Sun 23 Dec 22:22:59 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 2nuj-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2nuj-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2nuj-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2nuj-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/2nuj-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2nuj-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 22:23:08 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/2nuj-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2nuj-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 312 and 0 Target number of residues in the AU: 312 Target solvent content: 0.6372 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: 0.62 Input MTZ file: 2nuj-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: 91 Cell parameters: 78.401 78.401 151.418 90.000 90.000 90.000 Input sequence file: 2nuj-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 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 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: 78.401 3.800 Wilson plot Bfac: 70.25 4938 reflections ( 97.42 % complete ) and 0 restraints for refining 2908 atoms. Observations/parameters ratio is 0.42 ------------------------------------------------------ Starting model: R = 0.3422 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2951 (Rfree = 0.000) for 2908 atoms. Found 15 (15 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.45 2.93 Search for helices and strands: 0 residues in 0 chains, 2942 seeds are put forward NCS extension: 0 residues added, 2942 seeds are put forward Round 1: 152 peptides, 28 chains. Longest chain 10 peptides. Score 0.332 Round 2: 181 peptides, 26 chains. Longest chain 23 peptides. Score 0.465 Round 3: 182 peptides, 24 chains. Longest chain 16 peptides. Score 0.497 Round 4: 204 peptides, 27 chains. Longest chain 19 peptides. Score 0.523 Round 5: 195 peptides, 27 chains. Longest chain 16 peptides. Score 0.495 Taking the results from Round 4 Chains 27, Residues 177, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4938 reflections ( 97.42 % complete ) and 5084 restraints for refining 2359 atoms. 4403 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2775 (Rfree = 0.000) for 2359 atoms. Found 12 (12 requested) and removed 7 (6 requested) atoms. Cycle 2: After refmac, R = 0.2577 (Rfree = 0.000) for 2342 atoms. Found 8 (13 requested) and removed 8 (6 requested) atoms. Cycle 3: After refmac, R = 0.2513 (Rfree = 0.000) for 2335 atoms. Found 2 (12 requested) and removed 9 (6 requested) atoms. Cycle 4: After refmac, R = 0.2455 (Rfree = 0.000) for 2319 atoms. Found 4 (12 requested) and removed 6 (6 requested) atoms. Cycle 5: After refmac, R = 0.2430 (Rfree = 0.000) for 2310 atoms. Found 4 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.53 3.00 Search for helices and strands: 0 residues in 0 chains, 2377 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 2396 seeds are put forward Round 1: 166 peptides, 27 chains. Longest chain 15 peptides. Score 0.399 Round 2: 192 peptides, 28 chains. Longest chain 17 peptides. Score 0.472 Round 3: 198 peptides, 28 chains. Longest chain 20 peptides. Score 0.491 Round 4: 196 peptides, 25 chains. Longest chain 15 peptides. Score 0.526 Round 5: 198 peptides, 26 chains. Longest chain 26 peptides. Score 0.518 Taking the results from Round 4 Chains 26, Residues 171, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 4938 reflections ( 97.42 % complete ) and 5044 restraints for refining 2357 atoms. 4343 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2545 (Rfree = 0.000) for 2357 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 7: After refmac, R = 0.2481 (Rfree = 0.000) for 2330 atoms. Found 5 (12 requested) and removed 8 (6 requested) atoms. Cycle 8: After refmac, R = 0.2396 (Rfree = 0.000) for 2314 atoms. Found 5 (12 requested) and removed 7 (6 requested) atoms. Cycle 9: After refmac, R = 0.2391 (Rfree = 0.000) for 2304 atoms. Found 5 (12 requested) and removed 6 (6 requested) atoms. Cycle 10: After refmac, R = 0.2403 (Rfree = 0.000) for 2298 atoms. Found 3 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.54 3.01 Search for helices and strands: 0 residues in 0 chains, 2356 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 2371 seeds are put forward Round 1: 192 peptides, 33 chains. Longest chain 14 peptides. Score 0.399 Round 2: 209 peptides, 29 chains. Longest chain 16 peptides. Score 0.511 Round 3: 219 peptides, 28 chains. Longest chain 19 peptides. Score 0.553 Round 4: 201 peptides, 25 chains. Longest chain 20 peptides. Score 0.541 Round 5: 215 peptides, 27 chains. Longest chain 16 peptides. Score 0.555 Taking the results from Round 5 Chains 27, Residues 188, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 4938 reflections ( 97.42 % complete ) and 5090 restraints for refining 2358 atoms. 4346 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2741 (Rfree = 0.000) for 2358 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 12: After refmac, R = 0.2581 (Rfree = 0.000) for 2343 atoms. Found 3 (12 requested) and removed 9 (6 requested) atoms. Cycle 13: After refmac, R = 0.2539 (Rfree = 0.000) for 2326 atoms. Found 4 (12 requested) and removed 7 (6 requested) atoms. Cycle 14: After refmac, R = 0.2516 (Rfree = 0.000) for 2315 atoms. Found 7 (12 requested) and removed 7 (6 requested) atoms. Cycle 15: After refmac, R = 0.2461 (Rfree = 0.000) for 2310 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.45 2.93 Search for helices and strands: 0 residues in 0 chains, 2368 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 2384 seeds are put forward Round 1: 181 peptides, 28 chains. Longest chain 14 peptides. Score 0.436 Round 2: 210 peptides, 31 chains. Longest chain 15 peptides. Score 0.487 Round 3: 202 peptides, 31 chains. Longest chain 12 peptides. Score 0.461 Round 4: 222 peptides, 29 chains. Longest chain 17 peptides. Score 0.549 Round 5: 206 peptides, 27 chains. Longest chain 25 peptides. Score 0.529 Taking the results from Round 4 Chains 30, Residues 193, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 4938 reflections ( 97.42 % complete ) and 4916 restraints for refining 2358 atoms. 4126 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2704 (Rfree = 0.000) for 2358 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 17: After refmac, R = 0.2588 (Rfree = 0.000) for 2342 atoms. Found 6 (12 requested) and removed 6 (6 requested) atoms. Cycle 18: After refmac, R = 0.2544 (Rfree = 0.000) for 2332 atoms. Found 3 (12 requested) and removed 8 (6 requested) atoms. Cycle 19: After refmac, R = 0.2522 (Rfree = 0.000) for 2317 atoms. Found 4 (12 requested) and removed 7 (6 requested) atoms. Cycle 20: After refmac, R = 0.2486 (Rfree = 0.000) for 2307 atoms. Found 3 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.49 2.97 Search for helices and strands: 0 residues in 0 chains, 2357 seeds are put forward NCS extension: 28 residues added (0 deleted due to clashes), 2385 seeds are put forward Round 1: 166 peptides, 32 chains. Longest chain 9 peptides. Score 0.321 Round 2: 201 peptides, 29 chains. Longest chain 17 peptides. Score 0.486 Round 3: 210 peptides, 31 chains. Longest chain 13 peptides. Score 0.487 Round 4: 212 peptides, 30 chains. Longest chain 15 peptides. Score 0.506 Round 5: 207 peptides, 30 chains. Longest chain 14 peptides. Score 0.491 Taking the results from Round 4 Chains 32, Residues 182, Estimated correctness of the model 0.0 % 2 chains (16 residues) have been docked in sequence ------------------------------------------------------ 4938 reflections ( 97.42 % complete ) and 4968 restraints for refining 2358 atoms. 4204 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2775 (Rfree = 0.000) for 2358 atoms. Found 12 (12 requested) and removed 7 (6 requested) atoms. Cycle 22: After refmac, R = 0.2608 (Rfree = 0.000) for 2352 atoms. Found 8 (12 requested) and removed 7 (6 requested) atoms. Cycle 23: After refmac, R = 0.2544 (Rfree = 0.000) for 2346 atoms. Found 4 (12 requested) and removed 7 (6 requested) atoms. Cycle 24: After refmac, R = 0.2502 (Rfree = 0.000) for 2339 atoms. Found 5 (12 requested) and removed 7 (6 requested) atoms. Cycle 25: After refmac, R = 0.2465 (Rfree = 0.000) for 2332 atoms. Found 3 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.46 2.94 Search for helices and strands: 0 residues in 0 chains, 2384 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 2398 seeds are put forward Round 1: 172 peptides, 29 chains. Longest chain 15 peptides. Score 0.390 Round 2: 183 peptides, 24 chains. Longest chain 19 peptides. Score 0.500 Round 3: 182 peptides, 23 chains. Longest chain 19 peptides. Score 0.511 Round 4: 188 peptides, 25 chains. Longest chain 15 peptides. Score 0.502 Round 5: 177 peptides, 25 chains. Longest chain 16 peptides. Score 0.467 Taking the results from Round 3 Chains 23, Residues 159, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4938 reflections ( 97.42 % complete ) and 5411 restraints for refining 2359 atoms. 4798 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2670 (Rfree = 0.000) for 2359 atoms. Found 8 (12 requested) and removed 7 (6 requested) atoms. Cycle 27: After refmac, R = 0.2608 (Rfree = 0.000) for 2357 atoms. Found 4 (12 requested) and removed 7 (6 requested) atoms. Cycle 28: After refmac, R = 0.2578 (Rfree = 0.000) for 2353 atoms. Found 2 (12 requested) and removed 7 (6 requested) atoms. Cycle 29: After refmac, R = 0.2574 (Rfree = 0.000) for 2346 atoms. Found 3 (12 requested) and removed 6 (6 requested) atoms. Cycle 30: After refmac, R = 0.2564 (Rfree = 0.000) for 2340 atoms. Found 4 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.48 2.96 Search for helices and strands: 0 residues in 0 chains, 2385 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 2406 seeds are put forward Round 1: 168 peptides, 33 chains. Longest chain 9 peptides. Score 0.312 Round 2: 173 peptides, 27 chains. Longest chain 12 peptides. Score 0.424 Round 3: 190 peptides, 30 chains. Longest chain 12 peptides. Score 0.436 Round 4: 203 peptides, 33 chains. Longest chain 14 peptides. Score 0.436 Round 5: 211 peptides, 31 chains. Longest chain 19 peptides. Score 0.490 Taking the results from Round 5 Chains 31, Residues 180, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4938 reflections ( 97.42 % complete ) and 5224 restraints for refining 2359 atoms. 4535 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2821 (Rfree = 0.000) for 2359 atoms. Found 9 (12 requested) and removed 9 (6 requested) atoms. Cycle 32: After refmac, R = 0.2545 (Rfree = 0.000) for 2336 atoms. Found 6 (12 requested) and removed 7 (6 requested) atoms. Cycle 33: After refmac, R = 0.2450 (Rfree = 0.000) for 2325 atoms. Found 4 (12 requested) and removed 6 (6 requested) atoms. Cycle 34: After refmac, R = 0.2388 (Rfree = 0.000) for 2320 atoms. Found 2 (12 requested) and removed 6 (6 requested) atoms. Cycle 35: After refmac, R = 0.2358 (Rfree = 0.000) for 2312 atoms. Found 1 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.48 2.96 Search for helices and strands: 0 residues in 0 chains, 2357 seeds are put forward NCS extension: 28 residues added (3 deleted due to clashes), 2385 seeds are put forward Round 1: 149 peptides, 30 chains. Longest chain 8 peptides. Score 0.288 Round 2: 172 peptides, 31 chains. Longest chain 12 peptides. Score 0.359 Round 3: 174 peptides, 30 chains. Longest chain 12 peptides. Score 0.381 Round 4: 181 peptides, 30 chains. Longest chain 11 peptides. Score 0.406 Round 5: 176 peptides, 27 chains. Longest chain 12 peptides. Score 0.434 Taking the results from Round 5 Chains 27, Residues 149, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4938 reflections ( 97.42 % complete ) and 5428 restraints for refining 2359 atoms. 4859 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2479 (Rfree = 0.000) for 2359 atoms. Found 9 (12 requested) and removed 8 (6 requested) atoms. Cycle 37: After refmac, R = 0.2328 (Rfree = 0.000) for 2339 atoms. Found 8 (12 requested) and removed 7 (6 requested) atoms. Cycle 38: After refmac, R = 0.2251 (Rfree = 0.000) for 2331 atoms. Found 7 (12 requested) and removed 6 (6 requested) atoms. Cycle 39: After refmac, R = 0.2183 (Rfree = 0.000) for 2329 atoms. Found 3 (12 requested) and removed 7 (6 requested) atoms. Cycle 40: After refmac, R = 0.2175 (Rfree = 0.000) for 2322 atoms. Found 1 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.52 2.99 Search for helices and strands: 0 residues in 0 chains, 2385 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 2404 seeds are put forward Round 1: 148 peptides, 31 chains. Longest chain 9 peptides. Score 0.267 Round 2: 156 peptides, 30 chains. Longest chain 10 peptides. Score 0.315 Round 3: 168 peptides, 30 chains. Longest chain 12 peptides. Score 0.360 Round 4: 177 peptides, 28 chains. Longest chain 18 peptides. Score 0.422 Round 5: 189 peptides, 27 chains. Longest chain 20 peptides. Score 0.476 Taking the results from Round 5 Chains 27, Residues 162, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4938 reflections ( 97.42 % complete ) and 5228 restraints for refining 2359 atoms. 4607 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2526 (Rfree = 0.000) for 2359 atoms. Found 12 (12 requested) and removed 7 (6 requested) atoms. Cycle 42: After refmac, R = 0.2400 (Rfree = 0.000) for 2358 atoms. Found 6 (13 requested) and removed 9 (6 requested) atoms. Cycle 43: After refmac, R = 0.2343 (Rfree = 0.000) for 2350 atoms. Found 4 (12 requested) and removed 7 (6 requested) atoms. Cycle 44: After refmac, R = 0.2290 (Rfree = 0.000) for 2341 atoms. Found 1 (12 requested) and removed 6 (6 requested) atoms. Cycle 45: After refmac, R = 0.2263 (Rfree = 0.000) for 2333 atoms. Found 0 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.56 3.02 Search for helices and strands: 0 residues in 0 chains, 2387 seeds are put forward NCS extension: 26 residues added (0 deleted due to clashes), 2413 seeds are put forward Round 1: 139 peptides, 29 chains. Longest chain 8 peptides. Score 0.265 Round 2: 152 peptides, 26 chains. Longest chain 13 peptides. Score 0.365 Round 3: 170 peptides, 28 chains. Longest chain 14 peptides. Score 0.398 Round 4: 165 peptides, 26 chains. Longest chain 9 peptides. Score 0.411 Round 5: 176 peptides, 28 chains. Longest chain 14 peptides. Score 0.419 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 28, Residues 148, 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 2nuj-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4938 reflections ( 97.42 % complete ) and 5449 restraints for refining 2359 atoms. 4885 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2579 (Rfree = 0.000) for 2359 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.2460 (Rfree = 0.000) for 2347 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.2416 (Rfree = 0.000) for 2338 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.2395 (Rfree = 0.000) for 2332 atoms. TimeTaking 47.55