Mon 24 Dec 00:19:38 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vky-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vky-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vky-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vky-3.8-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/1vky-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vky-3.8-parrot-mrncs ############### 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 00:19:43 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/mrncs/ArpWArp/wArpResults/WorkingDir/1vky-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vky-3.8-parrot-mrncs/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 682 and 0 Target number of residues in the AU: 682 Target solvent content: 0.6175 Checking the provided sequence file Detected sequence length: 347 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 694 Adjusted target solvent content: 0.61 Input MTZ file: 1vky-3.8-parrot-mrncs.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: 23 Cell parameters: 119.363 122.591 131.880 90.000 90.000 90.000 Input sequence file: 1vky-3.8-parrot-mrncs.fasta_lf Building free atoms model in initial map for 5552 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: 41.380 3.800 Wilson plot Bfac: 60.08 9833 reflections ( 99.71 % complete ) and 0 restraints for refining 6174 atoms. Observations/parameters ratio is 0.40 ------------------------------------------------------ Starting model: R = 0.3157 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2954 (Rfree = 0.000) for 6174 atoms. Found 33 (33 requested) and removed 37 (16 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.38 2.91 Search for helices and strands: 0 residues in 0 chains, 6244 seeds are put forward NCS extension: 0 residues added, 6244 seeds are put forward Round 1: 318 peptides, 52 chains. Longest chain 37 peptides. Score 0.385 Round 2: 373 peptides, 50 chains. Longest chain 24 peptides. Score 0.489 Round 3: 378 peptides, 45 chains. Longest chain 19 peptides. Score 0.531 Round 4: 390 peptides, 45 chains. Longest chain 21 peptides. Score 0.548 Round 5: 402 peptides, 47 chains. Longest chain 22 peptides. Score 0.551 Taking the results from Round 5 Chains 47, Residues 355, Estimated correctness of the model 0.0 % 5 chains (35 residues) have been docked in sequence ------------------------------------------------------ 9833 reflections ( 99.71 % complete ) and 10995 restraints for refining 5019 atoms. 9516 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2463 (Rfree = 0.000) for 5019 atoms. Found 27 (27 requested) and removed 43 (13 requested) atoms. Cycle 2: After refmac, R = 0.2272 (Rfree = 0.000) for 4913 atoms. Found 26 (27 requested) and removed 46 (13 requested) atoms. Failed to save intermediate PDB Cycle 3: After refmac, R = 0.2181 (Rfree = 0.000) for 4861 atoms. Found 26 (26 requested) and removed 37 (13 requested) atoms. Cycle 4: After refmac, R = 0.2098 (Rfree = 0.000) for 4828 atoms. Found 26 (26 requested) and removed 28 (13 requested) atoms. Cycle 5: After refmac, R = 0.1985 (Rfree = 0.000) for 4810 atoms. Found 25 (26 requested) and removed 31 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.33 2.87 Search for helices and strands: 0 residues in 0 chains, 4958 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 4972 seeds are put forward Round 1: 371 peptides, 56 chains. Longest chain 15 peptides. Score 0.444 Round 2: 376 peptides, 47 chains. Longest chain 24 peptides. Score 0.514 Round 3: 385 peptides, 46 chains. Longest chain 23 peptides. Score 0.534 Round 4: 389 peptides, 42 chains. Longest chain 22 peptides. Score 0.566 Round 5: 387 peptides, 44 chains. Longest chain 26 peptides. Score 0.550 Taking the results from Round 4 Chains 45, Residues 347, Estimated correctness of the model 0.0 % 4 chains (43 residues) have been docked in sequence ------------------------------------------------------ 9833 reflections ( 99.71 % complete ) and 10948 restraints for refining 5021 atoms. 9458 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2349 (Rfree = 0.000) for 5021 atoms. Found 27 (27 requested) and removed 51 (13 requested) atoms. Cycle 7: After refmac, R = 0.2189 (Rfree = 0.000) for 4939 atoms. Found 27 (27 requested) and removed 36 (13 requested) atoms. Cycle 8: After refmac, R = 0.2140 (Rfree = 0.000) for 4905 atoms. Found 27 (27 requested) and removed 30 (13 requested) atoms. Cycle 9: After refmac, R = 0.2056 (Rfree = 0.000) for 4877 atoms. Found 25 (26 requested) and removed 19 (13 requested) atoms. Cycle 10: After refmac, R = 0.2078 (Rfree = 0.000) for 4855 atoms. Found 26 (26 requested) and removed 18 (13 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.33 2.87 Search for helices and strands: 0 residues in 0 chains, 4997 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 5011 seeds are put forward Round 1: 359 peptides, 53 chains. Longest chain 24 peptides. Score 0.446 Round 2: 398 peptides, 48 chains. Longest chain 33 peptides. Score 0.539 Round 3: 398 peptides, 46 chains. Longest chain 25 peptides. Score 0.552 Round 4: 386 peptides, 46 chains. Longest chain 28 peptides. Score 0.535 Round 5: 399 peptides, 46 chains. Longest chain 31 peptides. Score 0.554 Taking the results from Round 5 Chains 48, Residues 353, Estimated correctness of the model 0.0 % 4 chains (51 residues) have been docked in sequence ------------------------------------------------------ 9833 reflections ( 99.71 % complete ) and 10757 restraints for refining 5022 atoms. 9170 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2531 (Rfree = 0.000) for 5022 atoms. Found 27 (27 requested) and removed 44 (13 requested) atoms. Cycle 12: After refmac, R = 0.2259 (Rfree = 0.000) for 4953 atoms. Found 21 (27 requested) and removed 45 (13 requested) atoms. Cycle 13: After refmac, R = 0.2263 (Rfree = 0.000) for 4907 atoms. Found 27 (27 requested) and removed 40 (13 requested) atoms. Cycle 14: After refmac, R = 0.2181 (Rfree = 0.000) for 4880 atoms. Found 16 (26 requested) and removed 39 (13 requested) atoms. Cycle 15: After refmac, R = 0.2128 (Rfree = 0.000) for 4847 atoms. Found 21 (26 requested) and removed 30 (13 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.31 2.85 Search for helices and strands: 0 residues in 0 chains, 4960 seeds are put forward NCS extension: 23 residues added (6 deleted due to clashes), 4983 seeds are put forward Round 1: 378 peptides, 53 chains. Longest chain 30 peptides. Score 0.476 Round 2: 405 peptides, 53 chains. Longest chain 20 peptides. Score 0.517 Round 3: 392 peptides, 48 chains. Longest chain 26 peptides. Score 0.531 Round 4: 391 peptides, 47 chains. Longest chain 26 peptides. Score 0.536 Round 5: 401 peptides, 46 chains. Longest chain 39 peptides. Score 0.556 Taking the results from Round 5 Chains 48, Residues 355, Estimated correctness of the model 0.0 % 3 chains (68 residues) have been docked in sequence ------------------------------------------------------ 9833 reflections ( 99.71 % complete ) and 10602 restraints for refining 5022 atoms. 8930 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2443 (Rfree = 0.000) for 5022 atoms. Found 27 (27 requested) and removed 54 (13 requested) atoms. Cycle 17: After refmac, R = 0.2232 (Rfree = 0.000) for 4931 atoms. Found 21 (27 requested) and removed 34 (13 requested) atoms. Cycle 18: After refmac, R = 0.2137 (Rfree = 0.000) for 4885 atoms. Found 23 (27 requested) and removed 26 (13 requested) atoms. Cycle 19: After refmac, R = 0.2072 (Rfree = 0.000) for 4869 atoms. Found 18 (26 requested) and removed 34 (13 requested) atoms. Cycle 20: After refmac, R = 0.2026 (Rfree = 0.000) for 4842 atoms. Found 20 (26 requested) and removed 22 (13 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.29 2.83 Search for helices and strands: 0 residues in 0 chains, 4974 seeds are put forward NCS extension: 51 residues added (2 deleted due to clashes), 5025 seeds are put forward Round 1: 348 peptides, 55 chains. Longest chain 19 peptides. Score 0.413 Round 2: 374 peptides, 50 chains. Longest chain 20 peptides. Score 0.491 Round 3: 369 peptides, 46 chains. Longest chain 21 peptides. Score 0.511 Round 4: 380 peptides, 51 chains. Longest chain 31 peptides. Score 0.493 Round 5: 388 peptides, 51 chains. Longest chain 20 peptides. Score 0.505 Taking the results from Round 3 Chains 48, Residues 323, Estimated correctness of the model 0.0 % 3 chains (27 residues) have been docked in sequence ------------------------------------------------------ 9833 reflections ( 99.71 % complete ) and 11129 restraints for refining 5020 atoms. 9788 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2218 (Rfree = 0.000) for 5020 atoms. Found 27 (27 requested) and removed 52 (13 requested) atoms. Cycle 22: After refmac, R = 0.2153 (Rfree = 0.000) for 4971 atoms. Found 14 (27 requested) and removed 29 (13 requested) atoms. Cycle 23: After refmac, R = 0.2133 (Rfree = 0.000) for 4939 atoms. Found 27 (27 requested) and removed 33 (13 requested) atoms. Cycle 24: After refmac, R = 0.2030 (Rfree = 0.000) for 4921 atoms. Found 23 (27 requested) and removed 32 (13 requested) atoms. Failed to save intermediate PDB Cycle 25: After refmac, R = 0.2011 (Rfree = 0.000) for 4902 atoms. Found 27 (27 requested) and removed 26 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.33 2.87 Search for helices and strands: 0 residues in 0 chains, 5055 seeds are put forward NCS extension: 16 residues added (3 deleted due to clashes), 5071 seeds are put forward Round 1: 355 peptides, 59 chains. Longest chain 14 peptides. Score 0.395 Round 2: 381 peptides, 51 chains. Longest chain 21 peptides. Score 0.494 Round 3: 378 peptides, 50 chains. Longest chain 20 peptides. Score 0.497 Round 4: 365 peptides, 45 chains. Longest chain 16 peptides. Score 0.512 Round 5: 373 peptides, 48 chains. Longest chain 23 peptides. Score 0.503 Taking the results from Round 4 Chains 47, Residues 320, Estimated correctness of the model 0.0 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 9833 reflections ( 99.71 % complete ) and 11394 restraints for refining 5022 atoms. 10110 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2207 (Rfree = 0.000) for 5022 atoms. Found 27 (27 requested) and removed 38 (13 requested) atoms. Cycle 27: After refmac, R = 0.2109 (Rfree = 0.000) for 4983 atoms. Found 23 (27 requested) and removed 30 (13 requested) atoms. Cycle 28: After refmac, R = 0.2114 (Rfree = 0.000) for 4965 atoms. Found 27 (27 requested) and removed 36 (13 requested) atoms. Cycle 29: After refmac, R = 0.2012 (Rfree = 0.000) for 4935 atoms. Found 27 (27 requested) and removed 30 (13 requested) atoms. Cycle 30: After refmac, R = 0.1955 (Rfree = 0.000) for 4922 atoms. Found 27 (27 requested) and removed 26 (13 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.34 2.88 Search for helices and strands: 0 residues in 0 chains, 5079 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 5096 seeds are put forward Round 1: 292 peptides, 52 chains. Longest chain 11 peptides. Score 0.338 Round 2: 358 peptides, 52 chains. Longest chain 22 peptides. Score 0.452 Round 3: 369 peptides, 46 chains. Longest chain 27 peptides. Score 0.511 Round 4: 361 peptides, 50 chains. Longest chain 24 peptides. Score 0.471 Round 5: 373 peptides, 48 chains. Longest chain 23 peptides. Score 0.503 Taking the results from Round 3 Chains 48, Residues 323, Estimated correctness of the model 0.0 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ 9833 reflections ( 99.71 % complete ) and 11106 restraints for refining 5022 atoms. 9780 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2372 (Rfree = 0.000) for 5022 atoms. Found 27 (27 requested) and removed 50 (13 requested) atoms. Cycle 32: After refmac, R = 0.2269 (Rfree = 0.000) for 4968 atoms. Found 27 (27 requested) and removed 44 (13 requested) atoms. Cycle 33: After refmac, R = 0.2196 (Rfree = 0.000) for 4929 atoms. Found 27 (27 requested) and removed 43 (13 requested) atoms. Cycle 34: After refmac, R = 0.2079 (Rfree = 0.000) for 4897 atoms. Found 27 (27 requested) and removed 27 (13 requested) atoms. Cycle 35: After refmac, R = 0.1932 (Rfree = 0.000) for 4879 atoms. Found 26 (26 requested) and removed 38 (13 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.26 2.81 Search for helices and strands: 0 residues in 0 chains, 5013 seeds are put forward NCS extension: 29 residues added (3 deleted due to clashes), 5042 seeds are put forward Round 1: 333 peptides, 58 chains. Longest chain 17 peptides. Score 0.365 Round 2: 379 peptides, 56 chains. Longest chain 17 peptides. Score 0.456 Round 3: 388 peptides, 51 chains. Longest chain 19 peptides. Score 0.505 Round 4: 381 peptides, 48 chains. Longest chain 27 peptides. Score 0.515 Round 5: 371 peptides, 50 chains. Longest chain 19 peptides. Score 0.486 Taking the results from Round 4 Chains 49, Residues 333, Estimated correctness of the model 0.0 % 3 chains (31 residues) have been docked in sequence ------------------------------------------------------ 9833 reflections ( 99.71 % complete ) and 10895 restraints for refining 5022 atoms. 9508 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2385 (Rfree = 0.000) for 5022 atoms. Found 27 (27 requested) and removed 48 (13 requested) atoms. Cycle 37: After refmac, R = 0.2313 (Rfree = 0.000) for 4965 atoms. Found 27 (27 requested) and removed 36 (13 requested) atoms. Cycle 38: After refmac, R = 0.2191 (Rfree = 0.000) for 4932 atoms. Found 27 (27 requested) and removed 37 (13 requested) atoms. Cycle 39: After refmac, R = 0.1917 (Rfree = 0.000) for 4908 atoms. Found 15 (27 requested) and removed 18 (13 requested) atoms. Cycle 40: After refmac, R = 0.2121 (Rfree = 0.000) for 4896 atoms. Found 26 (26 requested) and removed 39 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.31 2.85 Search for helices and strands: 0 residues in 0 chains, 5023 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 5040 seeds are put forward Round 1: 326 peptides, 57 chains. Longest chain 13 peptides. Score 0.360 Round 2: 365 peptides, 53 chains. Longest chain 16 peptides. Score 0.456 Round 3: 380 peptides, 55 chains. Longest chain 16 peptides. Score 0.465 Round 4: 363 peptides, 51 chains. Longest chain 17 peptides. Score 0.467 Round 5: 382 peptides, 51 chains. Longest chain 20 peptides. Score 0.496 Taking the results from Round 5 Chains 51, Residues 331, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9833 reflections ( 99.71 % complete ) and 11383 restraints for refining 5022 atoms. 10110 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2415 (Rfree = 0.000) for 5022 atoms. Found 27 (27 requested) and removed 37 (13 requested) atoms. Cycle 42: After refmac, R = 0.2190 (Rfree = 0.000) for 4994 atoms. Found 27 (27 requested) and removed 38 (13 requested) atoms. Cycle 43: After refmac, R = 0.2243 (Rfree = 0.000) for 4972 atoms. Found 27 (27 requested) and removed 32 (13 requested) atoms. Cycle 44: After refmac, R = 0.2138 (Rfree = 0.000) for 4946 atoms. Found 27 (27 requested) and removed 28 (13 requested) atoms. Cycle 45: After refmac, R = 0.2055 (Rfree = 0.000) for 4935 atoms. Found 27 (27 requested) and removed 31 (13 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.37 2.90 Search for helices and strands: 0 residues in 0 chains, 5059 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 5082 seeds are put forward Round 1: 287 peptides, 53 chains. Longest chain 11 peptides. Score 0.321 Round 2: 321 peptides, 48 chains. Longest chain 16 peptides. Score 0.420 Round 3: 310 peptides, 43 chains. Longest chain 19 peptides. Score 0.440 Round 4: 323 peptides, 47 chains. Longest chain 23 peptides. Score 0.431 Round 5: 291 peptides, 40 chains. Longest chain 20 peptides. Score 0.431 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 43, Residues 267, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence Sequence coverage is 3 % Consider running further cycles of model building using 1vky-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 9833 reflections ( 99.71 % complete ) and 11526 restraints for refining 5022 atoms. 10449 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2308 (Rfree = 0.000) for 5022 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Cycle 47: After refmac, R = 0.2299 (Rfree = 0.000) for 4988 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Cycle 48: After refmac, R = 0.2158 (Rfree = 0.000) for 4958 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Cycle 49: After refmac, R = 0.2103 (Rfree = 0.000) for 4936 atoms. TimeTaking 65.5