Sun 23 Dec 23:41:27 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2ffj-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2ffj-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2ffj-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ffj-3.2-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2ffj-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ffj-3.2-parrot-mrncs ############### 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 23:41:32 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/mrncs/ArpWArp/wArpResults/WorkingDir/2ffj-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ffj-3.2-parrot-mrncs/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-mrncs.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-mrncs.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 5284 atoms. Observations/parameters ratio is 0.55 ------------------------------------------------------ Starting model: R = 0.3223 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3051 (Rfree = 0.000) for 5284 atoms. Found 47 (47 requested) and removed 49 (23 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.26 3.17 Search for helices and strands: 0 residues in 0 chains, 5400 seeds are put forward NCS extension: 0 residues added, 5400 seeds are put forward Round 1: 301 peptides, 54 chains. Longest chain 14 peptides. Score 0.391 Round 2: 367 peptides, 51 chains. Longest chain 19 peptides. Score 0.560 Round 3: 369 peptides, 52 chains. Longest chain 17 peptides. Score 0.556 Round 4: 378 peptides, 42 chains. Longest chain 47 peptides. Score 0.651 Round 5: 372 peptides, 45 chains. Longest chain 23 peptides. Score 0.618 Taking the results from Round 4 Chains 46, Residues 336, Estimated correctness of the model 54.1 % 4 chains (63 residues) have been docked in sequence ------------------------------------------------------ 11521 reflections ( 99.18 % complete ) and 9138 restraints for refining 4379 atoms. 7607 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3179 (Rfree = 0.000) for 4379 atoms. Found 37 (39 requested) and removed 71 (19 requested) atoms. Cycle 2: After refmac, R = 0.2956 (Rfree = 0.000) for 4261 atoms. Found 22 (38 requested) and removed 44 (19 requested) atoms. Cycle 3: After refmac, R = 0.2773 (Rfree = 0.000) for 4201 atoms. Found 20 (38 requested) and removed 28 (19 requested) atoms. Cycle 4: After refmac, R = 0.2670 (Rfree = 0.000) for 4171 atoms. Found 17 (37 requested) and removed 34 (18 requested) atoms. Cycle 5: After refmac, R = 0.2427 (Rfree = 0.000) for 4141 atoms. Found 12 (37 requested) and removed 25 (18 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.25 3.16 Search for helices and strands: 0 residues in 0 chains, 4321 seeds are put forward NCS extension: 27 residues added (1 deleted due to clashes), 4348 seeds are put forward Round 1: 345 peptides, 45 chains. Longest chain 17 peptides. Score 0.569 Round 2: 387 peptides, 48 chains. Longest chain 34 peptides. Score 0.620 Round 3: 384 peptides, 47 chains. Longest chain 27 peptides. Score 0.623 Round 4: 377 peptides, 40 chains. Longest chain 28 peptides. Score 0.664 Round 5: 383 peptides, 44 chains. Longest chain 24 peptides. Score 0.644 Taking the results from Round 4 Chains 40, Residues 337, Estimated correctness of the model 57.2 % 1 chains (18 residues) have been docked in sequence ------------------------------------------------------ 11521 reflections ( 99.18 % complete ) and 9175 restraints for refining 4230 atoms. 7804 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2688 (Rfree = 0.000) for 4230 atoms. Found 20 (37 requested) and removed 35 (18 requested) atoms. Cycle 7: After refmac, R = 0.2480 (Rfree = 0.000) for 4202 atoms. Found 18 (37 requested) and removed 21 (18 requested) atoms. Cycle 8: After refmac, R = 0.2419 (Rfree = 0.000) for 4190 atoms. Found 12 (37 requested) and removed 25 (18 requested) atoms. Cycle 9: After refmac, R = 0.2354 (Rfree = 0.000) for 4171 atoms. Found 27 (37 requested) and removed 20 (18 requested) atoms. Cycle 10: After refmac, R = 0.2278 (Rfree = 0.000) for 4167 atoms. Found 7 (37 requested) and removed 18 (18 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.27 3.18 Search for helices and strands: 0 residues in 0 chains, 4340 seeds are put forward NCS extension: 17 residues added (11 deleted due to clashes), 4357 seeds are put forward Round 1: 348 peptides, 51 chains. Longest chain 17 peptides. Score 0.523 Round 2: 383 peptides, 46 chains. Longest chain 21 peptides. Score 0.629 Round 3: 404 peptides, 50 chains. Longest chain 19 peptides. Score 0.634 Round 4: 389 peptides, 44 chains. Longest chain 23 peptides. Score 0.653 Round 5: 374 peptides, 45 chains. Longest chain 18 peptides. Score 0.621 Taking the results from Round 4 Chains 47, Residues 345, Estimated correctness of the model 54.6 % 3 chains (43 residues) have been docked in sequence ------------------------------------------------------ 11521 reflections ( 99.18 % complete ) and 9197 restraints for refining 4367 atoms. 7705 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2651 (Rfree = 0.000) for 4367 atoms. Found 24 (39 requested) and removed 38 (19 requested) atoms. Cycle 12: After refmac, R = 0.2553 (Rfree = 0.000) for 4329 atoms. Found 16 (39 requested) and removed 29 (19 requested) atoms. Cycle 13: After refmac, R = 0.2477 (Rfree = 0.000) for 4307 atoms. Found 10 (38 requested) and removed 22 (19 requested) atoms. Cycle 14: After refmac, R = 0.2505 (Rfree = 0.000) for 4287 atoms. Found 22 (38 requested) and removed 23 (19 requested) atoms. Cycle 15: After refmac, R = 0.2373 (Rfree = 0.000) for 4277 atoms. Found 4 (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, 4439 seeds are put forward NCS extension: 13 residues added (5 deleted due to clashes), 4452 seeds are put forward Round 1: 333 peptides, 48 chains. Longest chain 13 peptides. Score 0.520 Round 2: 376 peptides, 44 chains. Longest chain 28 peptides. Score 0.632 Round 3: 372 peptides, 44 chains. Longest chain 24 peptides. Score 0.626 Round 4: 379 peptides, 44 chains. Longest chain 23 peptides. Score 0.637 Round 5: 362 peptides, 43 chains. Longest chain 23 peptides. Score 0.616 Taking the results from Round 4 Chains 46, Residues 335, Estimated correctness of the model 50.7 % 1 chains (16 residues) have been docked in sequence ------------------------------------------------------ 11521 reflections ( 99.18 % complete ) and 9581 restraints for refining 4383 atoms. 8227 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2689 (Rfree = 0.000) for 4383 atoms. Found 22 (39 requested) and removed 30 (19 requested) atoms. Cycle 17: After refmac, R = 0.2531 (Rfree = 0.000) for 4367 atoms. Found 14 (39 requested) and removed 23 (19 requested) atoms. Cycle 18: After refmac, R = 0.2518 (Rfree = 0.000) for 4352 atoms. Found 15 (39 requested) and removed 24 (19 requested) atoms. Cycle 19: After refmac, R = 0.2468 (Rfree = 0.000) for 4337 atoms. Found 9 (38 requested) and removed 24 (19 requested) atoms. Cycle 20: After refmac, R = 0.2462 (Rfree = 0.000) for 4316 atoms. Found 13 (38 requested) and removed 20 (19 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.29 3.20 Search for helices and strands: 0 residues in 0 chains, 4465 seeds are put forward NCS extension: 32 residues added (1 deleted due to clashes), 4497 seeds are put forward Round 1: 349 peptides, 45 chains. Longest chain 22 peptides. Score 0.577 Round 2: 361 peptides, 41 chains. Longest chain 24 peptides. Score 0.630 Round 3: 370 peptides, 43 chains. Longest chain 25 peptides. Score 0.630 Round 4: 375 peptides, 44 chains. Longest chain 23 peptides. Score 0.631 Round 5: 388 peptides, 48 chains. Longest chain 23 peptides. Score 0.622 Taking the results from Round 4 Chains 48, Residues 331, Estimated correctness of the model 49.1 % 2 chains (28 residues) have been docked in sequence ------------------------------------------------------ 11521 reflections ( 99.18 % complete ) and 9440 restraints for refining 4382 atoms. 8040 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2550 (Rfree = 0.000) for 4382 atoms. Found 28 (39 requested) and removed 28 (19 requested) atoms. Cycle 22: After refmac, R = 0.2398 (Rfree = 0.000) for 4371 atoms. Found 12 (39 requested) and removed 26 (19 requested) atoms. Cycle 23: After refmac, R = 0.2317 (Rfree = 0.000) for 4348 atoms. Found 10 (39 requested) and removed 20 (19 requested) atoms. Cycle 24: After refmac, R = 0.2251 (Rfree = 0.000) for 4329 atoms. Found 8 (38 requested) and removed 21 (19 requested) atoms. Cycle 25: After refmac, R = 0.2240 (Rfree = 0.000) for 4309 atoms. Found 10 (38 requested) and removed 20 (19 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.27 3.18 Search for helices and strands: 0 residues in 0 chains, 4446 seeds are put forward NCS extension: 15 residues added (3 deleted due to clashes), 4461 seeds are put forward Round 1: 338 peptides, 50 chains. Longest chain 18 peptides. Score 0.512 Round 2: 368 peptides, 41 chains. Longest chain 27 peptides. Score 0.642 Round 3: 377 peptides, 43 chains. Longest chain 21 peptides. Score 0.642 Round 4: 373 peptides, 42 chains. Longest chain 25 peptides. Score 0.643 Round 5: 377 peptides, 43 chains. Longest chain 21 peptides. Score 0.642 Taking the results from Round 4 Chains 45, Residues 331, Estimated correctness of the model 52.1 % 4 chains (58 residues) have been docked in sequence ------------------------------------------------------ 11521 reflections ( 99.18 % complete ) and 9042 restraints for refining 4383 atoms. 7541 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2623 (Rfree = 0.000) for 4383 atoms. Found 32 (39 requested) and removed 33 (19 requested) atoms. Cycle 27: After refmac, R = 0.2464 (Rfree = 0.000) for 4369 atoms. Found 9 (39 requested) and removed 24 (19 requested) atoms. Cycle 28: After refmac, R = 0.2409 (Rfree = 0.000) for 4344 atoms. Found 4 (39 requested) and removed 28 (19 requested) atoms. Cycle 29: After refmac, R = 0.2342 (Rfree = 0.000) for 4315 atoms. Found 9 (38 requested) and removed 22 (19 requested) atoms. Cycle 30: After refmac, R = 0.2298 (Rfree = 0.000) for 4295 atoms. Found 5 (38 requested) and removed 21 (19 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.25 3.16 Search for helices and strands: 0 residues in 0 chains, 4415 seeds are put forward NCS extension: 40 residues added (6 deleted due to clashes), 4455 seeds are put forward Round 1: 310 peptides, 44 chains. Longest chain 19 peptides. Score 0.509 Round 2: 348 peptides, 44 chains. Longest chain 24 peptides. Score 0.583 Round 3: 355 peptides, 44 chains. Longest chain 22 peptides. Score 0.596 Round 4: 357 peptides, 43 chains. Longest chain 26 peptides. Score 0.608 Round 5: 340 peptides, 47 chains. Longest chain 16 peptides. Score 0.542 Taking the results from Round 4 Chains 44, Residues 314, Estimated correctness of the model 43.2 % 5 chains (61 residues) have been docked in sequence ------------------------------------------------------ 11521 reflections ( 99.18 % complete ) and 9155 restraints for refining 4383 atoms. 7714 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2624 (Rfree = 0.000) for 4383 atoms. Found 21 (39 requested) and removed 31 (19 requested) atoms. Cycle 32: After refmac, R = 0.2457 (Rfree = 0.000) for 4357 atoms. Found 23 (39 requested) and removed 27 (19 requested) atoms. Cycle 33: After refmac, R = 0.2351 (Rfree = 0.000) for 4343 atoms. Found 11 (39 requested) and removed 23 (19 requested) atoms. Cycle 34: After refmac, R = 0.2294 (Rfree = 0.000) for 4328 atoms. Found 10 (38 requested) and removed 20 (19 requested) atoms. Cycle 35: After refmac, R = 0.2230 (Rfree = 0.000) for 4314 atoms. Found 7 (38 requested) and removed 20 (19 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.27 3.18 Search for helices and strands: 0 residues in 0 chains, 4470 seeds are put forward NCS extension: 15 residues added (4 deleted due to clashes), 4485 seeds are put forward Round 1: 319 peptides, 47 chains. Longest chain 21 peptides. Score 0.500 Round 2: 319 peptides, 42 chains. Longest chain 28 peptides. Score 0.545 Round 3: 332 peptides, 42 chains. Longest chain 19 peptides. Score 0.570 Round 4: 333 peptides, 45 chains. Longest chain 21 peptides. Score 0.546 Round 5: 360 peptides, 43 chains. Longest chain 21 peptides. Score 0.613 Taking the results from Round 5 Chains 43, Residues 317, Estimated correctness of the model 44.5 % 1 chains (20 residues) have been docked in sequence ------------------------------------------------------ 11521 reflections ( 99.18 % complete ) and 9447 restraints for refining 4381 atoms. 8144 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2498 (Rfree = 0.000) for 4381 atoms. Found 28 (39 requested) and removed 26 (19 requested) atoms. Cycle 37: After refmac, R = 0.2405 (Rfree = 0.000) for 4374 atoms. Found 21 (39 requested) and removed 24 (19 requested) atoms. Cycle 38: After refmac, R = 0.2351 (Rfree = 0.000) for 4365 atoms. Found 16 (39 requested) and removed 19 (19 requested) atoms. Cycle 39: After refmac, R = 0.2313 (Rfree = 0.000) for 4355 atoms. Found 8 (39 requested) and removed 19 (19 requested) atoms. Cycle 40: After refmac, R = 0.2316 (Rfree = 0.000) for 4341 atoms. Found 17 (38 requested) and removed 19 (19 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.29 3.20 Search for helices and strands: 0 residues in 0 chains, 4508 seeds are put forward NCS extension: 27 residues added (5 deleted due to clashes), 4535 seeds are put forward Round 1: 269 peptides, 46 chains. Longest chain 21 peptides. Score 0.397 Round 2: 316 peptides, 46 chains. Longest chain 23 peptides. Score 0.503 Round 3: 327 peptides, 46 chains. Longest chain 24 peptides. Score 0.525 Round 4: 324 peptides, 44 chains. Longest chain 20 peptides. Score 0.537 Round 5: 314 peptides, 47 chains. Longest chain 21 peptides. Score 0.489 Taking the results from Round 4 Chains 44, Residues 280, Estimated correctness of the model 23.0 % 2 chains (26 residues) have been docked in sequence ------------------------------------------------------ 11521 reflections ( 99.18 % complete ) and 9614 restraints for refining 4383 atoms. 8440 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2523 (Rfree = 0.000) for 4383 atoms. Found 28 (39 requested) and removed 26 (19 requested) atoms. Cycle 42: After refmac, R = 0.2365 (Rfree = 0.000) for 4372 atoms. Found 19 (39 requested) and removed 22 (19 requested) atoms. Cycle 43: After refmac, R = 0.2310 (Rfree = 0.000) for 4361 atoms. Found 21 (39 requested) and removed 21 (19 requested) atoms. Cycle 44: After refmac, R = 0.2199 (Rfree = 0.000) for 4358 atoms. Found 8 (39 requested) and removed 20 (19 requested) atoms. Cycle 45: After refmac, R = 0.2143 (Rfree = 0.000) for 4339 atoms. Found 8 (39 requested) and removed 19 (19 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.24 3.15 Search for helices and strands: 0 residues in 0 chains, 4473 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 4496 seeds are put forward Round 1: 252 peptides, 43 chains. Longest chain 22 peptides. Score 0.387 Round 2: 281 peptides, 45 chains. Longest chain 23 peptides. Score 0.435 Round 3: 292 peptides, 42 chains. Longest chain 28 peptides. Score 0.489 Round 4: 290 peptides, 41 chains. Longest chain 21 peptides. Score 0.495 Round 5: 298 peptides, 44 chains. Longest chain 21 peptides. Score 0.483 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 44, Residues 249, Estimated correctness of the model 9.7 % 3 chains (41 residues) have been docked in sequence Sequence coverage is 16 % Consider running further cycles of model building using 2ffj-3_warpNtrace.pdb as input Building loops using Loopy2018 44 chains (249 residues) following loop building 3 chains (41 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 11521 reflections ( 99.18 % complete ) and 9638 restraints for refining 4383 atoms. 8546 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2359 (Rfree = 0.000) for 4383 atoms. Found 0 (39 requested) and removed 19 (19 requested) atoms. Cycle 47: After refmac, R = 0.2293 (Rfree = 0.000) for 4351 atoms. Found 0 (39 requested) and removed 9 (19 requested) atoms. Cycle 48: After refmac, R = 0.2253 (Rfree = 0.000) for 4337 atoms. Found 0 (38 requested) and removed 13 (19 requested) atoms. Cycle 49: After refmac, R = 0.2186 (Rfree = 0.000) for 4318 atoms. TimeTaking 55.13