null Mon 24 Dec 07:53:08 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vl5-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vl5-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vl5-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vl5-3.6-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/1vl5-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vl5-3.6-parrot-noncs ############### 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 07:53:13 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/noncs/ArpWArp/wArpResults/WorkingDir/1vl5-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vl5-3.6-parrot-noncs/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 783 and 0 Target number of residues in the AU: 783 Target solvent content: 0.6342 Checking the provided sequence file Detected sequence length: 260 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1040 Adjusted target solvent content: 0.51 Input MTZ file: 1vl5-3.6-parrot-noncs.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: 4 Cell parameters: 64.006 87.475 105.236 90.000 100.573 90.000 Input sequence file: 1vl5-3.6-parrot-noncs.fasta_lf Building free atoms model in initial map for 8320 target number of atoms Had to go as low as 0.75 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: 49.849 3.600 Wilson plot Bfac: 68.61 13375 reflections ( 99.90 % complete ) and 0 restraints for refining 9245 atoms. Observations/parameters ratio is 0.36 ------------------------------------------------------ Starting model: R = 0.3325 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2972 (Rfree = 0.000) for 9245 atoms. Found 59 (59 requested) and removed 71 (29 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.39 3.35 Search for helices and strands: 0 residues in 0 chains, 9390 seeds are put forward NCS extension: 0 residues added, 9390 seeds are put forward Round 1: 401 peptides, 76 chains. Longest chain 13 peptides. Score 0.326 Round 2: 516 peptides, 78 chains. Longest chain 14 peptides. Score 0.474 Round 3: 544 peptides, 76 chains. Longest chain 19 peptides. Score 0.519 Round 4: 563 peptides, 76 chains. Longest chain 18 peptides. Score 0.541 Round 5: 571 peptides, 69 chains. Longest chain 29 peptides. Score 0.585 Taking the results from Round 5 Chains 73, Residues 502, Estimated correctness of the model 8.7 % 5 chains (37 residues) have been docked in sequence ------------------------------------------------------ 13375 reflections ( 99.90 % complete ) and 17182 restraints for refining 7540 atoms. 15140 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2264 (Rfree = 0.000) for 7540 atoms. Found 22 (48 requested) and removed 58 (24 requested) atoms. Cycle 2: After refmac, R = 0.2143 (Rfree = 0.000) for 7381 atoms. Found 26 (48 requested) and removed 41 (24 requested) atoms. Cycle 3: After refmac, R = 0.1983 (Rfree = 0.000) for 7324 atoms. Found 9 (47 requested) and removed 38 (23 requested) atoms. Cycle 4: After refmac, R = 0.1991 (Rfree = 0.000) for 7257 atoms. Found 17 (46 requested) and removed 36 (23 requested) atoms. Cycle 5: After refmac, R = 0.1934 (Rfree = 0.000) for 7214 atoms. Found 16 (46 requested) and removed 32 (23 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.34 3.30 Search for helices and strands: 0 residues in 0 chains, 7510 seeds are put forward NCS extension: 28 residues added (1 deleted due to clashes), 7538 seeds are put forward Round 1: 473 peptides, 82 chains. Longest chain 16 peptides. Score 0.393 Round 2: 555 peptides, 78 chains. Longest chain 21 peptides. Score 0.522 Round 3: 534 peptides, 75 chains. Longest chain 24 peptides. Score 0.512 Round 4: 555 peptides, 76 chains. Longest chain 22 peptides. Score 0.532 Round 5: 550 peptides, 76 chains. Longest chain 18 peptides. Score 0.526 Taking the results from Round 4 Chains 78, Residues 479, Estimated correctness of the model 0.0 % 3 chains (41 residues) have been docked in sequence ------------------------------------------------------ 13375 reflections ( 99.90 % complete ) and 16589 restraints for refining 7403 atoms. 14595 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2260 (Rfree = 0.000) for 7403 atoms. Found 30 (47 requested) and removed 52 (23 requested) atoms. Cycle 7: After refmac, R = 0.2102 (Rfree = 0.000) for 7304 atoms. Found 25 (47 requested) and removed 50 (23 requested) atoms. Cycle 8: After refmac, R = 0.2040 (Rfree = 0.000) for 7241 atoms. Found 23 (46 requested) and removed 40 (23 requested) atoms. Cycle 9: After refmac, R = 0.1945 (Rfree = 0.000) for 7192 atoms. Found 21 (46 requested) and removed 36 (23 requested) atoms. Cycle 10: After refmac, R = 0.1911 (Rfree = 0.000) for 7156 atoms. Found 19 (46 requested) and removed 35 (23 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.36 3.32 Search for helices and strands: 0 residues in 0 chains, 7399 seeds are put forward NCS extension: 18 residues added (3 deleted due to clashes), 7417 seeds are put forward Round 1: 472 peptides, 82 chains. Longest chain 16 peptides. Score 0.392 Round 2: 546 peptides, 85 chains. Longest chain 19 peptides. Score 0.473 Round 3: 571 peptides, 77 chains. Longest chain 27 peptides. Score 0.545 Round 4: 582 peptides, 78 chains. Longest chain 25 peptides. Score 0.553 Round 5: 575 peptides, 78 chains. Longest chain 23 peptides. Score 0.545 Taking the results from Round 4 Chains 82, Residues 504, Estimated correctness of the model 0.0 % 6 chains (67 residues) have been docked in sequence ------------------------------------------------------ 13375 reflections ( 99.90 % complete ) and 16370 restraints for refining 7542 atoms. 14223 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2200 (Rfree = 0.000) for 7542 atoms. Found 25 (48 requested) and removed 71 (24 requested) atoms. Cycle 12: After refmac, R = 0.2126 (Rfree = 0.000) for 7448 atoms. Found 27 (48 requested) and removed 52 (24 requested) atoms. Cycle 13: After refmac, R = 0.2025 (Rfree = 0.000) for 7394 atoms. Found 17 (47 requested) and removed 41 (23 requested) atoms. Cycle 14: After refmac, R = 0.1994 (Rfree = 0.000) for 7341 atoms. Found 22 (47 requested) and removed 34 (23 requested) atoms. Cycle 15: After refmac, R = 0.1935 (Rfree = 0.000) for 7315 atoms. Found 19 (47 requested) and removed 32 (23 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.36 3.32 Search for helices and strands: 0 residues in 0 chains, 7544 seeds are put forward NCS extension: 27 residues added (0 deleted due to clashes), 7571 seeds are put forward Round 1: 459 peptides, 83 chains. Longest chain 16 peptides. Score 0.367 Round 2: 528 peptides, 77 chains. Longest chain 19 peptides. Score 0.494 Round 3: 535 peptides, 80 chains. Longest chain 18 peptides. Score 0.486 Round 4: 520 peptides, 75 chains. Longest chain 22 peptides. Score 0.495 Round 5: 518 peptides, 71 chains. Longest chain 18 peptides. Score 0.515 Taking the results from Round 5 Chains 75, Residues 447, Estimated correctness of the model 0.0 % 6 chains (45 residues) have been docked in sequence ------------------------------------------------------ 13375 reflections ( 99.90 % complete ) and 17129 restraints for refining 7542 atoms. 15283 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2183 (Rfree = 0.000) for 7542 atoms. Found 36 (48 requested) and removed 42 (24 requested) atoms. Cycle 17: After refmac, R = 0.2106 (Rfree = 0.000) for 7484 atoms. Found 45 (48 requested) and removed 41 (24 requested) atoms. Cycle 18: After refmac, R = 0.1986 (Rfree = 0.000) for 7448 atoms. Found 34 (48 requested) and removed 31 (24 requested) atoms. Cycle 19: After refmac, R = 0.1908 (Rfree = 0.000) for 7428 atoms. Found 35 (47 requested) and removed 32 (23 requested) atoms. Cycle 20: After refmac, R = 0.1859 (Rfree = 0.000) for 7408 atoms. Found 26 (47 requested) and removed 27 (23 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.39 3.35 Search for helices and strands: 0 residues in 0 chains, 7656 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 7677 seeds are put forward Round 1: 452 peptides, 84 chains. Longest chain 17 peptides. Score 0.351 Round 2: 508 peptides, 80 chains. Longest chain 22 peptides. Score 0.452 Round 3: 533 peptides, 87 chains. Longest chain 19 peptides. Score 0.445 Round 4: 536 peptides, 83 chains. Longest chain 14 peptides. Score 0.471 Round 5: 525 peptides, 81 chains. Longest chain 26 peptides. Score 0.468 Taking the results from Round 4 Chains 83, Residues 453, Estimated correctness of the model 0.0 % 6 chains (39 residues) have been docked in sequence ------------------------------------------------------ 13375 reflections ( 99.90 % complete ) and 17282 restraints for refining 7541 atoms. 15443 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2070 (Rfree = 0.000) for 7541 atoms. Found 29 (48 requested) and removed 37 (24 requested) atoms. Cycle 22: After refmac, R = 0.1945 (Rfree = 0.000) for 7505 atoms. Found 28 (48 requested) and removed 32 (24 requested) atoms. Cycle 23: After refmac, R = 0.1857 (Rfree = 0.000) for 7478 atoms. Found 26 (48 requested) and removed 35 (24 requested) atoms. Cycle 24: After refmac, R = 0.1804 (Rfree = 0.000) for 7448 atoms. Found 18 (47 requested) and removed 34 (23 requested) atoms. Cycle 25: After refmac, R = 0.1786 (Rfree = 0.000) for 7416 atoms. Found 20 (47 requested) and removed 33 (23 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.38 3.34 Search for helices and strands: 0 residues in 0 chains, 7662 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 7679 seeds are put forward Round 1: 460 peptides, 87 chains. Longest chain 14 peptides. Score 0.344 Round 2: 514 peptides, 85 chains. Longest chain 17 peptides. Score 0.431 Round 3: 546 peptides, 85 chains. Longest chain 15 peptides. Score 0.473 Round 4: 553 peptides, 87 chains. Longest chain 15 peptides. Score 0.471 Round 5: 532 peptides, 77 chains. Longest chain 13 peptides. Score 0.499 Taking the results from Round 5 Chains 79, Residues 455, Estimated correctness of the model 0.0 % 6 chains (42 residues) have been docked in sequence ------------------------------------------------------ 13375 reflections ( 99.90 % complete ) and 16948 restraints for refining 7542 atoms. 15087 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2099 (Rfree = 0.000) for 7542 atoms. Found 42 (48 requested) and removed 40 (24 requested) atoms. Cycle 27: After refmac, R = 0.2037 (Rfree = 0.000) for 7487 atoms. Found 43 (48 requested) and removed 36 (24 requested) atoms. Cycle 28: After refmac, R = 0.1708 (Rfree = 0.000) for 7471 atoms. Found 12 (48 requested) and removed 30 (24 requested) atoms. Cycle 29: After refmac, R = 0.1643 (Rfree = 0.000) for 7440 atoms. Found 9 (47 requested) and removed 30 (23 requested) atoms. Cycle 30: After refmac, R = 0.1610 (Rfree = 0.000) for 7408 atoms. Found 4 (47 requested) and removed 25 (23 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.37 3.33 Search for helices and strands: 0 residues in 0 chains, 7644 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 7657 seeds are put forward Round 1: 414 peptides, 81 chains. Longest chain 10 peptides. Score 0.313 Round 2: 466 peptides, 80 chains. Longest chain 12 peptides. Score 0.395 Round 3: 476 peptides, 75 chains. Longest chain 14 peptides. Score 0.439 Round 4: 488 peptides, 75 chains. Longest chain 20 peptides. Score 0.455 Round 5: 496 peptides, 80 chains. Longest chain 15 peptides. Score 0.436 Taking the results from Round 4 Chains 76, Residues 413, Estimated correctness of the model 0.0 % 3 chains (16 residues) have been docked in sequence ------------------------------------------------------ 13375 reflections ( 99.90 % complete ) and 17524 restraints for refining 7542 atoms. 15903 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2025 (Rfree = 0.000) for 7542 atoms. Found 27 (48 requested) and removed 34 (24 requested) atoms. Cycle 32: After refmac, R = 0.1962 (Rfree = 0.000) for 7510 atoms. Found 27 (48 requested) and removed 30 (24 requested) atoms. Cycle 33: After refmac, R = 0.1895 (Rfree = 0.000) for 7491 atoms. Found 18 (48 requested) and removed 26 (24 requested) atoms. Cycle 34: After refmac, R = 0.1613 (Rfree = 0.000) for 7470 atoms. Found 7 (48 requested) and removed 29 (24 requested) atoms. Cycle 35: After refmac, R = 0.1649 (Rfree = 0.000) for 7445 atoms. Found 10 (47 requested) and removed 23 (23 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.39 3.35 Search for helices and strands: 0 residues in 0 chains, 7680 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 7695 seeds are put forward Round 1: 389 peptides, 79 chains. Longest chain 11 peptides. Score 0.288 Round 2: 395 peptides, 66 chains. Longest chain 13 peptides. Score 0.381 Round 3: 456 peptides, 66 chains. Longest chain 17 peptides. Score 0.465 Round 4: 442 peptides, 67 chains. Longest chain 21 peptides. Score 0.440 Round 5: 435 peptides, 70 chains. Longest chain 13 peptides. Score 0.413 Taking the results from Round 3 Chains 66, Residues 390, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 13375 reflections ( 99.90 % complete ) and 17535 restraints for refining 7539 atoms. 16041 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2008 (Rfree = 0.000) for 7539 atoms. Found 33 (48 requested) and removed 38 (24 requested) atoms. Cycle 37: After refmac, R = 0.1931 (Rfree = 0.000) for 7500 atoms. Found 22 (48 requested) and removed 35 (24 requested) atoms. Cycle 38: After refmac, R = 0.1856 (Rfree = 0.000) for 7471 atoms. Found 36 (48 requested) and removed 31 (24 requested) atoms. Cycle 39: After refmac, R = 0.1520 (Rfree = 0.000) for 7465 atoms. Found 7 (47 requested) and removed 27 (23 requested) atoms. Cycle 40: After refmac, R = 0.1454 (Rfree = 0.000) for 7435 atoms. Found 4 (47 requested) and removed 26 (23 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.40 3.36 Search for helices and strands: 0 residues in 0 chains, 7629 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 7645 seeds are put forward Round 1: 378 peptides, 75 chains. Longest chain 14 peptides. Score 0.297 Round 2: 438 peptides, 73 chains. Longest chain 18 peptides. Score 0.399 Round 3: 455 peptides, 72 chains. Longest chain 15 peptides. Score 0.428 Round 4: 450 peptides, 73 chains. Longest chain 16 peptides. Score 0.415 Round 5: 456 peptides, 70 chains. Longest chain 16 peptides. Score 0.441 Taking the results from Round 5 Chains 70, Residues 386, Estimated correctness of the model 0.0 % 4 chains (24 residues) have been docked in sequence ------------------------------------------------------ 13375 reflections ( 99.90 % complete ) and 17283 restraints for refining 7541 atoms. 15715 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1989 (Rfree = 0.000) for 7541 atoms. Found 43 (48 requested) and removed 32 (24 requested) atoms. Cycle 42: After refmac, R = 0.1941 (Rfree = 0.000) for 7511 atoms. Found 35 (48 requested) and removed 30 (24 requested) atoms. Cycle 43: After refmac, R = 0.1929 (Rfree = 0.000) for 7500 atoms. Found 26 (48 requested) and removed 36 (24 requested) atoms. Cycle 44: After refmac, R = 0.1921 (Rfree = 0.000) for 7476 atoms. Found 38 (48 requested) and removed 32 (24 requested) atoms. Cycle 45: After refmac, R = 0.1875 (Rfree = 0.000) for 7474 atoms. Found 25 (48 requested) and removed 28 (24 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.38 3.34 Search for helices and strands: 0 residues in 0 chains, 7710 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 7732 seeds are put forward Round 1: 352 peptides, 73 chains. Longest chain 10 peptides. Score 0.269 Round 2: 378 peptides, 68 chains. Longest chain 13 peptides. Score 0.343 Round 3: 376 peptides, 64 chains. Longest chain 21 peptides. Score 0.366 Round 4: 378 peptides, 67 chains. Longest chain 14 peptides. Score 0.349 Round 5: 391 peptides, 64 chains. Longest chain 23 peptides. Score 0.388 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 64, Residues 327, 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 1vl5-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 13375 reflections ( 99.90 % complete ) and 17853 restraints for refining 7542 atoms. 16609 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2108 (Rfree = 0.000) for 7542 atoms. Found 0 (48 requested) and removed 24 (24 requested) atoms. Cycle 47: After refmac, R = 0.2027 (Rfree = 0.000) for 7488 atoms. Found 0 (48 requested) and removed 24 (24 requested) atoms. Cycle 48: After refmac, R = 0.1912 (Rfree = 0.000) for 7452 atoms. Found 0 (47 requested) and removed 23 (23 requested) atoms. Cycle 49: After refmac, R = 0.2050 (Rfree = 0.000) for 7420 atoms. Found 0 (47 requested) and removed 23 (23 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 09:06:19 GMT 2018 Job finished. TimeTaking 73.19 Used memory is bytes: 12949376