null Sun 23 Dec 22:23:08 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 2aj7-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2aj7-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2aj7-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2aj7-3.8-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/2aj7-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2aj7-3.8-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 ============================================================ Sun 23 Dec 22:23:18 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/2aj7-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2aj7-3.8-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 373 and 0 Target number of residues in the AU: 373 Target solvent content: 0.6433 Checking the provided sequence file Detected sequence length: 163 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 326 Adjusted target solvent content: 0.69 Input MTZ file: 2aj7-3.8-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: 173 Cell parameters: 108.801 108.801 82.811 90.000 90.000 120.000 Input sequence file: 2aj7-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 2608 target number of atoms Had to go as low as 1.15 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: 94.224 3.800 Wilson plot Bfac: 73.84 5579 reflections ( 99.91 % complete ) and 0 restraints for refining 2894 atoms. Observations/parameters ratio is 0.48 ------------------------------------------------------ Starting model: R = 0.3350 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3500 (Rfree = 0.000) for 2894 atoms. Found 15 (15 requested) and removed 103 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.63 2.78 Search for helices and strands: 0 residues in 0 chains, 2836 seeds are put forward NCS extension: 0 residues added, 2836 seeds are put forward Round 1: 157 peptides, 24 chains. Longest chain 19 peptides. Score 0.383 Round 2: 197 peptides, 22 chains. Longest chain 21 peptides. Score 0.520 Round 3: 197 peptides, 24 chains. Longest chain 23 peptides. Score 0.496 Round 4: 194 peptides, 27 chains. Longest chain 21 peptides. Score 0.451 Round 5: 222 peptides, 23 chains. Longest chain 33 peptides. Score 0.569 Taking the results from Round 5 Chains 25, Residues 199, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 5579 reflections ( 99.91 % complete ) and 5118 restraints for refining 2359 atoms. 4309 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3550 (Rfree = 0.000) for 2359 atoms. Found 12 (12 requested) and removed 32 (6 requested) atoms. Cycle 2: After refmac, R = 0.3342 (Rfree = 0.000) for 2290 atoms. Found 12 (12 requested) and removed 19 (6 requested) atoms. Cycle 3: After refmac, R = 0.3024 (Rfree = 0.000) for 2241 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 4: After refmac, R = 0.3006 (Rfree = 0.000) for 2217 atoms. Found 12 (12 requested) and removed 19 (6 requested) atoms. Cycle 5: After refmac, R = 0.3153 (Rfree = 0.000) for 2199 atoms. Found 12 (12 requested) and removed 20 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.65 2.80 Search for helices and strands: 0 residues in 0 chains, 2282 seeds are put forward NCS extension: 48 residues added (0 deleted due to clashes), 2330 seeds are put forward Round 1: 204 peptides, 24 chains. Longest chain 32 peptides. Score 0.514 Round 2: 227 peptides, 21 chains. Longest chain 36 peptides. Score 0.602 Round 3: 227 peptides, 20 chains. Longest chain 39 peptides. Score 0.613 Round 4: 233 peptides, 20 chains. Longest chain 40 peptides. Score 0.625 Round 5: 232 peptides, 20 chains. Longest chain 43 peptides. Score 0.623 Taking the results from Round 4 Chains 23, Residues 213, Estimated correctness of the model 10.2 % 2 chains (35 residues) have been docked in sequence ------------------------------------------------------ 5579 reflections ( 99.91 % complete ) and 4562 restraints for refining 2359 atoms. 3585 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3476 (Rfree = 0.000) for 2359 atoms. Found 12 (12 requested) and removed 19 (6 requested) atoms. Cycle 7: After refmac, R = 0.3186 (Rfree = 0.000) for 2303 atoms. Found 12 (12 requested) and removed 17 (6 requested) atoms. Cycle 8: After refmac, R = 0.3159 (Rfree = 0.000) for 2270 atoms. Found 10 (12 requested) and removed 16 (6 requested) atoms. Cycle 9: After refmac, R = 0.2954 (Rfree = 0.000) for 2240 atoms. Found 6 (12 requested) and removed 14 (6 requested) atoms. Cycle 10: After refmac, R = 0.2991 (Rfree = 0.000) for 2218 atoms. Found 4 (12 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 4.22 3.23 Search for helices and strands: 0 residues in 0 chains, 2278 seeds are put forward NCS extension: 22 residues added (5 deleted due to clashes), 2300 seeds are put forward Round 1: 193 peptides, 23 chains. Longest chain 17 peptides. Score 0.498 Round 2: 210 peptides, 22 chains. Longest chain 23 peptides. Score 0.552 Round 3: 210 peptides, 19 chains. Longest chain 23 peptides. Score 0.586 Round 4: 204 peptides, 18 chains. Longest chain 36 peptides. Score 0.584 Round 5: 210 peptides, 19 chains. Longest chain 29 peptides. Score 0.586 Taking the results from Round 5 Chains 19, Residues 191, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5579 reflections ( 99.91 % complete ) and 5236 restraints for refining 2359 atoms. 4491 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3346 (Rfree = 0.000) for 2359 atoms. Found 12 (12 requested) and removed 93 (6 requested) atoms. Cycle 12: After refmac, R = 0.3262 (Rfree = 0.000) for 2244 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. Cycle 13: After refmac, R = 0.2927 (Rfree = 0.000) for 2214 atoms. Found 8 (12 requested) and removed 11 (6 requested) atoms. Cycle 14: After refmac, R = 0.2953 (Rfree = 0.000) for 2190 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 15: After refmac, R = 0.2757 (Rfree = 0.000) for 2181 atoms. Found 6 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.62 2.77 Search for helices and strands: 0 residues in 0 chains, 2248 seeds are put forward NCS extension: 27 residues added (0 deleted due to clashes), 2275 seeds are put forward Round 1: 195 peptides, 29 chains. Longest chain 23 peptides. Score 0.429 Round 2: 209 peptides, 27 chains. Longest chain 18 peptides. Score 0.491 Round 3: 215 peptides, 25 chains. Longest chain 21 peptides. Score 0.530 Round 4: 216 peptides, 22 chains. Longest chain 30 peptides. Score 0.567 Round 5: 212 peptides, 25 chains. Longest chain 21 peptides. Score 0.523 Taking the results from Round 4 Chains 22, Residues 194, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5579 reflections ( 99.91 % complete ) and 5208 restraints for refining 2359 atoms. 4454 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3307 (Rfree = 0.000) for 2359 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 17: After refmac, R = 0.3123 (Rfree = 0.000) for 2336 atoms. Found 12 (12 requested) and removed 24 (6 requested) atoms. Cycle 18: After refmac, R = 0.3115 (Rfree = 0.000) for 2294 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 19: After refmac, R = 0.3164 (Rfree = 0.000) for 2259 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. Cycle 20: After refmac, R = 0.3022 (Rfree = 0.000) for 2232 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.60 2.76 Search for helices and strands: 0 residues in 0 chains, 2311 seeds are put forward NCS extension: 35 residues added (0 deleted due to clashes), 2346 seeds are put forward Round 1: 199 peptides, 25 chains. Longest chain 20 peptides. Score 0.489 Round 2: 220 peptides, 22 chains. Longest chain 37 peptides. Score 0.576 Round 3: 222 peptides, 26 chains. Longest chain 21 peptides. Score 0.536 Round 4: 215 peptides, 24 chains. Longest chain 26 peptides. Score 0.541 Round 5: 208 peptides, 26 chains. Longest chain 19 peptides. Score 0.501 Taking the results from Round 2 Chains 22, Residues 198, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5579 reflections ( 99.91 % complete ) and 4928 restraints for refining 2358 atoms. 4158 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3216 (Rfree = 0.000) for 2358 atoms. Found 12 (12 requested) and removed 25 (6 requested) atoms. Cycle 22: After refmac, R = 0.3175 (Rfree = 0.000) for 2323 atoms. Found 12 (12 requested) and removed 20 (6 requested) atoms. Cycle 23: After refmac, R = 0.2812 (Rfree = 0.000) for 2293 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 24: After refmac, R = 0.2819 (Rfree = 0.000) for 2288 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 25: After refmac, R = 0.2827 (Rfree = 0.000) for 2269 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.61 2.77 Search for helices and strands: 0 residues in 0 chains, 2348 seeds are put forward NCS extension: 48 residues added (6 deleted due to clashes), 2396 seeds are put forward Round 1: 207 peptides, 32 chains. Longest chain 13 peptides. Score 0.425 Round 2: 226 peptides, 24 chains. Longest chain 34 peptides. Score 0.568 Round 3: 223 peptides, 24 chains. Longest chain 26 peptides. Score 0.561 Round 4: 209 peptides, 24 chains. Longest chain 22 peptides. Score 0.527 Round 5: 224 peptides, 25 chains. Longest chain 30 peptides. Score 0.552 Taking the results from Round 2 Chains 25, Residues 202, Estimated correctness of the model 0.0 % 1 chains (25 residues) have been docked in sequence ------------------------------------------------------ 5579 reflections ( 99.91 % complete ) and 4728 restraints for refining 2359 atoms. 3836 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3051 (Rfree = 0.000) for 2359 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 27: After refmac, R = 0.2792 (Rfree = 0.000) for 2334 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 28: After refmac, R = 0.2616 (Rfree = 0.000) for 2320 atoms. Found 11 (12 requested) and removed 13 (6 requested) atoms. Cycle 29: After refmac, R = 0.2556 (Rfree = 0.000) for 2311 atoms. Found 11 (12 requested) and removed 14 (6 requested) atoms. Cycle 30: After refmac, R = 0.2703 (Rfree = 0.000) for 2302 atoms. Found 12 (12 requested) and removed 21 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.63 2.78 Search for helices and strands: 0 residues in 0 chains, 2361 seeds are put forward NCS extension: 0 residues added, 2361 seeds are put forward Round 1: 193 peptides, 27 chains. Longest chain 16 peptides. Score 0.448 Round 2: 217 peptides, 26 chains. Longest chain 22 peptides. Score 0.523 Round 3: 235 peptides, 27 chains. Longest chain 25 peptides. Score 0.556 Round 4: 227 peptides, 22 chains. Longest chain 28 peptides. Score 0.592 Round 5: 232 peptides, 22 chains. Longest chain 38 peptides. Score 0.603 Taking the results from Round 5 Chains 24, Residues 210, Estimated correctness of the model 0.3 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 5579 reflections ( 99.91 % complete ) and 4952 restraints for refining 2359 atoms. 4075 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3222 (Rfree = 0.000) for 2359 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 32: After refmac, R = 0.3031 (Rfree = 0.000) for 2340 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 33: After refmac, R = 0.2860 (Rfree = 0.000) for 2333 atoms. Found 7 (12 requested) and removed 14 (6 requested) atoms. Cycle 34: After refmac, R = 0.2917 (Rfree = 0.000) for 2307 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 35: After refmac, R = 0.2867 (Rfree = 0.000) for 2295 atoms. Found 10 (12 requested) and removed 13 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.66 2.80 Search for helices and strands: 0 residues in 0 chains, 2375 seeds are put forward NCS extension: 53 residues added (3 deleted due to clashes), 2428 seeds are put forward Round 1: 193 peptides, 27 chains. Longest chain 24 peptides. Score 0.448 Round 2: 210 peptides, 24 chains. Longest chain 24 peptides. Score 0.529 Round 3: 208 peptides, 25 chains. Longest chain 20 peptides. Score 0.513 Round 4: 214 peptides, 25 chains. Longest chain 27 peptides. Score 0.528 Round 5: 209 peptides, 23 chains. Longest chain 27 peptides. Score 0.538 Taking the results from Round 5 Chains 25, Residues 186, Estimated correctness of the model 0.0 % 3 chains (51 residues) have been docked in sequence ------------------------------------------------------ 5579 reflections ( 99.91 % complete ) and 4702 restraints for refining 2359 atoms. 3765 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3208 (Rfree = 0.000) for 2359 atoms. Found 12 (12 requested) and removed 17 (6 requested) atoms. Cycle 37: After refmac, R = 0.2986 (Rfree = 0.000) for 2313 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 38: After refmac, R = 0.2968 (Rfree = 0.000) for 2287 atoms. Found 12 (12 requested) and removed 16 (6 requested) atoms. Cycle 39: After refmac, R = 0.2802 (Rfree = 0.000) for 2267 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 40: After refmac, R = 0.2785 (Rfree = 0.000) for 2248 atoms. Found 8 (12 requested) and removed 13 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 4.22 3.23 Search for helices and strands: 0 residues in 0 chains, 2312 seeds are put forward NCS extension: 44 residues added (9 deleted due to clashes), 2356 seeds are put forward Round 1: 166 peptides, 29 chains. Longest chain 13 peptides. Score 0.342 Round 2: 187 peptides, 25 chains. Longest chain 14 peptides. Score 0.457 Round 3: 191 peptides, 25 chains. Longest chain 16 peptides. Score 0.468 Round 4: 202 peptides, 27 chains. Longest chain 17 peptides. Score 0.473 Round 5: 198 peptides, 22 chains. Longest chain 22 peptides. Score 0.523 Taking the results from Round 5 Chains 23, Residues 176, Estimated correctness of the model 0.0 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 5579 reflections ( 99.91 % complete ) and 5100 restraints for refining 2358 atoms. 4355 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3332 (Rfree = 0.000) for 2358 atoms. Found 12 (12 requested) and removed 19 (6 requested) atoms. Cycle 42: After refmac, R = 0.2975 (Rfree = 0.000) for 2332 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 43: After refmac, R = 0.2988 (Rfree = 0.000) for 2307 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 44: After refmac, R = 0.2919 (Rfree = 0.000) for 2296 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 45: After refmac, R = 0.2600 (Rfree = 0.000) for 2285 atoms. Found 6 (12 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.66 2.80 Search for helices and strands: 0 residues in 0 chains, 2340 seeds are put forward NCS extension: 34 residues added (0 deleted due to clashes), 2374 seeds are put forward Round 1: 184 peptides, 34 chains. Longest chain 12 peptides. Score 0.330 Round 2: 193 peptides, 25 chains. Longest chain 33 peptides. Score 0.473 Round 3: 191 peptides, 23 chains. Longest chain 35 peptides. Score 0.493 Round 4: 196 peptides, 23 chains. Longest chain 22 peptides. Score 0.506 Round 5: 186 peptides, 21 chains. Longest chain 31 peptides. Score 0.504 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 23, Residues 173, 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 2aj7-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5579 reflections ( 99.91 % complete ) and 5209 restraints for refining 2358 atoms. 4540 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3131 (Rfree = 0.000) for 2358 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.3034 (Rfree = 0.000) for 2335 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.3073 (Rfree = 0.000) for 2321 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.2862 (Rfree = 0.000) for 2298 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:18:47 GMT 2018 Job finished. TimeTaking 55.65 Used memory is bytes: 8860048