Mon 24 Dec 07:33:55 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vjn-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vjn-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vjn-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vjn-3.6-parrot-noncs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vjn-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vjn-3.6-parrot-noncs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Mon 24 Dec 07:33:59 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vjn-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vjn-3.6-parrot-noncs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 346 and 0 Target number of residues in the AU: 346 Target solvent content: 0.5649 Checking the provided sequence file Detected sequence length: 220 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 440 Adjusted target solvent content: 0.45 Input MTZ file: 1vjn-3.6-parrot-noncs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 1 Cell parameters: 43.059 45.719 63.384 73.681 89.271 64.860 Input sequence file: 1vjn-3.6-parrot-noncs.fasta_lf Building free atoms model in initial map for 3520 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 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: 60.370 3.600 Wilson plot Bfac: 39.98 4736 reflections ( 98.07 % complete ) and 0 restraints for refining 3916 atoms. Observations/parameters ratio is 0.30 ------------------------------------------------------ Starting model: R = 0.2916 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2898 (Rfree = 0.000) for 3916 atoms. Found 25 (25 requested) and removed 43 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.94 3.14 Search for helices and strands: 0 residues in 0 chains, 3938 seeds are put forward NCS extension: 0 residues added, 3938 seeds are put forward Round 1: 141 peptides, 31 chains. Longest chain 7 peptides. Score 0.243 Round 2: 192 peptides, 36 chains. Longest chain 11 peptides. Score 0.365 Round 3: 208 peptides, 37 chains. Longest chain 11 peptides. Score 0.409 Round 4: 217 peptides, 34 chains. Longest chain 16 peptides. Score 0.485 Round 5: 210 peptides, 33 chains. Longest chain 13 peptides. Score 0.476 Taking the results from Round 4 Chains 34, Residues 183, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 4736 reflections ( 98.07 % complete ) and 7401 restraints for refining 3191 atoms. 6661 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2160 (Rfree = 0.000) for 3191 atoms. Found 16 (20 requested) and removed 21 (10 requested) atoms. Cycle 2: After refmac, R = 0.1968 (Rfree = 0.000) for 3130 atoms. Found 15 (20 requested) and removed 15 (10 requested) atoms. Cycle 3: After refmac, R = 0.2037 (Rfree = 0.000) for 3108 atoms. Found 13 (20 requested) and removed 16 (10 requested) atoms. Cycle 4: After refmac, R = 0.1970 (Rfree = 0.000) for 3097 atoms. Found 19 (19 requested) and removed 15 (9 requested) atoms. Cycle 5: After refmac, R = 0.1823 (Rfree = 0.000) for 3092 atoms. Found 12 (19 requested) and removed 23 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.92 3.12 Search for helices and strands: 0 residues in 0 chains, 3156 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 3175 seeds are put forward Round 1: 183 peptides, 38 chains. Longest chain 9 peptides. Score 0.297 Round 2: 194 peptides, 32 chains. Longest chain 11 peptides. Score 0.436 Round 3: 207 peptides, 34 chains. Longest chain 15 peptides. Score 0.451 Round 4: 194 peptides, 31 chains. Longest chain 13 peptides. Score 0.451 Round 5: 219 peptides, 35 chains. Longest chain 14 peptides. Score 0.477 Taking the results from Round 5 Chains 35, Residues 184, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4736 reflections ( 98.07 % complete ) and 6935 restraints for refining 3036 atoms. 6234 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2082 (Rfree = 0.000) for 3036 atoms. Found 19 (19 requested) and removed 26 (9 requested) atoms. Cycle 7: After refmac, R = 0.1922 (Rfree = 0.000) for 3006 atoms. Found 11 (19 requested) and removed 25 (9 requested) atoms. Cycle 8: After refmac, R = 0.1851 (Rfree = 0.000) for 2981 atoms. Found 13 (19 requested) and removed 25 (9 requested) atoms. Cycle 9: After refmac, R = 0.1794 (Rfree = 0.000) for 2962 atoms. Found 14 (19 requested) and removed 27 (9 requested) atoms. Cycle 10: After refmac, R = 0.1644 (Rfree = 0.000) for 2943 atoms. Found 15 (18 requested) and removed 19 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.03 3.24 Search for helices and strands: 0 residues in 0 chains, 3025 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 3048 seeds are put forward Round 1: 206 peptides, 41 chains. Longest chain 10 peptides. Score 0.339 Round 2: 231 peptides, 39 chains. Longest chain 14 peptides. Score 0.460 Round 3: 223 peptides, 37 chains. Longest chain 11 peptides. Score 0.462 Round 4: 217 peptides, 37 chains. Longest chain 14 peptides. Score 0.441 Round 5: 217 peptides, 34 chains. Longest chain 19 peptides. Score 0.485 Taking the results from Round 5 Chains 34, Residues 183, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 4736 reflections ( 98.07 % complete ) and 7176 restraints for refining 3125 atoms. 6452 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1941 (Rfree = 0.000) for 3125 atoms. Found 14 (20 requested) and removed 43 (10 requested) atoms. Cycle 12: After refmac, R = 0.1847 (Rfree = 0.000) for 3086 atoms. Found 16 (19 requested) and removed 17 (9 requested) atoms. Cycle 13: After refmac, R = 0.1882 (Rfree = 0.000) for 3080 atoms. Found 11 (19 requested) and removed 18 (9 requested) atoms. Cycle 14: After refmac, R = 0.1853 (Rfree = 0.000) for 3071 atoms. Found 11 (19 requested) and removed 22 (9 requested) atoms. Cycle 15: After refmac, R = 0.1838 (Rfree = 0.000) for 3060 atoms. Found 11 (19 requested) and removed 18 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.99 3.20 Search for helices and strands: 0 residues in 0 chains, 3119 seeds are put forward NCS extension: 19 residues added (3 deleted due to clashes), 3138 seeds are put forward Round 1: 171 peptides, 34 chains. Longest chain 10 peptides. Score 0.316 Round 2: 195 peptides, 27 chains. Longest chain 17 peptides. Score 0.514 Round 3: 188 peptides, 29 chains. Longest chain 16 peptides. Score 0.461 Round 4: 183 peptides, 27 chains. Longest chain 13 peptides. Score 0.474 Round 5: 194 peptides, 28 chains. Longest chain 17 peptides. Score 0.496 Taking the results from Round 2 Chains 27, Residues 168, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4736 reflections ( 98.07 % complete ) and 7371 restraints for refining 3128 atoms. 6726 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1781 (Rfree = 0.000) for 3128 atoms. Found 14 (20 requested) and removed 38 (10 requested) atoms. Cycle 17: After refmac, R = 0.1921 (Rfree = 0.000) for 3098 atoms. Found 19 (19 requested) and removed 24 (9 requested) atoms. Cycle 18: After refmac, R = 0.1795 (Rfree = 0.000) for 3086 atoms. Found 19 (19 requested) and removed 16 (9 requested) atoms. Cycle 19: After refmac, R = 0.1817 (Rfree = 0.000) for 3088 atoms. Found 19 (19 requested) and removed 10 (9 requested) atoms. Cycle 20: After refmac, R = 0.1335 (Rfree = 0.000) for 3092 atoms. Found 9 (19 requested) and removed 13 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.00 3.21 Search for helices and strands: 0 residues in 0 chains, 3176 seeds are put forward NCS extension: 21 residues added (3 deleted due to clashes), 3197 seeds are put forward Round 1: 176 peptides, 34 chains. Longest chain 12 peptides. Score 0.336 Round 2: 186 peptides, 31 chains. Longest chain 11 peptides. Score 0.423 Round 3: 179 peptides, 27 chains. Longest chain 15 peptides. Score 0.460 Round 4: 190 peptides, 33 chains. Longest chain 16 peptides. Score 0.406 Round 5: 193 peptides, 28 chains. Longest chain 18 peptides. Score 0.493 Taking the results from Round 5 Chains 28, Residues 165, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 4736 reflections ( 98.07 % complete ) and 7556 restraints for refining 3190 atoms. 6902 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1705 (Rfree = 0.000) for 3190 atoms. Found 8 (20 requested) and removed 17 (10 requested) atoms. Cycle 22: After refmac, R = 0.1567 (Rfree = 0.000) for 3170 atoms. Found 5 (20 requested) and removed 19 (10 requested) atoms. Cycle 23: After refmac, R = 0.1555 (Rfree = 0.000) for 3154 atoms. Found 11 (20 requested) and removed 13 (10 requested) atoms. Cycle 24: After refmac, R = 0.1408 (Rfree = 0.000) for 3147 atoms. Found 2 (20 requested) and removed 18 (10 requested) atoms. Cycle 25: After refmac, R = 0.1430 (Rfree = 0.000) for 3128 atoms. Found 5 (20 requested) and removed 14 (10 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.96 3.16 Search for helices and strands: 0 residues in 0 chains, 3194 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 3216 seeds are put forward Round 1: 160 peptides, 31 chains. Longest chain 15 peptides. Score 0.323 Round 2: 190 peptides, 35 chains. Longest chain 15 peptides. Score 0.374 Round 3: 191 peptides, 32 chains. Longest chain 11 peptides. Score 0.425 Round 4: 191 peptides, 31 chains. Longest chain 15 peptides. Score 0.440 Round 5: 200 peptides, 33 chains. Longest chain 14 peptides. Score 0.442 Taking the results from Round 5 Chains 33, Residues 167, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 4736 reflections ( 98.07 % complete ) and 7498 restraints for refining 3191 atoms. 6844 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1866 (Rfree = 0.000) for 3191 atoms. Found 14 (20 requested) and removed 26 (10 requested) atoms. Cycle 27: After refmac, R = 0.1880 (Rfree = 0.000) for 3165 atoms. Found 15 (20 requested) and removed 23 (10 requested) atoms. Cycle 28: After refmac, R = 0.1748 (Rfree = 0.000) for 3154 atoms. Found 14 (20 requested) and removed 16 (10 requested) atoms. Cycle 29: After refmac, R = 0.1775 (Rfree = 0.000) for 3145 atoms. Found 16 (20 requested) and removed 18 (10 requested) atoms. Cycle 30: After refmac, R = 0.1622 (Rfree = 0.000) for 3140 atoms. Found 20 (20 requested) and removed 19 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.00 3.21 Search for helices and strands: 0 residues in 0 chains, 3215 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 3234 seeds are put forward Round 1: 165 peptides, 34 chains. Longest chain 9 peptides. Score 0.292 Round 2: 196 peptides, 35 chains. Longest chain 10 peptides. Score 0.396 Round 3: 199 peptides, 31 chains. Longest chain 14 peptides. Score 0.468 Round 4: 199 peptides, 35 chains. Longest chain 10 peptides. Score 0.407 Round 5: 190 peptides, 30 chains. Longest chain 14 peptides. Score 0.452 Taking the results from Round 3 Chains 31, Residues 168, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4736 reflections ( 98.07 % complete ) and 7505 restraints for refining 3190 atoms. 6864 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1679 (Rfree = 0.000) for 3190 atoms. Found 16 (20 requested) and removed 16 (10 requested) atoms. Cycle 32: After refmac, R = 0.1643 (Rfree = 0.000) for 3183 atoms. Found 11 (20 requested) and removed 17 (10 requested) atoms. Cycle 33: After refmac, R = 0.1772 (Rfree = 0.000) for 3171 atoms. Found 19 (20 requested) and removed 14 (10 requested) atoms. Cycle 34: After refmac, R = 0.1574 (Rfree = 0.000) for 3170 atoms. Found 15 (20 requested) and removed 13 (10 requested) atoms. Cycle 35: After refmac, R = 0.1302 (Rfree = 0.000) for 3170 atoms. Found 6 (20 requested) and removed 13 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.97 3.18 Search for helices and strands: 0 residues in 0 chains, 3217 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 3235 seeds are put forward Round 1: 153 peptides, 32 chains. Longest chain 9 peptides. Score 0.277 Round 2: 167 peptides, 31 chains. Longest chain 11 peptides. Score 0.351 Round 3: 179 peptides, 33 chains. Longest chain 11 peptides. Score 0.364 Round 4: 179 peptides, 30 chains. Longest chain 11 peptides. Score 0.413 Round 5: 192 peptides, 30 chains. Longest chain 19 peptides. Score 0.459 Taking the results from Round 5 Chains 30, Residues 162, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4736 reflections ( 98.07 % complete ) and 7425 restraints for refining 3166 atoms. 6807 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1870 (Rfree = 0.000) for 3166 atoms. Found 20 (20 requested) and removed 13 (10 requested) atoms. Cycle 37: After refmac, R = 0.1891 (Rfree = 0.000) for 3163 atoms. Found 20 (20 requested) and removed 17 (10 requested) atoms. Cycle 38: After refmac, R = 0.1767 (Rfree = 0.000) for 3156 atoms. Found 15 (20 requested) and removed 13 (10 requested) atoms. Cycle 39: After refmac, R = 0.1393 (Rfree = 0.000) for 3155 atoms. Found 3 (20 requested) and removed 10 (10 requested) atoms. Cycle 40: After refmac, R = 0.1298 (Rfree = 0.000) for 3143 atoms. Found 4 (20 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.00 3.21 Search for helices and strands: 0 residues in 0 chains, 3176 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 3191 seeds are put forward Round 1: 156 peptides, 33 chains. Longest chain 8 peptides. Score 0.272 Round 2: 174 peptides, 32 chains. Longest chain 12 peptides. Score 0.361 Round 3: 182 peptides, 29 chains. Longest chain 16 peptides. Score 0.439 Round 4: 173 peptides, 28 chains. Longest chain 13 peptides. Score 0.423 Round 5: 182 peptides, 28 chains. Longest chain 17 peptides. Score 0.455 Taking the results from Round 5 Chains 29, Residues 154, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4736 reflections ( 98.07 % complete ) and 7455 restraints for refining 3191 atoms. 6826 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1974 (Rfree = 0.000) for 3191 atoms. Found 20 (20 requested) and removed 24 (10 requested) atoms. Cycle 42: After refmac, R = 0.1427 (Rfree = 0.000) for 3176 atoms. Found 7 (20 requested) and removed 15 (10 requested) atoms. Cycle 43: After refmac, R = 0.1539 (Rfree = 0.000) for 3162 atoms. Found 20 (20 requested) and removed 18 (10 requested) atoms. Cycle 44: After refmac, R = 0.1928 (Rfree = 0.000) for 3162 atoms. Found 20 (20 requested) and removed 16 (10 requested) atoms. Cycle 45: After refmac, R = 0.1594 (Rfree = 0.000) for 3160 atoms. Found 19 (20 requested) and removed 12 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.01 3.22 Search for helices and strands: 0 residues in 0 chains, 3228 seeds are put forward NCS extension: 24 residues added (2 deleted due to clashes), 3252 seeds are put forward Round 1: 132 peptides, 30 chains. Longest chain 7 peptides. Score 0.222 Round 2: 136 peptides, 26 chains. Longest chain 10 peptides. Score 0.312 Round 3: 140 peptides, 25 chains. Longest chain 11 peptides. Score 0.346 Round 4: 137 peptides, 26 chains. Longest chain 9 peptides. Score 0.316 Round 5: 138 peptides, 23 chains. Longest chain 16 peptides. Score 0.373 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 23, Residues 115, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence Sequence coverage is 5 % Consider running further cycles of model building using 1vjn-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4736 reflections ( 98.07 % complete ) and 7679 restraints for refining 3187 atoms. 7222 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1815 (Rfree = 0.000) for 3187 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 47: After refmac, R = 0.1723 (Rfree = 0.000) for 3168 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 48: After refmac, R = 0.1712 (Rfree = 0.000) for 3151 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 49: After refmac, R = 0.1705 (Rfree = 0.000) for 3137 atoms. TimeTaking 39.75