null 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 1vjz-2.5-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vjz-2.5-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vjz-2.5-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjz-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/1vjz-2.5-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjz-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 ============================================================ Tue 25 Dec 19:28:07 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/1vjz-2.5-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjz-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 362 and 0 Target number of residues in the AU: 362 Target solvent content: 0.5371 Checking the provided sequence file Detected sequence length: 341 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 341 Adjusted target solvent content: 0.56 Input MTZ file: 1vjz-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: 96 Cell parameters: 64.677 64.677 202.367 90.000 90.000 90.000 Input sequence file: 1vjz-2.5-parrot-hancs.fasta_lf Building free atoms model in initial map for 2728 target number of atoms Had to go as low as 0.60 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: 61.607 2.501 Wilson plot Bfac: 31.92 15421 reflections ( 98.79 % complete ) and 0 restraints for refining 3052 atoms. Observations/parameters ratio is 1.26 ------------------------------------------------------ Starting model: R = 0.3289 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2894 (Rfree = 0.000) for 3052 atoms. Found 47 (55 requested) and removed 49 (27 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.43 2.24 Round 1: 207 peptides, 34 chains. Longest chain 14 peptides. Score 0.454 Round 2: 242 peptides, 27 chains. Longest chain 25 peptides. Score 0.653 Round 3: 255 peptides, 22 chains. Longest chain 39 peptides. Score 0.736 Round 4: 263 peptides, 22 chains. Longest chain 38 peptides. Score 0.751 Round 5: 268 peptides, 21 chains. Longest chain 27 peptides. Score 0.769 Taking the results from Round 5 Chains 26, Residues 247, Estimated correctness of the model 90.1 % 8 chains (146 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 212 A and 215 A Built loop between residues 234 A and 237 A Built loop between residues 258 A and 265 A 20 chains (252 residues) following loop building 5 chains (156 residues) in sequence following loop building ------------------------------------------------------ 15421 reflections ( 98.79 % complete ) and 4187 restraints for refining 2805 atoms. 2451 conditional restraints added. Observations/parameters ratio is 1.37 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3135 (Rfree = 0.000) for 2805 atoms. Found 50 (50 requested) and removed 39 (25 requested) atoms. Cycle 2: After refmac, R = 0.2967 (Rfree = 0.000) for 2797 atoms. Found 50 (50 requested) and removed 35 (25 requested) atoms. Cycle 3: After refmac, R = 0.2779 (Rfree = 0.000) for 2795 atoms. Found 37 (48 requested) and removed 28 (25 requested) atoms. Cycle 4: After refmac, R = 0.2807 (Rfree = 0.000) for 2799 atoms. Found 47 (47 requested) and removed 29 (25 requested) atoms. Cycle 5: After refmac, R = 0.2645 (Rfree = 0.000) for 2809 atoms. Found 29 (47 requested) and removed 29 (25 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.42 2.23 Round 1: 268 peptides, 20 chains. Longest chain 26 peptides. Score 0.778 Round 2: 283 peptides, 15 chains. Longest chain 49 peptides. Score 0.839 Round 3: 295 peptides, 13 chains. Longest chain 45 peptides. Score 0.866 Round 4: 297 peptides, 14 chains. Longest chain 90 peptides. Score 0.862 Round 5: 295 peptides, 18 chains. Longest chain 58 peptides. Score 0.834 Taking the results from Round 3 Chains 14, Residues 282, Estimated correctness of the model 96.3 % 9 chains (253 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 62 A and 65 A Built loop between residues 81 A and 89 A Built loop between residues 167 A and 171 A Built loop between residues 192 A and 195 A Built loop between residues 212 A and 215 A Built loop between residues 235 A and 238 A Built loop between residues 281 A and 284 A 6 chains (301 residues) following loop building 2 chains (273 residues) in sequence following loop building ------------------------------------------------------ 15421 reflections ( 98.79 % complete ) and 3356 restraints for refining 2942 atoms. 869 conditional restraints added. Observations/parameters ratio is 1.31 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2790 (Rfree = 0.000) for 2942 atoms. Found 48 (48 requested) and removed 38 (26 requested) atoms. Cycle 7: After refmac, R = 0.2519 (Rfree = 0.000) for 2929 atoms. Found 47 (47 requested) and removed 32 (26 requested) atoms. Cycle 8: After refmac, R = 0.2388 (Rfree = 0.000) for 2934 atoms. Found 37 (46 requested) and removed 30 (26 requested) atoms. Cycle 9: After refmac, R = 0.2337 (Rfree = 0.000) for 2931 atoms. Found 26 (45 requested) and removed 27 (26 requested) atoms. Cycle 10: After refmac, R = 0.2343 (Rfree = 0.000) for 2927 atoms. Found 25 (43 requested) and removed 29 (26 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.40 2.21 Round 1: 310 peptides, 8 chains. Longest chain 91 peptides. Score 0.908 Round 2: 309 peptides, 6 chains. Longest chain 114 peptides. Score 0.917 Round 3: 308 peptides, 10 chains. Longest chain 51 peptides. Score 0.896 Round 4: 305 peptides, 10 chains. Longest chain 60 peptides. Score 0.893 Round 5: 311 peptides, 8 chains. Longest chain 68 peptides. Score 0.909 Taking the results from Round 2 Chains 7, Residues 303, Estimated correctness of the model 98.5 % 3 chains (267 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 210 A and 214 A 5 chains (305 residues) following loop building 2 chains (270 residues) in sequence following loop building ------------------------------------------------------ 15421 reflections ( 98.79 % complete ) and 3275 restraints for refining 2857 atoms. 762 conditional restraints added. Observations/parameters ratio is 1.35 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2290 (Rfree = 0.000) for 2857 atoms. Found 41 (41 requested) and removed 31 (25 requested) atoms. Cycle 12: After refmac, R = 0.2218 (Rfree = 0.000) for 2857 atoms. Found 40 (40 requested) and removed 31 (25 requested) atoms. Cycle 13: After refmac, R = 0.2160 (Rfree = 0.000) for 2862 atoms. Found 39 (39 requested) and removed 26 (25 requested) atoms. Cycle 14: After refmac, R = 0.2117 (Rfree = 0.000) for 2872 atoms. Found 38 (38 requested) and removed 30 (26 requested) atoms. Cycle 15: After refmac, R = 0.2092 (Rfree = 0.000) for 2878 atoms. Found 33 (37 requested) and removed 27 (26 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.41 2.22 Round 1: 315 peptides, 6 chains. Longest chain 104 peptides. Score 0.921 Round 2: 314 peptides, 6 chains. Longest chain 127 peptides. Score 0.921 Round 3: 316 peptides, 5 chains. Longest chain 192 peptides. Score 0.927 Round 4: 314 peptides, 7 chains. Longest chain 82 peptides. Score 0.916 Round 5: 314 peptides, 9 chains. Longest chain 125 peptides. Score 0.906 Taking the results from Round 3 Chains 7, Residues 311, Estimated correctness of the model 98.8 % 5 chains (308 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 211 A and 215 A Built loop between residues 234 A and 237 A Built loop between residues 272 A and 275 A Built loop between residues 323 A and 327 A 1 chains (318 residues) following loop building 1 chains (318 residues) in sequence following loop building ------------------------------------------------------ 15421 reflections ( 98.79 % complete ) and 2988 restraints for refining 2907 atoms. 213 conditional restraints added. Observations/parameters ratio is 1.33 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2124 (Rfree = 0.000) for 2907 atoms. Found 36 (36 requested) and removed 32 (26 requested) atoms. Cycle 17: After refmac, R = 0.1996 (Rfree = 0.000) for 2909 atoms. Found 35 (35 requested) and removed 28 (26 requested) atoms. Cycle 18: After refmac, R = 0.1932 (Rfree = 0.000) for 2915 atoms. Found 34 (34 requested) and removed 28 (26 requested) atoms. Cycle 19: After refmac, R = 0.1894 (Rfree = 0.000) for 2918 atoms. Found 33 (33 requested) and removed 30 (26 requested) atoms. Cycle 20: After refmac, R = 0.1842 (Rfree = 0.000) for 2920 atoms. Found 32 (32 requested) and removed 28 (26 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.37 2.19 Round 1: 320 peptides, 4 chains. Longest chain 195 peptides. Score 0.933 Round 2: 313 peptides, 9 chains. Longest chain 78 peptides. Score 0.905 Round 3: 319 peptides, 6 chains. Longest chain 106 peptides. Score 0.924 Round 4: 315 peptides, 10 chains. Longest chain 81 peptides. Score 0.902 Round 5: 319 peptides, 6 chains. Longest chain 122 peptides. Score 0.924 Taking the results from Round 1 Chains 4, Residues 316, Estimated correctness of the model 99.0 % 4 chains (316 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 213 A and 215 A Built loop between residues 235 A and 238 A Built loop between residues 325 A and 328 A 1 chains (321 residues) following loop building 1 chains (321 residues) in sequence following loop building ------------------------------------------------------ 15421 reflections ( 98.79 % complete ) and 2933 restraints for refining 2904 atoms. 127 conditional restraints added. Observations/parameters ratio is 1.33 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1997 (Rfree = 0.000) for 2904 atoms. Found 31 (31 requested) and removed 30 (26 requested) atoms. Cycle 22: After refmac, R = 0.1892 (Rfree = 0.000) for 2901 atoms. Found 30 (30 requested) and removed 28 (26 requested) atoms. Cycle 23: After refmac, R = 0.1833 (Rfree = 0.000) for 2901 atoms. Found 29 (29 requested) and removed 26 (26 requested) atoms. Cycle 24: After refmac, R = 0.1801 (Rfree = 0.000) for 2903 atoms. Found 28 (28 requested) and removed 26 (26 requested) atoms. Cycle 25: After refmac, R = 0.1787 (Rfree = 0.000) for 2904 atoms. Found 27 (27 requested) and removed 26 (26 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.37 2.19 Round 1: 319 peptides, 5 chains. Longest chain 105 peptides. Score 0.928 Round 2: 317 peptides, 5 chains. Longest chain 109 peptides. Score 0.927 Round 3: 315 peptides, 8 chains. Longest chain 86 peptides. Score 0.912 Round 4: 317 peptides, 9 chains. Longest chain 69 peptides. Score 0.908 Round 5: 316 peptides, 8 chains. Longest chain 106 peptides. Score 0.912 Taking the results from Round 1 Chains 5, Residues 314, Estimated correctness of the model 98.8 % 5 chains (314 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 85 A and 88 A Built loop between residues 137 A and 140 A Built loop between residues 213 A and 215 A Built loop between residues 234 A and 237 A 1 chains (321 residues) following loop building 1 chains (321 residues) in sequence following loop building ------------------------------------------------------ 15421 reflections ( 98.79 % complete ) and 2920 restraints for refining 2887 atoms. 114 conditional restraints added. Observations/parameters ratio is 1.34 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1980 (Rfree = 0.000) for 2887 atoms. Found 26 (26 requested) and removed 31 (26 requested) atoms. Cycle 27: After refmac, R = 0.1882 (Rfree = 0.000) for 2880 atoms. Found 26 (26 requested) and removed 26 (26 requested) atoms. Cycle 28: After refmac, R = 0.1847 (Rfree = 0.000) for 2880 atoms. Found 26 (26 requested) and removed 26 (26 requested) atoms. Cycle 29: After refmac, R = 0.1843 (Rfree = 0.000) for 2880 atoms. Found 26 (26 requested) and removed 26 (26 requested) atoms. Cycle 30: After refmac, R = 0.1827 (Rfree = 0.000) for 2880 atoms. Found 26 (26 requested) and removed 28 (26 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.37 2.19 Round 1: 318 peptides, 3 chains. Longest chain 192 peptides. Score 0.937 Round 2: 320 peptides, 4 chains. Longest chain 113 peptides. Score 0.933 Round 3: 314 peptides, 7 chains. Longest chain 82 peptides. Score 0.916 Round 4: 315 peptides, 6 chains. Longest chain 120 peptides. Score 0.921 Round 5: 310 peptides, 8 chains. Longest chain 67 peptides. Score 0.908 Taking the results from Round 1 Chains 4, Residues 315, Estimated correctness of the model 99.1 % 3 chains (313 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 211 A and 215 A Built loop between residues 234 A and 237 A 1 chains (318 residues) following loop building 1 chains (318 residues) in sequence following loop building ------------------------------------------------------ 15421 reflections ( 98.79 % complete ) and 2978 restraints for refining 2887 atoms. 203 conditional restraints added. Observations/parameters ratio is 1.34 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2010 (Rfree = 0.000) for 2887 atoms. Found 26 (26 requested) and removed 29 (26 requested) atoms. Cycle 32: After refmac, R = 0.1891 (Rfree = 0.000) for 2884 atoms. Found 26 (26 requested) and removed 27 (26 requested) atoms. Cycle 33: After refmac, R = 0.1855 (Rfree = 0.000) for 2881 atoms. Found 26 (26 requested) and removed 27 (26 requested) atoms. Cycle 34: After refmac, R = 0.1850 (Rfree = 0.000) for 2879 atoms. Found 26 (26 requested) and removed 27 (26 requested) atoms. Cycle 35: After refmac, R = 0.1838 (Rfree = 0.000) for 2878 atoms. Found 26 (26 requested) and removed 26 (26 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.37 2.19 Round 1: 315 peptides, 6 chains. Longest chain 74 peptides. Score 0.921 Round 2: 318 peptides, 4 chains. Longest chain 137 peptides. Score 0.932 Round 3: 319 peptides, 5 chains. Longest chain 122 peptides. Score 0.928 Round 4: 313 peptides, 4 chains. Longest chain 111 peptides. Score 0.929 Round 5: 319 peptides, 5 chains. Longest chain 106 peptides. Score 0.928 Taking the results from Round 2 Chains 5, Residues 314, Estimated correctness of the model 98.9 % 4 chains (310 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 99 A and 102 A Built loop between residues 237 A and 240 A Built loop between residues 271 A and 274 A 2 chains (320 residues) following loop building 1 chains (316 residues) in sequence following loop building ------------------------------------------------------ 15421 reflections ( 98.79 % complete ) and 2985 restraints for refining 2890 atoms. 219 conditional restraints added. Observations/parameters ratio is 1.33 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2022 (Rfree = 0.000) for 2890 atoms. Found 26 (26 requested) and removed 29 (26 requested) atoms. Cycle 37: After refmac, R = 0.1889 (Rfree = 0.000) for 2882 atoms. Found 26 (26 requested) and removed 30 (26 requested) atoms. Cycle 38: After refmac, R = 0.1835 (Rfree = 0.000) for 2876 atoms. Found 26 (26 requested) and removed 27 (26 requested) atoms. Cycle 39: After refmac, R = 0.1832 (Rfree = 0.000) for 2874 atoms. Found 26 (26 requested) and removed 29 (26 requested) atoms. Cycle 40: After refmac, R = 0.1794 (Rfree = 0.000) for 2870 atoms. Found 26 (26 requested) and removed 27 (26 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.37 2.19 Round 1: 316 peptides, 8 chains. Longest chain 66 peptides. Score 0.912 Round 2: 320 peptides, 5 chains. Longest chain 109 peptides. Score 0.929 Round 3: 314 peptides, 8 chains. Longest chain 78 peptides. Score 0.911 Round 4: 321 peptides, 4 chains. Longest chain 132 peptides. Score 0.934 Round 5: 319 peptides, 6 chains. Longest chain 87 peptides. Score 0.924 Taking the results from Round 4 Chains 6, Residues 317, Estimated correctness of the model 99.0 % 4 chains (314 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 80 A and 83 A Built loop between residues 211 A and 215 A Built loop between residues 234 A and 237 A 2 chains (322 residues) following loop building 1 chains (321 residues) in sequence following loop building ------------------------------------------------------ 15421 reflections ( 98.79 % complete ) and 2942 restraints for refining 2905 atoms. 133 conditional restraints added. Observations/parameters ratio is 1.33 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1999 (Rfree = 0.000) for 2905 atoms. Found 26 (26 requested) and removed 31 (26 requested) atoms. Cycle 42: After refmac, R = 0.1868 (Rfree = 0.000) for 2898 atoms. Found 26 (26 requested) and removed 26 (26 requested) atoms. Cycle 43: After refmac, R = 0.1809 (Rfree = 0.000) for 2897 atoms. Found 26 (26 requested) and removed 26 (26 requested) atoms. Cycle 44: After refmac, R = 0.1791 (Rfree = 0.000) for 2896 atoms. Found 26 (26 requested) and removed 27 (26 requested) atoms. Cycle 45: After refmac, R = 0.1781 (Rfree = 0.000) for 2893 atoms. Found 26 (26 requested) and removed 28 (26 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.36 2.18 Round 1: 318 peptides, 5 chains. Longest chain 138 peptides. Score 0.928 Round 2: 315 peptides, 4 chains. Longest chain 169 peptides. Score 0.930 Round 3: 315 peptides, 9 chains. Longest chain 67 peptides. Score 0.907 Round 4: 321 peptides, 3 chains. Longest chain 192 peptides. Score 0.938 Round 5: 318 peptides, 7 chains. Longest chain 69 peptides. Score 0.919 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 4, Residues 318, Estimated correctness of the model 99.1 % 3 chains (316 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 100 A and 103 A Built loop between residues 148 A and 151 A 2 chains (322 residues) following loop building 1 chains (320 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 15421 reflections ( 98.79 % complete ) and 2804 restraints for refining 2716 atoms. Observations/parameters ratio is 1.42 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2396 (Rfree = 0.000) for 2716 atoms. Found 24 (24 requested) and removed 0 (24 requested) atoms. Cycle 47: After refmac, R = 0.2246 (Rfree = 0.000) for 2716 atoms. Found 15 (24 requested) and removed 0 (24 requested) atoms. Cycle 48: After refmac, R = 0.2176 (Rfree = 0.000) for 2716 atoms. Found 6 (24 requested) and removed 4 (24 requested) atoms. Cycle 49: After refmac, R = 0.2171 (Rfree = 0.000) for 2716 atoms. Found 6 (24 requested) and removed 4 (24 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:32:18 GMT 2018 Job finished. TimeTaking 64.36 Used memory is bytes: 22304384