null Sun 23 Dec 22:23:05 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 1vrb-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vrb-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vrb-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vrb-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/1vrb-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vrb-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 ============================================================ Sun 23 Dec 22:23:14 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/1vrb-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vrb-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 874 and 0 Target number of residues in the AU: 874 Target solvent content: 0.6664 Checking the provided sequence file Detected sequence length: 342 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1368 Adjusted target solvent content: 0.48 Input MTZ file: 1vrb-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: 47.576 104.273 285.843 90.000 90.000 90.000 Input sequence file: 1vrb-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 10944 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: 48.979 3.800 Wilson plot Bfac: 89.57 14699 reflections ( 99.13 % complete ) and 0 restraints for refining 12061 atoms. Observations/parameters ratio is 0.30 ------------------------------------------------------ Starting model: R = 0.3497 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3330 (Rfree = 0.000) for 12061 atoms. Found 66 (66 requested) and removed 160 (33 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.71 3.81 Search for helices and strands: 0 residues in 0 chains, 12206 seeds are put forward NCS extension: 0 residues added, 12206 seeds are put forward Round 1: 415 peptides, 78 chains. Longest chain 16 peptides. Score 0.311 Round 2: 538 peptides, 92 chains. Longest chain 13 peptides. Score 0.387 Round 3: 607 peptides, 91 chains. Longest chain 21 peptides. Score 0.468 Round 4: 599 peptides, 93 chains. Longest chain 18 peptides. Score 0.451 Round 5: 606 peptides, 89 chains. Longest chain 17 peptides. Score 0.477 Taking the results from Round 5 Chains 90, Residues 517, Estimated correctness of the model 0.0 % 7 chains (51 residues) have been docked in sequence ------------------------------------------------------ 14699 reflections ( 99.13 % complete ) and 23502 restraints for refining 9888 atoms. 21364 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2744 (Rfree = 0.000) for 9888 atoms. Found 41 (54 requested) and removed 92 (27 requested) atoms. Cycle 2: After refmac, R = 0.2504 (Rfree = 0.000) for 9638 atoms. Found 51 (54 requested) and removed 89 (27 requested) atoms. Cycle 3: After refmac, R = 0.2425 (Rfree = 0.000) for 9532 atoms. Found 50 (52 requested) and removed 68 (26 requested) atoms. Cycle 4: After refmac, R = 0.2403 (Rfree = 0.000) for 9466 atoms. Found 52 (52 requested) and removed 49 (26 requested) atoms. Cycle 5: After refmac, R = 0.2320 (Rfree = 0.000) for 9427 atoms. Found 49 (52 requested) and removed 64 (26 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.64 3.74 Search for helices and strands: 0 residues in 0 chains, 9770 seeds are put forward NCS extension: 19 residues added (3 deleted due to clashes), 9789 seeds are put forward Round 1: 506 peptides, 99 chains. Longest chain 12 peptides. Score 0.313 Round 2: 632 peptides, 100 chains. Longest chain 17 peptides. Score 0.453 Round 3: 645 peptides, 99 chains. Longest chain 18 peptides. Score 0.471 Round 4: 663 peptides, 98 chains. Longest chain 22 peptides. Score 0.494 Round 5: 653 peptides, 89 chains. Longest chain 25 peptides. Score 0.524 Taking the results from Round 5 Chains 93, Residues 564, Estimated correctness of the model 0.0 % 7 chains (54 residues) have been docked in sequence ------------------------------------------------------ 14699 reflections ( 99.13 % complete ) and 21646 restraints for refining 9612 atoms. 19295 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2474 (Rfree = 0.000) for 9612 atoms. Found 48 (52 requested) and removed 101 (26 requested) atoms. Cycle 7: After refmac, R = 0.2351 (Rfree = 0.000) for 9481 atoms. Found 50 (52 requested) and removed 60 (26 requested) atoms. Cycle 8: After refmac, R = 0.2211 (Rfree = 0.000) for 9409 atoms. Found 49 (52 requested) and removed 52 (26 requested) atoms. Cycle 9: After refmac, R = 0.1936 (Rfree = 0.000) for 9349 atoms. Found 19 (51 requested) and removed 40 (25 requested) atoms. Cycle 10: After refmac, R = 0.1831 (Rfree = 0.000) for 9285 atoms. Found 16 (51 requested) and removed 33 (25 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.70 3.80 Search for helices and strands: 0 residues in 0 chains, 9532 seeds are put forward NCS extension: 35 residues added (1 deleted due to clashes), 9567 seeds are put forward Round 1: 523 peptides, 104 chains. Longest chain 10 peptides. Score 0.308 Round 2: 609 peptides, 91 chains. Longest chain 18 peptides. Score 0.471 Round 3: 631 peptides, 95 chains. Longest chain 25 peptides. Score 0.475 Round 4: 631 peptides, 91 chains. Longest chain 17 peptides. Score 0.493 Round 5: 612 peptides, 88 chains. Longest chain 20 peptides. Score 0.487 Taking the results from Round 4 Chains 91, Residues 540, Estimated correctness of the model 0.0 % 4 chains (22 residues) have been docked in sequence ------------------------------------------------------ 14699 reflections ( 99.13 % complete ) and 21749 restraints for refining 9503 atoms. 19609 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2358 (Rfree = 0.000) for 9503 atoms. Found 49 (52 requested) and removed 87 (26 requested) atoms. Cycle 12: After refmac, R = 0.2221 (Rfree = 0.000) for 9393 atoms. Found 49 (52 requested) and removed 55 (26 requested) atoms. Cycle 13: After refmac, R = 0.2148 (Rfree = 0.000) for 9335 atoms. Found 51 (51 requested) and removed 58 (25 requested) atoms. Cycle 14: After refmac, R = 0.2131 (Rfree = 0.000) for 9293 atoms. Found 51 (51 requested) and removed 44 (25 requested) atoms. Cycle 15: After refmac, R = 0.2103 (Rfree = 0.000) for 9263 atoms. Found 51 (51 requested) and removed 48 (25 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.63 3.73 Search for helices and strands: 0 residues in 0 chains, 9609 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 9633 seeds are put forward Round 1: 520 peptides, 99 chains. Longest chain 15 peptides. Score 0.330 Round 2: 581 peptides, 99 chains. Longest chain 19 peptides. Score 0.402 Round 3: 604 peptides, 95 chains. Longest chain 16 peptides. Score 0.447 Round 4: 606 peptides, 90 chains. Longest chain 23 peptides. Score 0.472 Round 5: 589 peptides, 89 chains. Longest chain 16 peptides. Score 0.459 Taking the results from Round 4 Chains 90, Residues 516, Estimated correctness of the model 0.0 % 8 chains (55 residues) have been docked in sequence ------------------------------------------------------ 14699 reflections ( 99.13 % complete ) and 21829 restraints for refining 9659 atoms. 19653 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2333 (Rfree = 0.000) for 9659 atoms. Found 53 (53 requested) and removed 96 (26 requested) atoms. Cycle 17: After refmac, R = 0.2184 (Rfree = 0.000) for 9538 atoms. Found 52 (52 requested) and removed 58 (26 requested) atoms. Cycle 18: After refmac, R = 0.2071 (Rfree = 0.000) for 9480 atoms. Found 52 (52 requested) and removed 68 (26 requested) atoms. Cycle 19: After refmac, R = 0.1744 (Rfree = 0.000) for 9427 atoms. Found 14 (52 requested) and removed 41 (26 requested) atoms. Cycle 20: After refmac, R = 0.1899 (Rfree = 0.000) for 9383 atoms. Found 51 (51 requested) and removed 35 (25 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.69 3.79 Search for helices and strands: 0 residues in 0 chains, 9683 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 9708 seeds are put forward Round 1: 494 peptides, 99 chains. Longest chain 15 peptides. Score 0.298 Round 2: 553 peptides, 95 chains. Longest chain 16 peptides. Score 0.390 Round 3: 546 peptides, 90 chains. Longest chain 15 peptides. Score 0.407 Round 4: 553 peptides, 86 chains. Longest chain 16 peptides. Score 0.434 Round 5: 568 peptides, 90 chains. Longest chain 15 peptides. Score 0.431 Taking the results from Round 4 Chains 87, Residues 467, Estimated correctness of the model 0.0 % 7 chains (42 residues) have been docked in sequence ------------------------------------------------------ 14699 reflections ( 99.13 % complete ) and 22034 restraints for refining 9710 atoms. 20090 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2250 (Rfree = 0.000) for 9710 atoms. Found 52 (53 requested) and removed 85 (26 requested) atoms. Cycle 22: After refmac, R = 0.2132 (Rfree = 0.000) for 9633 atoms. Found 53 (53 requested) and removed 56 (26 requested) atoms. Cycle 23: After refmac, R = 0.2154 (Rfree = 0.000) for 9596 atoms. Found 52 (52 requested) and removed 53 (26 requested) atoms. Cycle 24: After refmac, R = 0.2072 (Rfree = 0.000) for 9565 atoms. Found 52 (52 requested) and removed 44 (26 requested) atoms. Cycle 25: After refmac, R = 0.2071 (Rfree = 0.000) for 9543 atoms. Found 52 (52 requested) and removed 45 (26 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.66 3.76 Search for helices and strands: 0 residues in 0 chains, 9831 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 9849 seeds are put forward Round 1: 444 peptides, 92 chains. Longest chain 9 peptides. Score 0.272 Round 2: 511 peptides, 91 chains. Longest chain 15 peptides. Score 0.361 Round 3: 501 peptides, 84 chains. Longest chain 17 peptides. Score 0.385 Round 4: 508 peptides, 82 chains. Longest chain 19 peptides. Score 0.403 Round 5: 525 peptides, 82 chains. Longest chain 19 peptides. Score 0.423 Taking the results from Round 5 Chains 84, Residues 443, Estimated correctness of the model 0.0 % 5 chains (45 residues) have been docked in sequence ------------------------------------------------------ 14699 reflections ( 99.13 % complete ) and 22995 restraints for refining 9897 atoms. 21147 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2253 (Rfree = 0.000) for 9897 atoms. Found 54 (54 requested) and removed 63 (27 requested) atoms. Cycle 27: After refmac, R = 0.2196 (Rfree = 0.000) for 9827 atoms. Found 54 (54 requested) and removed 49 (27 requested) atoms. Cycle 28: After refmac, R = 0.2139 (Rfree = 0.000) for 9792 atoms. Found 54 (54 requested) and removed 57 (27 requested) atoms. Cycle 29: After refmac, R = 0.1838 (Rfree = 0.000) for 9762 atoms. Found 19 (53 requested) and removed 36 (26 requested) atoms. Cycle 30: After refmac, R = 0.1809 (Rfree = 0.000) for 9727 atoms. Found 16 (53 requested) and removed 33 (26 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.68 3.78 Search for helices and strands: 0 residues in 0 chains, 9994 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 10019 seeds are put forward Round 1: 450 peptides, 91 chains. Longest chain 19 peptides. Score 0.285 Round 2: 500 peptides, 87 chains. Longest chain 19 peptides. Score 0.368 Round 3: 526 peptides, 92 chains. Longest chain 17 peptides. Score 0.373 Round 4: 519 peptides, 83 chains. Longest chain 14 peptides. Score 0.411 Round 5: 515 peptides, 80 chains. Longest chain 15 peptides. Score 0.421 Taking the results from Round 5 Chains 80, Residues 435, Estimated correctness of the model 0.0 % 5 chains (27 residues) have been docked in sequence ------------------------------------------------------ 14699 reflections ( 99.13 % complete ) and 23068 restraints for refining 9899 atoms. 21323 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2461 (Rfree = 0.000) for 9899 atoms. Found 54 (54 requested) and removed 68 (27 requested) atoms. Cycle 32: After refmac, R = 0.2317 (Rfree = 0.000) for 9846 atoms. Found 54 (54 requested) and removed 68 (27 requested) atoms. Cycle 33: After refmac, R = 0.2275 (Rfree = 0.000) for 9815 atoms. Found 54 (54 requested) and removed 58 (27 requested) atoms. Cycle 34: After refmac, R = 0.2243 (Rfree = 0.000) for 9794 atoms. Found 53 (53 requested) and removed 56 (26 requested) atoms. Cycle 35: After refmac, R = 0.1986 (Rfree = 0.000) for 9764 atoms. Found 20 (53 requested) and removed 33 (26 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.70 3.80 Search for helices and strands: 0 residues in 0 chains, 9985 seeds are put forward NCS extension: 15 residues added (3 deleted due to clashes), 10000 seeds are put forward Round 1: 415 peptides, 86 chains. Longest chain 9 peptides. Score 0.267 Round 2: 455 peptides, 82 chains. Longest chain 12 peptides. Score 0.340 Round 3: 464 peptides, 80 chains. Longest chain 13 peptides. Score 0.362 Round 4: 479 peptides, 78 chains. Longest chain 17 peptides. Score 0.390 Round 5: 484 peptides, 78 chains. Longest chain 16 peptides. Score 0.396 Taking the results from Round 5 Chains 78, Residues 406, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 14699 reflections ( 99.13 % complete ) and 23556 restraints for refining 9898 atoms. 21965 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2345 (Rfree = 0.000) for 9898 atoms. Found 54 (54 requested) and removed 82 (27 requested) atoms. Cycle 37: After refmac, R = 0.2211 (Rfree = 0.000) for 9843 atoms. Found 54 (54 requested) and removed 68 (27 requested) atoms. Cycle 38: After refmac, R = 0.2216 (Rfree = 0.000) for 9797 atoms. Found 54 (54 requested) and removed 47 (27 requested) atoms. Cycle 39: After refmac, R = 0.1942 (Rfree = 0.000) for 9788 atoms. Found 22 (53 requested) and removed 42 (26 requested) atoms. Cycle 40: After refmac, R = 0.1858 (Rfree = 0.000) for 9753 atoms. Found 11 (53 requested) and removed 39 (26 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.70 3.80 Search for helices and strands: 0 residues in 0 chains, 9980 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 9997 seeds are put forward Round 1: 350 peptides, 74 chains. Longest chain 9 peptides. Score 0.247 Round 2: 405 peptides, 73 chains. Longest chain 10 peptides. Score 0.326 Round 3: 414 peptides, 73 chains. Longest chain 13 peptides. Score 0.338 Round 4: 418 peptides, 77 chains. Longest chain 10 peptides. Score 0.321 Round 5: 455 peptides, 74 chains. Longest chain 15 peptides. Score 0.383 Taking the results from Round 5 Chains 74, Residues 381, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 14699 reflections ( 99.13 % complete ) and 23615 restraints for refining 9898 atoms. 22141 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2251 (Rfree = 0.000) for 9898 atoms. Found 54 (54 requested) and removed 48 (27 requested) atoms. Cycle 42: After refmac, R = 0.2190 (Rfree = 0.000) for 9876 atoms. Found 54 (54 requested) and removed 53 (27 requested) atoms. Cycle 43: After refmac, R = 0.2145 (Rfree = 0.000) for 9856 atoms. Found 54 (54 requested) and removed 39 (27 requested) atoms. Cycle 44: After refmac, R = 0.2198 (Rfree = 0.000) for 9846 atoms. Found 54 (54 requested) and removed 59 (27 requested) atoms. Cycle 45: After refmac, R = 0.2100 (Rfree = 0.000) for 9821 atoms. Found 54 (54 requested) and removed 39 (27 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.68 3.78 Search for helices and strands: 0 residues in 0 chains, 10085 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 10097 seeds are put forward Round 1: 288 peptides, 64 chains. Longest chain 7 peptides. Score 0.218 Round 2: 319 peptides, 59 chains. Longest chain 14 peptides. Score 0.294 Round 3: 340 peptides, 63 chains. Longest chain 15 peptides. Score 0.298 Round 4: 348 peptides, 63 chains. Longest chain 16 peptides. Score 0.309 Round 5: 377 peptides, 70 chains. Longest chain 13 peptides. Score 0.307 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 63, Residues 285, Estimated correctness of the model 0.0 % 3 chains (9 residues) have been docked in sequence Sequence coverage is 3 % Consider running further cycles of model building using 1vrb-3_warpNtrace.pdb as input Building loops using Loopy2018 63 chains (285 residues) following loop building 3 chains (9 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 14699 reflections ( 99.13 % complete ) and 24321 restraints for refining 9860 atoms. 23228 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2313 (Rfree = 0.000) for 9860 atoms. Found 0 (54 requested) and removed 27 (27 requested) atoms. Cycle 47: After refmac, R = 0.2361 (Rfree = 0.000) for 9807 atoms. Found 0 (54 requested) and removed 27 (27 requested) atoms. Cycle 48: After refmac, R = 0.2265 (Rfree = 0.000) for 9754 atoms. Found 0 (53 requested) and removed 26 (26 requested) atoms. Cycle 49: After refmac, R = 0.2040 (Rfree = 0.000) for 9717 atoms. Found 0 (53 requested) and removed 26 (26 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 00:11:58 GMT 2018 Job finished. TimeTaking 108.9 Used memory is bytes: 4781456