Mon 24 Dec 07:27:20 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 2i51-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2i51-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2i51-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2i51-3.4-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/2i51-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2i51-3.4-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 07:27:24 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/2i51-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2i51-3.4-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 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-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: 19 Cell parameters: 65.591 65.955 112.360 90.000 90.000 90.000 Input sequence file: 2i51-3.4-parrot-noncs.fasta_lf Building free atoms model in initial map for 3120 target number of atoms Had to go as low as 0.80 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 3476 atoms. Observations/parameters ratio is 0.44 ------------------------------------------------------ Starting model: R = 0.3407 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3043 (Rfree = 0.000) for 3476 atoms. Found 25 (26 requested) and removed 16 (13 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.19 2.90 Search for helices and strands: 0 residues in 0 chains, 3522 seeds are put forward NCS extension: 0 residues added, 3522 seeds are put forward Round 1: 159 peptides, 34 chains. Longest chain 7 peptides. Score 0.258 Round 2: 203 peptides, 36 chains. Longest chain 11 peptides. Score 0.385 Round 3: 215 peptides, 30 chains. Longest chain 25 peptides. Score 0.505 Round 4: 213 peptides, 32 chains. Longest chain 13 peptides. Score 0.473 Round 5: 218 peptides, 34 chains. Longest chain 19 peptides. Score 0.461 Taking the results from Round 3 Chains 30, Residues 185, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 6083 reflections ( 85.58 % complete ) and 6059 restraints for refining 2836 atoms. 5331 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2574 (Rfree = 0.000) for 2836 atoms. Found 12 (21 requested) and removed 12 (10 requested) atoms. Cycle 2: After refmac, R = 0.2455 (Rfree = 0.000) for 2800 atoms. Found 4 (21 requested) and removed 11 (10 requested) atoms. Cycle 3: After refmac, R = 0.2366 (Rfree = 0.000) for 2781 atoms. Found 3 (21 requested) and removed 11 (10 requested) atoms. Cycle 4: After refmac, R = 0.2419 (Rfree = 0.000) for 2767 atoms. Found 13 (20 requested) and removed 13 (10 requested) atoms. Cycle 5: After refmac, R = 0.2417 (Rfree = 0.000) for 2763 atoms. Found 9 (20 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.22 2.93 Search for helices and strands: 0 residues in 0 chains, 2820 seeds are put forward NCS extension: 37 residues added (1 deleted due to clashes), 2857 seeds are put forward Round 1: 195 peptides, 36 chains. Longest chain 14 peptides. Score 0.358 Round 2: 223 peptides, 35 chains. Longest chain 20 peptides. Score 0.463 Round 3: 222 peptides, 35 chains. Longest chain 16 peptides. Score 0.460 Round 4: 229 peptides, 36 chains. Longest chain 21 peptides. Score 0.468 Round 5: 234 peptides, 41 chains. Longest chain 18 peptides. Score 0.417 Taking the results from Round 4 Chains 38, Residues 193, Estimated correctness of the model 0.0 % 4 chains (24 residues) have been docked in sequence ------------------------------------------------------ 6083 reflections ( 85.58 % complete ) and 6071 restraints for refining 2837 atoms. 5255 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2544 (Rfree = 0.000) for 2837 atoms. Found 15 (21 requested) and removed 13 (10 requested) atoms. Cycle 7: After refmac, R = 0.2385 (Rfree = 0.000) for 2820 atoms. Found 9 (21 requested) and removed 26 (10 requested) atoms. Cycle 8: After refmac, R = 0.2308 (Rfree = 0.000) for 2792 atoms. Found 7 (21 requested) and removed 16 (10 requested) atoms. Cycle 9: After refmac, R = 0.2305 (Rfree = 0.000) for 2778 atoms. Found 4 (21 requested) and removed 11 (10 requested) atoms. Cycle 10: After refmac, R = 0.2205 (Rfree = 0.000) for 2768 atoms. Found 4 (20 requested) and removed 13 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.27 2.98 Search for helices and strands: 0 residues in 0 chains, 2815 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 2839 seeds are put forward Round 1: 197 peptides, 36 chains. Longest chain 11 peptides. Score 0.365 Round 2: 223 peptides, 37 chains. Longest chain 14 peptides. Score 0.436 Round 3: 233 peptides, 34 chains. Longest chain 23 peptides. Score 0.506 Round 4: 224 peptides, 35 chains. Longest chain 16 peptides. Score 0.466 Round 5: 218 peptides, 31 chains. Longest chain 16 peptides. Score 0.501 Taking the results from Round 3 Chains 34, Residues 199, Estimated correctness of the model 0.0 % 4 chains (19 residues) have been docked in sequence ------------------------------------------------------ 6083 reflections ( 85.58 % complete ) and 6098 restraints for refining 2837 atoms. 5273 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2504 (Rfree = 0.000) for 2837 atoms. Found 21 (21 requested) and removed 12 (10 requested) atoms. Cycle 12: After refmac, R = 0.2370 (Rfree = 0.000) for 2834 atoms. Found 11 (21 requested) and removed 13 (10 requested) atoms. Cycle 13: After refmac, R = 0.2315 (Rfree = 0.000) for 2828 atoms. Found 9 (21 requested) and removed 10 (10 requested) atoms. Cycle 14: After refmac, R = 0.2300 (Rfree = 0.000) for 2823 atoms. Found 5 (21 requested) and removed 12 (10 requested) atoms. Cycle 15: After refmac, R = 0.2262 (Rfree = 0.000) for 2809 atoms. Found 5 (21 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.23 2.94 Search for helices and strands: 0 residues in 0 chains, 2856 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 2875 seeds are put forward Round 1: 197 peptides, 35 chains. Longest chain 16 peptides. Score 0.380 Round 2: 218 peptides, 30 chains. Longest chain 23 peptides. Score 0.514 Round 3: 237 peptides, 34 chains. Longest chain 16 peptides. Score 0.517 Round 4: 222 peptides, 28 chains. Longest chain 27 peptides. Score 0.550 Round 5: 234 peptides, 31 chains. Longest chain 24 peptides. Score 0.546 Taking the results from Round 4 Chains 28, Residues 194, Estimated correctness of the model 11.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6083 reflections ( 85.58 % complete ) and 6209 restraints for refining 2837 atoms. 5461 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2341 (Rfree = 0.000) for 2837 atoms. Found 17 (21 requested) and removed 10 (10 requested) atoms. Cycle 17: After refmac, R = 0.2207 (Rfree = 0.000) for 2835 atoms. Found 2 (21 requested) and removed 10 (10 requested) atoms. Cycle 18: After refmac, R = 0.2154 (Rfree = 0.000) for 2820 atoms. Found 1 (21 requested) and removed 10 (10 requested) atoms. Cycle 19: After refmac, R = 0.2144 (Rfree = 0.000) for 2810 atoms. Found 5 (21 requested) and removed 10 (10 requested) atoms. Cycle 20: After refmac, R = 0.2130 (Rfree = 0.000) for 2803 atoms. Found 2 (21 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.22 2.93 Search for helices and strands: 0 residues in 0 chains, 2835 seeds are put forward NCS extension: 28 residues added (0 deleted due to clashes), 2863 seeds are put forward Round 1: 203 peptides, 38 chains. Longest chain 11 peptides. Score 0.356 Round 2: 237 peptides, 37 chains. Longest chain 13 peptides. Score 0.479 Round 3: 224 peptides, 35 chains. Longest chain 18 peptides. Score 0.466 Round 4: 224 peptides, 32 chains. Longest chain 22 peptides. Score 0.505 Round 5: 239 peptides, 36 chains. Longest chain 17 peptides. Score 0.498 Taking the results from Round 4 Chains 32, Residues 192, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6083 reflections ( 85.58 % complete ) and 6301 restraints for refining 2834 atoms. 5565 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2326 (Rfree = 0.000) for 2834 atoms. Found 16 (21 requested) and removed 11 (10 requested) atoms. Cycle 22: After refmac, R = 0.2171 (Rfree = 0.000) for 2826 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 23: After refmac, R = 0.2128 (Rfree = 0.000) for 2811 atoms. Found 2 (21 requested) and removed 10 (10 requested) atoms. Cycle 24: After refmac, R = 0.2105 (Rfree = 0.000) for 2803 atoms. Found 3 (21 requested) and removed 10 (10 requested) atoms. Cycle 25: After refmac, R = 0.2082 (Rfree = 0.000) for 2794 atoms. Found 3 (21 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.24 2.95 Search for helices and strands: 0 residues in 0 chains, 2831 seeds are put forward NCS extension: 40 residues added (0 deleted due to clashes), 2871 seeds are put forward Round 1: 183 peptides, 33 chains. Longest chain 15 peptides. Score 0.361 Round 2: 193 peptides, 28 chains. Longest chain 18 peptides. Score 0.466 Round 3: 202 peptides, 28 chains. Longest chain 15 peptides. Score 0.493 Round 4: 216 peptides, 32 chains. Longest chain 16 peptides. Score 0.482 Round 5: 220 peptides, 31 chains. Longest chain 19 peptides. Score 0.507 Taking the results from Round 5 Chains 31, Residues 189, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6083 reflections ( 85.58 % complete ) and 6370 restraints for refining 2837 atoms. 5645 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2369 (Rfree = 0.000) for 2837 atoms. Found 13 (21 requested) and removed 11 (10 requested) atoms. Cycle 27: After refmac, R = 0.2268 (Rfree = 0.000) for 2832 atoms. Found 4 (21 requested) and removed 10 (10 requested) atoms. Cycle 28: After refmac, R = 0.2257 (Rfree = 0.000) for 2826 atoms. Found 5 (21 requested) and removed 10 (10 requested) atoms. Cycle 29: After refmac, R = 0.2231 (Rfree = 0.000) for 2820 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 30: After refmac, R = 0.2246 (Rfree = 0.000) for 2810 atoms. Found 5 (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, 2846 seeds are put forward NCS extension: 29 residues added (3 deleted due to clashes), 2875 seeds are put forward Round 1: 197 peptides, 35 chains. Longest chain 15 peptides. Score 0.380 Round 2: 202 peptides, 28 chains. Longest chain 17 peptides. Score 0.493 Round 3: 217 peptides, 33 chains. Longest chain 13 peptides. Score 0.471 Round 4: 213 peptides, 32 chains. Longest chain 16 peptides. Score 0.473 Round 5: 207 peptides, 28 chains. Longest chain 15 peptides. Score 0.508 Taking the results from Round 5 Chains 28, Residues 179, Estimated correctness of the model 0.0 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ 6083 reflections ( 85.58 % complete ) and 6201 restraints for refining 2836 atoms. 5453 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2468 (Rfree = 0.000) for 2836 atoms. Found 16 (21 requested) and removed 10 (10 requested) atoms. Cycle 32: After refmac, R = 0.2347 (Rfree = 0.000) for 2838 atoms. Found 3 (21 requested) and removed 11 (10 requested) atoms. Cycle 33: After refmac, R = 0.2322 (Rfree = 0.000) for 2825 atoms. Found 5 (21 requested) and removed 10 (10 requested) atoms. Cycle 34: After refmac, R = 0.2305 (Rfree = 0.000) for 2817 atoms. Found 5 (21 requested) and removed 10 (10 requested) atoms. Cycle 35: After refmac, R = 0.2267 (Rfree = 0.000) for 2812 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.28 2.99 Search for helices and strands: 0 residues in 0 chains, 2844 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 2860 seeds are put forward Round 1: 192 peptides, 35 chains. Longest chain 12 peptides. Score 0.363 Round 2: 214 peptides, 31 chains. Longest chain 16 peptides. Score 0.489 Round 3: 202 peptides, 33 chains. Longest chain 16 peptides. Score 0.425 Round 4: 207 peptides, 34 chains. Longest chain 12 peptides. Score 0.427 Round 5: 186 peptides, 30 chains. Longest chain 10 peptides. Score 0.415 Taking the results from Round 2 Chains 31, Residues 183, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6083 reflections ( 85.58 % complete ) and 6354 restraints for refining 2837 atoms. 5653 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2418 (Rfree = 0.000) for 2837 atoms. Found 13 (21 requested) and removed 10 (10 requested) atoms. Cycle 37: After refmac, R = 0.2282 (Rfree = 0.000) for 2837 atoms. Found 5 (21 requested) and removed 10 (10 requested) atoms. Cycle 38: After refmac, R = 0.2234 (Rfree = 0.000) for 2831 atoms. Found 1 (21 requested) and removed 10 (10 requested) atoms. Cycle 39: After refmac, R = 0.2225 (Rfree = 0.000) for 2822 atoms. Found 1 (21 requested) and removed 10 (10 requested) atoms. Cycle 40: After refmac, R = 0.2201 (Rfree = 0.000) for 2811 atoms. Found 3 (21 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.26 2.97 Search for helices and strands: 0 residues in 0 chains, 2858 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 2871 seeds are put forward Round 1: 169 peptides, 29 chains. Longest chain 15 peptides. Score 0.372 Round 2: 199 peptides, 33 chains. Longest chain 12 peptides. Score 0.415 Round 3: 196 peptides, 26 chains. Longest chain 17 peptides. Score 0.502 Round 4: 185 peptides, 27 chains. Longest chain 14 peptides. Score 0.455 Round 5: 200 peptides, 28 chains. Longest chain 15 peptides. Score 0.487 Taking the results from Round 3 Chains 26, Residues 170, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6083 reflections ( 85.58 % complete ) and 6378 restraints for refining 2837 atoms. 5724 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2369 (Rfree = 0.000) for 2837 atoms. Found 16 (21 requested) and removed 11 (10 requested) atoms. Cycle 42: After refmac, R = 0.2306 (Rfree = 0.000) for 2836 atoms. Found 3 (21 requested) and removed 10 (10 requested) atoms. Cycle 43: After refmac, R = 0.2411 (Rfree = 0.000) for 2827 atoms. Found 7 (21 requested) and removed 10 (10 requested) atoms. Cycle 44: After refmac, R = 0.2379 (Rfree = 0.000) for 2822 atoms. Found 6 (21 requested) and removed 10 (10 requested) atoms. Cycle 45: After refmac, R = 0.2464 (Rfree = 0.000) for 2816 atoms. Found 17 (21 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.23 2.94 Search for helices and strands: 0 residues in 0 chains, 2868 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 2885 seeds are put forward Round 1: 145 peptides, 29 chains. Longest chain 12 peptides. Score 0.285 Round 2: 174 peptides, 27 chains. Longest chain 13 peptides. Score 0.419 Round 3: 173 peptides, 29 chains. Longest chain 13 peptides. Score 0.386 Round 4: 175 peptides, 26 chains. Longest chain 16 peptides. Score 0.437 Round 5: 162 peptides, 26 chains. Longest chain 17 peptides. Score 0.394 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 26, Residues 149, 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 6598 restraints for refining 2837 atoms. 6028 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2338 (Rfree = 0.000) for 2837 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 47: After refmac, R = 0.2288 (Rfree = 0.000) for 2824 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 48: After refmac, R = 0.2373 (Rfree = 0.000) for 2813 atoms. Found 0 (21 requested) and removed 6 (10 requested) atoms. Cycle 49: After refmac, R = 0.2462 (Rfree = 0.000) for 2805 atoms. TimeTaking 32.85