null Sun 23 Dec 22:22:46 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 2hag-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2hag-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2hag-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hag-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/2hag-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hag-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 22:22:56 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/2hag-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hag-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 335 and 0 Target number of residues in the AU: 335 Target solvent content: 0.6457 Checking the provided sequence file Detected sequence length: 312 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 312 Adjusted target solvent content: 0.67 Input MTZ file: 2hag-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: 96 Cell parameters: 94.680 94.680 114.160 90.000 90.000 90.000 Input sequence file: 2hag-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 2496 target number of atoms Had to go as low as 0.95 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 Loops will be built when appropriate and at the last cycle Resolution range: 29.659 3.400 Wilson plot Bfac: 74.93 7554 reflections ( 99.66 % complete ) and 0 restraints for refining 2771 atoms. Observations/parameters ratio is 0.68 ------------------------------------------------------ Starting model: R = 0.3284 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2828 (Rfree = 0.000) for 2771 atoms. Found 20 (20 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.43 2.71 Search for helices and strands: 0 residues in 0 chains, 2830 seeds are put forward Round 1: 188 peptides, 29 chains. Longest chain 15 peptides. Score 0.426 Round 2: 233 peptides, 24 chains. Longest chain 24 peptides. Score 0.611 Round 3: 238 peptides, 26 chains. Longest chain 22 peptides. Score 0.601 Round 4: 244 peptides, 18 chains. Longest chain 35 peptides. Score 0.697 Round 5: 230 peptides, 20 chains. Longest chain 33 peptides. Score 0.647 Taking the results from Round 4 Chains 18, Residues 226, Estimated correctness of the model 57.1 % 1 chains (34 residues) have been docked in sequence ------------------------------------------------------ 7554 reflections ( 99.66 % complete ) and 4295 restraints for refining 2303 atoms. 3259 conditional restraints added. Observations/parameters ratio is 0.82 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2692 (Rfree = 0.000) for 2303 atoms. Found 17 (17 requested) and removed 21 (8 requested) atoms. Cycle 2: After refmac, R = 0.2482 (Rfree = 0.000) for 2264 atoms. Found 12 (17 requested) and removed 13 (8 requested) atoms. Cycle 3: After refmac, R = 0.2451 (Rfree = 0.000) for 2241 atoms. Found 12 (17 requested) and removed 10 (8 requested) atoms. Cycle 4: After refmac, R = 0.2424 (Rfree = 0.000) for 2235 atoms. Found 6 (16 requested) and removed 10 (8 requested) atoms. Cycle 5: After refmac, R = 0.2414 (Rfree = 0.000) for 2218 atoms. Found 12 (16 requested) and removed 16 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.40 2.69 Search for helices and strands: 0 residues in 0 chains, 2290 seeds are put forward Round 1: 215 peptides, 25 chains. Longest chain 22 peptides. Score 0.555 Round 2: 231 peptides, 27 chains. Longest chain 29 peptides. Score 0.572 Round 3: 240 peptides, 26 chains. Longest chain 19 peptides. Score 0.605 Round 4: 222 peptides, 22 chains. Longest chain 19 peptides. Score 0.607 Round 5: 234 peptides, 24 chains. Longest chain 20 peptides. Score 0.613 Taking the results from Round 5 Chains 26, Residues 210, Estimated correctness of the model 32.9 % 3 chains (38 residues) have been docked in sequence ------------------------------------------------------ 7554 reflections ( 99.66 % complete ) and 4271 restraints for refining 2267 atoms. 3283 conditional restraints added. Observations/parameters ratio is 0.83 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2774 (Rfree = 0.000) for 2267 atoms. Found 17 (17 requested) and removed 16 (8 requested) atoms. Cycle 7: After refmac, R = 0.2591 (Rfree = 0.000) for 2252 atoms. Found 17 (17 requested) and removed 13 (8 requested) atoms. Cycle 8: After refmac, R = 0.2459 (Rfree = 0.000) for 2241 atoms. Found 11 (17 requested) and removed 13 (8 requested) atoms. Cycle 9: After refmac, R = 0.2388 (Rfree = 0.000) for 2233 atoms. Found 5 (16 requested) and removed 12 (8 requested) atoms. Cycle 10: After refmac, R = 0.2343 (Rfree = 0.000) for 2225 atoms. Found 3 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.42 2.70 Search for helices and strands: 0 residues in 0 chains, 2289 seeds are put forward Round 1: 223 peptides, 26 chains. Longest chain 22 peptides. Score 0.564 Round 2: 225 peptides, 20 chains. Longest chain 30 peptides. Score 0.636 Round 3: 230 peptides, 19 chains. Longest chain 33 peptides. Score 0.658 Round 4: 228 peptides, 17 chains. Longest chain 39 peptides. Score 0.675 Round 5: 224 peptides, 17 chains. Longest chain 33 peptides. Score 0.666 Taking the results from Round 4 Chains 17, Residues 211, Estimated correctness of the model 51.2 % 2 chains (64 residues) have been docked in sequence ------------------------------------------------------ 7554 reflections ( 99.66 % complete ) and 3977 restraints for refining 2269 atoms. 2873 conditional restraints added. Observations/parameters ratio is 0.83 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2852 (Rfree = 0.000) for 2269 atoms. Found 17 (17 requested) and removed 20 (8 requested) atoms. Cycle 12: After refmac, R = 0.2655 (Rfree = 0.000) for 2250 atoms. Found 5 (17 requested) and removed 14 (8 requested) atoms. Cycle 13: After refmac, R = 0.2608 (Rfree = 0.000) for 2228 atoms. Found 6 (16 requested) and removed 10 (8 requested) atoms. Cycle 14: After refmac, R = 0.2555 (Rfree = 0.000) for 2217 atoms. Found 1 (16 requested) and removed 14 (8 requested) atoms. Cycle 15: After refmac, R = 0.2531 (Rfree = 0.000) for 2198 atoms. Found 3 (16 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.39 2.68 Search for helices and strands: 0 residues in 0 chains, 2268 seeds are put forward Round 1: 196 peptides, 23 chains. Longest chain 20 peptides. Score 0.529 Round 2: 213 peptides, 20 chains. Longest chain 39 peptides. Score 0.609 Round 3: 222 peptides, 21 chains. Longest chain 24 peptides. Score 0.619 Round 4: 232 peptides, 22 chains. Longest chain 42 peptides. Score 0.630 Round 5: 235 peptides, 25 chains. Longest chain 22 peptides. Score 0.605 Taking the results from Round 4 Chains 22, Residues 210, Estimated correctness of the model 38.2 % 2 chains (45 residues) have been docked in sequence ------------------------------------------------------ 7554 reflections ( 99.66 % complete ) and 4283 restraints for refining 2268 atoms. 3276 conditional restraints added. Observations/parameters ratio is 0.83 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2728 (Rfree = 0.000) for 2268 atoms. Found 17 (17 requested) and removed 15 (8 requested) atoms. Cycle 17: After refmac, R = 0.2546 (Rfree = 0.000) for 2259 atoms. Found 7 (17 requested) and removed 18 (8 requested) atoms. Cycle 18: After refmac, R = 0.2394 (Rfree = 0.000) for 2240 atoms. Found 5 (16 requested) and removed 12 (8 requested) atoms. Cycle 19: After refmac, R = 0.2331 (Rfree = 0.000) for 2229 atoms. Found 4 (16 requested) and removed 8 (8 requested) atoms. Cycle 20: After refmac, R = 0.2281 (Rfree = 0.000) for 2224 atoms. Found 2 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.40 2.69 Search for helices and strands: 0 residues in 0 chains, 2292 seeds are put forward Round 1: 210 peptides, 24 chains. Longest chain 19 peptides. Score 0.554 Round 2: 237 peptides, 23 chains. Longest chain 43 peptides. Score 0.631 Round 3: 224 peptides, 25 chains. Longest chain 24 peptides. Score 0.578 Round 4: 230 peptides, 24 chains. Longest chain 36 peptides. Score 0.604 Round 5: 225 peptides, 26 chains. Longest chain 21 peptides. Score 0.569 Taking the results from Round 2 Chains 24, Residues 214, Estimated correctness of the model 38.5 % 1 chains (37 residues) have been docked in sequence ------------------------------------------------------ 7554 reflections ( 99.66 % complete ) and 4343 restraints for refining 2269 atoms. 3341 conditional restraints added. Observations/parameters ratio is 0.83 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2635 (Rfree = 0.000) for 2269 atoms. Found 13 (17 requested) and removed 13 (8 requested) atoms. Cycle 22: After refmac, R = 0.2457 (Rfree = 0.000) for 2254 atoms. Found 5 (17 requested) and removed 17 (8 requested) atoms. Cycle 23: After refmac, R = 0.2435 (Rfree = 0.000) for 2236 atoms. Found 2 (16 requested) and removed 11 (8 requested) atoms. Cycle 24: After refmac, R = 0.2475 (Rfree = 0.000) for 2218 atoms. Found 12 (16 requested) and removed 10 (8 requested) atoms. Cycle 25: After refmac, R = 0.2370 (Rfree = 0.000) for 2213 atoms. Found 8 (16 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.35 2.65 Search for helices and strands: 0 residues in 0 chains, 2286 seeds are put forward Round 1: 201 peptides, 24 chains. Longest chain 29 peptides. Score 0.530 Round 2: 232 peptides, 23 chains. Longest chain 42 peptides. Score 0.620 Round 3: 234 peptides, 22 chains. Longest chain 42 peptides. Score 0.635 Round 4: 237 peptides, 22 chains. Longest chain 26 peptides. Score 0.642 Round 5: 233 peptides, 23 chains. Longest chain 26 peptides. Score 0.622 Taking the results from Round 4 Chains 25, Residues 215, Estimated correctness of the model 41.8 % 4 chains (64 residues) have been docked in sequence ------------------------------------------------------ 7554 reflections ( 99.66 % complete ) and 4115 restraints for refining 2269 atoms. 3002 conditional restraints added. Observations/parameters ratio is 0.83 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2737 (Rfree = 0.000) for 2269 atoms. Found 17 (17 requested) and removed 16 (8 requested) atoms. Cycle 27: After refmac, R = 0.2595 (Rfree = 0.000) for 2255 atoms. Found 16 (17 requested) and removed 14 (8 requested) atoms. Cycle 28: After refmac, R = 0.2465 (Rfree = 0.000) for 2245 atoms. Found 4 (17 requested) and removed 9 (8 requested) atoms. Cycle 29: After refmac, R = 0.2377 (Rfree = 0.000) for 2237 atoms. Found 2 (16 requested) and removed 12 (8 requested) atoms. Cycle 30: After refmac, R = 0.2336 (Rfree = 0.000) for 2223 atoms. Found 6 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.37 2.66 Search for helices and strands: 0 residues in 0 chains, 2284 seeds are put forward Round 1: 218 peptides, 27 chains. Longest chain 20 peptides. Score 0.539 Round 2: 215 peptides, 23 chains. Longest chain 33 peptides. Score 0.579 Round 3: 215 peptides, 21 chains. Longest chain 28 peptides. Score 0.602 Round 4: 231 peptides, 22 chains. Longest chain 33 peptides. Score 0.628 Round 5: 217 peptides, 21 chains. Longest chain 25 peptides. Score 0.607 Taking the results from Round 4 Chains 23, Residues 209, Estimated correctness of the model 37.5 % 2 chains (31 residues) have been docked in sequence ------------------------------------------------------ 7554 reflections ( 99.66 % complete ) and 4511 restraints for refining 2269 atoms. 3570 conditional restraints added. Observations/parameters ratio is 0.83 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2605 (Rfree = 0.000) for 2269 atoms. Found 13 (17 requested) and removed 15 (8 requested) atoms. Cycle 32: After refmac, R = 0.2570 (Rfree = 0.000) for 2258 atoms. Found 8 (17 requested) and removed 12 (8 requested) atoms. Cycle 33: After refmac, R = 0.2371 (Rfree = 0.000) for 2250 atoms. Found 5 (17 requested) and removed 9 (8 requested) atoms. Cycle 34: After refmac, R = 0.2260 (Rfree = 0.000) for 2240 atoms. Found 5 (16 requested) and removed 10 (8 requested) atoms. Cycle 35: After refmac, R = 0.2179 (Rfree = 0.000) for 2231 atoms. Found 3 (16 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.40 2.69 Search for helices and strands: 0 residues in 0 chains, 2301 seeds are put forward Round 1: 194 peptides, 28 chains. Longest chain 17 peptides. Score 0.458 Round 2: 225 peptides, 28 chains. Longest chain 23 peptides. Score 0.545 Round 3: 219 peptides, 27 chains. Longest chain 17 peptides. Score 0.541 Round 4: 223 peptides, 24 chains. Longest chain 31 peptides. Score 0.587 Round 5: 242 peptides, 22 chains. Longest chain 33 peptides. Score 0.653 Taking the results from Round 5 Chains 25, Residues 220, Estimated correctness of the model 45.0 % 4 chains (63 residues) have been docked in sequence ------------------------------------------------------ 7554 reflections ( 99.66 % complete ) and 4083 restraints for refining 2269 atoms. 2971 conditional restraints added. Observations/parameters ratio is 0.83 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2749 (Rfree = 0.000) for 2269 atoms. Found 17 (17 requested) and removed 22 (8 requested) atoms. Cycle 37: After refmac, R = 0.2522 (Rfree = 0.000) for 2247 atoms. Found 10 (17 requested) and removed 15 (8 requested) atoms. Cycle 38: After refmac, R = 0.2391 (Rfree = 0.000) for 2234 atoms. Found 5 (16 requested) and removed 9 (8 requested) atoms. Cycle 39: After refmac, R = 0.2448 (Rfree = 0.000) for 2227 atoms. Found 14 (16 requested) and removed 10 (8 requested) atoms. Cycle 40: After refmac, R = 0.2326 (Rfree = 0.000) for 2227 atoms. Found 9 (16 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.39 2.68 Search for helices and strands: 0 residues in 0 chains, 2266 seeds are put forward Round 1: 190 peptides, 26 chains. Longest chain 20 peptides. Score 0.473 Round 2: 213 peptides, 24 chains. Longest chain 25 peptides. Score 0.562 Round 3: 218 peptides, 23 chains. Longest chain 30 peptides. Score 0.586 Round 4: 223 peptides, 24 chains. Longest chain 29 peptides. Score 0.587 Round 5: 217 peptides, 24 chains. Longest chain 24 peptides. Score 0.572 Taking the results from Round 4 Chains 25, Residues 199, Estimated correctness of the model 24.4 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 7554 reflections ( 99.66 % complete ) and 4767 restraints for refining 2269 atoms. 3927 conditional restraints added. Observations/parameters ratio is 0.83 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2539 (Rfree = 0.000) for 2269 atoms. Found 17 (17 requested) and removed 9 (8 requested) atoms. Cycle 42: After refmac, R = 0.2350 (Rfree = 0.000) for 2272 atoms. Found 7 (17 requested) and removed 8 (8 requested) atoms. Cycle 43: After refmac, R = 0.2228 (Rfree = 0.000) for 2259 atoms. Found 2 (17 requested) and removed 9 (8 requested) atoms. Cycle 44: After refmac, R = 0.2163 (Rfree = 0.000) for 2250 atoms. Found 4 (17 requested) and removed 8 (8 requested) atoms. Cycle 45: After refmac, R = 0.2139 (Rfree = 0.000) for 2243 atoms. Found 3 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.42 2.70 Search for helices and strands: 0 residues in 0 chains, 2305 seeds are put forward Round 1: 201 peptides, 28 chains. Longest chain 16 peptides. Score 0.479 Round 2: 220 peptides, 25 chains. Longest chain 28 peptides. Score 0.568 Round 3: 213 peptides, 27 chains. Longest chain 19 peptides. Score 0.525 Round 4: 214 peptides, 24 chains. Longest chain 27 peptides. Score 0.564 Round 5: 222 peptides, 28 chains. Longest chain 21 peptides. Score 0.537 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 28, Residues 195, Estimated correctness of the model 17.9 % 2 chains (33 residues) have been docked in sequence Sequence coverage is 16 % Consider running further cycles of model building using 2hag-3_warpNtrace.pdb as input Building loops using Loopy2018 28 chains (195 residues) following loop building 2 chains (33 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7554 reflections ( 99.66 % complete ) and 4481 restraints for refining 2269 atoms. 3573 conditional restraints added. Observations/parameters ratio is 0.83 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2457 (Rfree = 0.000) for 2269 atoms. Found 0 (17 requested) and removed 4 (8 requested) atoms. Cycle 47: After refmac, R = 0.2384 (Rfree = 0.000) for 2260 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.2335 (Rfree = 0.000) for 2244 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.2317 (Rfree = 0.000) for 2230 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:13:02 GMT 2018 Job finished. TimeTaking 50.27 Used memory is bytes: 360224