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 2ppv-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ppv-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ppv-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ppv-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/2ppv-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ppv-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 ============================================================ Tue 25 Dec 19:28:12 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/2ppv-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ppv-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 302 and 0 Target number of residues in the AU: 302 Target solvent content: 0.6807 Checking the provided sequence file Detected sequence length: 332 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 332 Adjusted target solvent content: 0.65 Input MTZ file: 2ppv-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: 20 Cell parameters: 133.390 136.620 56.180 90.000 90.000 90.000 Input sequence file: 2ppv-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 2656 target number of atoms Had to go as low as 0.90 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: 29.185 3.400 Wilson plot Bfac: 101.11 7339 reflections ( 99.23 % complete ) and 0 restraints for refining 2929 atoms. Observations/parameters ratio is 0.63 ------------------------------------------------------ Starting model: R = 0.3503 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3185 (Rfree = 0.000) for 2929 atoms. Found 20 (22 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.74 3.04 Search for helices and strands: 0 residues in 0 chains, 2996 seeds are put forward Round 1: 174 peptides, 30 chains. Longest chain 10 peptides. Score 0.367 Round 2: 195 peptides, 25 chains. Longest chain 18 peptides. Score 0.501 Round 3: 204 peptides, 21 chains. Longest chain 21 peptides. Score 0.575 Round 4: 222 peptides, 22 chains. Longest chain 19 peptides. Score 0.607 Round 5: 224 peptides, 24 chains. Longest chain 22 peptides. Score 0.589 Taking the results from Round 4 Chains 23, Residues 200, Estimated correctness of the model 30.9 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 7339 reflections ( 99.23 % complete ) and 5211 restraints for refining 2415 atoms. 4396 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2980 (Rfree = 0.000) for 2415 atoms. Found 18 (18 requested) and removed 19 (9 requested) atoms. Cycle 2: After refmac, R = 0.2682 (Rfree = 0.000) for 2366 atoms. Found 13 (18 requested) and removed 13 (9 requested) atoms. Cycle 3: After refmac, R = 0.2570 (Rfree = 0.000) for 2345 atoms. Found 9 (17 requested) and removed 14 (8 requested) atoms. Cycle 4: After refmac, R = 0.2401 (Rfree = 0.000) for 2327 atoms. Found 9 (17 requested) and removed 9 (8 requested) atoms. Cycle 5: After refmac, R = 0.2389 (Rfree = 0.000) for 2317 atoms. Found 3 (17 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.69 3.00 Search for helices and strands: 0 residues in 0 chains, 2378 seeds are put forward Round 1: 201 peptides, 24 chains. Longest chain 19 peptides. Score 0.530 Round 2: 212 peptides, 26 chains. Longest chain 16 peptides. Score 0.535 Round 3: 228 peptides, 24 chains. Longest chain 21 peptides. Score 0.599 Round 4: 238 peptides, 22 chains. Longest chain 49 peptides. Score 0.644 Round 5: 225 peptides, 23 chains. Longest chain 21 peptides. Score 0.603 Taking the results from Round 4 Chains 23, Residues 216, Estimated correctness of the model 42.4 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 7339 reflections ( 99.23 % complete ) and 5075 restraints for refining 2415 atoms. 4203 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2665 (Rfree = 0.000) for 2415 atoms. Found 18 (18 requested) and removed 19 (9 requested) atoms. Cycle 7: After refmac, R = 0.2411 (Rfree = 0.000) for 2384 atoms. Found 14 (18 requested) and removed 16 (9 requested) atoms. Cycle 8: After refmac, R = 0.2370 (Rfree = 0.000) for 2358 atoms. Found 15 (17 requested) and removed 9 (8 requested) atoms. Cycle 9: After refmac, R = 0.2194 (Rfree = 0.000) for 2353 atoms. Found 9 (17 requested) and removed 11 (8 requested) atoms. Cycle 10: After refmac, R = 0.2198 (Rfree = 0.000) for 2343 atoms. Found 7 (17 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.73 3.04 Search for helices and strands: 0 residues in 0 chains, 2424 seeds are put forward Round 1: 209 peptides, 28 chains. Longest chain 20 peptides. Score 0.502 Round 2: 217 peptides, 22 chains. Longest chain 21 peptides. Score 0.595 Round 3: 229 peptides, 26 chains. Longest chain 25 peptides. Score 0.579 Round 4: 237 peptides, 28 chains. Longest chain 27 peptides. Score 0.576 Round 5: 236 peptides, 22 chains. Longest chain 29 peptides. Score 0.639 Taking the results from Round 5 Chains 23, Residues 214, Estimated correctness of the model 40.9 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 7339 reflections ( 99.23 % complete ) and 5077 restraints for refining 2415 atoms. 4204 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2893 (Rfree = 0.000) for 2415 atoms. Found 18 (18 requested) and removed 15 (9 requested) atoms. Cycle 12: After refmac, R = 0.2564 (Rfree = 0.000) for 2392 atoms. Found 18 (18 requested) and removed 13 (9 requested) atoms. Cycle 13: After refmac, R = 0.2462 (Rfree = 0.000) for 2383 atoms. Found 18 (18 requested) and removed 11 (9 requested) atoms. Cycle 14: After refmac, R = 0.2351 (Rfree = 0.000) for 2388 atoms. Found 1 (18 requested) and removed 13 (9 requested) atoms. Cycle 15: After refmac, R = 0.2330 (Rfree = 0.000) for 2370 atoms. Found 3 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.74 3.04 Search for helices and strands: 0 residues in 0 chains, 2451 seeds are put forward Round 1: 201 peptides, 27 chains. Longest chain 15 peptides. Score 0.492 Round 2: 218 peptides, 19 chains. Longest chain 27 peptides. Score 0.632 Round 3: 217 peptides, 26 chains. Longest chain 24 peptides. Score 0.548 Round 4: 216 peptides, 24 chains. Longest chain 18 peptides. Score 0.570 Round 5: 214 peptides, 25 chains. Longest chain 31 peptides. Score 0.552 Taking the results from Round 2 Chains 19, Residues 199, Estimated correctness of the model 38.8 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 7339 reflections ( 99.23 % complete ) and 5091 restraints for refining 2415 atoms. 4269 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2535 (Rfree = 0.000) for 2415 atoms. Found 12 (18 requested) and removed 13 (9 requested) atoms. Cycle 17: After refmac, R = 0.2375 (Rfree = 0.000) for 2399 atoms. Found 7 (18 requested) and removed 9 (9 requested) atoms. Cycle 18: After refmac, R = 0.2319 (Rfree = 0.000) for 2388 atoms. Found 5 (18 requested) and removed 12 (9 requested) atoms. Cycle 19: After refmac, R = 0.2239 (Rfree = 0.000) for 2378 atoms. Found 4 (17 requested) and removed 10 (8 requested) atoms. Cycle 20: After refmac, R = 0.2141 (Rfree = 0.000) for 2364 atoms. Found 1 (17 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.72 3.03 Search for helices and strands: 0 residues in 0 chains, 2460 seeds are put forward Round 1: 190 peptides, 26 chains. Longest chain 18 peptides. Score 0.473 Round 2: 218 peptides, 28 chains. Longest chain 20 peptides. Score 0.526 Round 3: 209 peptides, 23 chains. Longest chain 20 peptides. Score 0.564 Round 4: 207 peptides, 24 chains. Longest chain 20 peptides. Score 0.546 Round 5: 207 peptides, 24 chains. Longest chain 24 peptides. Score 0.546 Taking the results from Round 3 Chains 23, Residues 186, Estimated correctness of the model 16.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7339 reflections ( 99.23 % complete ) and 5260 restraints for refining 2405 atoms. 4539 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2442 (Rfree = 0.000) for 2405 atoms. Found 11 (18 requested) and removed 15 (9 requested) atoms. Cycle 22: After refmac, R = 0.2311 (Rfree = 0.000) for 2378 atoms. Found 11 (18 requested) and removed 18 (9 requested) atoms. Cycle 23: After refmac, R = 0.2192 (Rfree = 0.000) for 2360 atoms. Found 3 (17 requested) and removed 12 (8 requested) atoms. Cycle 24: After refmac, R = 0.2090 (Rfree = 0.000) for 2341 atoms. Found 4 (17 requested) and removed 9 (8 requested) atoms. Cycle 25: After refmac, R = 0.1996 (Rfree = 0.000) for 2332 atoms. Found 3 (17 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.67 2.99 Search for helices and strands: 0 residues in 0 chains, 2425 seeds are put forward Round 1: 181 peptides, 29 chains. Longest chain 13 peptides. Score 0.404 Round 2: 212 peptides, 27 chains. Longest chain 24 peptides. Score 0.522 Round 3: 206 peptides, 23 chains. Longest chain 23 peptides. Score 0.556 Round 4: 213 peptides, 21 chains. Longest chain 23 peptides. Score 0.597 Round 5: 216 peptides, 26 chains. Longest chain 25 peptides. Score 0.546 Taking the results from Round 4 Chains 21, Residues 192, Estimated correctness of the model 27.7 % 2 chains (40 residues) have been docked in sequence ------------------------------------------------------ 7339 reflections ( 99.23 % complete ) and 4796 restraints for refining 2415 atoms. 3886 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2498 (Rfree = 0.000) for 2415 atoms. Found 17 (18 requested) and removed 15 (9 requested) atoms. Cycle 27: After refmac, R = 0.2335 (Rfree = 0.000) for 2389 atoms. Found 7 (18 requested) and removed 13 (9 requested) atoms. Cycle 28: After refmac, R = 0.2253 (Rfree = 0.000) for 2379 atoms. Found 3 (17 requested) and removed 13 (8 requested) atoms. Cycle 29: After refmac, R = 0.2195 (Rfree = 0.000) for 2361 atoms. Found 3 (17 requested) and removed 8 (8 requested) atoms. Cycle 30: After refmac, R = 0.2118 (Rfree = 0.000) for 2356 atoms. Found 3 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.69 3.00 Search for helices and strands: 0 residues in 0 chains, 2422 seeds are put forward Round 1: 192 peptides, 28 chains. Longest chain 18 peptides. Score 0.452 Round 2: 214 peptides, 23 chains. Longest chain 29 peptides. Score 0.576 Round 3: 215 peptides, 27 chains. Longest chain 26 peptides. Score 0.531 Round 4: 220 peptides, 23 chains. Longest chain 23 peptides. Score 0.591 Round 5: 221 peptides, 24 chains. Longest chain 26 peptides. Score 0.582 Taking the results from Round 4 Chains 24, Residues 197, Estimated correctness of the model 25.7 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 7339 reflections ( 99.23 % complete ) and 5057 restraints for refining 2415 atoms. 4260 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2484 (Rfree = 0.000) for 2415 atoms. Found 18 (18 requested) and removed 11 (9 requested) atoms. Cycle 32: After refmac, R = 0.2310 (Rfree = 0.000) for 2402 atoms. Found 16 (18 requested) and removed 11 (9 requested) atoms. Cycle 33: After refmac, R = 0.2175 (Rfree = 0.000) for 2396 atoms. Found 2 (18 requested) and removed 12 (9 requested) atoms. Cycle 34: After refmac, R = 0.2211 (Rfree = 0.000) for 2373 atoms. Found 9 (18 requested) and removed 10 (9 requested) atoms. Cycle 35: After refmac, R = 0.2087 (Rfree = 0.000) for 2367 atoms. Found 8 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.67 2.99 Search for helices and strands: 0 residues in 0 chains, 2477 seeds are put forward Round 1: 162 peptides, 21 chains. Longest chain 18 peptides. Score 0.458 Round 2: 198 peptides, 26 chains. Longest chain 19 peptides. Score 0.496 Round 3: 212 peptides, 25 chains. Longest chain 22 peptides. Score 0.547 Round 4: 217 peptides, 23 chains. Longest chain 18 peptides. Score 0.584 Round 5: 209 peptides, 25 chains. Longest chain 22 peptides. Score 0.539 Taking the results from Round 4 Chains 25, Residues 194, Estimated correctness of the model 23.4 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 7339 reflections ( 99.23 % complete ) and 4983 restraints for refining 2414 atoms. 4183 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2338 (Rfree = 0.000) for 2414 atoms. Found 17 (18 requested) and removed 10 (9 requested) atoms. Cycle 37: After refmac, R = 0.2192 (Rfree = 0.000) for 2405 atoms. Found 9 (18 requested) and removed 11 (9 requested) atoms. Cycle 38: After refmac, R = 0.2136 (Rfree = 0.000) for 2397 atoms. Found 7 (18 requested) and removed 12 (9 requested) atoms. Cycle 39: After refmac, R = 0.2334 (Rfree = 0.000) for 2381 atoms. Found 16 (18 requested) and removed 18 (9 requested) atoms. Cycle 40: After refmac, R = 0.2114 (Rfree = 0.000) for 2373 atoms. Found 7 (17 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.70 3.01 Search for helices and strands: 0 residues in 0 chains, 2433 seeds are put forward Round 1: 176 peptides, 28 chains. Longest chain 15 peptides. Score 0.402 Round 2: 203 peptides, 20 chains. Longest chain 25 peptides. Score 0.584 Round 3: 191 peptides, 23 chains. Longest chain 18 peptides. Score 0.515 Round 4: 205 peptides, 25 chains. Longest chain 22 peptides. Score 0.528 Round 5: 213 peptides, 26 chains. Longest chain 18 peptides. Score 0.538 Taking the results from Round 2 Chains 20, Residues 183, Estimated correctness of the model 23.4 % 1 chains (16 residues) have been docked in sequence ------------------------------------------------------ 7339 reflections ( 99.23 % complete ) and 5122 restraints for refining 2413 atoms. 4349 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2486 (Rfree = 0.000) for 2413 atoms. Found 18 (18 requested) and removed 14 (9 requested) atoms. Cycle 42: After refmac, R = 0.2199 (Rfree = 0.000) for 2401 atoms. Found 9 (18 requested) and removed 16 (9 requested) atoms. Cycle 43: After refmac, R = 0.2424 (Rfree = 0.000) for 2384 atoms. Found 13 (18 requested) and removed 16 (9 requested) atoms. Cycle 44: After refmac, R = 0.2117 (Rfree = 0.000) for 2379 atoms. Found 8 (17 requested) and removed 10 (8 requested) atoms. Cycle 45: After refmac, R = 0.2652 (Rfree = 0.000) for 2372 atoms. Found 17 (17 requested) and removed 18 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.72 3.03 Search for helices and strands: 0 residues in 0 chains, 2458 seeds are put forward Round 1: 170 peptides, 27 chains. Longest chain 12 peptides. Score 0.397 Round 2: 189 peptides, 22 chains. Longest chain 23 peptides. Score 0.523 Round 3: 189 peptides, 22 chains. Longest chain 20 peptides. Score 0.523 Round 4: 184 peptides, 23 chains. Longest chain 20 peptides. Score 0.496 Round 5: 192 peptides, 22 chains. Longest chain 20 peptides. Score 0.531 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 22, Residues 170, Estimated correctness of the model 4.6 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2ppv-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7339 reflections ( 99.23 % complete ) and 5344 restraints for refining 2415 atoms. 4686 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2836 (Rfree = 0.000) for 2415 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.2155 (Rfree = 0.000) for 2392 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.2021 (Rfree = 0.000) for 2376 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.2068 (Rfree = 0.000) for 2365 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:29:46 GMT 2018 Job finished. TimeTaking 61.82 Used memory is bytes: 3541632