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 2nuj-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2nuj-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2nuj-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2nuj-3.6-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-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2nuj-3.6-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 19:28:07 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-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2nuj-3.6-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 322 and 0 Target number of residues in the AU: 322 Target solvent content: 0.6255 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-3.6-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-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 2608 target number of atoms Had to go as low as 0.85 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 3.600 Wilson plot Bfac: 63.74 5780 reflections ( 97.59 % complete ) and 0 restraints for refining 2875 atoms. Observations/parameters ratio is 0.50 ------------------------------------------------------ Starting model: R = 0.3323 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3088 (Rfree = 0.000) for 2875 atoms. Found 18 (18 requested) and removed 19 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.36 2.85 Search for helices and strands: 0 residues in 0 chains, 2924 seeds are put forward NCS extension: 0 residues added, 2924 seeds are put forward Round 1: 173 peptides, 32 chains. Longest chain 10 peptides. Score 0.347 Round 2: 227 peptides, 31 chains. Longest chain 15 peptides. Score 0.537 Round 3: 227 peptides, 27 chains. Longest chain 19 peptides. Score 0.588 Round 4: 217 peptides, 26 chains. Longest chain 22 peptides. Score 0.573 Round 5: 232 peptides, 25 chains. Longest chain 34 peptides. Score 0.624 Taking the results from Round 5 Chains 25, Residues 207, Estimated correctness of the model 23.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5780 reflections ( 97.59 % complete ) and 4798 restraints for refining 2364 atoms. 3995 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2709 (Rfree = 0.000) for 2364 atoms. Found 15 (15 requested) and removed 11 (7 requested) atoms. Cycle 2: After refmac, R = 0.2505 (Rfree = 0.000) for 2332 atoms. Found 15 (15 requested) and removed 7 (7 requested) atoms. Cycle 3: After refmac, R = 0.2429 (Rfree = 0.000) for 2320 atoms. Found 15 (15 requested) and removed 11 (7 requested) atoms. Cycle 4: After refmac, R = 0.2372 (Rfree = 0.000) for 2303 atoms. Found 14 (14 requested) and removed 11 (7 requested) atoms. Failed to save intermediate PDB Cycle 5: After refmac, R = 0.2369 (Rfree = 0.000) for 2295 atoms. Found 14 (14 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.27 2.78 Search for helices and strands: 0 residues in 0 chains, 2379 seeds are put forward NCS extension: 52 residues added (4 deleted due to clashes), 2431 seeds are put forward Round 1: 201 peptides, 30 chains. Longest chain 15 peptides. Score 0.472 Round 2: 208 peptides, 24 chains. Longest chain 33 peptides. Score 0.573 Round 3: 235 peptides, 28 chains. Longest chain 24 peptides. Score 0.597 Round 4: 230 peptides, 24 chains. Longest chain 35 peptides. Score 0.631 Round 5: 225 peptides, 24 chains. Longest chain 33 peptides. Score 0.618 Taking the results from Round 4 Chains 26, Residues 206, Estimated correctness of the model 26.4 % 2 chains (44 residues) have been docked in sequence ------------------------------------------------------ 5780 reflections ( 97.59 % complete ) and 4464 restraints for refining 2364 atoms. 3491 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2468 (Rfree = 0.000) for 2364 atoms. Found 15 (15 requested) and removed 10 (7 requested) atoms. Cycle 7: After refmac, R = 0.2279 (Rfree = 0.000) for 2352 atoms. Found 11 (15 requested) and removed 11 (7 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.2196 (Rfree = 0.000) for 2336 atoms. Found 5 (15 requested) and removed 8 (7 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.2370 (Rfree = 0.000) for 2330 atoms. Found 11 (14 requested) and removed 10 (7 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.2283 (Rfree = 0.000) for 2325 atoms. Found 11 (14 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.32 2.82 Search for helices and strands: 0 residues in 0 chains, 2383 seeds are put forward NCS extension: 38 residues added (9 deleted due to clashes), 2421 seeds are put forward Round 1: 208 peptides, 29 chains. Longest chain 17 peptides. Score 0.508 Round 2: 233 peptides, 29 chains. Longest chain 25 peptides. Score 0.579 Round 3: 223 peptides, 28 chains. Longest chain 33 peptides. Score 0.564 Round 4: 239 peptides, 24 chains. Longest chain 39 peptides. Score 0.652 Round 5: 230 peptides, 27 chains. Longest chain 27 peptides. Score 0.595 Taking the results from Round 4 Chains 28, Residues 215, Estimated correctness of the model 33.9 % 2 chains (41 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 5780 reflections ( 97.59 % complete ) and 4495 restraints for refining 2364 atoms. 3520 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2430 (Rfree = 0.000) for 2364 atoms. Found 15 (15 requested) and removed 19 (7 requested) atoms. Cycle 12: After refmac, R = 0.2338 (Rfree = 0.000) for 2350 atoms. Found 7 (15 requested) and removed 8 (7 requested) atoms. Cycle 13: After refmac, R = 0.2317 (Rfree = 0.000) for 2337 atoms. Found 12 (15 requested) and removed 8 (7 requested) atoms. Cycle 14: After refmac, R = 0.2353 (Rfree = 0.000) for 2335 atoms. Found 15 (15 requested) and removed 10 (7 requested) atoms. Failed to save intermediate PDB Cycle 15: After refmac, R = 0.2280 (Rfree = 0.000) for 2331 atoms. Found 11 (15 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.33 2.83 Search for helices and strands: 0 residues in 0 chains, 2414 seeds are put forward NCS extension: 29 residues added (3 deleted due to clashes), 2443 seeds are put forward Round 1: 205 peptides, 31 chains. Longest chain 17 peptides. Score 0.471 Round 2: 222 peptides, 27 chains. Longest chain 32 peptides. Score 0.574 Round 3: 230 peptides, 28 chains. Longest chain 27 peptides. Score 0.583 Round 4: 229 peptides, 30 chains. Longest chain 21 peptides. Score 0.556 Round 5: 221 peptides, 25 chains. Longest chain 19 peptides. Score 0.596 Taking the results from Round 5 Chains 25, Residues 196, Estimated correctness of the model 13.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 5780 reflections ( 97.59 % complete ) and 5055 restraints for refining 2364 atoms. 4296 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2727 (Rfree = 0.000) for 2364 atoms. Found 15 (15 requested) and removed 16 (7 requested) atoms. Failed to save intermediate PDB Cycle 17: After refmac, R = 0.2552 (Rfree = 0.000) for 2345 atoms. Found 15 (15 requested) and removed 9 (7 requested) atoms. Cycle 18: After refmac, R = 0.2363 (Rfree = 0.000) for 2338 atoms. Found 15 (15 requested) and removed 12 (7 requested) atoms. Cycle 19: After refmac, R = 0.2301 (Rfree = 0.000) for 2331 atoms. Found 12 (15 requested) and removed 10 (7 requested) atoms. Cycle 20: After refmac, R = 0.2221 (Rfree = 0.000) for 2325 atoms. Found 14 (14 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.29 2.80 Search for helices and strands: 0 residues in 0 chains, 2422 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 2440 seeds are put forward Round 1: 198 peptides, 31 chains. Longest chain 16 peptides. Score 0.448 Round 2: 226 peptides, 25 chains. Longest chain 28 peptides. Score 0.609 Round 3: 217 peptides, 27 chains. Longest chain 24 peptides. Score 0.560 Round 4: 223 peptides, 28 chains. Longest chain 21 peptides. Score 0.564 Round 5: 214 peptides, 29 chains. Longest chain 20 peptides. Score 0.526 Taking the results from Round 2 Chains 25, Residues 201, Estimated correctness of the model 18.1 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 5780 reflections ( 97.59 % complete ) and 4888 restraints for refining 2363 atoms. 4083 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2278 (Rfree = 0.000) for 2363 atoms. Found 15 (15 requested) and removed 9 (7 requested) atoms. Cycle 22: After refmac, R = 0.2295 (Rfree = 0.000) for 2350 atoms. Found 15 (15 requested) and removed 8 (7 requested) atoms. Cycle 23: After refmac, R = 0.2207 (Rfree = 0.000) for 2352 atoms. Found 8 (15 requested) and removed 9 (7 requested) atoms. Cycle 24: After refmac, R = 0.2181 (Rfree = 0.000) for 2347 atoms. Found 14 (15 requested) and removed 12 (7 requested) atoms. Cycle 25: After refmac, R = 0.2119 (Rfree = 0.000) for 2347 atoms. Found 14 (15 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.36 2.85 Search for helices and strands: 0 residues in 0 chains, 2443 seeds are put forward NCS extension: 23 residues added (4 deleted due to clashes), 2466 seeds are put forward Round 1: 197 peptides, 29 chains. Longest chain 23 peptides. Score 0.474 Round 2: 215 peptides, 25 chains. Longest chain 27 peptides. Score 0.580 Round 3: 214 peptides, 22 chains. Longest chain 29 peptides. Score 0.614 Round 4: 204 peptides, 23 chains. Longest chain 28 peptides. Score 0.575 Round 5: 211 peptides, 27 chains. Longest chain 16 peptides. Score 0.543 Taking the results from Round 3 Chains 22, Residues 192, Estimated correctness of the model 20.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 5780 reflections ( 97.59 % complete ) and 4924 restraints for refining 2364 atoms. 4151 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2416 (Rfree = 0.000) for 2364 atoms. Found 15 (15 requested) and removed 12 (7 requested) atoms. Cycle 27: After refmac, R = 0.2247 (Rfree = 0.000) for 2361 atoms. Found 15 (15 requested) and removed 10 (7 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.2154 (Rfree = 0.000) for 2363 atoms. Found 15 (15 requested) and removed 7 (7 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.2210 (Rfree = 0.000) for 2369 atoms. Found 15 (15 requested) and removed 8 (7 requested) atoms. Cycle 30: After refmac, R = 0.2086 (Rfree = 0.000) for 2373 atoms. Found 15 (15 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.33 2.83 Search for helices and strands: 0 residues in 0 chains, 2459 seeds are put forward NCS extension: 38 residues added (3 deleted due to clashes), 2497 seeds are put forward Round 1: 200 peptides, 30 chains. Longest chain 15 peptides. Score 0.469 Round 2: 222 peptides, 28 chains. Longest chain 24 peptides. Score 0.562 Round 3: 230 peptides, 24 chains. Longest chain 35 peptides. Score 0.631 Round 4: 210 peptides, 23 chains. Longest chain 31 peptides. Score 0.592 Round 5: 213 peptides, 24 chains. Longest chain 28 peptides. Score 0.587 Taking the results from Round 3 Chains 24, Residues 206, Estimated correctness of the model 26.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5780 reflections ( 97.59 % complete ) and 4857 restraints for refining 2364 atoms. 4057 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2376 (Rfree = 0.000) for 2364 atoms. Found 15 (15 requested) and removed 9 (7 requested) atoms. Cycle 32: After refmac, R = 0.2203 (Rfree = 0.000) for 2355 atoms. Found 15 (15 requested) and removed 9 (7 requested) atoms. Failed to save intermediate PDB Cycle 33: After refmac, R = 0.2190 (Rfree = 0.000) for 2352 atoms. Found 15 (15 requested) and removed 10 (7 requested) atoms. Cycle 34: After refmac, R = 0.2131 (Rfree = 0.000) for 2353 atoms. Found 11 (15 requested) and removed 7 (7 requested) atoms. Cycle 35: After refmac, R = 0.2114 (Rfree = 0.000) for 2356 atoms. Found 15 (15 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.33 2.83 Search for helices and strands: 0 residues in 0 chains, 2421 seeds are put forward NCS extension: 29 residues added (8 deleted due to clashes), 2450 seeds are put forward Round 1: 195 peptides, 27 chains. Longest chain 33 peptides. Score 0.495 Round 2: 215 peptides, 24 chains. Longest chain 27 peptides. Score 0.592 Round 3: 216 peptides, 25 chains. Longest chain 41 peptides. Score 0.583 Round 4: 214 peptides, 26 chains. Longest chain 20 peptides. Score 0.565 Round 5: 224 peptides, 25 chains. Longest chain 45 peptides. Score 0.604 Taking the results from Round 5 Chains 27, Residues 199, Estimated correctness of the model 16.2 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 5780 reflections ( 97.59 % complete ) and 4734 restraints for refining 2364 atoms. 3903 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2449 (Rfree = 0.000) for 2364 atoms. Found 15 (15 requested) and removed 9 (7 requested) atoms. Cycle 37: After refmac, R = 0.2269 (Rfree = 0.000) for 2349 atoms. Found 7 (15 requested) and removed 8 (7 requested) atoms. Cycle 38: After refmac, R = 0.2107 (Rfree = 0.000) for 2344 atoms. Found 4 (15 requested) and removed 8 (7 requested) atoms. Failed to save intermediate PDB Cycle 39: After refmac, R = 0.2143 (Rfree = 0.000) for 2339 atoms. Found 4 (15 requested) and removed 9 (7 requested) atoms. Cycle 40: After refmac, R = 0.2123 (Rfree = 0.000) for 2333 atoms. Found 4 (14 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.37 2.86 Search for helices and strands: 0 residues in 0 chains, 2389 seeds are put forward NCS extension: 59 residues added (7 deleted due to clashes), 2448 seeds are put forward Round 1: 188 peptides, 30 chains. Longest chain 21 peptides. Score 0.430 Round 2: 199 peptides, 28 chains. Longest chain 24 peptides. Score 0.494 Round 3: 202 peptides, 24 chains. Longest chain 28 peptides. Score 0.557 Round 4: 186 peptides, 25 chains. Longest chain 30 peptides. Score 0.495 Round 5: 203 peptides, 28 chains. Longest chain 28 peptides. Score 0.506 Taking the results from Round 3 Chains 25, Residues 178, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 5780 reflections ( 97.59 % complete ) and 5045 restraints for refining 2362 atoms. 4326 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2347 (Rfree = 0.000) for 2362 atoms. Found 15 (15 requested) and removed 10 (7 requested) atoms. Failed to save intermediate PDB Cycle 42: After refmac, R = 0.2132 (Rfree = 0.000) for 2347 atoms. Found 14 (15 requested) and removed 7 (7 requested) atoms. Cycle 43: After refmac, R = 0.2152 (Rfree = 0.000) for 2350 atoms. Found 9 (15 requested) and removed 7 (7 requested) atoms. Cycle 44: After refmac, R = 0.2126 (Rfree = 0.000) for 2347 atoms. Found 15 (15 requested) and removed 9 (7 requested) atoms. Cycle 45: After refmac, R = 0.2038 (Rfree = 0.000) for 2346 atoms. Found 8 (15 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.34 2.84 Search for helices and strands: 0 residues in 0 chains, 2418 seeds are put forward NCS extension: 33 residues added (0 deleted due to clashes), 2451 seeds are put forward Round 1: 159 peptides, 28 chains. Longest chain 10 peptides. Score 0.358 Round 2: 178 peptides, 21 chains. Longest chain 30 peptides. Score 0.527 Round 3: 188 peptides, 26 chains. Longest chain 23 peptides. Score 0.488 Round 4: 187 peptides, 28 chains. Longest chain 16 peptides. Score 0.456 Round 5: 191 peptides, 28 chains. Longest chain 28 peptides. Score 0.469 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 25, Residues 157, Estimated correctness of the model 0.0 % 2 chains (22 residues) have been docked in sequence Sequence coverage is 13 % Consider running further cycles of model building using 2nuj-3_warpNtrace.pdb as input Building loops using Loopy2018 25 chains (157 residues) following loop building 2 chains (22 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5780 reflections ( 97.59 % complete ) and 4924 restraints for refining 2364 atoms. 4245 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2246 (Rfree = 0.000) for 2364 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Failed to save intermediate PDB Cycle 47: After refmac, R = 0.2131 (Rfree = 0.000) for 2344 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.2079 (Rfree = 0.000) for 2336 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.2076 (Rfree = 0.000) for 2327 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Writing output files ... TimeTaking 52.98