Mon 24 Dec 07:53:36 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2ffj-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2ffj-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2ffj-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ffj-3.2-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2ffj-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ffj-3.2-parrot-noncs ############### 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 ============================================================ Mon 24 Dec 07:53:40 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/noncs/ArpWArp/wArpResults/WorkingDir/2ffj-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ffj-3.2-parrot-noncs/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-noncs.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-noncs.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 Failed to save intermediate PDB 11521 reflections ( 99.18 % complete ) and 0 restraints for refining 5329 atoms. Observations/parameters ratio is 0.54 ------------------------------------------------------ Starting model: R = 0.3351 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3208 (Rfree = 0.000) for 5329 atoms. Found 47 (47 requested) and removed 73 (23 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.27 3.18 Search for helices and strands: 0 residues in 0 chains, 5431 seeds are put forward NCS extension: 0 residues added, 5431 seeds are put forward Round 1: 260 peptides, 50 chains. Longest chain 11 peptides. Score 0.332 Round 2: 316 peptides, 48 chains. Longest chain 13 peptides. Score 0.484 Round 3: 335 peptides, 45 chains. Longest chain 20 peptides. Score 0.550 Round 4: 329 peptides, 45 chains. Longest chain 20 peptides. Score 0.538 Round 5: 348 peptides, 53 chains. Longest chain 19 peptides. Score 0.505 Taking the results from Round 3 Chains 45, Residues 290, Estimated correctness of the model 26.9 % 1 chains (19 residues) have been docked in sequence ------------------------------------------------------ 11521 reflections ( 99.18 % complete ) and 9874 restraints for refining 4381 atoms. 8686 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2931 (Rfree = 0.000) for 4381 atoms. Found 35 (39 requested) and removed 64 (19 requested) atoms. Cycle 2: After refmac, R = 0.2895 (Rfree = 0.000) for 4304 atoms. Found 22 (39 requested) and removed 43 (19 requested) atoms. Cycle 3: After refmac, R = 0.2755 (Rfree = 0.000) for 4265 atoms. Found 15 (38 requested) and removed 36 (19 requested) atoms. Cycle 4: After refmac, R = 0.2719 (Rfree = 0.000) for 4232 atoms. Found 11 (38 requested) and removed 25 (19 requested) atoms. Cycle 5: After refmac, R = 0.2590 (Rfree = 0.000) for 4209 atoms. Found 4 (37 requested) and removed 21 (18 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.25 3.16 Search for helices and strands: 0 residues in 0 chains, 4383 seeds are put forward NCS extension: 18 residues added (3 deleted due to clashes), 4401 seeds are put forward Round 1: 324 peptides, 49 chains. Longest chain 16 peptides. Score 0.492 Round 2: 352 peptides, 43 chains. Longest chain 22 peptides. Score 0.599 Round 3: 353 peptides, 44 chains. Longest chain 18 peptides. Score 0.592 Round 4: 359 peptides, 44 chains. Longest chain 22 peptides. Score 0.603 Round 5: 360 peptides, 44 chains. Longest chain 20 peptides. Score 0.605 Taking the results from Round 5 Chains 45, Residues 316, Estimated correctness of the model 42.4 % 3 chains (43 residues) have been docked in sequence ------------------------------------------------------ 11521 reflections ( 99.18 % complete ) and 9302 restraints for refining 4373 atoms. 7933 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2905 (Rfree = 0.000) for 4373 atoms. Found 39 (39 requested) and removed 56 (19 requested) atoms. Cycle 7: After refmac, R = 0.2708 (Rfree = 0.000) for 4339 atoms. Found 18 (39 requested) and removed 30 (19 requested) atoms. Cycle 8: After refmac, R = 0.2642 (Rfree = 0.000) for 4314 atoms. Found 20 (38 requested) and removed 27 (19 requested) atoms. Cycle 9: After refmac, R = 0.2592 (Rfree = 0.000) for 4294 atoms. Found 15 (38 requested) and removed 25 (19 requested) atoms. Cycle 10: After refmac, R = 0.2561 (Rfree = 0.000) for 4274 atoms. Found 11 (38 requested) and removed 24 (19 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.26 3.17 Search for helices and strands: 0 residues in 0 chains, 4428 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 4447 seeds are put forward Round 1: 306 peptides, 44 chains. Longest chain 19 peptides. Score 0.500 Round 2: 336 peptides, 44 chains. Longest chain 27 peptides. Score 0.561 Round 3: 341 peptides, 40 chains. Longest chain 21 peptides. Score 0.604 Round 4: 335 peptides, 42 chains. Longest chain 22 peptides. Score 0.576 Round 5: 360 peptides, 46 chains. Longest chain 24 peptides. Score 0.589 Taking the results from Round 3 Chains 40, Residues 301, Estimated correctness of the model 42.1 % 3 chains (43 residues) have been docked in sequence ------------------------------------------------------ 11521 reflections ( 99.18 % complete ) and 9251 restraints for refining 4347 atoms. 7914 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2768 (Rfree = 0.000) for 4347 atoms. Found 21 (39 requested) and removed 40 (19 requested) atoms. Cycle 12: After refmac, R = 0.2642 (Rfree = 0.000) for 4308 atoms. Found 22 (38 requested) and removed 30 (19 requested) atoms. Cycle 13: After refmac, R = 0.2574 (Rfree = 0.000) for 4291 atoms. Found 12 (38 requested) and removed 30 (19 requested) atoms. Cycle 14: After refmac, R = 0.2544 (Rfree = 0.000) for 4261 atoms. Found 12 (38 requested) and removed 24 (19 requested) atoms. Cycle 15: After refmac, R = 0.2568 (Rfree = 0.000) for 4242 atoms. Found 13 (38 requested) and removed 24 (19 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.26 3.17 Search for helices and strands: 0 residues in 0 chains, 4379 seeds are put forward NCS extension: 17 residues added (4 deleted due to clashes), 4396 seeds are put forward Round 1: 288 peptides, 44 chains. Longest chain 17 peptides. Score 0.461 Round 2: 322 peptides, 39 chains. Longest chain 24 peptides. Score 0.577 Round 3: 350 peptides, 45 chains. Longest chain 19 peptides. Score 0.579 Round 4: 334 peptides, 40 chains. Longest chain 25 peptides. Score 0.591 Round 5: 340 peptides, 47 chains. Longest chain 17 peptides. Score 0.542 Taking the results from Round 4 Chains 45, Residues 294, Estimated correctness of the model 38.6 % 4 chains (50 residues) have been docked in sequence ------------------------------------------------------ 11521 reflections ( 99.18 % complete ) and 9364 restraints for refining 4383 atoms. 8053 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2827 (Rfree = 0.000) for 4383 atoms. Found 39 (39 requested) and removed 38 (19 requested) atoms. Cycle 17: After refmac, R = 0.2746 (Rfree = 0.000) for 4366 atoms. Found 24 (39 requested) and removed 36 (19 requested) atoms. Cycle 18: After refmac, R = 0.2728 (Rfree = 0.000) for 4344 atoms. Found 16 (39 requested) and removed 30 (19 requested) atoms. Cycle 19: After refmac, R = 0.2685 (Rfree = 0.000) for 4319 atoms. Found 13 (38 requested) and removed 26 (19 requested) atoms. Cycle 20: After refmac, R = 0.2598 (Rfree = 0.000) for 4301 atoms. Found 12 (38 requested) and removed 23 (19 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.24 3.15 Search for helices and strands: 0 residues in 0 chains, 4454 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 4473 seeds are put forward Round 1: 302 peptides, 46 chains. Longest chain 14 peptides. Score 0.473 Round 2: 335 peptides, 45 chains. Longest chain 20 peptides. Score 0.550 Round 3: 340 peptides, 43 chains. Longest chain 22 peptides. Score 0.577 Round 4: 332 peptides, 44 chains. Longest chain 20 peptides. Score 0.553 Round 5: 330 peptides, 44 chains. Longest chain 18 peptides. Score 0.549 Taking the results from Round 3 Chains 46, Residues 297, Estimated correctness of the model 34.7 % 3 chains (35 residues) have been docked in sequence ------------------------------------------------------ 11521 reflections ( 99.18 % complete ) and 9429 restraints for refining 4383 atoms. 8158 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2719 (Rfree = 0.000) for 4383 atoms. Found 39 (39 requested) and removed 39 (19 requested) atoms. Cycle 22: After refmac, R = 0.2575 (Rfree = 0.000) for 4368 atoms. Found 16 (39 requested) and removed 31 (19 requested) atoms. Cycle 23: After refmac, R = 0.2508 (Rfree = 0.000) for 4346 atoms. Found 10 (39 requested) and removed 21 (19 requested) atoms. Cycle 24: After refmac, R = 0.2471 (Rfree = 0.000) for 4327 atoms. Found 17 (38 requested) and removed 20 (19 requested) atoms. Cycle 25: After refmac, R = 0.2429 (Rfree = 0.000) for 4315 atoms. Found 17 (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, 4474 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 4488 seeds are put forward Round 1: 282 peptides, 47 chains. Longest chain 12 peptides. Score 0.417 Round 2: 334 peptides, 46 chains. Longest chain 20 peptides. Score 0.539 Round 3: 327 peptides, 44 chains. Longest chain 25 peptides. Score 0.543 Round 4: 318 peptides, 46 chains. Longest chain 17 peptides. Score 0.507 Round 5: 317 peptides, 41 chains. Longest chain 27 peptides. Score 0.550 Taking the results from Round 5 Chains 41, Residues 276, Estimated correctness of the model 26.9 % 1 chains (23 residues) have been docked in sequence ------------------------------------------------------ 11521 reflections ( 99.18 % complete ) and 9593 restraints for refining 4382 atoms. 8433 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2620 (Rfree = 0.000) for 4382 atoms. Found 36 (39 requested) and removed 26 (19 requested) atoms. Cycle 27: After refmac, R = 0.2502 (Rfree = 0.000) for 4375 atoms. Found 15 (39 requested) and removed 23 (19 requested) atoms. Cycle 28: After refmac, R = 0.2459 (Rfree = 0.000) for 4355 atoms. Found 19 (39 requested) and removed 23 (19 requested) atoms. Cycle 29: After refmac, R = 0.2430 (Rfree = 0.000) for 4347 atoms. Found 21 (39 requested) and removed 21 (19 requested) atoms. Cycle 30: After refmac, R = 0.2449 (Rfree = 0.000) for 4342 atoms. Found 21 (39 requested) and removed 20 (19 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.26 3.17 Search for helices and strands: 0 residues in 0 chains, 4512 seeds are put forward NCS extension: 28 residues added (4 deleted due to clashes), 4540 seeds are put forward Round 1: 266 peptides, 43 chains. Longest chain 15 peptides. Score 0.421 Round 2: 312 peptides, 43 chains. Longest chain 16 peptides. Score 0.522 Round 3: 307 peptides, 46 chains. Longest chain 17 peptides. Score 0.483 Round 4: 307 peptides, 45 chains. Longest chain 22 peptides. Score 0.493 Round 5: 313 peptides, 47 chains. Longest chain 18 peptides. Score 0.487 Taking the results from Round 2 Chains 43, Residues 269, Estimated correctness of the model 18.3 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 11521 reflections ( 99.18 % complete ) and 9852 restraints for refining 4382 atoms. 8804 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2569 (Rfree = 0.000) for 4382 atoms. Found 29 (39 requested) and removed 26 (19 requested) atoms. Cycle 32: After refmac, R = 0.2607 (Rfree = 0.000) for 4372 atoms. Found 25 (39 requested) and removed 23 (19 requested) atoms. Cycle 33: After refmac, R = 0.2661 (Rfree = 0.000) for 4368 atoms. Found 34 (39 requested) and removed 29 (19 requested) atoms. Cycle 34: After refmac, R = 0.2639 (Rfree = 0.000) for 4364 atoms. Found 20 (39 requested) and removed 69 (19 requested) atoms. Cycle 35: After refmac, R = 0.2586 (Rfree = 0.000) for 4308 atoms. Found 16 (38 requested) and removed 25 (19 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.21 3.13 Search for helices and strands: 0 residues in 0 chains, 4487 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 4501 seeds are put forward Round 1: 273 peptides, 52 chains. Longest chain 11 peptides. Score 0.343 Round 2: 296 peptides, 43 chains. Longest chain 15 peptides. Score 0.488 Round 3: 302 peptides, 48 chains. Longest chain 18 peptides. Score 0.453 Round 4: 306 peptides, 48 chains. Longest chain 16 peptides. Score 0.462 Round 5: 293 peptides, 38 chains. Longest chain 20 peptides. Score 0.529 Taking the results from Round 5 Chains 38, Residues 255, Estimated correctness of the model 20.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 11521 reflections ( 99.18 % complete ) and 10145 restraints for refining 4383 atoms. 9163 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2618 (Rfree = 0.000) for 4383 atoms. Found 37 (39 requested) and removed 26 (19 requested) atoms. Cycle 37: After refmac, R = 0.2440 (Rfree = 0.000) for 4379 atoms. Found 11 (39 requested) and removed 27 (19 requested) atoms. Cycle 38: After refmac, R = 0.2406 (Rfree = 0.000) for 4357 atoms. Found 13 (39 requested) and removed 20 (19 requested) atoms. Cycle 39: After refmac, R = 0.2386 (Rfree = 0.000) for 4348 atoms. Found 8 (39 requested) and removed 25 (19 requested) atoms. Cycle 40: After refmac, R = 0.2443 (Rfree = 0.000) for 4325 atoms. Found 27 (38 requested) and removed 23 (19 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.22 3.14 Search for helices and strands: 0 residues in 0 chains, 4504 seeds are put forward NCS extension: 27 residues added (3 deleted due to clashes), 4531 seeds are put forward Round 1: 246 peptides, 46 chains. Longest chain 13 peptides. Score 0.339 Round 2: 284 peptides, 45 chains. Longest chain 15 peptides. Score 0.442 Round 3: 287 peptides, 43 chains. Longest chain 14 peptides. Score 0.469 Round 4: 292 peptides, 42 chains. Longest chain 18 peptides. Score 0.489 Round 5: 288 peptides, 42 chains. Longest chain 17 peptides. Score 0.481 Taking the results from Round 4 Chains 44, Residues 250, Estimated correctness of the model 7.7 % 4 chains (46 residues) have been docked in sequence ------------------------------------------------------ 11521 reflections ( 99.18 % complete ) and 9543 restraints for refining 4383 atoms. 8421 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2509 (Rfree = 0.000) for 4383 atoms. Found 21 (39 requested) and removed 24 (19 requested) atoms. Cycle 42: After refmac, R = 0.2592 (Rfree = 0.000) for 4368 atoms. Found 20 (39 requested) and removed 29 (19 requested) atoms. Cycle 43: After refmac, R = 0.2513 (Rfree = 0.000) for 4356 atoms. Found 16 (39 requested) and removed 26 (19 requested) atoms. Cycle 44: After refmac, R = 0.2385 (Rfree = 0.000) for 4336 atoms. Found 10 (39 requested) and removed 19 (19 requested) atoms. Cycle 45: After refmac, R = 0.2412 (Rfree = 0.000) for 4319 atoms. Found 19 (38 requested) and removed 20 (19 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.22 3.14 Search for helices and strands: 0 residues in 0 chains, 4472 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 4493 seeds are put forward Round 1: 243 peptides, 43 chains. Longest chain 15 peptides. Score 0.365 Round 2: 276 peptides, 41 chains. Longest chain 24 peptides. Score 0.464 Round 3: 263 peptides, 40 chains. Longest chain 17 peptides. Score 0.444 Round 4: 273 peptides, 41 chains. Longest chain 18 peptides. Score 0.457 Round 5: 274 peptides, 40 chains. Longest chain 18 peptides. Score 0.469 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 41, Residues 234, Estimated correctness of the model 1.0 % 1 chains (13 residues) have been docked in sequence Sequence coverage is 5 % 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 9908 restraints for refining 4383 atoms. 8963 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2541 (Rfree = 0.000) for 4383 atoms. Found 0 (39 requested) and removed 19 (19 requested) atoms. Cycle 47: After refmac, R = 0.2556 (Rfree = 0.000) for 4354 atoms. Found 0 (39 requested) and removed 19 (19 requested) atoms. Cycle 48: After refmac, R = 0.2525 (Rfree = 0.000) for 4331 atoms. Found 0 (38 requested) and removed 14 (19 requested) atoms. Cycle 49: After refmac, R = 0.2494 (Rfree = 0.000) for 4314 atoms. TimeTaking 45.53