null Tue 25 Dec 19:27:57 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 1vky-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vky-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vky-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vky-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/1vky-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vky-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 19:28:06 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/1vky-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vky-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 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-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: 23 Cell parameters: 119.363 122.591 131.880 90.000 90.000 90.000 Input sequence file: 1vky-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 5552 target number of atoms Had to go as low as 0.80 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 6184 atoms. Observations/parameters ratio is 0.40 ------------------------------------------------------ Starting model: R = 0.3266 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3161 (Rfree = 0.000) for 6184 atoms. Found 34 (34 requested) and removed 83 (17 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.32 2.86 Search for helices and strands: 0 residues in 0 chains, 6235 seeds are put forward NCS extension: 0 residues added, 6235 seeds are put forward Round 1: 306 peptides, 54 chains. Longest chain 14 peptides. Score 0.348 Round 2: 365 peptides, 49 chains. Longest chain 23 peptides. Score 0.484 Round 3: 367 peptides, 48 chains. Longest chain 22 peptides. Score 0.494 Round 4: 371 peptides, 44 chains. Longest chain 27 peptides. Score 0.527 Round 5: 388 peptides, 48 chains. Longest chain 16 peptides. Score 0.525 Taking the results from Round 4 Chains 50, Residues 327, Estimated correctness of the model 0.0 % 5 chains (64 residues) have been docked in sequence ------------------------------------------------------ 9833 reflections ( 99.71 % complete ) and 10737 restraints for refining 5019 atoms. 9227 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2650 (Rfree = 0.000) for 5019 atoms. Found 27 (27 requested) and removed 37 (13 requested) atoms. Cycle 2: After refmac, R = 0.2638 (Rfree = 0.000) for 4908 atoms. Found 27 (27 requested) and removed 29 (13 requested) atoms. Cycle 3: After refmac, R = 0.2514 (Rfree = 0.000) for 4846 atoms. Found 26 (26 requested) and removed 30 (13 requested) atoms. Cycle 4: After refmac, R = 0.2419 (Rfree = 0.000) for 4797 atoms. Found 26 (26 requested) and removed 31 (13 requested) atoms. Cycle 5: After refmac, R = 0.2315 (Rfree = 0.000) for 4754 atoms. Found 26 (26 requested) and removed 29 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.35 2.89 Search for helices and strands: 0 residues in 0 chains, 4904 seeds are put forward NCS extension: 28 residues added (2 deleted due to clashes), 4932 seeds are put forward Round 1: 334 peptides, 52 chains. Longest chain 18 peptides. Score 0.412 Round 2: 394 peptides, 49 chains. Longest chain 21 peptides. Score 0.527 Round 3: 388 peptides, 46 chains. Longest chain 17 peptides. Score 0.538 Round 4: 399 peptides, 47 chains. Longest chain 20 peptides. Score 0.547 Round 5: 382 peptides, 42 chains. Longest chain 22 peptides. Score 0.556 Taking the results from Round 5 Chains 48, Residues 340, Estimated correctness of the model 0.0 % 4 chains (48 residues) have been docked in sequence ------------------------------------------------------ 9833 reflections ( 99.71 % complete ) and 10846 restraints for refining 5021 atoms. 9338 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2618 (Rfree = 0.000) for 5021 atoms. Found 27 (27 requested) and removed 50 (13 requested) atoms. Cycle 7: After refmac, R = 0.2591 (Rfree = 0.000) for 4955 atoms. Found 27 (27 requested) and removed 41 (13 requested) atoms. Cycle 8: After refmac, R = 0.2555 (Rfree = 0.000) for 4902 atoms. Found 27 (27 requested) and removed 39 (13 requested) atoms. Cycle 9: After refmac, R = 0.2490 (Rfree = 0.000) for 4855 atoms. Found 26 (26 requested) and removed 44 (13 requested) atoms. Cycle 10: After refmac, R = 0.2466 (Rfree = 0.000) for 4813 atoms. Found 26 (26 requested) and removed 30 (13 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.33 2.87 Search for helices and strands: 0 residues in 0 chains, 4943 seeds are put forward NCS extension: 31 residues added (2 deleted due to clashes), 4974 seeds are put forward Round 1: 354 peptides, 54 chains. Longest chain 15 peptides. Score 0.431 Round 2: 389 peptides, 52 chains. Longest chain 19 peptides. Score 0.500 Round 3: 376 peptides, 53 chains. Longest chain 16 peptides. Score 0.473 Round 4: 379 peptides, 53 chains. Longest chain 20 peptides. Score 0.477 Round 5: 365 peptides, 52 chains. Longest chain 18 peptides. Score 0.463 Taking the results from Round 2 Chains 55, Residues 337, Estimated correctness of the model 0.0 % 3 chains (22 residues) have been docked in sequence ------------------------------------------------------ 9833 reflections ( 99.71 % complete ) and 11212 restraints for refining 5022 atoms. 9846 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2630 (Rfree = 0.000) for 5022 atoms. Found 27 (27 requested) and removed 61 (13 requested) atoms. Cycle 12: After refmac, R = 0.2487 (Rfree = 0.000) for 4942 atoms. Found 27 (27 requested) and removed 47 (13 requested) atoms. Cycle 13: After refmac, R = 0.2390 (Rfree = 0.000) for 4881 atoms. Found 27 (27 requested) and removed 40 (13 requested) atoms. Cycle 14: After refmac, R = 0.2393 (Rfree = 0.000) for 4838 atoms. Found 26 (26 requested) and removed 50 (13 requested) atoms. Cycle 15: After refmac, R = 0.2262 (Rfree = 0.000) for 4795 atoms. Found 26 (26 requested) and removed 35 (13 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.35 2.89 Search for helices and strands: 0 residues in 0 chains, 4911 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 4936 seeds are put forward Round 1: 326 peptides, 54 chains. Longest chain 14 peptides. Score 0.383 Round 2: 362 peptides, 54 chains. Longest chain 16 peptides. Score 0.444 Round 3: 381 peptides, 53 chains. Longest chain 30 peptides. Score 0.481 Round 4: 352 peptides, 52 chains. Longest chain 19 peptides. Score 0.442 Round 5: 360 peptides, 52 chains. Longest chain 20 peptides. Score 0.455 Taking the results from Round 3 Chains 53, Residues 328, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9833 reflections ( 99.71 % complete ) and 11333 restraints for refining 5021 atoms. 10074 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2518 (Rfree = 0.000) for 5021 atoms. Found 27 (27 requested) and removed 49 (13 requested) atoms. Cycle 17: After refmac, R = 0.2258 (Rfree = 0.000) for 4957 atoms. Found 27 (27 requested) and removed 54 (13 requested) atoms. Cycle 18: After refmac, R = 0.2244 (Rfree = 0.000) for 4903 atoms. Found 27 (27 requested) and removed 47 (13 requested) atoms. Cycle 19: After refmac, R = 0.2199 (Rfree = 0.000) for 4869 atoms. Found 26 (26 requested) and removed 30 (13 requested) atoms. Cycle 20: After refmac, R = 0.2172 (Rfree = 0.000) for 4855 atoms. Found 26 (26 requested) and removed 42 (13 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.33 2.87 Search for helices and strands: 0 residues in 0 chains, 4980 seeds are put forward NCS extension: 38 residues added (2 deleted due to clashes), 5018 seeds are put forward Round 1: 339 peptides, 62 chains. Longest chain 13 peptides. Score 0.345 Round 2: 361 peptides, 56 chains. Longest chain 24 peptides. Score 0.427 Round 3: 367 peptides, 55 chains. Longest chain 16 peptides. Score 0.444 Round 4: 357 peptides, 54 chains. Longest chain 13 peptides. Score 0.435 Round 5: 375 peptides, 53 chains. Longest chain 20 peptides. Score 0.471 Taking the results from Round 5 Chains 53, Residues 322, Estimated correctness of the model 0.0 % 1 chains (17 residues) have been docked in sequence ------------------------------------------------------ 9833 reflections ( 99.71 % complete ) and 11391 restraints for refining 5022 atoms. 10095 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2391 (Rfree = 0.000) for 5022 atoms. Found 27 (27 requested) and removed 34 (13 requested) atoms. Cycle 22: After refmac, R = 0.2416 (Rfree = 0.000) for 4976 atoms. Found 27 (27 requested) and removed 46 (13 requested) atoms. Cycle 23: After refmac, R = 0.2319 (Rfree = 0.000) for 4943 atoms. Found 27 (27 requested) and removed 45 (13 requested) atoms. Cycle 24: After refmac, R = 0.2295 (Rfree = 0.000) for 4913 atoms. Found 27 (27 requested) and removed 47 (13 requested) atoms. Cycle 25: After refmac, R = 0.2174 (Rfree = 0.000) for 4886 atoms. Found 26 (26 requested) and removed 40 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.35 2.89 Search for helices and strands: 0 residues in 0 chains, 4993 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 5013 seeds are put forward Round 1: 330 peptides, 57 chains. Longest chain 11 peptides. Score 0.367 Round 2: 347 peptides, 52 chains. Longest chain 15 peptides. Score 0.434 Round 3: 362 peptides, 57 chains. Longest chain 14 peptides. Score 0.422 Round 4: 365 peptides, 52 chains. Longest chain 20 peptides. Score 0.463 Round 5: 356 peptides, 48 chains. Longest chain 18 peptides. Score 0.477 Taking the results from Round 5 Chains 51, Residues 308, Estimated correctness of the model 0.0 % 2 chains (21 residues) have been docked in sequence ------------------------------------------------------ 9833 reflections ( 99.71 % complete ) and 11387 restraints for refining 5021 atoms. 10157 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2715 (Rfree = 0.000) for 5021 atoms. Found 27 (27 requested) and removed 41 (13 requested) atoms. Cycle 27: After refmac, R = 0.2554 (Rfree = 0.000) for 4963 atoms. Found 27 (27 requested) and removed 37 (13 requested) atoms. Cycle 28: After refmac, R = 0.2154 (Rfree = 0.000) for 4930 atoms. Found 12 (27 requested) and removed 29 (13 requested) atoms. Cycle 29: After refmac, R = 0.2406 (Rfree = 0.000) for 4906 atoms. Found 27 (27 requested) and removed 29 (13 requested) atoms. Cycle 30: After refmac, R = 0.2123 (Rfree = 0.000) for 4897 atoms. Found 12 (26 requested) and removed 27 (13 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.36 2.90 Search for helices and strands: 0 residues in 0 chains, 5010 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 5035 seeds are put forward Round 1: 310 peptides, 56 chains. Longest chain 13 peptides. Score 0.339 Round 2: 345 peptides, 55 chains. Longest chain 11 peptides. Score 0.408 Round 3: 350 peptides, 54 chains. Longest chain 19 peptides. Score 0.424 Round 4: 368 peptides, 54 chains. Longest chain 20 peptides. Score 0.453 Round 5: 353 peptides, 51 chains. Longest chain 20 peptides. Score 0.451 Taking the results from Round 4 Chains 57, Residues 314, Estimated correctness of the model 0.0 % 3 chains (39 residues) have been docked in sequence ------------------------------------------------------ 9833 reflections ( 99.71 % complete ) and 11049 restraints for refining 5021 atoms. 9680 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2665 (Rfree = 0.000) for 5021 atoms. Found 27 (27 requested) and removed 38 (13 requested) atoms. Cycle 32: After refmac, R = 0.2471 (Rfree = 0.000) for 4969 atoms. Found 27 (27 requested) and removed 38 (13 requested) atoms. Cycle 33: After refmac, R = 0.2483 (Rfree = 0.000) for 4949 atoms. Found 27 (27 requested) and removed 34 (13 requested) atoms. Cycle 34: After refmac, R = 0.2417 (Rfree = 0.000) for 4927 atoms. Found 27 (27 requested) and removed 24 (13 requested) atoms. Cycle 35: After refmac, R = 0.2461 (Rfree = 0.000) for 4912 atoms. Found 27 (27 requested) and removed 32 (13 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.39 2.92 Search for helices and strands: 0 residues in 0 chains, 5024 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 5039 seeds are put forward Round 1: 294 peptides, 58 chains. Longest chain 11 peptides. Score 0.293 Round 2: 316 peptides, 50 chains. Longest chain 17 peptides. Score 0.397 Round 3: 333 peptides, 54 chains. Longest chain 18 peptides. Score 0.395 Round 4: 334 peptides, 49 chains. Longest chain 19 peptides. Score 0.434 Round 5: 341 peptides, 53 chains. Longest chain 14 peptides. Score 0.416 Taking the results from Round 4 Chains 49, Residues 285, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9833 reflections ( 99.71 % complete ) and 11585 restraints for refining 5021 atoms. 10494 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2611 (Rfree = 0.000) for 5021 atoms. Found 27 (27 requested) and removed 33 (13 requested) atoms. Cycle 37: After refmac, R = 0.2442 (Rfree = 0.000) for 4983 atoms. Found 27 (27 requested) and removed 23 (13 requested) atoms. Cycle 38: After refmac, R = 0.2064 (Rfree = 0.000) for 4960 atoms. Found 16 (27 requested) and removed 22 (13 requested) atoms. Cycle 39: After refmac, R = 0.2241 (Rfree = 0.000) for 4940 atoms. Found 27 (27 requested) and removed 21 (13 requested) atoms. Cycle 40: After refmac, R = 0.2350 (Rfree = 0.000) for 4938 atoms. Found 27 (27 requested) and removed 25 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.33 2.87 Search for helices and strands: 0 residues in 0 chains, 5052 seeds are put forward NCS extension: 31 residues added (2 deleted due to clashes), 5083 seeds are put forward Round 1: 263 peptides, 51 chains. Longest chain 10 peptides. Score 0.291 Round 2: 299 peptides, 46 chains. Longest chain 17 peptides. Score 0.398 Round 3: 305 peptides, 50 chains. Longest chain 16 peptides. Score 0.377 Round 4: 287 peptides, 45 chains. Longest chain 20 peptides. Score 0.385 Round 5: 305 peptides, 47 chains. Longest chain 18 peptides. Score 0.401 Taking the results from Round 5 Chains 47, Residues 258, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 9833 reflections ( 99.71 % complete ) and 11585 restraints for refining 5022 atoms. 10561 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2504 (Rfree = 0.000) for 5022 atoms. Found 27 (27 requested) and removed 50 (13 requested) atoms. Cycle 42: After refmac, R = 0.2445 (Rfree = 0.000) for 4958 atoms. Found 27 (27 requested) and removed 33 (13 requested) atoms. Cycle 43: After refmac, R = 0.2354 (Rfree = 0.000) for 4932 atoms. Found 27 (27 requested) and removed 28 (13 requested) atoms. Cycle 44: After refmac, R = 0.1937 (Rfree = 0.000) for 4913 atoms. Found 14 (27 requested) and removed 26 (13 requested) atoms. Cycle 45: After refmac, R = 0.1905 (Rfree = 0.000) for 4893 atoms. Found 6 (26 requested) and removed 26 (13 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.34 2.88 Search for helices and strands: 0 residues in 0 chains, 4996 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 5017 seeds are put forward Round 1: 267 peptides, 50 chains. Longest chain 13 peptides. Score 0.307 Round 2: 280 peptides, 44 chains. Longest chain 22 peptides. Score 0.380 Round 3: 304 peptides, 48 chains. Longest chain 17 peptides. Score 0.391 Round 4: 300 peptides, 46 chains. Longest chain 14 peptides. Score 0.400 Round 5: 292 peptides, 46 chains. Longest chain 17 peptides. Score 0.386 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 46, Residues 254, 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 1vky-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 9833 reflections ( 99.71 % complete ) and 11671 restraints for refining 5022 atoms. 10701 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2474 (Rfree = 0.000) for 5022 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Cycle 47: After refmac, R = 0.2406 (Rfree = 0.000) for 4980 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Cycle 48: After refmac, R = 0.2275 (Rfree = 0.000) for 4953 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Cycle 49: After refmac, R = 0.1870 (Rfree = 0.000) for 4934 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:49:01 GMT 2018 Job finished. TimeTaking 81.07 Used memory is bytes: 10925888