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 2i51-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2i51-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2i51-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2i51-3.8-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/2i51-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2i51-3.8-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/2i51-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2i51-3.8-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 322 and 0 Target number of residues in the AU: 322 Target solvent content: 0.6415 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: 2i51-3.8-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: 2i51-3.8-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 3.800 Wilson plot Bfac: 72.52 4372 reflections ( 84.88 % complete ) and 0 restraints for refining 3455 atoms. Observations/parameters ratio is 0.32 ------------------------------------------------------ Starting model: R = 0.3481 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3137 (Rfree = 0.000) for 3455 atoms. Found 19 (19 requested) and removed 22 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.56 3.24 Search for helices and strands: 0 residues in 0 chains, 3494 seeds are put forward NCS extension: 0 residues added, 3494 seeds are put forward Round 1: 123 peptides, 25 chains. Longest chain 9 peptides. Score 0.265 Round 2: 177 peptides, 30 chains. Longest chain 12 peptides. Score 0.385 Round 3: 208 peptides, 33 chains. Longest chain 14 peptides. Score 0.444 Round 4: 217 peptides, 37 chains. Longest chain 12 peptides. Score 0.417 Round 5: 201 peptides, 34 chains. Longest chain 15 peptides. Score 0.407 Taking the results from Round 3 Chains 33, Residues 175, Estimated correctness of the model 0.0 % 3 chains (13 residues) have been docked in sequence ------------------------------------------------------ 4372 reflections ( 84.88 % complete ) and 6198 restraints for refining 2822 atoms. 5482 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2557 (Rfree = 0.000) for 2822 atoms. Found 9 (15 requested) and removed 14 (7 requested) atoms. Cycle 2: After refmac, R = 0.2454 (Rfree = 0.000) for 2764 atoms. Found 8 (15 requested) and removed 23 (7 requested) atoms. Cycle 3: After refmac, R = 0.2169 (Rfree = 0.000) for 2725 atoms. Found 7 (15 requested) and removed 17 (7 requested) atoms. Cycle 4: After refmac, R = 0.2267 (Rfree = 0.000) for 2703 atoms. Found 10 (14 requested) and removed 12 (7 requested) atoms. Cycle 5: After refmac, R = 0.2238 (Rfree = 0.000) for 2690 atoms. Found 8 (14 requested) and removed 25 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.47 3.16 Search for helices and strands: 0 residues in 0 chains, 2748 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 2764 seeds are put forward Round 1: 166 peptides, 33 chains. Longest chain 10 peptides. Score 0.300 Round 2: 181 peptides, 31 chains. Longest chain 11 peptides. Score 0.384 Round 3: 198 peptides, 31 chains. Longest chain 12 peptides. Score 0.440 Round 4: 199 peptides, 29 chains. Longest chain 15 peptides. Score 0.471 Round 5: 195 peptides, 31 chains. Longest chain 17 peptides. Score 0.430 Taking the results from Round 4 Chains 29, Residues 170, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 4372 reflections ( 84.88 % complete ) and 6438 restraints for refining 2821 atoms. 5765 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2532 (Rfree = 0.000) for 2821 atoms. Found 15 (15 requested) and removed 11 (7 requested) atoms. Cycle 7: After refmac, R = 0.2250 (Rfree = 0.000) for 2810 atoms. Found 14 (15 requested) and removed 12 (7 requested) atoms. Cycle 8: After refmac, R = 0.2167 (Rfree = 0.000) for 2794 atoms. Found 10 (15 requested) and removed 13 (7 requested) atoms. Cycle 9: After refmac, R = 0.2144 (Rfree = 0.000) for 2780 atoms. Found 11 (15 requested) and removed 10 (7 requested) atoms. Cycle 10: After refmac, R = 0.2040 (Rfree = 0.000) for 2770 atoms. Found 6 (15 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.51 3.20 Search for helices and strands: 0 residues in 0 chains, 2812 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 2826 seeds are put forward Round 1: 178 peptides, 36 chains. Longest chain 12 peptides. Score 0.298 Round 2: 185 peptides, 32 chains. Longest chain 11 peptides. Score 0.383 Round 3: 201 peptides, 33 chains. Longest chain 10 peptides. Score 0.421 Round 4: 205 peptides, 34 chains. Longest chain 12 peptides. Score 0.420 Round 5: 202 peptides, 30 chains. Longest chain 15 peptides. Score 0.466 Taking the results from Round 5 Chains 31, Residues 172, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4372 reflections ( 84.88 % complete ) and 6441 restraints for refining 2822 atoms. 5738 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2281 (Rfree = 0.000) for 2822 atoms. Found 6 (15 requested) and removed 14 (7 requested) atoms. Cycle 12: After refmac, R = 0.2182 (Rfree = 0.000) for 2797 atoms. Found 10 (15 requested) and removed 10 (7 requested) atoms. Cycle 13: After refmac, R = 0.2027 (Rfree = 0.000) for 2787 atoms. Found 5 (15 requested) and removed 13 (7 requested) atoms. Cycle 14: After refmac, R = 0.1886 (Rfree = 0.000) for 2772 atoms. Found 3 (15 requested) and removed 10 (7 requested) atoms. Cycle 15: After refmac, R = 0.1893 (Rfree = 0.000) for 2761 atoms. Found 2 (15 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.47 3.16 Search for helices and strands: 0 residues in 0 chains, 2807 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 2827 seeds are put forward Round 1: 178 peptides, 34 chains. Longest chain 14 peptides. Score 0.328 Round 2: 205 peptides, 36 chains. Longest chain 12 peptides. Score 0.392 Round 3: 190 peptides, 32 chains. Longest chain 11 peptides. Score 0.400 Round 4: 213 peptides, 35 chains. Longest chain 13 peptides. Score 0.432 Round 5: 206 peptides, 32 chains. Longest chain 12 peptides. Score 0.451 Taking the results from Round 5 Chains 32, Residues 174, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 4372 reflections ( 84.88 % complete ) and 6317 restraints for refining 2822 atoms. 5628 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2324 (Rfree = 0.000) for 2822 atoms. Found 10 (15 requested) and removed 17 (7 requested) atoms. Cycle 17: After refmac, R = 0.2091 (Rfree = 0.000) for 2790 atoms. Found 14 (15 requested) and removed 12 (7 requested) atoms. Cycle 18: After refmac, R = 0.1777 (Rfree = 0.000) for 2775 atoms. Found 8 (15 requested) and removed 9 (7 requested) atoms. Cycle 19: After refmac, R = 0.1747 (Rfree = 0.000) for 2764 atoms. Found 3 (15 requested) and removed 9 (7 requested) atoms. Cycle 20: After refmac, R = 0.1776 (Rfree = 0.000) for 2749 atoms. Found 8 (15 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.46 3.15 Search for helices and strands: 0 residues in 0 chains, 2805 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 2820 seeds are put forward Round 1: 152 peptides, 29 chains. Longest chain 11 peptides. Score 0.311 Round 2: 180 peptides, 33 chains. Longest chain 14 peptides. Score 0.351 Round 3: 203 peptides, 34 chains. Longest chain 12 peptides. Score 0.414 Round 4: 200 peptides, 31 chains. Longest chain 13 peptides. Score 0.446 Round 5: 202 peptides, 32 chains. Longest chain 13 peptides. Score 0.439 Taking the results from Round 4 Chains 31, Residues 169, Estimated correctness of the model 0.0 % 5 chains (25 residues) have been docked in sequence ------------------------------------------------------ 4372 reflections ( 84.88 % complete ) and 6250 restraints for refining 2822 atoms. 5521 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2037 (Rfree = 0.000) for 2822 atoms. Found 11 (15 requested) and removed 11 (7 requested) atoms. Cycle 22: After refmac, R = 0.1931 (Rfree = 0.000) for 2808 atoms. Found 7 (15 requested) and removed 12 (7 requested) atoms. Cycle 23: After refmac, R = 0.1852 (Rfree = 0.000) for 2798 atoms. Found 2 (15 requested) and removed 9 (7 requested) atoms. Cycle 24: After refmac, R = 0.1845 (Rfree = 0.000) for 2785 atoms. Found 7 (15 requested) and removed 9 (7 requested) atoms. Cycle 25: After refmac, R = 0.1766 (Rfree = 0.000) for 2773 atoms. Found 5 (15 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.50 3.19 Search for helices and strands: 0 residues in 0 chains, 2817 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 2836 seeds are put forward Round 1: 172 peptides, 35 chains. Longest chain 9 peptides. Score 0.291 Round 2: 195 peptides, 31 chains. Longest chain 16 peptides. Score 0.430 Round 3: 181 peptides, 32 chains. Longest chain 10 peptides. Score 0.369 Round 4: 185 peptides, 28 chains. Longest chain 17 peptides. Score 0.441 Round 5: 187 peptides, 30 chains. Longest chain 10 peptides. Score 0.418 Taking the results from Round 4 Chains 28, Residues 157, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4372 reflections ( 84.88 % complete ) and 6468 restraints for refining 2822 atoms. 5868 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1960 (Rfree = 0.000) for 2822 atoms. Found 11 (15 requested) and removed 9 (7 requested) atoms. Cycle 27: After refmac, R = 0.1851 (Rfree = 0.000) for 2814 atoms. Found 4 (15 requested) and removed 8 (7 requested) atoms. Cycle 28: After refmac, R = 0.1755 (Rfree = 0.000) for 2806 atoms. Found 5 (15 requested) and removed 8 (7 requested) atoms. Cycle 29: After refmac, R = 0.1740 (Rfree = 0.000) for 2800 atoms. Found 5 (15 requested) and removed 8 (7 requested) atoms. Cycle 30: After refmac, R = 0.1651 (Rfree = 0.000) for 2794 atoms. Found 3 (15 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.52 3.20 Search for helices and strands: 0 residues in 0 chains, 2847 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 2862 seeds are put forward Round 1: 148 peptides, 29 chains. Longest chain 8 peptides. Score 0.296 Round 2: 176 peptides, 30 chains. Longest chain 10 peptides. Score 0.382 Round 3: 167 peptides, 28 chains. Longest chain 13 peptides. Score 0.381 Round 4: 168 peptides, 29 chains. Longest chain 11 peptides. Score 0.369 Round 5: 176 peptides, 26 chains. Longest chain 12 peptides. Score 0.440 Taking the results from Round 5 Chains 26, Residues 150, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4372 reflections ( 84.88 % complete ) and 6559 restraints for refining 2822 atoms. 5985 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1886 (Rfree = 0.000) for 2822 atoms. Found 8 (15 requested) and removed 8 (7 requested) atoms. Cycle 32: After refmac, R = 0.1915 (Rfree = 0.000) for 2810 atoms. Found 8 (15 requested) and removed 8 (7 requested) atoms. Cycle 33: After refmac, R = 0.1818 (Rfree = 0.000) for 2802 atoms. Found 11 (15 requested) and removed 9 (7 requested) atoms. Cycle 34: After refmac, R = 0.1653 (Rfree = 0.000) for 2798 atoms. Found 4 (15 requested) and removed 7 (7 requested) atoms. Cycle 35: After refmac, R = 0.1631 (Rfree = 0.000) for 2789 atoms. Found 5 (15 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.49 3.18 Search for helices and strands: 0 residues in 0 chains, 2846 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 2858 seeds are put forward Round 1: 146 peptides, 30 chains. Longest chain 10 peptides. Score 0.273 Round 2: 165 peptides, 31 chains. Longest chain 10 peptides. Score 0.328 Round 3: 162 peptides, 26 chains. Longest chain 12 peptides. Score 0.394 Round 4: 157 peptides, 25 chains. Longest chain 12 peptides. Score 0.392 Round 5: 164 peptides, 27 chains. Longest chain 12 peptides. Score 0.385 Taking the results from Round 3 Chains 26, Residues 136, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4372 reflections ( 84.88 % complete ) and 6722 restraints for refining 2822 atoms. 6204 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2195 (Rfree = 0.000) for 2822 atoms. Found 15 (15 requested) and removed 8 (7 requested) atoms. Cycle 37: After refmac, R = 0.1985 (Rfree = 0.000) for 2818 atoms. Found 15 (15 requested) and removed 9 (7 requested) atoms. Cycle 38: After refmac, R = 0.1642 (Rfree = 0.000) for 2822 atoms. Found 3 (15 requested) and removed 8 (7 requested) atoms. Cycle 39: After refmac, R = 0.1582 (Rfree = 0.000) for 2812 atoms. Found 2 (15 requested) and removed 7 (7 requested) atoms. Cycle 40: After refmac, R = 0.1800 (Rfree = 0.000) for 2805 atoms. Found 12 (15 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.53 3.21 Search for helices and strands: 0 residues in 0 chains, 2845 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 2857 seeds are put forward Round 1: 149 peptides, 33 chains. Longest chain 9 peptides. Score 0.236 Round 2: 161 peptides, 31 chains. Longest chain 8 peptides. Score 0.313 Round 3: 173 peptides, 30 chains. Longest chain 12 peptides. Score 0.371 Round 4: 174 peptides, 31 chains. Longest chain 9 peptides. Score 0.360 Round 5: 171 peptides, 30 chains. Longest chain 13 peptides. Score 0.364 Taking the results from Round 3 Chains 30, Residues 143, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 4372 reflections ( 84.88 % complete ) and 6551 restraints for refining 2822 atoms. 5989 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1963 (Rfree = 0.000) for 2822 atoms. Found 14 (15 requested) and removed 8 (7 requested) atoms. Cycle 42: After refmac, R = 0.1793 (Rfree = 0.000) for 2822 atoms. Found 4 (15 requested) and removed 8 (7 requested) atoms. Cycle 43: After refmac, R = 0.1727 (Rfree = 0.000) for 2813 atoms. Found 4 (15 requested) and removed 8 (7 requested) atoms. Cycle 44: After refmac, R = 0.1690 (Rfree = 0.000) for 2804 atoms. Found 1 (15 requested) and removed 7 (7 requested) atoms. Cycle 45: After refmac, R = 0.1651 (Rfree = 0.000) for 2798 atoms. Found 2 (15 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.53 3.21 Search for helices and strands: 0 residues in 0 chains, 2832 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 2846 seeds are put forward Round 1: 141 peptides, 31 chains. Longest chain 6 peptides. Score 0.237 Round 2: 147 peptides, 27 chains. Longest chain 10 peptides. Score 0.325 Round 3: 161 peptides, 29 chains. Longest chain 11 peptides. Score 0.344 Round 4: 153 peptides, 27 chains. Longest chain 11 peptides. Score 0.347 Round 5: 154 peptides, 27 chains. Longest chain 10 peptides. Score 0.350 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 27, Residues 127, 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. 4372 reflections ( 84.88 % complete ) and 6653 restraints for refining 2822 atoms. 6172 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1938 (Rfree = 0.000) for 2822 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.1974 (Rfree = 0.000) for 2802 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.2107 (Rfree = 0.000) for 2790 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.1952 (Rfree = 0.000) for 2778 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:20:15 GMT 2018 Job finished. TimeTaking 52.31 Used memory is bytes: 22285832