Sun 23 Dec 22:22:42 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-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ffj-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ffj-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ffj-3.2-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-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ffj-3.2-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/2ffj-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ffj-3.2-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 451 and 0 Target number of residues in the AU: 451 Target solvent content: 0.6362 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-3.2-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-3.2-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 3.200 Wilson plot Bfac: 69.70 11521 reflections ( 99.18 % complete ) and 0 restraints for refining 5302 atoms. Observations/parameters ratio is 0.54 ------------------------------------------------------ Starting model: R = 0.3227 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3097 (Rfree = 0.000) for 5302 atoms. Found 47 (47 requested) and removed 56 (23 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.28 3.19 Search for helices and strands: 0 residues in 0 chains, 5405 seeds are put forward NCS extension: 0 residues added, 5405 seeds are put forward Round 1: 279 peptides, 47 chains. Longest chain 13 peptides. Score 0.410 Round 2: 340 peptides, 51 chains. Longest chain 15 peptides. Score 0.507 Round 3: 376 peptides, 45 chains. Longest chain 22 peptides. Score 0.625 Round 4: 382 peptides, 43 chains. Longest chain 26 peptides. Score 0.650 Round 5: 393 peptides, 42 chains. Longest chain 30 peptides. Score 0.674 Taking the results from Round 5 Chains 45, Residues 351, Estimated correctness of the model 59.5 % 2 chains (25 residues) have been docked in sequence ------------------------------------------------------ 11521 reflections ( 99.18 % complete ) and 9411 restraints for refining 4383 atoms. 7947 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2863 (Rfree = 0.000) for 4383 atoms. Found 39 (39 requested) and removed 72 (19 requested) atoms. Cycle 2: After refmac, R = 0.2656 (Rfree = 0.000) for 4276 atoms. Found 17 (39 requested) and removed 36 (19 requested) atoms. Cycle 3: After refmac, R = 0.2630 (Rfree = 0.000) for 4227 atoms. Found 19 (38 requested) and removed 35 (19 requested) atoms. Cycle 4: After refmac, R = 0.2490 (Rfree = 0.000) for 4201 atoms. Found 15 (37 requested) and removed 24 (18 requested) atoms. Cycle 5: After refmac, R = 0.2502 (Rfree = 0.000) for 4183 atoms. Found 10 (37 requested) and removed 21 (18 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.26 3.17 Search for helices and strands: 0 residues in 0 chains, 4337 seeds are put forward NCS extension: 15 residues added (3 deleted due to clashes), 4352 seeds are put forward Round 1: 333 peptides, 45 chains. Longest chain 17 peptides. Score 0.546 Round 2: 388 peptides, 47 chains. Longest chain 24 peptides. Score 0.630 Round 3: 383 peptides, 43 chains. Longest chain 31 peptides. Score 0.651 Round 4: 374 peptides, 43 chains. Longest chain 31 peptides. Score 0.637 Round 5: 371 peptides, 42 chains. Longest chain 22 peptides. Score 0.639 Taking the results from Round 3 Chains 47, Residues 340, Estimated correctness of the model 54.1 % 5 chains (56 residues) have been docked in sequence ------------------------------------------------------ 11521 reflections ( 99.18 % complete ) and 9177 restraints for refining 4318 atoms. 7655 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2692 (Rfree = 0.000) for 4318 atoms. Found 32 (38 requested) and removed 51 (19 requested) atoms. Cycle 7: After refmac, R = 0.2509 (Rfree = 0.000) for 4279 atoms. Found 10 (38 requested) and removed 28 (19 requested) atoms. Cycle 8: After refmac, R = 0.2482 (Rfree = 0.000) for 4244 atoms. Found 11 (38 requested) and removed 25 (19 requested) atoms. Cycle 9: After refmac, R = 0.2390 (Rfree = 0.000) for 4224 atoms. Found 8 (37 requested) and removed 25 (18 requested) atoms. Cycle 10: After refmac, R = 0.2408 (Rfree = 0.000) for 4189 atoms. Found 14 (37 requested) and removed 21 (18 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.25 3.16 Search for helices and strands: 0 residues in 0 chains, 4348 seeds are put forward NCS extension: 26 residues added (4 deleted due to clashes), 4374 seeds are put forward Round 1: 362 peptides, 51 chains. Longest chain 17 peptides. Score 0.551 Round 2: 360 peptides, 43 chains. Longest chain 23 peptides. Score 0.613 Round 3: 388 peptides, 46 chains. Longest chain 23 peptides. Score 0.637 Round 4: 394 peptides, 46 chains. Longest chain 26 peptides. Score 0.647 Round 5: 395 peptides, 44 chains. Longest chain 23 peptides. Score 0.663 Taking the results from Round 5 Chains 49, Residues 351, Estimated correctness of the model 56.9 % 4 chains (55 residues) have been docked in sequence ------------------------------------------------------ 11521 reflections ( 99.18 % complete ) and 9073 restraints for refining 4383 atoms. 7512 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2699 (Rfree = 0.000) for 4383 atoms. Found 26 (39 requested) and removed 48 (19 requested) atoms. Cycle 12: After refmac, R = 0.2481 (Rfree = 0.000) for 4344 atoms. Found 7 (39 requested) and removed 30 (19 requested) atoms. Cycle 13: After refmac, R = 0.2586 (Rfree = 0.000) for 4310 atoms. Found 14 (38 requested) and removed 26 (19 requested) atoms. Cycle 14: After refmac, R = 0.2384 (Rfree = 0.000) for 4286 atoms. Found 7 (38 requested) and removed 34 (19 requested) atoms. Cycle 15: After refmac, R = 0.2294 (Rfree = 0.000) for 4255 atoms. Found 3 (38 requested) and removed 25 (19 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.26 3.17 Search for helices and strands: 0 residues in 0 chains, 4358 seeds are put forward NCS extension: 23 residues added (6 deleted due to clashes), 4381 seeds are put forward Round 1: 344 peptides, 48 chains. Longest chain 19 peptides. Score 0.542 Round 2: 356 peptides, 42 chains. Longest chain 29 peptides. Score 0.614 Round 3: 367 peptides, 41 chains. Longest chain 31 peptides. Score 0.640 Round 4: 362 peptides, 41 chains. Longest chain 25 peptides. Score 0.632 Round 5: 364 peptides, 43 chains. Longest chain 21 peptides. Score 0.620 Taking the results from Round 3 Chains 41, Residues 326, Estimated correctness of the model 51.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 11521 reflections ( 99.18 % complete ) and 9624 restraints for refining 4331 atoms. 8361 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2529 (Rfree = 0.000) for 4331 atoms. Found 26 (38 requested) and removed 35 (19 requested) atoms. Cycle 17: After refmac, R = 0.2391 (Rfree = 0.000) for 4311 atoms. Found 11 (38 requested) and removed 26 (19 requested) atoms. Cycle 18: After refmac, R = 0.2383 (Rfree = 0.000) for 4292 atoms. Found 9 (38 requested) and removed 22 (19 requested) atoms. Cycle 19: After refmac, R = 0.2314 (Rfree = 0.000) for 4275 atoms. Found 14 (38 requested) and removed 21 (19 requested) atoms. Cycle 20: After refmac, R = 0.2206 (Rfree = 0.000) for 4263 atoms. Found 8 (38 requested) and removed 19 (19 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.28 3.19 Search for helices and strands: 0 residues in 0 chains, 4419 seeds are put forward NCS extension: 20 residues added (5 deleted due to clashes), 4439 seeds are put forward Round 1: 352 peptides, 53 chains. Longest chain 19 peptides. Score 0.513 Round 2: 380 peptides, 43 chains. Longest chain 38 peptides. Score 0.646 Round 3: 366 peptides, 45 chains. Longest chain 30 peptides. Score 0.608 Round 4: 379 peptides, 42 chains. Longest chain 31 peptides. Score 0.652 Round 5: 384 peptides, 45 chains. Longest chain 30 peptides. Score 0.638 Taking the results from Round 4 Chains 47, Residues 337, Estimated correctness of the model 54.3 % 4 chains (74 residues) have been docked in sequence ------------------------------------------------------ 11521 reflections ( 99.18 % complete ) and 8807 restraints for refining 4383 atoms. 7210 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2619 (Rfree = 0.000) for 4383 atoms. Found 26 (39 requested) and removed 39 (19 requested) atoms. Cycle 22: After refmac, R = 0.2455 (Rfree = 0.000) for 4362 atoms. Found 18 (39 requested) and removed 25 (19 requested) atoms. Cycle 23: After refmac, R = 0.2448 (Rfree = 0.000) for 4346 atoms. Found 9 (39 requested) and removed 26 (19 requested) atoms. Cycle 24: After refmac, R = 0.2689 (Rfree = 0.000) for 4326 atoms. Found 36 (38 requested) and removed 28 (19 requested) atoms. Cycle 25: After refmac, R = 0.2430 (Rfree = 0.000) for 4325 atoms. Found 14 (38 requested) and removed 24 (19 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.28 3.19 Search for helices and strands: 0 residues in 0 chains, 4484 seeds are put forward NCS extension: 45 residues added (3 deleted due to clashes), 4529 seeds are put forward Round 1: 323 peptides, 49 chains. Longest chain 16 peptides. Score 0.490 Round 2: 350 peptides, 40 chains. Longest chain 30 peptides. Score 0.619 Round 3: 347 peptides, 42 chains. Longest chain 20 peptides. Score 0.598 Round 4: 353 peptides, 48 chains. Longest chain 29 peptides. Score 0.559 Round 5: 356 peptides, 42 chains. Longest chain 30 peptides. Score 0.614 Taking the results from Round 2 Chains 44, Residues 310, Estimated correctness of the model 46.1 % 5 chains (70 residues) have been docked in sequence ------------------------------------------------------ 11521 reflections ( 99.18 % complete ) and 9009 restraints for refining 4383 atoms. 7534 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2575 (Rfree = 0.000) for 4383 atoms. Found 16 (39 requested) and removed 35 (19 requested) atoms. Cycle 27: After refmac, R = 0.2529 (Rfree = 0.000) for 4357 atoms. Found 15 (39 requested) and removed 22 (19 requested) atoms. Cycle 28: After refmac, R = 0.2391 (Rfree = 0.000) for 4344 atoms. Found 5 (39 requested) and removed 21 (19 requested) atoms. Cycle 29: After refmac, R = 0.2353 (Rfree = 0.000) for 4322 atoms. Found 9 (38 requested) and removed 20 (19 requested) atoms. Cycle 30: After refmac, R = 0.2305 (Rfree = 0.000) for 4305 atoms. Found 13 (38 requested) and removed 19 (19 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.27 3.18 Search for helices and strands: 0 residues in 0 chains, 4458 seeds are put forward NCS extension: 20 residues added (6 deleted due to clashes), 4478 seeds are put forward Round 1: 305 peptides, 46 chains. Longest chain 17 peptides. Score 0.479 Round 2: 346 peptides, 43 chains. Longest chain 28 peptides. Score 0.588 Round 3: 331 peptides, 42 chains. Longest chain 29 peptides. Score 0.568 Round 4: 335 peptides, 40 chains. Longest chain 22 peptides. Score 0.593 Round 5: 333 peptides, 47 chains. Longest chain 27 peptides. Score 0.529 Taking the results from Round 4 Chains 43, Residues 295, Estimated correctness of the model 39.2 % 2 chains (33 residues) have been docked in sequence ------------------------------------------------------ 11521 reflections ( 99.18 % complete ) and 9562 restraints for refining 4382 atoms. 8312 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2591 (Rfree = 0.000) for 4382 atoms. Found 25 (39 requested) and removed 32 (19 requested) atoms. Cycle 32: After refmac, R = 0.2465 (Rfree = 0.000) for 4367 atoms. Found 14 (39 requested) and removed 22 (19 requested) atoms. Failed to save intermediate PDB Cycle 33: After refmac, R = 0.2450 (Rfree = 0.000) for 4356 atoms. Found 19 (39 requested) and removed 21 (19 requested) atoms. Cycle 34: After refmac, R = 0.2388 (Rfree = 0.000) for 4349 atoms. Found 6 (39 requested) and removed 19 (19 requested) atoms. Cycle 35: After refmac, R = 0.2378 (Rfree = 0.000) for 4333 atoms. Found 12 (38 requested) and removed 21 (19 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.28 3.19 Search for helices and strands: 0 residues in 0 chains, 4493 seeds are put forward NCS extension: 18 residues added (5 deleted due to clashes), 4511 seeds are put forward Round 1: 281 peptides, 47 chains. Longest chain 20 peptides. Score 0.415 Round 2: 322 peptides, 41 chains. Longest chain 31 peptides. Score 0.560 Round 3: 326 peptides, 42 chains. Longest chain 17 peptides. Score 0.559 Round 4: 317 peptides, 40 chains. Longest chain 23 peptides. Score 0.559 Round 5: 310 peptides, 42 chains. Longest chain 16 peptides. Score 0.527 Taking the results from Round 2 Chains 41, Residues 281, Estimated correctness of the model 29.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 11521 reflections ( 99.18 % complete ) and 9976 restraints for refining 4373 atoms. 8893 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2419 (Rfree = 0.000) for 4373 atoms. Found 22 (39 requested) and removed 24 (19 requested) atoms. Cycle 37: After refmac, R = 0.2323 (Rfree = 0.000) for 4365 atoms. Found 11 (39 requested) and removed 22 (19 requested) atoms. Cycle 38: After refmac, R = 0.2299 (Rfree = 0.000) for 4348 atoms. Found 13 (39 requested) and removed 21 (19 requested) atoms. Cycle 39: After refmac, R = 0.2229 (Rfree = 0.000) for 4339 atoms. Found 11 (38 requested) and removed 19 (19 requested) atoms. Cycle 40: After refmac, R = 0.2239 (Rfree = 0.000) for 4330 atoms. Found 9 (38 requested) and removed 20 (19 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.28 3.19 Search for helices and strands: 0 residues in 0 chains, 4489 seeds are put forward NCS extension: 53 residues added (6 deleted due to clashes), 4542 seeds are put forward Round 1: 280 peptides, 49 chains. Longest chain 15 peptides. Score 0.392 Round 2: 336 peptides, 47 chains. Longest chain 23 peptides. Score 0.535 Round 3: 352 peptides, 49 chains. Longest chain 29 peptides. Score 0.549 Round 4: 338 peptides, 47 chains. Longest chain 36 peptides. Score 0.539 Round 5: 331 peptides, 45 chains. Longest chain 35 peptides. Score 0.542 Taking the results from Round 3 Chains 49, Residues 303, Estimated correctness of the model 26.6 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 11521 reflections ( 99.18 % complete ) and 9843 restraints for refining 4382 atoms. 8649 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2397 (Rfree = 0.000) for 4382 atoms. Found 20 (39 requested) and removed 21 (19 requested) atoms. Cycle 42: After refmac, R = 0.2306 (Rfree = 0.000) for 4374 atoms. Found 14 (39 requested) and removed 20 (19 requested) atoms. Cycle 43: After refmac, R = 0.2242 (Rfree = 0.000) for 4365 atoms. Found 4 (39 requested) and removed 19 (19 requested) atoms. Cycle 44: After refmac, R = 0.2253 (Rfree = 0.000) for 4341 atoms. Found 13 (39 requested) and removed 19 (19 requested) atoms. Cycle 45: After refmac, R = 0.2208 (Rfree = 0.000) for 4331 atoms. Found 7 (38 requested) and removed 19 (19 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.25 3.16 Search for helices and strands: 0 residues in 0 chains, 4488 seeds are put forward NCS extension: 25 residues added (4 deleted due to clashes), 4513 seeds are put forward Round 1: 254 peptides, 45 chains. Longest chain 18 peptides. Score 0.370 Round 2: 305 peptides, 46 chains. Longest chain 27 peptides. Score 0.479 Round 3: 311 peptides, 42 chains. Longest chain 27 peptides. Score 0.529 Round 4: 302 peptides, 43 chains. Longest chain 27 peptides. Score 0.501 Round 5: 313 peptides, 43 chains. Longest chain 27 peptides. Score 0.524 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 42, Residues 269, Estimated correctness of the model 20.5 % 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. 11521 reflections ( 99.18 % complete ) and 10059 restraints for refining 4383 atoms. 9025 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2411 (Rfree = 0.000) for 4383 atoms. Found 0 (39 requested) and removed 17 (19 requested) atoms. Cycle 47: After refmac, R = 0.2351 (Rfree = 0.000) for 4353 atoms. Found 0 (39 requested) and removed 9 (19 requested) atoms. Cycle 48: After refmac, R = 0.2368 (Rfree = 0.000) for 4342 atoms. Found 0 (38 requested) and removed 9 (19 requested) atoms. Cycle 49: After refmac, R = 0.2303 (Rfree = 0.000) for 4331 atoms. Found 0 (38 requested) and removed 10 (19 requested) atoms. Writing output files ... TimeTaking 114.58