptides. Score 0.917 Taking the results from Round 3 Chains 5, Residues 351, Estimated correctness of the model 99.0 % 4 chains (346 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 149 A and 160 A Built loop between residues 244 A and 247 A Built loop between residues 295 A and 298 A 1 chains (360 residues) following loop building 1 chains (360 residues) in sequence following loop building ------------------------------------------------------ 16512 reflections ( 95.21 % complete ) and 2950 restraints for refining 2990 atoms. 89 conditional restraints added. Observations/parameters ratio is 1.38 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1909 (Rfree = 0.000) for 2990 atoms. Found 28 (28 requested) and removed 31 (28 requested) atoms. Cycle 42: After refmac, R = 0.1818 (Rfree = 0.000) for 2984 atoms. Found 28 (28 requested) and removed 30 (28 requested) atoms. Cycle 43: After refmac, R = 0.1801 (Rfree = 0.000) for 2981 atoms. Found 28 (28 requested) and removed 29 (28 requested) atoms. Cycle 44: After refmac, R = 0.1807 (Rfree = 0.000) for 2978 atoms. Found 28 (28 requested) and removed 33 (28 requested) atoms. Cycle 45: After refmac, R = 0.1807 (Rfree = 0.000) for 2973 atoms. Found 28 (28 requested) and removed 29 (28 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.42 2.17 Round 1: 346 peptides, 9 chains. Longest chain 127 peptides. Score 0.908 Round 2: 359 peptides, 3 chains. Longest chain 209 peptides. Score 0.941 Round 3: 353 peptides, 8 chains. Longest chain 95 peptides. Score 0.917 Round 4: 354 peptides, 6 chains. Longest chain 109 peptides. Score 0.926 Round 5: 354 peptides, 8 chains. Longest chain 81 peptides. Score 0.918 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 3, Residues 356, Estimated correctness of the model 99.2 % 3 chains (356 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 125 A and 128 A Built loop between residues 155 A and 158 A 1 chains (360 residues) following loop building 1 chains (360 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 16512 reflections ( 95.21 % complete ) and 2861 restraints for refining 2808 atoms. Observations/parameters ratio is 1.47 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2177 (Rfree = 0.000) for 2808 atoms. Found 24 (26 requested) and removed 0 (26 requested) atoms. Cycle 47: After refmac, R = 0.2019 (Rfree = 0.000) for 2808 atoms. Found 9 (26 requested) and removed 1 (26 requested) atoms. Cycle 48: After refmac, R = 0.1987 (Rfree = 0.000) for 2808 atoms. Found 1 (26 requested) and removed 0 (26 requested) atoms. Cycle 49: After refmac, R = 0.1966 (Rfree = 0.000) for 2808 atoms. TimeTaking 70.27