Sun 23 Dec 22:22:53 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 2ffj-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ffj-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ffj-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ffj-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/2ffj-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ffj-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 22:23:03 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/2ffj-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ffj-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 437 and 0 Target number of residues in the AU: 437 Target solvent content: 0.6475 Checking the provided sequence file Detected sequence length: 300 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 600 Adjusted target solvent content: 0.52 Input MTZ file: 2ffj-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: 19 Cell parameters: 68.806 80.677 120.868 90.000 90.000 90.000 Input sequence file: 2ffj-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 4800 target number of atoms Had to go as low as 0.55 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: 29.898 3.400 Wilson plot Bfac: 76.26 9629 reflections ( 99.03 % complete ) and 0 restraints for refining 5285 atoms. Observations/parameters ratio is 0.46 ------------------------------------------------------ Starting model: R = 0.3251 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3372 (Rfree = 0.000) for 5285 atoms. Found 39 (39 requested) and removed 46 (19 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.43 3.34 Search for helices and strands: 0 residues in 0 chains, 5409 seeds are put forward NCS extension: 0 residues added, 5409 seeds are put forward Round 1: 261 peptides, 49 chains. Longest chain 11 peptides. Score 0.345 Round 2: 335 peptides, 44 chains. Longest chain 26 peptides. Score 0.559 Round 3: 348 peptides, 43 chains. Longest chain 28 peptides. Score 0.592 Round 4: 341 peptides, 42 chains. Longest chain 20 peptides. Score 0.587 Round 5: 349 peptides, 45 chains. Longest chain 24 peptides. Score 0.577 Taking the results from Round 3 Chains 43, Residues 305, Estimated correctness of the model 26.0 % 3 chains (40 residues) have been docked in sequence ------------------------------------------------------ 9629 reflections ( 99.03 % complete ) and 9479 restraints for refining 4365 atoms. 8163 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2855 (Rfree = 0.000) for 4365 atoms. Found 25 (32 requested) and removed 47 (16 requested) atoms. Cycle 2: After refmac, R = 0.2846 (Rfree = 0.000) for 4240 atoms. Found 32 (32 requested) and removed 34 (16 requested) atoms. Cycle 3: After refmac, R = 0.2807 (Rfree = 0.000) for 4186 atoms. Found 29 (31 requested) and removed 39 (15 requested) atoms. Cycle 4: After refmac, R = 0.2400 (Rfree = 0.000) for 4146 atoms. Found 16 (31 requested) and removed 34 (15 requested) atoms. Cycle 5: After refmac, R = 0.2341 (Rfree = 0.000) for 4113 atoms. Found 4 (31 requested) and removed 18 (15 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.45 3.36 Search for helices and strands: 0 residues in 0 chains, 4286 seeds are put forward NCS extension: 37 residues added (5 deleted due to clashes), 4323 seeds are put forward Round 1: 326 peptides, 46 chains. Longest chain 16 peptides. Score 0.523 Round 2: 355 peptides, 42 chains. Longest chain 20 peptides. Score 0.612 Round 3: 361 peptides, 45 chains. Longest chain 25 peptides. Score 0.599 Round 4: 367 peptides, 40 chains. Longest chain 22 peptides. Score 0.648 Round 5: 370 peptides, 43 chains. Longest chain 19 peptides. Score 0.630 Taking the results from Round 4 Chains 41, Residues 327, Estimated correctness of the model 43.6 % 2 chains (29 residues) have been docked in sequence ------------------------------------------------------ 9629 reflections ( 99.03 % complete ) and 9091 restraints for refining 4219 atoms. 7712 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2828 (Rfree = 0.000) for 4219 atoms. Found 23 (31 requested) and removed 49 (15 requested) atoms. Cycle 7: After refmac, R = 0.2615 (Rfree = 0.000) for 4167 atoms. Found 17 (31 requested) and removed 28 (15 requested) atoms. Cycle 8: After refmac, R = 0.2510 (Rfree = 0.000) for 4146 atoms. Found 15 (31 requested) and removed 23 (15 requested) atoms. Cycle 9: After refmac, R = 0.2475 (Rfree = 0.000) for 4128 atoms. Found 9 (31 requested) and removed 22 (15 requested) atoms. Cycle 10: After refmac, R = 0.2481 (Rfree = 0.000) for 4113 atoms. Found 6 (31 requested) and removed 18 (15 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.45 3.36 Search for helices and strands: 0 residues in 0 chains, 4285 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 4301 seeds are put forward Round 1: 321 peptides, 45 chains. Longest chain 15 peptides. Score 0.522 Round 2: 340 peptides, 41 chains. Longest chain 21 peptides. Score 0.594 Round 3: 344 peptides, 42 chains. Longest chain 20 peptides. Score 0.593 Round 4: 345 peptides, 37 chains. Longest chain 31 peptides. Score 0.635 Round 5: 358 peptides, 44 chains. Longest chain 35 peptides. Score 0.601 Taking the results from Round 4 Chains 38, Residues 308, Estimated correctness of the model 39.7 % 4 chains (61 residues) have been docked in sequence ------------------------------------------------------ 9629 reflections ( 99.03 % complete ) and 9247 restraints for refining 4363 atoms. 7833 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2780 (Rfree = 0.000) for 4363 atoms. Found 21 (32 requested) and removed 56 (16 requested) atoms. Cycle 12: After refmac, R = 0.2568 (Rfree = 0.000) for 4287 atoms. Found 8 (32 requested) and removed 32 (16 requested) atoms. Failed to save intermediate PDB Cycle 13: After refmac, R = 0.2442 (Rfree = 0.000) for 4248 atoms. Found 10 (32 requested) and removed 24 (16 requested) atoms. Cycle 14: After refmac, R = 0.2409 (Rfree = 0.000) for 4227 atoms. Found 4 (31 requested) and removed 22 (15 requested) atoms. Cycle 15: After refmac, R = 0.2386 (Rfree = 0.000) for 4201 atoms. Found 4 (31 requested) and removed 17 (15 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.43 3.34 Search for helices and strands: 0 residues in 0 chains, 4330 seeds are put forward NCS extension: 15 residues added (4 deleted due to clashes), 4345 seeds are put forward Round 1: 312 peptides, 47 chains. Longest chain 20 peptides. Score 0.485 Round 2: 329 peptides, 47 chains. Longest chain 17 peptides. Score 0.520 Round 3: 329 peptides, 45 chains. Longest chain 15 peptides. Score 0.538 Round 4: 322 peptides, 42 chains. Longest chain 16 peptides. Score 0.551 Round 5: 334 peptides, 44 chains. Longest chain 20 peptides. Score 0.557 Taking the results from Round 5 Chains 45, Residues 290, Estimated correctness of the model 14.0 % 3 chains (22 residues) have been docked in sequence ------------------------------------------------------ 9629 reflections ( 99.03 % complete ) and 9880 restraints for refining 4365 atoms. 8690 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2770 (Rfree = 0.000) for 4365 atoms. Found 22 (32 requested) and removed 32 (16 requested) atoms. Cycle 17: After refmac, R = 0.2586 (Rfree = 0.000) for 4333 atoms. Found 17 (32 requested) and removed 23 (16 requested) atoms. Cycle 18: After refmac, R = 0.2584 (Rfree = 0.000) for 4322 atoms. Found 13 (32 requested) and removed 22 (16 requested) atoms. Cycle 19: After refmac, R = 0.2325 (Rfree = 0.000) for 4303 atoms. Found 5 (32 requested) and removed 22 (16 requested) atoms. Cycle 20: After refmac, R = 0.2333 (Rfree = 0.000) for 4279 atoms. Found 7 (32 requested) and removed 20 (16 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.45 3.36 Search for helices and strands: 0 residues in 0 chains, 4446 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 4467 seeds are put forward Round 1: 299 peptides, 48 chains. Longest chain 20 peptides. Score 0.446 Round 2: 338 peptides, 48 chains. Longest chain 21 peptides. Score 0.530 Round 3: 329 peptides, 47 chains. Longest chain 21 peptides. Score 0.520 Round 4: 323 peptides, 46 chains. Longest chain 16 peptides. Score 0.517 Round 5: 314 peptides, 39 chains. Longest chain 23 peptides. Score 0.562 Taking the results from Round 5 Chains 42, Residues 275, Estimated correctness of the model 15.8 % 2 chains (30 residues) have been docked in sequence ------------------------------------------------------ 9629 reflections ( 99.03 % complete ) and 9773 restraints for refining 4365 atoms. 8603 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2783 (Rfree = 0.000) for 4365 atoms. Found 28 (32 requested) and removed 32 (16 requested) atoms. Cycle 22: After refmac, R = 0.2581 (Rfree = 0.000) for 4339 atoms. Found 32 (32 requested) and removed 21 (16 requested) atoms. Cycle 23: After refmac, R = 0.2645 (Rfree = 0.000) for 4334 atoms. Found 32 (32 requested) and removed 22 (16 requested) atoms. Cycle 24: After refmac, R = 0.2408 (Rfree = 0.000) for 4330 atoms. Found 12 (32 requested) and removed 26 (16 requested) atoms. Cycle 25: After refmac, R = 0.2408 (Rfree = 0.000) for 4302 atoms. Found 28 (32 requested) and removed 21 (16 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.42 3.33 Search for helices and strands: 0 residues in 0 chains, 4490 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 4510 seeds are put forward Round 1: 266 peptides, 47 chains. Longest chain 11 peptides. Score 0.379 Round 2: 303 peptides, 48 chains. Longest chain 13 peptides. Score 0.455 Round 3: 309 peptides, 47 chains. Longest chain 18 peptides. Score 0.478 Round 4: 305 peptides, 43 chains. Longest chain 14 peptides. Score 0.507 Round 5: 309 peptides, 45 chains. Longest chain 14 peptides. Score 0.497 Taking the results from Round 4 Chains 45, Residues 262, Estimated correctness of the model 0.0 % 2 chains (21 residues) have been docked in sequence ------------------------------------------------------ 9629 reflections ( 99.03 % complete ) and 9860 restraints for refining 4365 atoms. 8785 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2692 (Rfree = 0.000) for 4365 atoms. Failed to save intermediate PDB Found 32 (32 requested) and removed 35 (16 requested) atoms. Cycle 27: After refmac, R = 0.2436 (Rfree = 0.000) for 4350 atoms. Found 17 (32 requested) and removed 29 (16 requested) atoms. Cycle 28: After refmac, R = 0.2385 (Rfree = 0.000) for 4324 atoms. Found 18 (32 requested) and removed 23 (16 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.2363 (Rfree = 0.000) for 4312 atoms. Found 14 (32 requested) and removed 19 (16 requested) atoms. Cycle 30: After refmac, R = 0.2329 (Rfree = 0.000) for 4295 atoms. Found 11 (32 requested) and removed 22 (16 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.41 3.32 Search for helices and strands: 0 residues in 0 chains, 4457 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 4470 seeds are put forward Round 1: 277 peptides, 50 chains. Longest chain 12 peptides. Score 0.374 Round 2: 309 peptides, 47 chains. Longest chain 13 peptides. Score 0.478 Round 3: 314 peptides, 42 chains. Longest chain 16 peptides. Score 0.535 Round 4: 321 peptides, 48 chains. Longest chain 17 peptides. Score 0.495 Round 5: 303 peptides, 45 chains. Longest chain 13 peptides. Score 0.484 Taking the results from Round 3 Chains 42, Residues 272, Estimated correctness of the model 6.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9629 reflections ( 99.03 % complete ) and 9872 restraints for refining 4353 atoms. 8826 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2663 (Rfree = 0.000) for 4353 atoms. Found 32 (32 requested) and removed 34 (16 requested) atoms. Cycle 32: After refmac, R = 0.2475 (Rfree = 0.000) for 4331 atoms. Found 25 (32 requested) and removed 23 (16 requested) atoms. Cycle 33: After refmac, R = 0.2353 (Rfree = 0.000) for 4327 atoms. Found 11 (32 requested) and removed 26 (16 requested) atoms. Cycle 34: After refmac, R = 0.2296 (Rfree = 0.000) for 4303 atoms. Found 7 (32 requested) and removed 23 (16 requested) atoms. Cycle 35: After refmac, R = 0.2233 (Rfree = 0.000) for 4281 atoms. Found 10 (32 requested) and removed 18 (16 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.40 3.31 Search for helices and strands: 0 residues in 0 chains, 4457 seeds are put forward NCS extension: 15 residues added (3 deleted due to clashes), 4472 seeds are put forward Round 1: 260 peptides, 48 chains. Longest chain 13 peptides. Score 0.353 Round 2: 301 peptides, 48 chains. Longest chain 14 peptides. Score 0.451 Round 3: 288 peptides, 43 chains. Longest chain 15 peptides. Score 0.471 Round 4: 297 peptides, 45 chains. Longest chain 15 peptides. Score 0.471 Round 5: 302 peptides, 44 chains. Longest chain 14 peptides. Score 0.492 Taking the results from Round 5 Chains 44, Residues 258, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 9629 reflections ( 99.03 % complete ) and 9978 restraints for refining 4365 atoms. 8975 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2529 (Rfree = 0.000) for 4365 atoms. Found 25 (32 requested) and removed 26 (16 requested) atoms. Cycle 37: After refmac, R = 0.2274 (Rfree = 0.000) for 4339 atoms. Found 16 (32 requested) and removed 23 (16 requested) atoms. Cycle 38: After refmac, R = 0.2225 (Rfree = 0.000) for 4323 atoms. Found 16 (32 requested) and removed 22 (16 requested) atoms. Cycle 39: After refmac, R = 0.2141 (Rfree = 0.000) for 4314 atoms. Found 15 (32 requested) and removed 20 (16 requested) atoms. Cycle 40: After refmac, R = 0.2121 (Rfree = 0.000) for 4307 atoms. Found 10 (32 requested) and removed 20 (16 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.44 3.35 Search for helices and strands: 0 residues in 0 chains, 4454 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 4468 seeds are put forward Round 1: 225 peptides, 45 chains. Longest chain 12 peptides. Score 0.295 Round 2: 264 peptides, 43 chains. Longest chain 14 peptides. Score 0.416 Round 3: 261 peptides, 42 chains. Longest chain 15 peptides. Score 0.419 Round 4: 273 peptides, 43 chains. Longest chain 15 peptides. Score 0.437 Round 5: 275 peptides, 41 chains. Longest chain 15 peptides. Score 0.462 Taking the results from Round 5 Chains 41, Residues 234, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9629 reflections ( 99.03 % complete ) and 10139 restraints for refining 4365 atoms. 9244 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2471 (Rfree = 0.000) for 4365 atoms. Found 21 (32 requested) and removed 23 (16 requested) atoms. Cycle 42: After refmac, R = 0.2302 (Rfree = 0.000) for 4355 atoms. Found 15 (32 requested) and removed 20 (16 requested) atoms. Cycle 43: After refmac, R = 0.2245 (Rfree = 0.000) for 4344 atoms. Found 10 (32 requested) and removed 18 (16 requested) atoms. Cycle 44: After refmac, R = 0.2253 (Rfree = 0.000) for 4332 atoms. Found 20 (32 requested) and removed 21 (16 requested) atoms. Cycle 45: After refmac, R = 0.2191 (Rfree = 0.000) for 4325 atoms. Found 18 (32 requested) and removed 20 (16 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.40 3.31 Search for helices and strands: 0 residues in 0 chains, 4482 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 4497 seeds are put forward Round 1: 236 peptides, 47 chains. Longest chain 11 peptides. Score 0.302 Round 2: 253 peptides, 42 chains. Longest chain 15 peptides. Score 0.400 Round 3: 252 peptides, 37 chains. Longest chain 19 peptides. Score 0.450 Round 4: 256 peptides, 41 chains. Longest chain 16 peptides. Score 0.418 Round 5: 250 peptides, 36 chains. Longest chain 16 peptides. Score 0.455 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 36, Residues 214, 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 2ffj-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 9629 reflections ( 99.03 % complete ) and 10095 restraints for refining 4365 atoms. 9275 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2432 (Rfree = 0.000) for 4365 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 47: After refmac, R = 0.2301 (Rfree = 0.000) for 4334 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 48: After refmac, R = 0.2184 (Rfree = 0.000) for 4314 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 49: After refmac, R = 0.2221 (Rfree = 0.000) for 4296 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Writing output files ... Failed to save intermediate PDB TimeTaking 63.25