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 2i51-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2i51-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2i51-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2i51-3.6-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/2i51-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2i51-3.6-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/2i51-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2i51-3.6-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 330 and 0 Target number of residues in the AU: 330 Target solvent content: 0.6326 Checking the provided sequence file Detected sequence length: 195 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 390 Adjusted target solvent content: 0.57 Input MTZ file: 2i51-3.6-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: 65.591 65.955 112.360 90.000 90.000 90.000 Input sequence file: 2i51-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 3120 target number of atoms Had to go as low as 0.85 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: 56.880 3.600 Wilson plot Bfac: 67.45 5129 reflections ( 85.23 % complete ) and 0 restraints for refining 3471 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Starting model: R = 0.3364 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3215 (Rfree = 0.000) for 3471 atoms. Found 22 (22 requested) and removed 19 (11 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.36 3.06 Search for helices and strands: 0 residues in 0 chains, 3527 seeds are put forward NCS extension: 0 residues added, 3527 seeds are put forward Round 1: 156 peptides, 33 chains. Longest chain 9 peptides. Score 0.263 Round 2: 201 peptides, 32 chains. Longest chain 14 peptides. Score 0.435 Round 3: 232 peptides, 36 chains. Longest chain 15 peptides. Score 0.477 Round 4: 214 peptides, 29 chains. Longest chain 23 peptides. Score 0.515 Round 5: 217 peptides, 32 chains. Longest chain 17 peptides. Score 0.485 Taking the results from Round 4 Chains 30, Residues 185, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 5129 reflections ( 85.23 % complete ) and 6122 restraints for refining 2826 atoms. 5353 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2820 (Rfree = 0.000) for 2826 atoms. Found 18 (18 requested) and removed 27 (9 requested) atoms. Cycle 2: After refmac, R = 0.2568 (Rfree = 0.000) for 2783 atoms. Found 17 (18 requested) and removed 20 (9 requested) atoms. Cycle 3: After refmac, R = 0.2421 (Rfree = 0.000) for 2768 atoms. Found 6 (17 requested) and removed 11 (8 requested) atoms. Cycle 4: After refmac, R = 0.2294 (Rfree = 0.000) for 2758 atoms. Found 10 (17 requested) and removed 18 (8 requested) atoms. Cycle 5: After refmac, R = 0.2337 (Rfree = 0.000) for 2745 atoms. Found 10 (17 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.38 3.08 Search for helices and strands: 0 residues in 0 chains, 2829 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 2843 seeds are put forward Round 1: 199 peptides, 37 chains. Longest chain 12 peptides. Score 0.357 Round 2: 211 peptides, 34 chains. Longest chain 20 peptides. Score 0.439 Round 3: 211 peptides, 28 chains. Longest chain 16 peptides. Score 0.520 Round 4: 227 peptides, 31 chains. Longest chain 18 peptides. Score 0.527 Round 5: 216 peptides, 33 chains. Longest chain 12 peptides. Score 0.468 Taking the results from Round 4 Chains 32, Residues 196, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 5129 reflections ( 85.23 % complete ) and 6081 restraints for refining 2828 atoms. 5276 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2428 (Rfree = 0.000) for 2828 atoms. Found 12 (18 requested) and removed 20 (9 requested) atoms. Cycle 7: After refmac, R = 0.2276 (Rfree = 0.000) for 2797 atoms. Found 14 (18 requested) and removed 12 (9 requested) atoms. Cycle 8: After refmac, R = 0.2067 (Rfree = 0.000) for 2784 atoms. Found 10 (17 requested) and removed 11 (8 requested) atoms. Cycle 9: After refmac, R = 0.2002 (Rfree = 0.000) for 2780 atoms. Found 5 (17 requested) and removed 14 (8 requested) atoms. Cycle 10: After refmac, R = 0.1863 (Rfree = 0.000) for 2761 atoms. Found 6 (17 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.38 3.08 Search for helices and strands: 0 residues in 0 chains, 2826 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 2852 seeds are put forward Round 1: 226 peptides, 42 chains. Longest chain 10 peptides. Score 0.377 Round 2: 218 peptides, 41 chains. Longest chain 10 peptides. Score 0.364 Round 3: 216 peptides, 36 chains. Longest chain 12 peptides. Score 0.428 Round 4: 220 peptides, 30 chains. Longest chain 23 peptides. Score 0.520 Round 5: 229 peptides, 35 chains. Longest chain 20 peptides. Score 0.481 Taking the results from Round 4 Chains 34, Residues 190, Estimated correctness of the model 0.0 % 3 chains (33 residues) have been docked in sequence ------------------------------------------------------ 5129 reflections ( 85.23 % complete ) and 5998 restraints for refining 2827 atoms. 5138 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2460 (Rfree = 0.000) for 2827 atoms. Found 18 (18 requested) and removed 18 (9 requested) atoms. Cycle 12: After refmac, R = 0.2262 (Rfree = 0.000) for 2798 atoms. Found 17 (18 requested) and removed 14 (9 requested) atoms. Cycle 13: After refmac, R = 0.2141 (Rfree = 0.000) for 2788 atoms. Found 12 (17 requested) and removed 9 (8 requested) atoms. Cycle 14: After refmac, R = 0.2045 (Rfree = 0.000) for 2780 atoms. Found 12 (17 requested) and removed 10 (8 requested) atoms. Cycle 15: After refmac, R = 0.1968 (Rfree = 0.000) for 2780 atoms. Found 14 (17 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.36 3.06 Search for helices and strands: 0 residues in 0 chains, 2837 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 2849 seeds are put forward Round 1: 208 peptides, 39 chains. Longest chain 15 peptides. Score 0.359 Round 2: 216 peptides, 36 chains. Longest chain 15 peptides. Score 0.428 Round 3: 217 peptides, 34 chains. Longest chain 16 peptides. Score 0.458 Round 4: 240 peptides, 34 chains. Longest chain 16 peptides. Score 0.526 Round 5: 225 peptides, 34 chains. Longest chain 16 peptides. Score 0.482 Taking the results from Round 4 Chains 35, Residues 206, Estimated correctness of the model 0.0 % 2 chains (19 residues) have been docked in sequence ------------------------------------------------------ 5129 reflections ( 85.23 % complete ) and 6053 restraints for refining 2828 atoms. 5197 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2291 (Rfree = 0.000) for 2828 atoms. Found 10 (18 requested) and removed 14 (9 requested) atoms. Cycle 17: After refmac, R = 0.2138 (Rfree = 0.000) for 2810 atoms. Found 16 (18 requested) and removed 12 (9 requested) atoms. Cycle 18: After refmac, R = 0.2059 (Rfree = 0.000) for 2809 atoms. Found 13 (18 requested) and removed 12 (9 requested) atoms. Cycle 19: After refmac, R = 0.1962 (Rfree = 0.000) for 2803 atoms. Found 6 (18 requested) and removed 12 (9 requested) atoms. Cycle 20: After refmac, R = 0.1825 (Rfree = 0.000) for 2794 atoms. Found 9 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.39 3.09 Search for helices and strands: 0 residues in 0 chains, 2875 seeds are put forward NCS extension: 0 residues added, 2875 seeds are put forward Round 1: 188 peptides, 37 chains. Longest chain 11 peptides. Score 0.319 Round 2: 196 peptides, 32 chains. Longest chain 10 peptides. Score 0.419 Round 3: 202 peptides, 34 chains. Longest chain 12 peptides. Score 0.410 Round 4: 199 peptides, 33 chains. Longest chain 12 peptides. Score 0.415 Round 5: 198 peptides, 31 chains. Longest chain 16 peptides. Score 0.440 Taking the results from Round 5 Chains 32, Residues 167, Estimated correctness of the model 0.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 5129 reflections ( 85.23 % complete ) and 6204 restraints for refining 2828 atoms. 5511 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2320 (Rfree = 0.000) for 2828 atoms. Found 11 (18 requested) and removed 16 (9 requested) atoms. Cycle 22: After refmac, R = 0.2163 (Rfree = 0.000) for 2809 atoms. Found 5 (18 requested) and removed 12 (9 requested) atoms. Cycle 23: After refmac, R = 0.2121 (Rfree = 0.000) for 2789 atoms. Found 10 (17 requested) and removed 8 (8 requested) atoms. Cycle 24: After refmac, R = 0.2033 (Rfree = 0.000) for 2786 atoms. Found 3 (17 requested) and removed 10 (8 requested) atoms. Cycle 25: After refmac, R = 0.1922 (Rfree = 0.000) for 2775 atoms. Found 5 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.40 3.10 Search for helices and strands: 0 residues in 0 chains, 2826 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 2850 seeds are put forward Round 1: 183 peptides, 35 chains. Longest chain 12 peptides. Score 0.331 Round 2: 192 peptides, 30 chains. Longest chain 14 peptides. Score 0.435 Round 3: 200 peptides, 29 chains. Longest chain 19 peptides. Score 0.474 Round 4: 194 peptides, 26 chains. Longest chain 21 peptides. Score 0.496 Round 5: 198 peptides, 31 chains. Longest chain 17 peptides. Score 0.440 Taking the results from Round 4 Chains 30, Residues 168, Estimated correctness of the model 0.0 % 3 chains (39 residues) have been docked in sequence ------------------------------------------------------ 5129 reflections ( 85.23 % complete ) and 6039 restraints for refining 2828 atoms. 5249 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2459 (Rfree = 0.000) for 2828 atoms. Found 18 (18 requested) and removed 16 (9 requested) atoms. Cycle 27: After refmac, R = 0.2216 (Rfree = 0.000) for 2817 atoms. Found 16 (18 requested) and removed 13 (9 requested) atoms. Cycle 28: After refmac, R = 0.2088 (Rfree = 0.000) for 2810 atoms. Found 12 (18 requested) and removed 12 (9 requested) atoms. Cycle 29: After refmac, R = 0.1900 (Rfree = 0.000) for 2799 atoms. Found 4 (18 requested) and removed 11 (9 requested) atoms. Cycle 30: After refmac, R = 0.1832 (Rfree = 0.000) for 2791 atoms. Found 1 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.39 3.09 Search for helices and strands: 0 residues in 0 chains, 2829 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 2848 seeds are put forward Round 1: 151 peptides, 29 chains. Longest chain 10 peptides. Score 0.308 Round 2: 194 peptides, 29 chains. Longest chain 16 peptides. Score 0.455 Round 3: 209 peptides, 31 chains. Longest chain 15 peptides. Score 0.474 Round 4: 199 peptides, 28 chains. Longest chain 19 peptides. Score 0.484 Round 5: 193 peptides, 28 chains. Longest chain 14 peptides. Score 0.466 Taking the results from Round 4 Chains 29, Residues 171, Estimated correctness of the model 0.0 % 4 chains (25 residues) have been docked in sequence ------------------------------------------------------ 5129 reflections ( 85.23 % complete ) and 6195 restraints for refining 2828 atoms. 5453 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2430 (Rfree = 0.000) for 2828 atoms. Found 10 (18 requested) and removed 14 (9 requested) atoms. Cycle 32: After refmac, R = 0.2229 (Rfree = 0.000) for 2810 atoms. Found 17 (18 requested) and removed 13 (9 requested) atoms. Cycle 33: After refmac, R = 0.2195 (Rfree = 0.000) for 2806 atoms. Found 12 (18 requested) and removed 25 (9 requested) atoms. Cycle 34: After refmac, R = 0.2092 (Rfree = 0.000) for 2786 atoms. Found 12 (17 requested) and removed 22 (8 requested) atoms. Cycle 35: After refmac, R = 0.1890 (Rfree = 0.000) for 2773 atoms. Found 6 (17 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.43 3.12 Search for helices and strands: 0 residues in 0 chains, 2816 seeds are put forward NCS extension: 32 residues added (0 deleted due to clashes), 2848 seeds are put forward Round 1: 164 peptides, 31 chains. Longest chain 10 peptides. Score 0.324 Round 2: 175 peptides, 31 chains. Longest chain 11 peptides. Score 0.363 Round 3: 186 peptides, 30 chains. Longest chain 13 peptides. Score 0.415 Round 4: 193 peptides, 33 chains. Longest chain 12 peptides. Score 0.395 Round 5: 209 peptides, 34 chains. Longest chain 13 peptides. Score 0.433 Taking the results from Round 5 Chains 34, Residues 175, Estimated correctness of the model 0.0 % 3 chains (15 residues) have been docked in sequence ------------------------------------------------------ 5129 reflections ( 85.23 % complete ) and 6323 restraints for refining 2828 atoms. 5610 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2383 (Rfree = 0.000) for 2828 atoms. Found 18 (18 requested) and removed 11 (9 requested) atoms. Cycle 37: After refmac, R = 0.2656 (Rfree = 0.000) for 2823 atoms. Found 13 (18 requested) and removed 32 (9 requested) atoms. Cycle 38: After refmac, R = 0.2004 (Rfree = 0.000) for 2801 atoms. Found 12 (17 requested) and removed 21 (8 requested) atoms. Cycle 39: After refmac, R = 0.2041 (Rfree = 0.000) for 2788 atoms. Found 5 (17 requested) and removed 21 (8 requested) atoms. Cycle 40: After refmac, R = 0.2134 (Rfree = 0.000) for 2770 atoms. Found 17 (17 requested) and removed 15 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.37 3.07 Search for helices and strands: 0 residues in 0 chains, 2815 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 2834 seeds are put forward Round 1: 155 peptides, 31 chains. Longest chain 10 peptides. Score 0.291 Round 2: 160 peptides, 26 chains. Longest chain 12 peptides. Score 0.387 Round 3: 166 peptides, 30 chains. Longest chain 10 peptides. Score 0.347 Round 4: 166 peptides, 28 chains. Longest chain 17 peptides. Score 0.377 Round 5: 173 peptides, 29 chains. Longest chain 14 peptides. Score 0.386 Taking the results from Round 2 Chains 26, Residues 134, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5129 reflections ( 85.23 % complete ) and 6693 restraints for refining 2828 atoms. 6183 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2353 (Rfree = 0.000) for 2828 atoms. Found 18 (18 requested) and removed 10 (9 requested) atoms. Cycle 42: After refmac, R = 0.2133 (Rfree = 0.000) for 2827 atoms. Found 18 (18 requested) and removed 11 (9 requested) atoms. Cycle 43: After refmac, R = 0.2007 (Rfree = 0.000) for 2830 atoms. Found 18 (18 requested) and removed 14 (9 requested) atoms. Cycle 44: After refmac, R = 0.1901 (Rfree = 0.000) for 2829 atoms. Found 18 (18 requested) and removed 11 (9 requested) atoms. Cycle 45: After refmac, R = 0.1956 (Rfree = 0.000) for 2834 atoms. Found 18 (18 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.41 3.10 Search for helices and strands: 0 residues in 0 chains, 2884 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 2902 seeds are put forward Round 1: 129 peptides, 26 chains. Longest chain 10 peptides. Score 0.272 Round 2: 155 peptides, 27 chains. Longest chain 15 peptides. Score 0.354 Round 3: 167 peptides, 27 chains. Longest chain 17 peptides. Score 0.396 Round 4: 164 peptides, 25 chains. Longest chain 29 peptides. Score 0.416 Round 5: 162 peptides, 26 chains. Longest chain 29 peptides. Score 0.394 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 25, Residues 139, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2i51-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5129 reflections ( 85.23 % complete ) and 6636 restraints for refining 2827 atoms. 6105 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2207 (Rfree = 0.000) for 2827 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.2229 (Rfree = 0.000) for 2813 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.1988 (Rfree = 0.000) for 2797 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.2097 (Rfree = 0.000) for 2780 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:19:54 GMT 2018 Job finished. TimeTaking 51.95 Used memory is bytes: 11068264