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 1vqy-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vqy-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vqy-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vqy-3.8-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/1vqy-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vqy-3.8-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/1vqy-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vqy-3.8-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 721 and 0 Target number of residues in the AU: 721 Target solvent content: 0.6016 Checking the provided sequence file Detected sequence length: 116 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 8 Adjusted target number of residues: 928 Adjusted target solvent content: 0.49 Input MTZ file: 1vqy-3.8-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: 19 Cell parameters: 68.026 110.931 129.804 90.000 90.000 90.000 Input sequence file: 1vqy-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 7424 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: 29.074 3.800 Wilson plot Bfac: 53.20 9994 reflections ( 98.35 % complete ) and 0 restraints for refining 8202 atoms. Observations/parameters ratio is 0.30 ------------------------------------------------------ Starting model: R = 0.2891 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2844 (Rfree = 0.000) for 8202 atoms. Found 42 (45 requested) and removed 41 (22 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.26 3.30 Search for helices and strands: 0 residues in 0 chains, 8328 seeds are put forward NCS extension: 0 residues added, 8328 seeds are put forward Round 1: 351 peptides, 71 chains. Longest chain 12 peptides. Score 0.296 Round 2: 470 peptides, 75 chains. Longest chain 15 peptides. Score 0.465 Round 3: 499 peptides, 76 chains. Longest chain 21 peptides. Score 0.501 Round 4: 499 peptides, 65 chains. Longest chain 18 peptides. Score 0.567 Round 5: 528 peptides, 67 chains. Longest chain 24 peptides. Score 0.593 Taking the results from Round 5 Chains 67, Residues 461, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 9994 reflections ( 98.35 % complete ) and 15099 restraints for refining 6715 atoms. 13272 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2434 (Rfree = 0.000) for 6715 atoms. Found 34 (36 requested) and removed 68 (18 requested) atoms. Cycle 2: After refmac, R = 0.2381 (Rfree = 0.000) for 6582 atoms. Found 30 (36 requested) and removed 47 (18 requested) atoms. Cycle 3: After refmac, R = 0.1988 (Rfree = 0.000) for 6510 atoms. Found 17 (36 requested) and removed 36 (18 requested) atoms. Cycle 4: After refmac, R = 0.2211 (Rfree = 0.000) for 6467 atoms. Found 28 (35 requested) and removed 46 (17 requested) atoms. Cycle 5: After refmac, R = 0.2288 (Rfree = 0.000) for 6419 atoms. Found 35 (35 requested) and removed 40 (17 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.30 3.34 Search for helices and strands: 0 residues in 0 chains, 6676 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 6688 seeds are put forward Round 1: 436 peptides, 73 chains. Longest chain 15 peptides. Score 0.426 Round 2: 517 peptides, 74 chains. Longest chain 20 peptides. Score 0.538 Round 3: 493 peptides, 68 chains. Longest chain 21 peptides. Score 0.542 Round 4: 507 peptides, 65 chains. Longest chain 26 peptides. Score 0.578 Round 5: 517 peptides, 66 chains. Longest chain 22 peptides. Score 0.585 Taking the results from Round 5 Chains 68, Residues 451, Estimated correctness of the model 0.0 % 3 chains (40 residues) have been docked in sequence ------------------------------------------------------ 9994 reflections ( 98.35 % complete ) and 14989 restraints for refining 6713 atoms. 13088 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2275 (Rfree = 0.000) for 6713 atoms. Found 30 (36 requested) and removed 59 (18 requested) atoms. Cycle 7: After refmac, R = 0.2232 (Rfree = 0.000) for 6620 atoms. Found 36 (36 requested) and removed 51 (18 requested) atoms. Cycle 8: After refmac, R = 0.2020 (Rfree = 0.000) for 6576 atoms. Found 32 (36 requested) and removed 38 (18 requested) atoms. Cycle 9: After refmac, R = 0.1945 (Rfree = 0.000) for 6547 atoms. Found 25 (36 requested) and removed 36 (18 requested) atoms. Cycle 10: After refmac, R = 0.1911 (Rfree = 0.000) for 6530 atoms. Found 26 (35 requested) and removed 42 (17 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.28 3.32 Search for helices and strands: 0 residues in 0 chains, 6744 seeds are put forward NCS extension: 32 residues added (0 deleted due to clashes), 6776 seeds are put forward Round 1: 447 peptides, 80 chains. Longest chain 17 peptides. Score 0.395 Round 2: 500 peptides, 73 chains. Longest chain 19 peptides. Score 0.521 Round 3: 511 peptides, 70 chains. Longest chain 30 peptides. Score 0.554 Round 4: 519 peptides, 70 chains. Longest chain 21 peptides. Score 0.564 Round 5: 531 peptides, 73 chains. Longest chain 20 peptides. Score 0.563 Taking the results from Round 4 Chains 70, Residues 449, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9994 reflections ( 98.35 % complete ) and 15454 restraints for refining 6715 atoms. 13728 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2520 (Rfree = 0.000) for 6715 atoms. Found 36 (36 requested) and removed 66 (18 requested) atoms. Cycle 12: After refmac, R = 0.2071 (Rfree = 0.000) for 6633 atoms. Found 31 (36 requested) and removed 40 (18 requested) atoms. Cycle 13: After refmac, R = 0.1706 (Rfree = 0.000) for 6596 atoms. Found 12 (36 requested) and removed 31 (18 requested) atoms. Cycle 14: After refmac, R = 0.1651 (Rfree = 0.000) for 6566 atoms. Found 11 (36 requested) and removed 23 (18 requested) atoms. Cycle 15: After refmac, R = 0.1934 (Rfree = 0.000) for 6547 atoms. Found 36 (36 requested) and removed 32 (18 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.28 3.32 Search for helices and strands: 0 residues in 0 chains, 6836 seeds are put forward NCS extension: 31 residues added (0 deleted due to clashes), 6867 seeds are put forward Round 1: 415 peptides, 74 chains. Longest chain 16 peptides. Score 0.385 Round 2: 459 peptides, 66 chains. Longest chain 22 peptides. Score 0.507 Round 3: 486 peptides, 68 chains. Longest chain 28 peptides. Score 0.532 Round 4: 497 peptides, 70 chains. Longest chain 18 peptides. Score 0.535 Round 5: 504 peptides, 69 chains. Longest chain 24 peptides. Score 0.550 Taking the results from Round 5 Chains 70, Residues 435, Estimated correctness of the model 0.0 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ 9994 reflections ( 98.35 % complete ) and 15196 restraints for refining 6712 atoms. 13463 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2211 (Rfree = 0.000) for 6712 atoms. Found 27 (36 requested) and removed 50 (18 requested) atoms. Cycle 17: After refmac, R = 0.2176 (Rfree = 0.000) for 6658 atoms. Found 30 (36 requested) and removed 46 (18 requested) atoms. Cycle 18: After refmac, R = 0.2304 (Rfree = 0.000) for 6611 atoms. Found 36 (36 requested) and removed 45 (18 requested) atoms. Cycle 19: After refmac, R = 0.2041 (Rfree = 0.000) for 6566 atoms. Found 36 (36 requested) and removed 25 (18 requested) atoms. Cycle 20: After refmac, R = 0.2053 (Rfree = 0.000) for 6560 atoms. Found 36 (36 requested) and removed 28 (18 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.30 3.34 Search for helices and strands: 0 residues in 0 chains, 6788 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 6811 seeds are put forward Round 1: 399 peptides, 74 chains. Longest chain 20 peptides. Score 0.358 Round 2: 491 peptides, 81 chains. Longest chain 23 peptides. Score 0.457 Round 3: 498 peptides, 74 chains. Longest chain 28 peptides. Score 0.512 Round 4: 474 peptides, 69 chains. Longest chain 24 peptides. Score 0.509 Round 5: 492 peptides, 70 chains. Longest chain 20 peptides. Score 0.528 Taking the results from Round 5 Chains 70, Residues 422, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9994 reflections ( 98.35 % complete ) and 15492 restraints for refining 6714 atoms. 13874 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2358 (Rfree = 0.000) for 6714 atoms. Found 36 (36 requested) and removed 40 (18 requested) atoms. Cycle 22: After refmac, R = 0.2237 (Rfree = 0.000) for 6664 atoms. Found 36 (36 requested) and removed 41 (18 requested) atoms. Cycle 23: After refmac, R = 0.2072 (Rfree = 0.000) for 6622 atoms. Found 29 (36 requested) and removed 35 (18 requested) atoms. Cycle 24: After refmac, R = 0.2120 (Rfree = 0.000) for 6592 atoms. Found 36 (36 requested) and removed 27 (18 requested) atoms. Cycle 25: After refmac, R = 0.2137 (Rfree = 0.000) for 6584 atoms. Found 36 (36 requested) and removed 36 (18 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.28 3.32 Search for helices and strands: 0 residues in 0 chains, 6792 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 6804 seeds are put forward Round 1: 395 peptides, 77 chains. Longest chain 13 peptides. Score 0.329 Round 2: 450 peptides, 81 chains. Longest chain 12 peptides. Score 0.393 Round 3: 429 peptides, 71 chains. Longest chain 14 peptides. Score 0.428 Round 4: 453 peptides, 73 chains. Longest chain 13 peptides. Score 0.452 Round 5: 451 peptides, 74 chains. Longest chain 16 peptides. Score 0.442 Taking the results from Round 4 Chains 73, Residues 380, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9994 reflections ( 98.35 % complete ) and 15692 restraints for refining 6713 atoms. 14245 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2533 (Rfree = 0.000) for 6713 atoms. Found 36 (36 requested) and removed 58 (18 requested) atoms. Cycle 27: After refmac, R = 0.2544 (Rfree = 0.000) for 6649 atoms. Found 36 (36 requested) and removed 63 (18 requested) atoms. Cycle 28: After refmac, R = 0.2206 (Rfree = 0.000) for 6579 atoms. Found 36 (36 requested) and removed 37 (18 requested) atoms. Cycle 29: After refmac, R = 0.2157 (Rfree = 0.000) for 6562 atoms. Found 36 (36 requested) and removed 39 (18 requested) atoms. Cycle 30: After refmac, R = 0.2077 (Rfree = 0.000) for 6546 atoms. Found 36 (36 requested) and removed 33 (18 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.28 3.32 Search for helices and strands: 0 residues in 0 chains, 6754 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 6769 seeds are put forward Round 1: 378 peptides, 79 chains. Longest chain 10 peptides. Score 0.284 Round 2: 439 peptides, 75 chains. Longest chain 12 peptides. Score 0.417 Round 3: 468 peptides, 79 chains. Longest chain 13 peptides. Score 0.435 Round 4: 470 peptides, 80 chains. Longest chain 15 peptides. Score 0.432 Round 5: 469 peptides, 73 chains. Longest chain 13 peptides. Score 0.476 Taking the results from Round 5 Chains 73, Residues 396, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9994 reflections ( 98.35 % complete ) and 15702 restraints for refining 6715 atoms. 14191 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2262 (Rfree = 0.000) for 6715 atoms. Found 36 (36 requested) and removed 52 (18 requested) atoms. Cycle 32: After refmac, R = 0.2116 (Rfree = 0.000) for 6654 atoms. Found 36 (36 requested) and removed 46 (18 requested) atoms. Cycle 33: After refmac, R = 0.1972 (Rfree = 0.000) for 6621 atoms. Found 36 (36 requested) and removed 32 (18 requested) atoms. Cycle 34: After refmac, R = 0.1878 (Rfree = 0.000) for 6599 atoms. Found 36 (36 requested) and removed 33 (18 requested) atoms. Cycle 35: After refmac, R = 0.1772 (Rfree = 0.000) for 6591 atoms. Found 36 (36 requested) and removed 27 (18 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.27 3.31 Search for helices and strands: 0 residues in 0 chains, 6797 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 6810 seeds are put forward Round 1: 341 peptides, 73 chains. Longest chain 10 peptides. Score 0.262 Round 2: 420 peptides, 77 chains. Longest chain 12 peptides. Score 0.372 Round 3: 421 peptides, 73 chains. Longest chain 11 peptides. Score 0.402 Round 4: 428 peptides, 71 chains. Longest chain 14 peptides. Score 0.427 Round 5: 415 peptides, 69 chains. Longest chain 13 peptides. Score 0.420 Taking the results from Round 4 Chains 71, Residues 357, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9994 reflections ( 98.35 % complete ) and 15923 restraints for refining 6715 atoms. 14566 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2175 (Rfree = 0.000) for 6715 atoms. Found 35 (36 requested) and removed 37 (18 requested) atoms. Cycle 37: After refmac, R = 0.2064 (Rfree = 0.000) for 6680 atoms. Found 36 (36 requested) and removed 34 (18 requested) atoms. Cycle 38: After refmac, R = 0.2023 (Rfree = 0.000) for 6664 atoms. Found 36 (36 requested) and removed 39 (18 requested) atoms. Cycle 39: After refmac, R = 0.1908 (Rfree = 0.000) for 6643 atoms. Found 36 (36 requested) and removed 31 (18 requested) atoms. Cycle 40: After refmac, R = 0.1828 (Rfree = 0.000) for 6633 atoms. Found 36 (36 requested) and removed 32 (18 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.23 3.27 Search for helices and strands: 0 residues in 0 chains, 6856 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 6875 seeds are put forward Round 1: 343 peptides, 71 chains. Longest chain 10 peptides. Score 0.281 Round 2: 366 peptides, 66 chains. Longest chain 12 peptides. Score 0.360 Round 3: 361 peptides, 61 chains. Longest chain 12 peptides. Score 0.388 Round 4: 372 peptides, 63 chains. Longest chain 17 peptides. Score 0.392 Round 5: 379 peptides, 60 chains. Longest chain 17 peptides. Score 0.425 Taking the results from Round 5 Chains 60, Residues 319, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9994 reflections ( 98.35 % complete ) and 16147 restraints for refining 6715 atoms. 14931 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2138 (Rfree = 0.000) for 6715 atoms. Found 36 (36 requested) and removed 34 (18 requested) atoms. Cycle 42: After refmac, R = 0.2014 (Rfree = 0.000) for 6696 atoms. Found 36 (36 requested) and removed 37 (18 requested) atoms. Cycle 43: After refmac, R = 0.1979 (Rfree = 0.000) for 6676 atoms. Found 36 (36 requested) and removed 31 (18 requested) atoms. Cycle 44: After refmac, R = 0.1619 (Rfree = 0.000) for 6671 atoms. Found 7 (36 requested) and removed 24 (18 requested) atoms. Cycle 45: After refmac, R = 0.1496 (Rfree = 0.000) for 6640 atoms. Found 9 (36 requested) and removed 21 (18 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.28 3.32 Search for helices and strands: 0 residues in 0 chains, 6815 seeds are put forward NCS extension: 26 residues added (2 deleted due to clashes), 6841 seeds are put forward Round 1: 311 peptides, 66 chains. Longest chain 9 peptides. Score 0.260 Round 2: 359 peptides, 66 chains. Longest chain 11 peptides. Score 0.348 Round 3: 372 peptides, 64 chains. Longest chain 16 peptides. Score 0.385 Round 4: 368 peptides, 64 chains. Longest chain 16 peptides. Score 0.378 Round 5: 365 peptides, 63 chains. Longest chain 12 peptides. Score 0.380 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 64, Residues 308, 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 1vqy-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 9994 reflections ( 98.35 % complete ) and 16184 restraints for refining 6715 atoms. 15016 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2014 (Rfree = 0.000) for 6715 atoms. Found 0 (36 requested) and removed 18 (18 requested) atoms. Cycle 47: After refmac, R = 0.2010 (Rfree = 0.000) for 6680 atoms. Found 0 (36 requested) and removed 18 (18 requested) atoms. Cycle 48: After refmac, R = 0.2094 (Rfree = 0.000) for 6651 atoms. Found 0 (36 requested) and removed 18 (18 requested) atoms. Cycle 49: After refmac, R = 0.1974 (Rfree = 0.000) for 6622 atoms. Found 0 (36 requested) and removed 18 (18 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 21:02:36 GMT 2018 Job finished. TimeTaking 94.68 Used memory is bytes: 4839640