null Sun 23 Dec 22:22:49 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 2i51-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2i51-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2i51-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2i51-3.4-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/2i51-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2i51-3.4-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 22:22:59 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/hancs/ArpWArp/wArpResults/WorkingDir/2i51-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2i51-3.4-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 341 and 0 Target number of residues in the AU: 341 Target solvent content: 0.6203 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: 2i51-3.4-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: 2i51-3.4-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 3.400 Wilson plot Bfac: 61.45 6083 reflections ( 85.58 % complete ) and 0 restraints for refining 3451 atoms. Observations/parameters ratio is 0.44 ------------------------------------------------------ Starting model: R = 0.3326 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2841 (Rfree = 0.000) for 3451 atoms. Found 26 (26 requested) and removed 21 (13 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.19 2.90 Search for helices and strands: 0 residues in 0 chains, 3501 seeds are put forward NCS extension: 0 residues added, 3501 seeds are put forward Round 1: 152 peptides, 31 chains. Longest chain 8 peptides. Score 0.280 Round 2: 201 peptides, 31 chains. Longest chain 12 peptides. Score 0.449 Round 3: 236 peptides, 36 chains. Longest chain 15 peptides. Score 0.489 Round 4: 245 peptides, 34 chains. Longest chain 15 peptides. Score 0.540 Round 5: 255 peptides, 35 chains. Longest chain 20 peptides. Score 0.554 Taking the results from Round 5 Chains 35, Residues 220, Estimated correctness of the model 13.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 6083 reflections ( 85.58 % complete ) and 5965 restraints for refining 2837 atoms. 5082 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2493 (Rfree = 0.000) for 2837 atoms. Found 21 (21 requested) and removed 13 (10 requested) atoms. Cycle 2: After refmac, R = 0.2315 (Rfree = 0.000) for 2814 atoms. Found 10 (21 requested) and removed 14 (10 requested) atoms. Cycle 3: After refmac, R = 0.2237 (Rfree = 0.000) for 2797 atoms. Found 11 (21 requested) and removed 10 (10 requested) atoms. Cycle 4: After refmac, R = 0.2174 (Rfree = 0.000) for 2791 atoms. Found 4 (21 requested) and removed 10 (10 requested) atoms. Cycle 5: After refmac, R = 0.2132 (Rfree = 0.000) for 2780 atoms. Found 4 (21 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.23 2.94 Search for helices and strands: 0 residues in 0 chains, 2834 seeds are put forward NCS extension: 31 residues added (1 deleted due to clashes), 2865 seeds are put forward Round 1: 216 peptides, 35 chains. Longest chain 19 peptides. Score 0.441 Round 2: 258 peptides, 32 chains. Longest chain 24 peptides. Score 0.597 Round 3: 266 peptides, 35 chains. Longest chain 21 peptides. Score 0.583 Round 4: 249 peptides, 30 chains. Longest chain 23 peptides. Score 0.597 Round 5: 238 peptides, 31 chains. Longest chain 18 peptides. Score 0.557 Taking the results from Round 4 Chains 31, Residues 219, Estimated correctness of the model 27.7 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 6083 reflections ( 85.58 % complete ) and 6065 restraints for refining 2837 atoms. 5172 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2442 (Rfree = 0.000) for 2837 atoms. Found 21 (21 requested) and removed 16 (10 requested) atoms. Cycle 7: After refmac, R = 0.2263 (Rfree = 0.000) for 2835 atoms. Found 4 (21 requested) and removed 10 (10 requested) atoms. Cycle 8: After refmac, R = 0.2216 (Rfree = 0.000) for 2825 atoms. Found 7 (21 requested) and removed 10 (10 requested) atoms. Cycle 9: After refmac, R = 0.2192 (Rfree = 0.000) for 2816 atoms. Found 7 (21 requested) and removed 12 (10 requested) atoms. Cycle 10: After refmac, R = 0.2145 (Rfree = 0.000) for 2809 atoms. Found 6 (21 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.25 2.96 Search for helices and strands: 0 residues in 0 chains, 2867 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 2891 seeds are put forward Round 1: 215 peptides, 35 chains. Longest chain 16 peptides. Score 0.438 Round 2: 241 peptides, 30 chains. Longest chain 26 peptides. Score 0.577 Round 3: 236 peptides, 28 chains. Longest chain 24 peptides. Score 0.587 Round 4: 247 peptides, 27 chains. Longest chain 21 peptides. Score 0.626 Round 5: 242 peptides, 28 chains. Longest chain 22 peptides. Score 0.602 Taking the results from Round 4 Chains 29, Residues 220, Estimated correctness of the model 36.9 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 6083 reflections ( 85.58 % complete ) and 5970 restraints for refining 2837 atoms. 5050 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2528 (Rfree = 0.000) for 2837 atoms. Found 20 (21 requested) and removed 12 (10 requested) atoms. Cycle 12: After refmac, R = 0.2396 (Rfree = 0.000) for 2837 atoms. Found 5 (21 requested) and removed 10 (10 requested) atoms. Cycle 13: After refmac, R = 0.2365 (Rfree = 0.000) for 2828 atoms. Found 4 (21 requested) and removed 10 (10 requested) atoms. Cycle 14: After refmac, R = 0.2313 (Rfree = 0.000) for 2822 atoms. Found 3 (21 requested) and removed 10 (10 requested) atoms. Cycle 15: After refmac, R = 0.2268 (Rfree = 0.000) for 2813 atoms. Found 3 (21 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.26 2.97 Search for helices and strands: 0 residues in 0 chains, 2870 seeds are put forward NCS extension: 21 residues added (3 deleted due to clashes), 2891 seeds are put forward Round 1: 222 peptides, 34 chains. Longest chain 16 peptides. Score 0.473 Round 2: 250 peptides, 34 chains. Longest chain 20 peptides. Score 0.553 Round 3: 250 peptides, 31 chains. Longest chain 16 peptides. Score 0.588 Round 4: 251 peptides, 36 chains. Longest chain 16 peptides. Score 0.532 Round 5: 246 peptides, 31 chains. Longest chain 23 peptides. Score 0.578 Taking the results from Round 3 Chains 31, Residues 219, Estimated correctness of the model 24.7 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 6083 reflections ( 85.58 % complete ) and 6080 restraints for refining 2836 atoms. 5197 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2498 (Rfree = 0.000) for 2836 atoms. Found 21 (21 requested) and removed 13 (10 requested) atoms. Cycle 17: After refmac, R = 0.2348 (Rfree = 0.000) for 2835 atoms. Found 9 (21 requested) and removed 10 (10 requested) atoms. Cycle 18: After refmac, R = 0.2314 (Rfree = 0.000) for 2833 atoms. Found 3 (21 requested) and removed 10 (10 requested) atoms. Cycle 19: After refmac, R = 0.2279 (Rfree = 0.000) for 2824 atoms. Found 4 (21 requested) and removed 10 (10 requested) atoms. Cycle 20: After refmac, R = 0.2278 (Rfree = 0.000) for 2817 atoms. Found 5 (21 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.27 2.98 Search for helices and strands: 0 residues in 0 chains, 2850 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 2865 seeds are put forward Round 1: 205 peptides, 36 chains. Longest chain 14 peptides. Score 0.392 Round 2: 220 peptides, 31 chains. Longest chain 16 peptides. Score 0.507 Round 3: 219 peptides, 28 chains. Longest chain 16 peptides. Score 0.542 Round 4: 227 peptides, 32 chains. Longest chain 15 peptides. Score 0.514 Round 5: 228 peptides, 27 chains. Longest chain 18 peptides. Score 0.578 Taking the results from Round 5 Chains 29, Residues 201, Estimated correctness of the model 21.3 % 3 chains (37 residues) have been docked in sequence ------------------------------------------------------ 6083 reflections ( 85.58 % complete ) and 5863 restraints for refining 2835 atoms. 4935 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2547 (Rfree = 0.000) for 2835 atoms. Found 19 (21 requested) and removed 16 (10 requested) atoms. Cycle 22: After refmac, R = 0.2374 (Rfree = 0.000) for 2819 atoms. Found 6 (21 requested) and removed 12 (10 requested) atoms. Cycle 23: After refmac, R = 0.2299 (Rfree = 0.000) for 2812 atoms. Found 4 (21 requested) and removed 11 (10 requested) atoms. Cycle 24: After refmac, R = 0.2240 (Rfree = 0.000) for 2803 atoms. Found 7 (21 requested) and removed 10 (10 requested) atoms. Cycle 25: After refmac, R = 0.2234 (Rfree = 0.000) for 2799 atoms. Found 8 (21 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.26 2.97 Search for helices and strands: 0 residues in 0 chains, 2859 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 2878 seeds are put forward Round 1: 209 peptides, 29 chains. Longest chain 23 peptides. Score 0.501 Round 2: 241 peptides, 31 chains. Longest chain 25 peptides. Score 0.565 Round 3: 247 peptides, 30 chains. Longest chain 25 peptides. Score 0.592 Round 4: 246 peptides, 32 chains. Longest chain 19 peptides. Score 0.566 Round 5: 243 peptides, 29 chains. Longest chain 23 peptides. Score 0.593 Taking the results from Round 5 Chains 30, Residues 214, Estimated correctness of the model 26.4 % 3 chains (36 residues) have been docked in sequence ------------------------------------------------------ 6083 reflections ( 85.58 % complete ) and 5854 restraints for refining 2837 atoms. 4875 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2424 (Rfree = 0.000) for 2837 atoms. Found 16 (21 requested) and removed 17 (10 requested) atoms. Cycle 27: After refmac, R = 0.2190 (Rfree = 0.000) for 2826 atoms. Found 9 (21 requested) and removed 17 (10 requested) atoms. Cycle 28: After refmac, R = 0.2113 (Rfree = 0.000) for 2818 atoms. Found 1 (21 requested) and removed 10 (10 requested) atoms. Cycle 29: After refmac, R = 0.2084 (Rfree = 0.000) for 2808 atoms. Found 2 (21 requested) and removed 10 (10 requested) atoms. Cycle 30: After refmac, R = 0.2078 (Rfree = 0.000) for 2800 atoms. Found 4 (21 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.26 2.97 Search for helices and strands: 0 residues in 0 chains, 2852 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 2864 seeds are put forward Round 1: 219 peptides, 34 chains. Longest chain 17 peptides. Score 0.464 Round 2: 233 peptides, 30 chains. Longest chain 19 peptides. Score 0.556 Round 3: 238 peptides, 32 chains. Longest chain 17 peptides. Score 0.545 Round 4: 239 peptides, 32 chains. Longest chain 16 peptides. Score 0.547 Round 5: 245 peptides, 35 chains. Longest chain 16 peptides. Score 0.527 Taking the results from Round 2 Chains 30, Residues 203, Estimated correctness of the model 13.7 % 2 chains (32 residues) have been docked in sequence ------------------------------------------------------ 6083 reflections ( 85.58 % complete ) and 5809 restraints for refining 2837 atoms. 4887 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2339 (Rfree = 0.000) for 2837 atoms. Found 21 (21 requested) and removed 17 (10 requested) atoms. Cycle 32: After refmac, R = 0.2195 (Rfree = 0.000) for 2834 atoms. Found 10 (21 requested) and removed 12 (10 requested) atoms. Cycle 33: After refmac, R = 0.2107 (Rfree = 0.000) for 2830 atoms. Found 8 (21 requested) and removed 10 (10 requested) atoms. Cycle 34: After refmac, R = 0.2075 (Rfree = 0.000) for 2826 atoms. Found 6 (21 requested) and removed 10 (10 requested) atoms. Cycle 35: After refmac, R = 0.2046 (Rfree = 0.000) for 2821 atoms. Found 3 (21 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.25 2.96 Search for helices and strands: 0 residues in 0 chains, 2847 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 2872 seeds are put forward Round 1: 197 peptides, 34 chains. Longest chain 15 peptides. Score 0.394 Round 2: 226 peptides, 32 chains. Longest chain 18 peptides. Score 0.511 Round 3: 224 peptides, 34 chains. Longest chain 18 peptides. Score 0.479 Round 4: 234 peptides, 33 chains. Longest chain 15 peptides. Score 0.521 Round 5: 227 peptides, 32 chains. Longest chain 17 peptides. Score 0.514 Taking the results from Round 4 Chains 34, Residues 201, Estimated correctness of the model 0.8 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 6083 reflections ( 85.58 % complete ) and 6187 restraints for refining 2837 atoms. 5383 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2282 (Rfree = 0.000) for 2837 atoms. Found 18 (21 requested) and removed 13 (10 requested) atoms. Cycle 37: After refmac, R = 0.2081 (Rfree = 0.000) for 2838 atoms. Found 9 (21 requested) and removed 11 (10 requested) atoms. Cycle 38: After refmac, R = 0.2017 (Rfree = 0.000) for 2833 atoms. Found 4 (21 requested) and removed 11 (10 requested) atoms. Cycle 39: After refmac, R = 0.1996 (Rfree = 0.000) for 2826 atoms. Found 3 (21 requested) and removed 10 (10 requested) atoms. Cycle 40: After refmac, R = 0.1982 (Rfree = 0.000) for 2819 atoms. Found 3 (21 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.24 2.95 Search for helices and strands: 0 residues in 0 chains, 2866 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 2877 seeds are put forward Round 1: 198 peptides, 35 chains. Longest chain 16 peptides. Score 0.383 Round 2: 224 peptides, 35 chains. Longest chain 17 peptides. Score 0.466 Round 3: 223 peptides, 34 chains. Longest chain 17 peptides. Score 0.476 Round 4: 227 peptides, 31 chains. Longest chain 17 peptides. Score 0.527 Round 5: 221 peptides, 29 chains. Longest chain 24 peptides. Score 0.535 Taking the results from Round 5 Chains 29, Residues 192, Estimated correctness of the model 6.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6083 reflections ( 85.58 % complete ) and 6315 restraints for refining 2837 atoms. 5576 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2248 (Rfree = 0.000) for 2837 atoms. Found 21 (21 requested) and removed 11 (10 requested) atoms. Cycle 42: After refmac, R = 0.2093 (Rfree = 0.000) for 2845 atoms. Found 5 (21 requested) and removed 10 (10 requested) atoms. Cycle 43: After refmac, R = 0.2061 (Rfree = 0.000) for 2835 atoms. Found 9 (21 requested) and removed 10 (10 requested) atoms. Cycle 44: After refmac, R = 0.2006 (Rfree = 0.000) for 2833 atoms. Found 3 (21 requested) and removed 12 (10 requested) atoms. Cycle 45: After refmac, R = 0.2011 (Rfree = 0.000) for 2822 atoms. Found 5 (21 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.24 2.95 Search for helices and strands: 0 residues in 0 chains, 2872 seeds are put forward NCS extension: 40 residues added (3 deleted due to clashes), 2912 seeds are put forward Round 1: 195 peptides, 32 chains. Longest chain 15 peptides. Score 0.416 Round 2: 208 peptides, 28 chains. Longest chain 18 peptides. Score 0.511 Round 3: 203 peptides, 27 chains. Longest chain 19 peptides. Score 0.509 Round 4: 211 peptides, 29 chains. Longest chain 16 peptides. Score 0.506 Round 5: 193 peptides, 26 chains. Longest chain 21 peptides. Score 0.493 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 28, Residues 180, 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. 6083 reflections ( 85.58 % complete ) and 6424 restraints for refining 2837 atoms. 5732 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2148 (Rfree = 0.000) for 2837 atoms. Found 0 (21 requested) and removed 5 (10 requested) atoms. Cycle 47: After refmac, R = 0.2078 (Rfree = 0.000) for 2828 atoms. Found 0 (21 requested) and removed 3 (10 requested) atoms. Cycle 48: After refmac, R = 0.2054 (Rfree = 0.000) for 2825 atoms. Found 0 (21 requested) and removed 1 (10 requested) atoms. Cycle 49: After refmac, R = 0.2040 (Rfree = 0.000) for 2824 atoms. Found 0 (21 requested) and removed 1 (10 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:13:27 GMT 2018 Job finished. TimeTaking 50.63 Used memory is bytes: 20228176