Mon 24 Dec 08:00:28 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 1vll-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vll-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vll-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vll-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/1vll-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vll-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 08:00:33 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/1vll-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vll-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 437 and 0 Target number of residues in the AU: 437 Target solvent content: 0.6678 Checking the provided sequence file Detected sequence length: 334 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 668 Adjusted target solvent content: 0.49 Input MTZ file: 1vll-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: 57.294 93.405 133.015 90.000 90.000 90.000 Input sequence file: 1vll-3.2-parrot-noncs.fasta_lf Building free atoms model in initial map for 5344 target number of atoms Had to go as low as 0.70 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: 76.441 3.200 Wilson plot Bfac: 90.38 Failed to save intermediate PDB 12307 reflections ( 99.98 % complete ) and 0 restraints for refining 5887 atoms. Observations/parameters ratio is 0.52 ------------------------------------------------------ Starting model: R = 0.3606 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2941 (Rfree = 0.000) for 5887 atoms. Found 30 (52 requested) and removed 47 (26 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.52 3.57 Search for helices and strands: 0 residues in 0 chains, 5997 seeds are put forward NCS extension: 0 residues added, 5997 seeds are put forward Round 1: 328 peptides, 56 chains. Longest chain 17 peptides. Score 0.422 Round 2: 375 peptides, 50 chains. Longest chain 23 peptides. Score 0.567 Round 3: 384 peptides, 50 chains. Longest chain 21 peptides. Score 0.583 Round 4: 389 peptides, 45 chains. Longest chain 33 peptides. Score 0.629 Round 5: 391 peptides, 42 chains. Longest chain 44 peptides. Score 0.653 Taking the results from Round 5 Chains 46, Residues 349, Estimated correctness of the model 54.6 % 6 chains (84 residues) have been docked in sequence ------------------------------------------------------ 12307 reflections ( 99.98 % complete ) and 10303 restraints for refining 4877 atoms. 8657 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2801 (Rfree = 0.000) for 4877 atoms. Found 18 (43 requested) and removed 49 (21 requested) atoms. Cycle 2: After refmac, R = 0.2617 (Rfree = 0.000) for 4775 atoms. Found 10 (43 requested) and removed 30 (21 requested) atoms. Cycle 3: After refmac, R = 0.2594 (Rfree = 0.000) for 4732 atoms. Found 9 (42 requested) and removed 27 (21 requested) atoms. Cycle 4: After refmac, R = 0.2534 (Rfree = 0.000) for 4703 atoms. Found 5 (42 requested) and removed 26 (21 requested) atoms. Cycle 5: After refmac, R = 0.2531 (Rfree = 0.000) for 4671 atoms. Found 4 (42 requested) and removed 22 (21 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.50 3.55 Search for helices and strands: 0 residues in 0 chains, 4838 seeds are put forward NCS extension: 54 residues added (1 deleted due to clashes), 4892 seeds are put forward Round 1: 346 peptides, 55 chains. Longest chain 26 peptides. Score 0.470 Round 2: 371 peptides, 49 chains. Longest chain 26 peptides. Score 0.568 Round 3: 363 peptides, 49 chains. Longest chain 21 peptides. Score 0.554 Round 4: 366 peptides, 47 chains. Longest chain 26 peptides. Score 0.575 Round 5: 370 peptides, 50 chains. Longest chain 24 peptides. Score 0.558 Taking the results from Round 4 Chains 49, Residues 319, Estimated correctness of the model 34.1 % 5 chains (37 residues) have been docked in sequence ------------------------------------------------------ 12307 reflections ( 99.98 % complete ) and 10998 restraints for refining 4878 atoms. 9645 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2650 (Rfree = 0.000) for 4878 atoms. Found 15 (43 requested) and removed 35 (21 requested) atoms. Cycle 7: After refmac, R = 0.2479 (Rfree = 0.000) for 4833 atoms. Found 6 (43 requested) and removed 28 (21 requested) atoms. Cycle 8: After refmac, R = 0.2422 (Rfree = 0.000) for 4799 atoms. Found 5 (43 requested) and removed 21 (21 requested) atoms. Cycle 9: After refmac, R = 0.2347 (Rfree = 0.000) for 4775 atoms. Found 3 (42 requested) and removed 22 (21 requested) atoms. Cycle 10: After refmac, R = 0.2337 (Rfree = 0.000) for 4751 atoms. Found 0 (42 requested) and removed 21 (21 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.49 3.54 Search for helices and strands: 0 residues in 0 chains, 4904 seeds are put forward NCS extension: 25 residues added (3 deleted due to clashes), 4929 seeds are put forward Round 1: 318 peptides, 54 chains. Longest chain 18 peptides. Score 0.419 Round 2: 341 peptides, 47 chains. Longest chain 24 peptides. Score 0.529 Round 3: 371 peptides, 48 chains. Longest chain 29 peptides. Score 0.576 Round 4: 353 peptides, 47 chains. Longest chain 33 peptides. Score 0.552 Round 5: 352 peptides, 43 chains. Longest chain 24 peptides. Score 0.583 Taking the results from Round 5 Chains 44, Residues 309, Estimated correctness of the model 36.4 % 4 chains (55 residues) have been docked in sequence ------------------------------------------------------ 12307 reflections ( 99.98 % complete ) and 10849 restraints for refining 4878 atoms. 9465 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2581 (Rfree = 0.000) for 4878 atoms. Found 11 (43 requested) and removed 47 (21 requested) atoms. Cycle 12: After refmac, R = 0.2498 (Rfree = 0.000) for 4811 atoms. Found 5 (43 requested) and removed 28 (21 requested) atoms. Cycle 13: After refmac, R = 0.2470 (Rfree = 0.000) for 4783 atoms. Found 8 (42 requested) and removed 27 (21 requested) atoms. Cycle 14: After refmac, R = 0.2424 (Rfree = 0.000) for 4758 atoms. Found 2 (42 requested) and removed 25 (21 requested) atoms. Cycle 15: After refmac, R = 0.2372 (Rfree = 0.000) for 4730 atoms. Found 2 (42 requested) and removed 24 (21 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.48 3.53 Search for helices and strands: 0 residues in 0 chains, 4871 seeds are put forward NCS extension: 39 residues added (0 deleted due to clashes), 4910 seeds are put forward Round 1: 286 peptides, 49 chains. Longest chain 14 peptides. Score 0.396 Round 2: 343 peptides, 45 chains. Longest chain 24 peptides. Score 0.550 Round 3: 332 peptides, 46 chains. Longest chain 22 peptides. Score 0.521 Round 4: 344 peptides, 46 chains. Longest chain 28 peptides. Score 0.543 Round 5: 349 peptides, 47 chains. Longest chain 25 peptides. Score 0.545 Taking the results from Round 2 Chains 49, Residues 298, Estimated correctness of the model 26.9 % 5 chains (44 residues) have been docked in sequence ------------------------------------------------------ 12307 reflections ( 99.98 % complete ) and 10704 restraints for refining 4877 atoms. 9405 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2502 (Rfree = 0.000) for 4877 atoms. Found 15 (43 requested) and removed 29 (21 requested) atoms. Cycle 17: After refmac, R = 0.2392 (Rfree = 0.000) for 4849 atoms. Found 8 (43 requested) and removed 26 (21 requested) atoms. Cycle 18: After refmac, R = 0.2360 (Rfree = 0.000) for 4824 atoms. Found 6 (43 requested) and removed 23 (21 requested) atoms. Cycle 19: After refmac, R = 0.2302 (Rfree = 0.000) for 4802 atoms. Found 6 (43 requested) and removed 21 (21 requested) atoms. Cycle 20: After refmac, R = 0.2267 (Rfree = 0.000) for 4778 atoms. Found 4 (42 requested) and removed 21 (21 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.48 3.53 Search for helices and strands: 0 residues in 0 chains, 4903 seeds are put forward NCS extension: 27 residues added (0 deleted due to clashes), 4930 seeds are put forward Round 1: 316 peptides, 57 chains. Longest chain 13 peptides. Score 0.386 Round 2: 344 peptides, 52 chains. Longest chain 25 peptides. Score 0.492 Round 3: 356 peptides, 49 chains. Longest chain 20 peptides. Score 0.541 Round 4: 346 peptides, 42 chains. Longest chain 27 peptides. Score 0.580 Round 5: 346 peptides, 44 chains. Longest chain 29 peptides. Score 0.564 Taking the results from Round 4 Chains 44, Residues 304, Estimated correctness of the model 35.6 % 4 chains (51 residues) have been docked in sequence ------------------------------------------------------ 12307 reflections ( 99.98 % complete ) and 10710 restraints for refining 4878 atoms. 9368 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2513 (Rfree = 0.000) for 4878 atoms. Found 16 (43 requested) and removed 36 (21 requested) atoms. Cycle 22: After refmac, R = 0.2348 (Rfree = 0.000) for 4846 atoms. Found 9 (43 requested) and removed 23 (21 requested) atoms. Cycle 23: After refmac, R = 0.2321 (Rfree = 0.000) for 4828 atoms. Found 6 (43 requested) and removed 21 (21 requested) atoms. Cycle 24: After refmac, R = 0.2276 (Rfree = 0.000) for 4811 atoms. Found 5 (43 requested) and removed 21 (21 requested) atoms. Cycle 25: After refmac, R = 0.2237 (Rfree = 0.000) for 4789 atoms. Found 3 (43 requested) and removed 21 (21 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.49 3.54 Search for helices and strands: 0 residues in 0 chains, 4950 seeds are put forward NCS extension: 27 residues added (5 deleted due to clashes), 4977 seeds are put forward Round 1: 300 peptides, 53 chains. Longest chain 13 peptides. Score 0.389 Round 2: 314 peptides, 45 chains. Longest chain 21 peptides. Score 0.494 Round 3: 325 peptides, 48 chains. Longest chain 15 peptides. Score 0.489 Round 4: 324 peptides, 49 chains. Longest chain 14 peptides. Score 0.478 Round 5: 319 peptides, 46 chains. Longest chain 20 peptides. Score 0.495 Taking the results from Round 5 Chains 50, Residues 273, Estimated correctness of the model 9.7 % 3 chains (30 residues) have been docked in sequence ------------------------------------------------------ 12307 reflections ( 99.98 % complete ) and 11068 restraints for refining 4878 atoms. 9923 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2501 (Rfree = 0.000) for 4878 atoms. Found 13 (43 requested) and removed 28 (21 requested) atoms. Cycle 27: After refmac, R = 0.2379 (Rfree = 0.000) for 4850 atoms. Found 12 (43 requested) and removed 22 (21 requested) atoms. Cycle 28: After refmac, R = 0.2349 (Rfree = 0.000) for 4834 atoms. Found 12 (43 requested) and removed 21 (21 requested) atoms. Cycle 29: After refmac, R = 0.2327 (Rfree = 0.000) for 4818 atoms. Found 8 (43 requested) and removed 21 (21 requested) atoms. Cycle 30: After refmac, R = 0.2262 (Rfree = 0.000) for 4797 atoms. Found 4 (43 requested) and removed 21 (21 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.48 3.53 Search for helices and strands: 0 residues in 0 chains, 4942 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 4962 seeds are put forward Round 1: 279 peptides, 49 chains. Longest chain 13 peptides. Score 0.380 Round 2: 324 peptides, 49 chains. Longest chain 16 peptides. Score 0.478 Round 3: 318 peptides, 49 chains. Longest chain 16 peptides. Score 0.466 Round 4: 328 peptides, 41 chains. Longest chain 20 peptides. Score 0.556 Round 5: 334 peptides, 44 chains. Longest chain 19 peptides. Score 0.542 Taking the results from Round 4 Chains 42, Residues 287, Estimated correctness of the model 28.7 % 3 chains (21 residues) have been docked in sequence ------------------------------------------------------ 12307 reflections ( 99.98 % complete ) and 11167 restraints for refining 4878 atoms. 9998 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2529 (Rfree = 0.000) for 4878 atoms. Found 18 (43 requested) and removed 29 (21 requested) atoms. Cycle 32: After refmac, R = 0.2435 (Rfree = 0.000) for 4850 atoms. Found 5 (43 requested) and removed 29 (21 requested) atoms. Cycle 33: After refmac, R = 0.2371 (Rfree = 0.000) for 4819 atoms. Found 8 (43 requested) and removed 23 (21 requested) atoms. Cycle 34: After refmac, R = 0.2301 (Rfree = 0.000) for 4797 atoms. Found 4 (43 requested) and removed 21 (21 requested) atoms. Cycle 35: After refmac, R = 0.2267 (Rfree = 0.000) for 4778 atoms. Found 2 (42 requested) and removed 21 (21 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.49 3.54 Search for helices and strands: 0 residues in 0 chains, 4910 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 4926 seeds are put forward Round 1: 271 peptides, 47 chains. Longest chain 19 peptides. Score 0.381 Round 2: 310 peptides, 43 chains. Longest chain 23 peptides. Score 0.504 Round 3: 310 peptides, 47 chains. Longest chain 18 peptides. Score 0.467 Round 4: 321 peptides, 48 chains. Longest chain 16 peptides. Score 0.481 Round 5: 332 peptides, 43 chains. Longest chain 21 peptides. Score 0.546 Taking the results from Round 5 Chains 45, Residues 289, Estimated correctness of the model 25.7 % 3 chains (29 residues) have been docked in sequence ------------------------------------------------------ 12307 reflections ( 99.98 % complete ) and 10864 restraints for refining 4878 atoms. 9643 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2717 (Rfree = 0.000) for 4878 atoms. Found 22 (43 requested) and removed 36 (21 requested) atoms. Cycle 37: After refmac, R = 0.2433 (Rfree = 0.000) for 4852 atoms. Found 21 (43 requested) and removed 30 (21 requested) atoms. Cycle 38: After refmac, R = 0.2606 (Rfree = 0.000) for 4831 atoms. Found 36 (43 requested) and removed 31 (21 requested) atoms. Cycle 39: After refmac, R = 0.2822 (Rfree = 0.000) for 4834 atoms. Found 43 (43 requested) and removed 38 (21 requested) atoms. Cycle 40: After refmac, R = 0.2271 (Rfree = 0.000) for 4818 atoms. Found 14 (43 requested) and removed 27 (21 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.48 3.53 Search for helices and strands: 0 residues in 0 chains, 4962 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 4985 seeds are put forward Round 1: 251 peptides, 47 chains. Longest chain 13 peptides. Score 0.334 Round 2: 284 peptides, 42 chains. Longest chain 23 peptides. Score 0.459 Round 3: 286 peptides, 40 chains. Longest chain 21 peptides. Score 0.482 Round 4: 303 peptides, 42 chains. Longest chain 20 peptides. Score 0.499 Round 5: 299 peptides, 46 chains. Longest chain 21 peptides. Score 0.454 Taking the results from Round 4 Chains 43, Residues 261, Estimated correctness of the model 11.0 % 5 chains (41 residues) have been docked in sequence ------------------------------------------------------ 12307 reflections ( 99.98 % complete ) and 10797 restraints for refining 4878 atoms. 9649 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2814 (Rfree = 0.000) for 4878 atoms. Found 43 (43 requested) and removed 40 (21 requested) atoms. Cycle 42: After refmac, R = 0.2344 (Rfree = 0.000) for 4861 atoms. Found 21 (43 requested) and removed 35 (21 requested) atoms. Cycle 43: After refmac, R = 0.2429 (Rfree = 0.000) for 4834 atoms. Found 33 (43 requested) and removed 23 (21 requested) atoms. Cycle 44: After refmac, R = 0.2039 (Rfree = 0.000) for 4833 atoms. Found 4 (43 requested) and removed 22 (21 requested) atoms. Cycle 45: After refmac, R = 0.2020 (Rfree = 0.000) for 4811 atoms. Found 3 (43 requested) and removed 22 (21 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.47 3.52 Search for helices and strands: 0 residues in 0 chains, 4950 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 4967 seeds are put forward Round 1: 201 peptides, 33 chains. Longest chain 15 peptides. Score 0.361 Round 2: 228 peptides, 33 chains. Longest chain 24 peptides. Score 0.425 Round 3: 238 peptides, 34 chains. Longest chain 15 peptides. Score 0.437 Round 4: 246 peptides, 32 chains. Longest chain 26 peptides. Score 0.475 Round 5: 246 peptides, 31 chains. Longest chain 17 peptides. Score 0.484 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 32, Residues 215, Estimated correctness of the model 6.1 % 3 chains (29 residues) have been docked in sequence Sequence coverage is 13 % Consider running further cycles of model building using 1vll-3_warpNtrace.pdb as input Building loops using Loopy2018 32 chains (215 residues) following loop building 3 chains (29 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 12307 reflections ( 99.98 % complete ) and 11182 restraints for refining 4878 atoms. 10249 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2233 (Rfree = 0.000) for 4878 atoms. Found 0 (43 requested) and removed 19 (21 requested) atoms. Cycle 47: After refmac, R = 0.2169 (Rfree = 0.000) for 4854 atoms. Found 0 (43 requested) and removed 4 (21 requested) atoms. Cycle 48: After refmac, R = 0.2215 (Rfree = 0.000) for 4847 atoms. Found 0 (43 requested) and removed 17 (21 requested) atoms. Cycle 49: After refmac, R = 0.2141 (Rfree = 0.000) for 4827 atoms. Found 0 (43 requested) and removed 21 (21 requested) atoms. Writing output files ... TimeTaking 52