null Tue 25 Dec 19:27:55 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 2ajr-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ajr-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ajr-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ajr-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/2ajr-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ajr-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 ============================================================ Tue 25 Dec 19:28:05 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/hancs/ArpWArp/wArpResults/WorkingDir/2ajr-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ajr-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 591 and 0 Target number of residues in the AU: 591 Target solvent content: 0.6173 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-3.2-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: 92 Cell parameters: 115.754 115.754 124.745 90.000 90.000 90.000 Input sequence file: 2ajr-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 5296 target number of atoms Had to go as low as 0.65 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 3.200 Wilson plot Bfac: 59.93 14494 reflections ( 99.68 % complete ) and 0 restraints for refining 5881 atoms. Observations/parameters ratio is 0.62 ------------------------------------------------------ Starting model: R = 0.3579 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3621 (Rfree = 0.000) for 5881 atoms. Found 52 (52 requested) and removed 74 (26 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.16 2.88 Search for helices and strands: 0 residues in 0 chains, 5950 seeds are put forward NCS extension: 0 residues added, 5950 seeds are put forward Round 1: 295 peptides, 57 chains. Longest chain 10 peptides. Score 0.318 Round 2: 359 peptides, 59 chains. Longest chain 13 peptides. Score 0.428 Round 3: 393 peptides, 60 chains. Longest chain 22 peptides. Score 0.481 Round 4: 393 peptides, 55 chains. Longest chain 24 peptides. Score 0.519 Round 5: 374 peptides, 50 chains. Longest chain 20 peptides. Score 0.524 Taking the results from Round 5 Chains 50, Residues 324, Estimated correctness of the model 19.0 % 3 chains (21 residues) have been docked in sequence ------------------------------------------------------ 14494 reflections ( 99.68 % complete ) and 10687 restraints for refining 4833 atoms. 9381 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3000 (Rfree = 0.000) for 4833 atoms. Found 43 (43 requested) and removed 40 (21 requested) atoms. Cycle 2: After refmac, R = 0.2778 (Rfree = 0.000) for 4794 atoms. Found 17 (43 requested) and removed 34 (21 requested) atoms. Cycle 3: After refmac, R = 0.2742 (Rfree = 0.000) for 4762 atoms. Found 11 (42 requested) and removed 28 (21 requested) atoms. Cycle 4: After refmac, R = 0.2697 (Rfree = 0.000) for 4730 atoms. Found 16 (42 requested) and removed 28 (21 requested) atoms. Cycle 5: After refmac, R = 0.2620 (Rfree = 0.000) for 4713 atoms. Found 9 (42 requested) and removed 26 (21 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.13 2.85 Search for helices and strands: 0 residues in 0 chains, 4869 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 4888 seeds are put forward Round 1: 370 peptides, 58 chains. Longest chain 19 peptides. Score 0.456 Round 2: 404 peptides, 54 chains. Longest chain 22 peptides. Score 0.544 Round 3: 390 peptides, 52 chains. Longest chain 19 peptides. Score 0.536 Round 4: 380 peptides, 43 chains. Longest chain 48 peptides. Score 0.584 Round 5: 381 peptides, 48 chains. Longest chain 19 peptides. Score 0.550 Taking the results from Round 4 Chains 46, Residues 337, Estimated correctness of the model 36.7 % 5 chains (54 residues) have been docked in sequence ------------------------------------------------------ 14494 reflections ( 99.68 % complete ) and 10250 restraints for refining 4835 atoms. 8786 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2911 (Rfree = 0.000) for 4835 atoms. Found 40 (43 requested) and removed 48 (21 requested) atoms. Cycle 7: After refmac, R = 0.2813 (Rfree = 0.000) for 4791 atoms. Found 43 (43 requested) and removed 37 (21 requested) atoms. Cycle 8: After refmac, R = 0.2812 (Rfree = 0.000) for 4779 atoms. Found 32 (43 requested) and removed 31 (21 requested) atoms. Cycle 9: After refmac, R = 0.2792 (Rfree = 0.000) for 4762 atoms. Found 37 (42 requested) and removed 31 (21 requested) atoms. Cycle 10: After refmac, R = 0.2743 (Rfree = 0.000) for 4752 atoms. Found 41 (42 requested) and removed 27 (21 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.16 2.88 Search for helices and strands: 0 residues in 0 chains, 4898 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 4922 seeds are put forward Round 1: 360 peptides, 56 chains. Longest chain 23 peptides. Score 0.454 Round 2: 392 peptides, 50 chains. Longest chain 20 peptides. Score 0.553 Round 3: 406 peptides, 48 chains. Longest chain 36 peptides. Score 0.589 Round 4: 423 peptides, 47 chains. Longest chain 22 peptides. Score 0.620 Round 5: 425 peptides, 48 chains. Longest chain 35 peptides. Score 0.616 Taking the results from Round 4 Chains 49, Residues 376, Estimated correctness of the model 46.3 % 4 chains (40 residues) have been docked in sequence ------------------------------------------------------ 14494 reflections ( 99.68 % complete ) and 10068 restraints for refining 4833 atoms. 8464 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2877 (Rfree = 0.000) for 4833 atoms. Found 43 (43 requested) and removed 42 (21 requested) atoms. Cycle 12: After refmac, R = 0.2870 (Rfree = 0.000) for 4812 atoms. Found 34 (43 requested) and removed 30 (21 requested) atoms. Cycle 13: After refmac, R = 0.2841 (Rfree = 0.000) for 4794 atoms. Found 38 (43 requested) and removed 31 (21 requested) atoms. Cycle 14: After refmac, R = 0.2770 (Rfree = 0.000) for 4786 atoms. Found 38 (43 requested) and removed 26 (21 requested) atoms. Cycle 15: After refmac, R = 0.2756 (Rfree = 0.000) for 4778 atoms. Found 41 (43 requested) and removed 28 (21 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.15 2.87 Search for helices and strands: 0 residues in 0 chains, 4951 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 4970 seeds are put forward Round 1: 370 peptides, 57 chains. Longest chain 24 peptides. Score 0.464 Round 2: 395 peptides, 55 chains. Longest chain 18 peptides. Score 0.522 Round 3: 421 peptides, 54 chains. Longest chain 32 peptides. Score 0.570 Round 4: 393 peptides, 50 chains. Longest chain 21 peptides. Score 0.555 Round 5: 395 peptides, 51 chains. Longest chain 30 peptides. Score 0.551 Taking the results from Round 3 Chains 61, Residues 367, Estimated correctness of the model 32.7 % 6 chains (63 residues) have been docked in sequence ------------------------------------------------------ 14494 reflections ( 99.68 % complete ) and 9759 restraints for refining 4835 atoms. 8140 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2779 (Rfree = 0.000) for 4835 atoms. Found 43 (43 requested) and removed 42 (21 requested) atoms. Cycle 17: After refmac, R = 0.2744 (Rfree = 0.000) for 4809 atoms. Found 35 (43 requested) and removed 32 (21 requested) atoms. Cycle 18: After refmac, R = 0.2726 (Rfree = 0.000) for 4787 atoms. Found 43 (43 requested) and removed 29 (21 requested) atoms. Cycle 19: After refmac, R = 0.2499 (Rfree = 0.000) for 4796 atoms. Found 9 (43 requested) and removed 24 (21 requested) atoms. Cycle 20: After refmac, R = 0.2449 (Rfree = 0.000) for 4768 atoms. Found 12 (42 requested) and removed 25 (21 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.15 2.87 Search for helices and strands: 0 residues in 0 chains, 4908 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 4929 seeds are put forward Round 1: 365 peptides, 54 chains. Longest chain 25 peptides. Score 0.479 Round 2: 382 peptides, 51 chains. Longest chain 20 peptides. Score 0.530 Round 3: 409 peptides, 52 chains. Longest chain 24 peptides. Score 0.566 Round 4: 404 peptides, 51 chains. Longest chain 25 peptides. Score 0.565 Round 5: 419 peptides, 52 chains. Longest chain 20 peptides. Score 0.581 Taking the results from Round 5 Chains 52, Residues 367, Estimated correctness of the model 35.8 % 1 chains (16 residues) have been docked in sequence ------------------------------------------------------ 14494 reflections ( 99.68 % complete ) and 10231 restraints for refining 4835 atoms. 8757 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2743 (Rfree = 0.000) for 4835 atoms. Found 28 (43 requested) and removed 33 (21 requested) atoms. Cycle 22: After refmac, R = 0.2728 (Rfree = 0.000) for 4814 atoms. Found 36 (43 requested) and removed 24 (21 requested) atoms. Cycle 23: After refmac, R = 0.2689 (Rfree = 0.000) for 4810 atoms. Found 40 (43 requested) and removed 23 (21 requested) atoms. Cycle 24: After refmac, R = 0.2664 (Rfree = 0.000) for 4822 atoms. Found 32 (43 requested) and removed 30 (21 requested) atoms. Cycle 25: After refmac, R = 0.2451 (Rfree = 0.000) for 4817 atoms. Found 16 (43 requested) and removed 24 (21 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.15 2.87 Search for helices and strands: 0 residues in 0 chains, 4946 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 4959 seeds are put forward Round 1: 368 peptides, 54 chains. Longest chain 17 peptides. Score 0.484 Round 2: 391 peptides, 50 chains. Longest chain 24 peptides. Score 0.552 Round 3: 387 peptides, 55 chains. Longest chain 17 peptides. Score 0.509 Round 4: 408 peptides, 50 chains. Longest chain 24 peptides. Score 0.578 Round 5: 402 peptides, 50 chains. Longest chain 17 peptides. Score 0.569 Taking the results from Round 4 Chains 52, Residues 358, Estimated correctness of the model 35.0 % 4 chains (37 residues) have been docked in sequence ------------------------------------------------------ 14494 reflections ( 99.68 % complete ) and 10089 restraints for refining 4834 atoms. 8585 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2659 (Rfree = 0.000) for 4834 atoms. Found 29 (43 requested) and removed 37 (21 requested) atoms. Cycle 27: After refmac, R = 0.2616 (Rfree = 0.000) for 4814 atoms. Found 27 (43 requested) and removed 28 (21 requested) atoms. Cycle 28: After refmac, R = 0.2598 (Rfree = 0.000) for 4803 atoms. Found 32 (43 requested) and removed 23 (21 requested) atoms. Cycle 29: After refmac, R = 0.2397 (Rfree = 0.000) for 4802 atoms. Found 14 (43 requested) and removed 23 (21 requested) atoms. Cycle 30: After refmac, R = 0.2341 (Rfree = 0.000) for 4786 atoms. Found 12 (43 requested) and removed 22 (21 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.16 2.88 Search for helices and strands: 0 residues in 0 chains, 4908 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 4921 seeds are put forward Round 1: 349 peptides, 52 chains. Longest chain 20 peptides. Score 0.466 Round 2: 395 peptides, 54 chains. Longest chain 26 peptides. Score 0.529 Round 3: 391 peptides, 47 chains. Longest chain 28 peptides. Score 0.573 Round 4: 393 peptides, 47 chains. Longest chain 28 peptides. Score 0.576 Round 5: 384 peptides, 49 chains. Longest chain 20 peptides. Score 0.548 Taking the results from Round 4 Chains 49, Residues 346, Estimated correctness of the model 34.4 % 5 chains (47 residues) have been docked in sequence ------------------------------------------------------ 14494 reflections ( 99.68 % complete ) and 10034 restraints for refining 4835 atoms. 8554 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2682 (Rfree = 0.000) for 4835 atoms. Found 31 (43 requested) and removed 29 (21 requested) atoms. Cycle 32: After refmac, R = 0.2700 (Rfree = 0.000) for 4824 atoms. Found 43 (43 requested) and removed 27 (21 requested) atoms. Cycle 33: After refmac, R = 0.2681 (Rfree = 0.000) for 4826 atoms. Found 43 (43 requested) and removed 31 (21 requested) atoms. Cycle 34: After refmac, R = 0.2596 (Rfree = 0.000) for 4830 atoms. Found 38 (43 requested) and removed 23 (21 requested) atoms. Cycle 35: After refmac, R = 0.2576 (Rfree = 0.000) for 4835 atoms. Found 40 (43 requested) and removed 23 (21 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.14 2.86 Search for helices and strands: 0 residues in 0 chains, 4988 seeds are put forward NCS extension: 31 residues added (6 deleted due to clashes), 5019 seeds are put forward Round 1: 332 peptides, 48 chains. Longest chain 22 peptides. Score 0.467 Round 2: 368 peptides, 50 chains. Longest chain 22 peptides. Score 0.514 Round 3: 350 peptides, 47 chains. Longest chain 18 peptides. Score 0.507 Round 4: 364 peptides, 50 chains. Longest chain 23 peptides. Score 0.508 Round 5: 375 peptides, 47 chains. Longest chain 24 peptides. Score 0.548 Taking the results from Round 5 Chains 47, Residues 328, Estimated correctness of the model 26.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 14494 reflections ( 99.68 % complete ) and 10528 restraints for refining 4835 atoms. 9263 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2630 (Rfree = 0.000) for 4835 atoms. Found 43 (43 requested) and removed 28 (21 requested) atoms. Cycle 37: After refmac, R = 0.2610 (Rfree = 0.000) for 4836 atoms. Found 43 (43 requested) and removed 27 (21 requested) atoms. Cycle 38: After refmac, R = 0.2496 (Rfree = 0.000) for 4847 atoms. Found 43 (43 requested) and removed 27 (21 requested) atoms. Cycle 39: After refmac, R = 0.2484 (Rfree = 0.000) for 4855 atoms. Found 38 (43 requested) and removed 26 (21 requested) atoms. Cycle 40: After refmac, R = 0.2376 (Rfree = 0.000) for 4860 atoms. Found 25 (43 requested) and removed 28 (21 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.12 2.84 Search for helices and strands: 0 residues in 0 chains, 5004 seeds are put forward NCS extension: 29 residues added (1 deleted due to clashes), 5033 seeds are put forward Round 1: 327 peptides, 59 chains. Longest chain 14 peptides. Score 0.366 Round 2: 356 peptides, 53 chains. Longest chain 18 peptides. Score 0.470 Round 3: 370 peptides, 52 chains. Longest chain 22 peptides. Score 0.503 Round 4: 381 peptides, 57 chains. Longest chain 23 peptides. Score 0.483 Round 5: 362 peptides, 55 chains. Longest chain 14 peptides. Score 0.465 Taking the results from Round 3 Chains 54, Residues 318, Estimated correctness of the model 12.3 % 4 chains (35 residues) have been docked in sequence ------------------------------------------------------ 14494 reflections ( 99.68 % complete ) and 10064 restraints for refining 4834 atoms. 8716 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2535 (Rfree = 0.000) for 4834 atoms. Found 43 (43 requested) and removed 30 (21 requested) atoms. Cycle 42: After refmac, R = 0.2368 (Rfree = 0.000) for 4833 atoms. Found 17 (43 requested) and removed 24 (21 requested) atoms. Cycle 43: After refmac, R = 0.2327 (Rfree = 0.000) for 4817 atoms. Found 23 (43 requested) and removed 25 (21 requested) atoms. Cycle 44: After refmac, R = 0.2302 (Rfree = 0.000) for 4806 atoms. Found 22 (43 requested) and removed 22 (21 requested) atoms. Cycle 45: After refmac, R = 0.2277 (Rfree = 0.000) for 4800 atoms. Found 15 (43 requested) and removed 21 (21 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.16 2.88 Search for helices and strands: 0 residues in 0 chains, 4890 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 4911 seeds are put forward Round 1: 317 peptides, 58 chains. Longest chain 16 peptides. Score 0.355 Round 2: 339 peptides, 51 chains. Longest chain 16 peptides. Score 0.456 Round 3: 342 peptides, 49 chains. Longest chain 18 peptides. Score 0.477 Round 4: 328 peptides, 50 chains. Longest chain 15 peptides. Score 0.444 Round 5: 332 peptides, 50 chains. Longest chain 14 peptides. Score 0.451 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 51, Residues 293, Estimated correctness of the model 3.7 % 1 chains (12 residues) have been docked in sequence Sequence coverage is 4 % Consider running further cycles of model building using 2ajr-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 14494 reflections ( 99.68 % complete ) and 10516 restraints for refining 4835 atoms. 9339 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2491 (Rfree = 0.000) for 4835 atoms. Found 0 (43 requested) and removed 21 (21 requested) atoms. Cycle 47: After refmac, R = 0.2413 (Rfree = 0.000) for 4802 atoms. Found 0 (43 requested) and removed 21 (21 requested) atoms. Cycle 48: After refmac, R = 0.2395 (Rfree = 0.000) for 4772 atoms. Found 0 (42 requested) and removed 21 (21 requested) atoms. Cycle 49: After refmac, R = 0.2363 (Rfree = 0.000) for 4748 atoms. Found 0 (42 requested) and removed 10 (21 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:48:05 GMT 2018 Job finished. TimeTaking 80.17 Used memory is bytes: 22925224