null Sun 23 Dec 22:22:46 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 1vku-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vku-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vku-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vku-3.4-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/1vku-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vku-3.4-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 ============================================================ Sun 23 Dec 22:22:55 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/1vku-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vku-3.4-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 59 and 0 Target number of residues in the AU: 59 Target solvent content: 0.6398 Checking the provided sequence file Detected sequence length: 100 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 100 Adjusted target solvent content: 0.39 Input MTZ file: 1vku-3.4-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: 154 Cell parameters: 45.440 45.440 74.373 90.000 90.000 120.000 Input sequence file: 1vku-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 800 target number of atoms Had to go as low as 0.60 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 Loops will be built when appropriate and at the last cycle Resolution range: 39.352 3.401 Wilson plot Bfac: 71.98 1371 reflections ( 99.42 % complete ) and 0 restraints for refining 887 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Starting model: R = 0.3316 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3200 (Rfree = 0.000) for 887 atoms. Found 4 (6 requested) and removed 7 (3 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.67 4.26 Search for helices and strands: 0 residues in 0 chains, 899 seeds are put forward Round 1: 31 peptides, 6 chains. Longest chain 6 peptides. Score 0.317 Round 2: 38 peptides, 7 chains. Longest chain 9 peptides. Score 0.370 Round 3: 37 peptides, 6 chains. Longest chain 12 peptides. Score 0.430 Round 4: 41 peptides, 5 chains. Longest chain 12 peptides. Score 0.567 Round 5: 47 peptides, 7 chains. Longest chain 12 peptides. Score 0.523 Taking the results from Round 4 Chains 5, Residues 36, Estimated correctness of the model 17.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1371 reflections ( 99.42 % complete ) and 1734 restraints for refining 721 atoms. 1595 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3201 (Rfree = 0.000) for 721 atoms. Found 5 (5 requested) and removed 8 (2 requested) atoms. Cycle 2: After refmac, R = 0.2771 (Rfree = 0.000) for 715 atoms. Found 3 (5 requested) and removed 5 (2 requested) atoms. Cycle 3: After refmac, R = 0.2702 (Rfree = 0.000) for 709 atoms. Found 2 (5 requested) and removed 2 (2 requested) atoms. Cycle 4: After refmac, R = 0.2666 (Rfree = 0.000) for 707 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 5: After refmac, R = 0.2591 (Rfree = 0.000) for 707 atoms. Found 3 (5 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.45 4.00 Search for helices and strands: 0 residues in 0 chains, 733 seeds are put forward Round 1: 23 peptides, 5 chains. Longest chain 6 peptides. Score 0.237 Round 2: 29 peptides, 5 chains. Longest chain 9 peptides. Score 0.362 Round 3: 32 peptides, 6 chains. Longest chain 10 peptides. Score 0.337 Round 4: 27 peptides, 4 chains. Longest chain 10 peptides. Score 0.409 Round 5: 29 peptides, 5 chains. Longest chain 10 peptides. Score 0.362 Taking the results from Round 4 Chains 4, Residues 23, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1371 reflections ( 99.42 % complete ) and 1731 restraints for refining 673 atoms. 1643 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2778 (Rfree = 0.000) for 673 atoms. Found 5 (5 requested) and removed 2 (2 requested) atoms. Cycle 7: After refmac, R = 0.2597 (Rfree = 0.000) for 676 atoms. Found 1 (5 requested) and removed 2 (2 requested) atoms. Cycle 8: After refmac, R = 0.2528 (Rfree = 0.000) for 675 atoms. Found 1 (5 requested) and removed 2 (2 requested) atoms. Cycle 9: After refmac, R = 0.2543 (Rfree = 0.000) for 674 atoms. Found 2 (5 requested) and removed 3 (2 requested) atoms. Cycle 10: After refmac, R = 0.2512 (Rfree = 0.000) for 673 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.46 4.02 Search for helices and strands: 0 residues in 0 chains, 699 seeds are put forward Round 1: 31 peptides, 6 chains. Longest chain 9 peptides. Score 0.317 Round 2: 37 peptides, 6 chains. Longest chain 11 peptides. Score 0.430 Round 3: 44 peptides, 8 chains. Longest chain 10 peptides. Score 0.402 Round 4: 40 peptides, 6 chains. Longest chain 12 peptides. Score 0.481 Round 5: 47 peptides, 8 chains. Longest chain 11 peptides. Score 0.453 Taking the results from Round 4 Chains 6, Residues 34, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1371 reflections ( 99.42 % complete ) and 1576 restraints for refining 655 atoms. 1446 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2976 (Rfree = 0.000) for 655 atoms. Found 4 (4 requested) and removed 2 (2 requested) atoms. Cycle 12: After refmac, R = 0.2864 (Rfree = 0.000) for 657 atoms. Found 4 (4 requested) and removed 2 (2 requested) atoms. Cycle 13: After refmac, R = 0.2767 (Rfree = 0.000) for 657 atoms. Found 4 (4 requested) and removed 2 (2 requested) atoms. Cycle 14: After refmac, R = 0.2703 (Rfree = 0.000) for 658 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 15: After refmac, R = 0.2707 (Rfree = 0.000) for 655 atoms. Found 1 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.44 3.99 Search for helices and strands: 0 residues in 0 chains, 683 seeds are put forward Round 1: 42 peptides, 8 chains. Longest chain 8 peptides. Score 0.366 Round 2: 46 peptides, 7 chains. Longest chain 11 peptides. Score 0.507 Round 3: 47 peptides, 7 chains. Longest chain 13 peptides. Score 0.523 Round 4: 42 peptides, 6 chains. Longest chain 11 peptides. Score 0.513 Round 5: 39 peptides, 5 chains. Longest chain 16 peptides. Score 0.536 Taking the results from Round 5 Chains 5, Residues 34, Estimated correctness of the model 6.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1371 reflections ( 99.42 % complete ) and 1527 restraints for refining 653 atoms. 1396 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2896 (Rfree = 0.000) for 653 atoms. Found 4 (4 requested) and removed 13 (2 requested) atoms. Cycle 17: After refmac, R = 0.2657 (Rfree = 0.000) for 644 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 18: After refmac, R = 0.2596 (Rfree = 0.000) for 641 atoms. Found 1 (4 requested) and removed 2 (2 requested) atoms. Cycle 19: After refmac, R = 0.2574 (Rfree = 0.000) for 638 atoms. Found 1 (4 requested) and removed 2 (2 requested) atoms. Cycle 20: After refmac, R = 0.2513 (Rfree = 0.000) for 637 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.43 3.98 Search for helices and strands: 0 residues in 0 chains, 658 seeds are put forward Round 1: 31 peptides, 6 chains. Longest chain 7 peptides. Score 0.317 Round 2: 43 peptides, 8 chains. Longest chain 11 peptides. Score 0.384 Round 3: 44 peptides, 7 chains. Longest chain 11 peptides. Score 0.475 Round 4: 46 peptides, 6 chains. Longest chain 13 peptides. Score 0.573 Round 5: 46 peptides, 6 chains. Longest chain 13 peptides. Score 0.573 Taking the results from Round 5 Chains 6, Residues 40, Estimated correctness of the model 19.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1371 reflections ( 99.42 % complete ) and 1502 restraints for refining 643 atoms. 1348 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3065 (Rfree = 0.000) for 643 atoms. Found 4 (4 requested) and removed 2 (2 requested) atoms. Cycle 22: After refmac, R = 0.2817 (Rfree = 0.000) for 644 atoms. Found 3 (4 requested) and removed 2 (2 requested) atoms. Cycle 23: After refmac, R = 0.2661 (Rfree = 0.000) for 645 atoms. Found 2 (4 requested) and removed 2 (2 requested) atoms. Cycle 24: After refmac, R = 0.2585 (Rfree = 0.000) for 645 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 25: After refmac, R = 0.2549 (Rfree = 0.000) for 643 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.35 3.89 Search for helices and strands: 0 residues in 0 chains, 666 seeds are put forward Round 1: 32 peptides, 6 chains. Longest chain 8 peptides. Score 0.337 Round 2: 40 peptides, 7 chains. Longest chain 9 peptides. Score 0.406 Round 3: 41 peptides, 7 chains. Longest chain 10 peptides. Score 0.424 Round 4: 46 peptides, 8 chains. Longest chain 10 peptides. Score 0.437 Round 5: 49 peptides, 7 chains. Longest chain 9 peptides. Score 0.553 Taking the results from Round 5 Chains 7, Residues 42, Estimated correctness of the model 12.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1371 reflections ( 99.42 % complete ) and 1373 restraints for refining 644 atoms. 1212 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3031 (Rfree = 0.000) for 644 atoms. Found 3 (4 requested) and removed 3 (2 requested) atoms. Cycle 27: After refmac, R = 0.2748 (Rfree = 0.000) for 642 atoms. Found 1 (4 requested) and removed 2 (2 requested) atoms. Cycle 28: After refmac, R = 0.2614 (Rfree = 0.000) for 639 atoms. Found 1 (4 requested) and removed 2 (2 requested) atoms. Cycle 29: After refmac, R = 0.2493 (Rfree = 0.000) for 638 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 30: After refmac, R = 0.2490 (Rfree = 0.000) for 635 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.36 3.90 Search for helices and strands: 0 residues in 0 chains, 646 seeds are put forward Round 1: 30 peptides, 5 chains. Longest chain 10 peptides. Score 0.382 Round 2: 37 peptides, 7 chains. Longest chain 8 peptides. Score 0.351 Round 3: 36 peptides, 5 chains. Longest chain 14 peptides. Score 0.488 Round 4: 32 peptides, 6 chains. Longest chain 9 peptides. Score 0.337 Round 5: 32 peptides, 5 chains. Longest chain 12 peptides. Score 0.419 Taking the results from Round 3 Chains 5, Residues 31, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1371 reflections ( 99.42 % complete ) and 1457 restraints for refining 629 atoms. 1338 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2523 (Rfree = 0.000) for 629 atoms. Found 2 (4 requested) and removed 3 (2 requested) atoms. Cycle 32: After refmac, R = 0.2406 (Rfree = 0.000) for 627 atoms. Found 4 (4 requested) and removed 2 (2 requested) atoms. Cycle 33: After refmac, R = 0.2331 (Rfree = 0.000) for 629 atoms. Found 2 (4 requested) and removed 2 (2 requested) atoms. Cycle 34: After refmac, R = 0.2280 (Rfree = 0.000) for 629 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 35: After refmac, R = 0.2256 (Rfree = 0.000) for 627 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.38 3.92 Search for helices and strands: 0 residues in 0 chains, 656 seeds are put forward Round 1: 30 peptides, 5 chains. Longest chain 11 peptides. Score 0.382 Round 2: 36 peptides, 6 chains. Longest chain 12 peptides. Score 0.412 Round 3: 33 peptides, 6 chains. Longest chain 9 peptides. Score 0.356 Round 4: 40 peptides, 7 chains. Longest chain 12 peptides. Score 0.406 Round 5: 38 peptides, 6 chains. Longest chain 14 peptides. Score 0.447 Taking the results from Round 5 Chains 6, Residues 32, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1371 reflections ( 99.42 % complete ) and 1439 restraints for refining 625 atoms. 1317 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2566 (Rfree = 0.000) for 625 atoms. Found 4 (4 requested) and removed 3 (2 requested) atoms. Cycle 37: After refmac, R = 0.2347 (Rfree = 0.000) for 626 atoms. Found 1 (4 requested) and removed 3 (2 requested) atoms. Cycle 38: After refmac, R = 0.2285 (Rfree = 0.000) for 624 atoms. Found 2 (4 requested) and removed 2 (2 requested) atoms. Cycle 39: After refmac, R = 0.2224 (Rfree = 0.000) for 624 atoms. Found 1 (4 requested) and removed 2 (2 requested) atoms. Cycle 40: After refmac, R = 0.2250 (Rfree = 0.000) for 622 atoms. Found 2 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.35 3.89 Search for helices and strands: 0 residues in 0 chains, 645 seeds are put forward Round 1: 31 peptides, 6 chains. Longest chain 8 peptides. Score 0.317 Round 2: 36 peptides, 6 chains. Longest chain 12 peptides. Score 0.412 Round 3: 35 peptides, 6 chains. Longest chain 10 peptides. Score 0.394 Round 4: 36 peptides, 6 chains. Longest chain 12 peptides. Score 0.412 Round 5: 32 peptides, 6 chains. Longest chain 9 peptides. Score 0.337 Taking the results from Round 4 Chains 6, Residues 30, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1371 reflections ( 99.42 % complete ) and 1473 restraints for refining 622 atoms. 1359 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2430 (Rfree = 0.000) for 622 atoms. Found 0 (4 requested) and removed 4 (2 requested) atoms. Cycle 42: After refmac, R = 0.2354 (Rfree = 0.000) for 618 atoms. Found 1 (4 requested) and removed 2 (2 requested) atoms. Cycle 43: After refmac, R = 0.2264 (Rfree = 0.000) for 617 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 44: After refmac, R = 0.2207 (Rfree = 0.000) for 615 atoms. Found 1 (4 requested) and removed 2 (2 requested) atoms. Cycle 45: After refmac, R = 0.2166 (Rfree = 0.000) for 614 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.36 3.90 Search for helices and strands: 0 residues in 0 chains, 648 seeds are put forward Round 1: 19 peptides, 4 chains. Longest chain 7 peptides. Score 0.242 Round 2: 21 peptides, 4 chains. Longest chain 7 peptides. Score 0.287 Round 3: 23 peptides, 4 chains. Longest chain 8 peptides. Score 0.330 Round 4: 19 peptides, 3 chains. Longest chain 8 peptides. Score 0.341 Round 5: 19 peptides, 3 chains. Longest chain 8 peptides. Score 0.341 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 3, Residues 16, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 1vku-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 1371 reflections ( 99.42 % complete ) and 1544 restraints for refining 611 atoms. 1483 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2178 (Rfree = 0.000) for 611 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 47: After refmac, R = 0.2122 (Rfree = 0.000) for 609 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 48: After refmac, R = 0.2121 (Rfree = 0.000) for 607 atoms. Found 0 (4 requested) and removed 1 (2 requested) atoms. Cycle 49: After refmac, R = 0.2136 (Rfree = 0.000) for 606 atoms. Found 0 (4 requested) and removed 1 (2 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:43:11 GMT 2018 Job finished. TimeTaking 20.42 Used memory is bytes: 13694192