Mon 24 Dec 01:09:00 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 2ajr-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2ajr-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2ajr-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ajr-3.6-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/2ajr-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ajr-3.6-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 ============================================================ Mon 24 Dec 01:09:05 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/2ajr-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ajr-3.6-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 559 and 0 Target number of residues in the AU: 559 Target solvent content: 0.6380 Checking the provided sequence file Detected sequence length: 331 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 662 Adjusted target solvent content: 0.57 Input MTZ file: 2ajr-3.6-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: 92 Cell parameters: 115.754 115.754 124.745 90.000 90.000 90.000 Input sequence file: 2ajr-3.6-parrot-mrncs.fasta_lf Building free atoms model in initial map for 5296 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: 29.168 3.600 Wilson plot Bfac: 70.60 10268 reflections ( 99.54 % complete ) and 0 restraints for refining 5867 atoms. Observations/parameters ratio is 0.44 ------------------------------------------------------ Starting model: R = 0.3620 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3584 (Rfree = 0.000) for 5867 atoms. Found 37 (37 requested) and removed 63 (18 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.42 3.11 Search for helices and strands: 0 residues in 0 chains, 5938 seeds are put forward NCS extension: 0 residues added, 5938 seeds are put forward Round 1: 245 peptides, 48 chains. Longest chain 12 peptides. Score 0.293 Round 2: 319 peptides, 53 chains. Longest chain 16 peptides. Score 0.402 Round 3: 352 peptides, 60 chains. Longest chain 15 peptides. Score 0.407 Round 4: 365 peptides, 50 chains. Longest chain 20 peptides. Score 0.509 Round 5: 351 peptides, 51 chains. Longest chain 18 peptides. Score 0.477 Taking the results from Round 4 Chains 52, Residues 315, Estimated correctness of the model 0.0 % 4 chains (37 residues) have been docked in sequence ------------------------------------------------------ 10268 reflections ( 99.54 % complete ) and 10525 restraints for refining 4799 atoms. 9199 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3059 (Rfree = 0.000) for 4799 atoms. Found 30 (30 requested) and removed 39 (15 requested) atoms. Cycle 2: After refmac, R = 0.2945 (Rfree = 0.000) for 4702 atoms. Found 30 (30 requested) and removed 38 (15 requested) atoms. Cycle 3: After refmac, R = 0.2947 (Rfree = 0.000) for 4644 atoms. Found 30 (30 requested) and removed 30 (15 requested) atoms. Cycle 4: After refmac, R = 0.2868 (Rfree = 0.000) for 4609 atoms. Found 29 (29 requested) and removed 34 (14 requested) atoms. Cycle 5: After refmac, R = 0.2582 (Rfree = 0.000) for 4582 atoms. Found 29 (29 requested) and removed 22 (14 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.44 3.13 Search for helices and strands: 0 residues in 0 chains, 4775 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 4793 seeds are put forward Round 1: 317 peptides, 52 chains. Longest chain 14 peptides. Score 0.406 Round 2: 360 peptides, 46 chains. Longest chain 21 peptides. Score 0.531 Round 3: 360 peptides, 50 chains. Longest chain 17 peptides. Score 0.501 Round 4: 354 peptides, 47 chains. Longest chain 19 peptides. Score 0.514 Round 5: 349 peptides, 48 chains. Longest chain 19 peptides. Score 0.497 Taking the results from Round 2 Chains 48, Residues 314, Estimated correctness of the model 0.0 % 5 chains (45 residues) have been docked in sequence ------------------------------------------------------ 10268 reflections ( 99.54 % complete ) and 10259 restraints for refining 4716 atoms. 8919 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2730 (Rfree = 0.000) for 4716 atoms. Found 30 (30 requested) and removed 40 (15 requested) atoms. Cycle 7: After refmac, R = 0.2790 (Rfree = 0.000) for 4665 atoms. Found 30 (30 requested) and removed 32 (15 requested) atoms. Cycle 8: After refmac, R = 0.2713 (Rfree = 0.000) for 4631 atoms. Found 29 (29 requested) and removed 28 (14 requested) atoms. Cycle 9: After refmac, R = 0.2642 (Rfree = 0.000) for 4621 atoms. Found 29 (29 requested) and removed 37 (14 requested) atoms. Cycle 10: After refmac, R = 0.2631 (Rfree = 0.000) for 4593 atoms. Found 29 (29 requested) and removed 26 (14 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.38 3.08 Search for helices and strands: 0 residues in 0 chains, 4802 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 4824 seeds are put forward Round 1: 317 peptides, 58 chains. Longest chain 11 peptides. Score 0.355 Round 2: 374 peptides, 50 chains. Longest chain 17 peptides. Score 0.524 Round 3: 384 peptides, 53 chains. Longest chain 21 peptides. Score 0.519 Round 4: 393 peptides, 52 chains. Longest chain 16 peptides. Score 0.541 Round 5: 376 peptides, 50 chains. Longest chain 23 peptides. Score 0.528 Taking the results from Round 4 Chains 53, Residues 341, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 10268 reflections ( 99.54 % complete ) and 10530 restraints for refining 4801 atoms. 9188 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2905 (Rfree = 0.000) for 4801 atoms. Found 30 (30 requested) and removed 40 (15 requested) atoms. Cycle 12: After refmac, R = 0.2764 (Rfree = 0.000) for 4753 atoms. Found 30 (30 requested) and removed 32 (15 requested) atoms. Cycle 13: After refmac, R = 0.2704 (Rfree = 0.000) for 4724 atoms. Found 30 (30 requested) and removed 25 (15 requested) atoms. Cycle 14: After refmac, R = 0.2613 (Rfree = 0.000) for 4698 atoms. Found 29 (30 requested) and removed 27 (15 requested) atoms. Cycle 15: After refmac, R = 0.2597 (Rfree = 0.000) for 4679 atoms. Found 30 (30 requested) and removed 24 (15 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.41 3.10 Search for helices and strands: 0 residues in 0 chains, 4904 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 4921 seeds are put forward Round 1: 309 peptides, 57 chains. Longest chain 16 peptides. Score 0.347 Round 2: 360 peptides, 53 chains. Longest chain 24 peptides. Score 0.478 Round 3: 355 peptides, 50 chains. Longest chain 17 peptides. Score 0.492 Round 4: 344 peptides, 50 chains. Longest chain 15 peptides. Score 0.473 Round 5: 361 peptides, 48 chains. Longest chain 27 peptides. Score 0.518 Taking the results from Round 5 Chains 50, Residues 313, Estimated correctness of the model 0.0 % 3 chains (22 residues) have been docked in sequence ------------------------------------------------------ 10268 reflections ( 99.54 % complete ) and 10499 restraints for refining 4800 atoms. 9225 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2870 (Rfree = 0.000) for 4800 atoms. Found 30 (30 requested) and removed 40 (15 requested) atoms. Cycle 17: After refmac, R = 0.2704 (Rfree = 0.000) for 4752 atoms. Found 30 (30 requested) and removed 33 (15 requested) atoms. Cycle 18: After refmac, R = 0.2601 (Rfree = 0.000) for 4730 atoms. Found 30 (30 requested) and removed 28 (15 requested) atoms. Cycle 19: After refmac, R = 0.2606 (Rfree = 0.000) for 4714 atoms. Found 30 (30 requested) and removed 32 (15 requested) atoms. Cycle 20: After refmac, R = 0.2502 (Rfree = 0.000) for 4695 atoms. Found 30 (30 requested) and removed 31 (15 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.43 3.12 Search for helices and strands: 0 residues in 0 chains, 4868 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 4882 seeds are put forward Round 1: 303 peptides, 53 chains. Longest chain 13 peptides. Score 0.370 Round 2: 345 peptides, 55 chains. Longest chain 20 peptides. Score 0.434 Round 3: 353 peptides, 49 chains. Longest chain 21 peptides. Score 0.496 Round 4: 352 peptides, 52 chains. Longest chain 16 peptides. Score 0.471 Round 5: 358 peptides, 50 chains. Longest chain 22 peptides. Score 0.497 Taking the results from Round 5 Chains 50, Residues 308, Estimated correctness of the model 0.0 % 3 chains (20 residues) have been docked in sequence ------------------------------------------------------ 10268 reflections ( 99.54 % complete ) and 10696 restraints for refining 4799 atoms. 9456 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2792 (Rfree = 0.000) for 4799 atoms. Found 30 (30 requested) and removed 32 (15 requested) atoms. Cycle 22: After refmac, R = 0.2594 (Rfree = 0.000) for 4758 atoms. Found 30 (30 requested) and removed 27 (15 requested) atoms. Cycle 23: After refmac, R = 0.2529 (Rfree = 0.000) for 4730 atoms. Found 30 (30 requested) and removed 27 (15 requested) atoms. Cycle 24: After refmac, R = 0.2451 (Rfree = 0.000) for 4713 atoms. Found 30 (30 requested) and removed 29 (15 requested) atoms. Cycle 25: After refmac, R = 0.2145 (Rfree = 0.000) for 4708 atoms. Found 14 (30 requested) and removed 21 (15 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.46 3.15 Search for helices and strands: 0 residues in 0 chains, 4813 seeds are put forward NCS extension: 29 residues added (0 deleted due to clashes), 4842 seeds are put forward Round 1: 292 peptides, 52 chains. Longest chain 12 peptides. Score 0.357 Round 2: 332 peptides, 50 chains. Longest chain 13 peptides. Score 0.451 Round 3: 333 peptides, 52 chains. Longest chain 12 peptides. Score 0.437 Round 4: 332 peptides, 51 chains. Longest chain 17 peptides. Score 0.443 Round 5: 325 peptides, 48 chains. Longest chain 18 peptides. Score 0.455 Taking the results from Round 5 Chains 48, Residues 277, Estimated correctness of the model 0.0 % 2 chains (23 residues) have been docked in sequence ------------------------------------------------------ 10268 reflections ( 99.54 % complete ) and 10782 restraints for refining 4799 atoms. 9642 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2745 (Rfree = 0.000) for 4799 atoms. Found 30 (30 requested) and removed 27 (15 requested) atoms. Cycle 27: After refmac, R = 0.2545 (Rfree = 0.000) for 4773 atoms. Found 30 (30 requested) and removed 30 (15 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.2242 (Rfree = 0.000) for 4754 atoms. Found 10 (30 requested) and removed 18 (15 requested) atoms. Cycle 29: After refmac, R = 0.2345 (Rfree = 0.000) for 4741 atoms. Found 23 (30 requested) and removed 27 (15 requested) atoms. Cycle 30: After refmac, R = 0.2425 (Rfree = 0.000) for 4730 atoms. Found 30 (30 requested) and removed 22 (15 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.43 3.12 Search for helices and strands: 0 residues in 0 chains, 4848 seeds are put forward NCS extension: 28 residues added (0 deleted due to clashes), 4876 seeds are put forward Round 1: 297 peptides, 53 chains. Longest chain 20 peptides. Score 0.358 Round 2: 331 peptides, 52 chains. Longest chain 15 peptides. Score 0.433 Round 3: 311 peptides, 45 chains. Longest chain 17 peptides. Score 0.454 Round 4: 338 peptides, 49 chains. Longest chain 17 peptides. Score 0.470 Round 5: 335 peptides, 48 chains. Longest chain 17 peptides. Score 0.473 Taking the results from Round 5 Chains 48, Residues 287, Estimated correctness of the model 0.0 % 4 chains (19 residues) have been docked in sequence ------------------------------------------------------ 10268 reflections ( 99.54 % complete ) and 10795 restraints for refining 4798 atoms. 9651 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2715 (Rfree = 0.000) for 4798 atoms. Found 30 (30 requested) and removed 23 (15 requested) atoms. Cycle 32: After refmac, R = 0.2531 (Rfree = 0.000) for 4774 atoms. Found 25 (30 requested) and removed 23 (15 requested) atoms. Cycle 33: After refmac, R = 0.2513 (Rfree = 0.000) for 4757 atoms. Found 30 (30 requested) and removed 26 (15 requested) atoms. Cycle 34: After refmac, R = 0.2409 (Rfree = 0.000) for 4754 atoms. Found 26 (30 requested) and removed 21 (15 requested) atoms. Cycle 35: After refmac, R = 0.2255 (Rfree = 0.000) for 4753 atoms. Found 10 (30 requested) and removed 18 (15 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.43 3.12 Search for helices and strands: 0 residues in 0 chains, 4858 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 4870 seeds are put forward Round 1: 292 peptides, 54 chains. Longest chain 17 peptides. Score 0.339 Round 2: 340 peptides, 52 chains. Longest chain 17 peptides. Score 0.450 Round 3: 341 peptides, 48 chains. Longest chain 30 peptides. Score 0.483 Round 4: 343 peptides, 50 chains. Longest chain 19 peptides. Score 0.471 Round 5: 341 peptides, 47 chains. Longest chain 25 peptides. Score 0.491 Taking the results from Round 5 Chains 47, Residues 294, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 10268 reflections ( 99.54 % complete ) and 10855 restraints for refining 4800 atoms. 9711 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2621 (Rfree = 0.000) for 4800 atoms. Found 29 (30 requested) and removed 28 (15 requested) atoms. Cycle 37: After refmac, R = 0.2528 (Rfree = 0.000) for 4775 atoms. Found 23 (30 requested) and removed 21 (15 requested) atoms. Cycle 38: After refmac, R = 0.2301 (Rfree = 0.000) for 4762 atoms. Found 17 (30 requested) and removed 24 (15 requested) atoms. Cycle 39: After refmac, R = 0.2271 (Rfree = 0.000) for 4740 atoms. Found 6 (30 requested) and removed 26 (15 requested) atoms. Cycle 40: After refmac, R = 0.2208 (Rfree = 0.000) for 4717 atoms. Found 2 (30 requested) and removed 17 (15 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.42 3.11 Search for helices and strands: 0 residues in 0 chains, 4812 seeds are put forward NCS extension: 42 residues added (1 deleted due to clashes), 4854 seeds are put forward Round 1: 280 peptides, 57 chains. Longest chain 11 peptides. Score 0.286 Round 2: 312 peptides, 50 chains. Longest chain 16 peptides. Score 0.414 Round 3: 305 peptides, 50 chains. Longest chain 13 peptides. Score 0.400 Round 4: 301 peptides, 43 chains. Longest chain 19 peptides. Score 0.452 Round 5: 301 peptides, 48 chains. Longest chain 14 peptides. Score 0.409 Taking the results from Round 4 Chains 43, Residues 258, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 10268 reflections ( 99.54 % complete ) and 10983 restraints for refining 4801 atoms. 9970 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2578 (Rfree = 0.000) for 4801 atoms. Found 30 (30 requested) and removed 24 (15 requested) atoms. Cycle 42: After refmac, R = 0.2497 (Rfree = 0.000) for 4787 atoms. Found 30 (30 requested) and removed 26 (15 requested) atoms. Cycle 43: After refmac, R = 0.2255 (Rfree = 0.000) for 4777 atoms. Found 16 (30 requested) and removed 21 (15 requested) atoms. Cycle 44: After refmac, R = 0.2233 (Rfree = 0.000) for 4758 atoms. Found 8 (30 requested) and removed 17 (15 requested) atoms. Cycle 45: After refmac, R = 0.2221 (Rfree = 0.000) for 4746 atoms. Found 5 (30 requested) and removed 19 (15 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.42 3.11 Search for helices and strands: 0 residues in 0 chains, 4868 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 4887 seeds are put forward Round 1: 254 peptides, 47 chains. Longest chain 11 peptides. Score 0.322 Round 2: 276 peptides, 45 chains. Longest chain 15 peptides. Score 0.386 Round 3: 283 peptides, 44 chains. Longest chain 12 peptides. Score 0.409 Round 4: 280 peptides, 41 chains. Longest chain 13 peptides. Score 0.429 Round 5: 256 peptides, 41 chains. Longest chain 15 peptides. Score 0.382 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 41, Residues 239, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence Sequence coverage is 3 % Consider running further cycles of model building using 2ajr-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 10268 reflections ( 99.54 % complete ) and 11018 restraints for refining 4801 atoms. 10069 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2530 (Rfree = 0.000) for 4801 atoms. Found 0 (30 requested) and removed 15 (15 requested) atoms. Cycle 47: After refmac, R = 0.2468 (Rfree = 0.000) for 4760 atoms. Found 0 (30 requested) and removed 15 (15 requested) atoms. Cycle 48: After refmac, R = 0.2509 (Rfree = 0.000) for 4729 atoms. Found 0 (30 requested) and removed 15 (15 requested) atoms. Cycle 49: After refmac, R = 0.2424 (Rfree = 0.000) for 4695 atoms. TimeTaking 53.9