null Sun 23 Dec 22:23:10 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 1vr0-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vr0-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vr0-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vr0-3.8-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/1vr0-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vr0-3.8-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 22:23:18 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/1vr0-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vr0-3.8-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 479 and 0 Target number of residues in the AU: 479 Target solvent content: 0.6461 Checking the provided sequence file Detected sequence length: 247 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 3 Adjusted target number of residues: 741 Adjusted target solvent content: 0.45 Input MTZ file: 1vr0-3.8-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: 20 Cell parameters: 46.686 69.193 453.518 90.000 90.000 90.000 Input sequence file: 1vr0-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 5928 target number of atoms Had to go as low as 0.70 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: 226.759 3.800 Wilson plot Bfac: 75.70 7656 reflections ( 99.57 % complete ) and 0 restraints for refining 6524 atoms. Observations/parameters ratio is 0.29 ------------------------------------------------------ Starting model: R = 0.3307 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3310 (Rfree = 0.000) for 6524 atoms. Found 35 (35 requested) and removed 52 (17 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.60 3.85 Search for helices and strands: 0 residues in 0 chains, 6625 seeds are put forward NCS extension: 0 residues added, 6625 seeds are put forward Round 1: 249 peptides, 51 chains. Longest chain 10 peptides. Score 0.284 Round 2: 335 peptides, 57 chains. Longest chain 12 peptides. Score 0.423 Round 3: 357 peptides, 54 chains. Longest chain 21 peptides. Score 0.494 Round 4: 378 peptides, 53 chains. Longest chain 23 peptides. Score 0.541 Round 5: 377 peptides, 54 chains. Longest chain 28 peptides. Score 0.531 Taking the results from Round 4 Chains 53, Residues 325, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7656 reflections ( 99.57 % complete ) and 12605 restraints for refining 5362 atoms. 11358 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2468 (Rfree = 0.000) for 5362 atoms. Found 16 (29 requested) and removed 42 (14 requested) atoms. Cycle 2: After refmac, R = 0.2282 (Rfree = 0.000) for 5255 atoms. Found 21 (29 requested) and removed 42 (14 requested) atoms. Cycle 3: After refmac, R = 0.2211 (Rfree = 0.000) for 5196 atoms. Found 28 (28 requested) and removed 34 (14 requested) atoms. Cycle 4: After refmac, R = 0.2128 (Rfree = 0.000) for 5172 atoms. Found 23 (28 requested) and removed 34 (14 requested) atoms. Cycle 5: After refmac, R = 0.1669 (Rfree = 0.000) for 5149 atoms. Found 5 (28 requested) and removed 21 (14 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.51 3.75 Search for helices and strands: 0 residues in 0 chains, 5356 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 5377 seeds are put forward Round 1: 315 peptides, 62 chains. Longest chain 11 peptides. Score 0.332 Round 2: 363 peptides, 54 chains. Longest chain 17 peptides. Score 0.505 Round 3: 373 peptides, 52 chains. Longest chain 17 peptides. Score 0.540 Round 4: 390 peptides, 55 chains. Longest chain 17 peptides. Score 0.547 Round 5: 380 peptides, 50 chains. Longest chain 17 peptides. Score 0.568 Taking the results from Round 5 Chains 50, Residues 330, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 7656 reflections ( 99.57 % complete ) and 12480 restraints for refining 5360 atoms. 11166 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2165 (Rfree = 0.000) for 5360 atoms. Found 29 (29 requested) and removed 59 (14 requested) atoms. Cycle 7: After refmac, R = 0.2137 (Rfree = 0.000) for 5293 atoms. Found 29 (29 requested) and removed 35 (14 requested) atoms. Cycle 8: After refmac, R = 0.1951 (Rfree = 0.000) for 5259 atoms. Found 29 (29 requested) and removed 23 (14 requested) atoms. Cycle 9: After refmac, R = 0.2027 (Rfree = 0.000) for 5237 atoms. Found 28 (28 requested) and removed 37 (14 requested) atoms. Cycle 10: After refmac, R = 0.1873 (Rfree = 0.000) for 5207 atoms. Found 28 (28 requested) and removed 25 (14 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.52 3.76 Search for helices and strands: 0 residues in 0 chains, 5389 seeds are put forward NCS extension: 15 residues added (3 deleted due to clashes), 5404 seeds are put forward Round 1: 301 peptides, 59 chains. Longest chain 16 peptides. Score 0.328 Round 2: 350 peptides, 57 chains. Longest chain 16 peptides. Score 0.454 Round 3: 337 peptides, 55 chains. Longest chain 11 peptides. Score 0.445 Round 4: 333 peptides, 48 chains. Longest chain 15 peptides. Score 0.498 Round 5: 331 peptides, 47 chains. Longest chain 14 peptides. Score 0.503 Taking the results from Round 5 Chains 47, Residues 284, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7656 reflections ( 99.57 % complete ) and 12971 restraints for refining 5359 atoms. 11882 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2037 (Rfree = 0.000) for 5359 atoms. Found 25 (29 requested) and removed 63 (14 requested) atoms. Cycle 12: After refmac, R = 0.2056 (Rfree = 0.000) for 5291 atoms. Found 29 (29 requested) and removed 28 (14 requested) atoms. Cycle 13: After refmac, R = 0.2015 (Rfree = 0.000) for 5282 atoms. Found 29 (29 requested) and removed 39 (14 requested) atoms. Cycle 14: After refmac, R = 0.1534 (Rfree = 0.000) for 5264 atoms. Found 6 (28 requested) and removed 25 (14 requested) atoms. Cycle 15: After refmac, R = 0.1434 (Rfree = 0.000) for 5232 atoms. Found 5 (28 requested) and removed 23 (14 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.53 3.77 Search for helices and strands: 0 residues in 0 chains, 5401 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 5424 seeds are put forward Round 1: 291 peptides, 61 chains. Longest chain 8 peptides. Score 0.285 Round 2: 310 peptides, 57 chains. Longest chain 11 peptides. Score 0.368 Round 3: 323 peptides, 54 chains. Longest chain 12 peptides. Score 0.425 Round 4: 336 peptides, 53 chains. Longest chain 13 peptides. Score 0.461 Round 5: 332 peptides, 51 chains. Longest chain 15 peptides. Score 0.470 Taking the results from Round 5 Chains 51, Residues 281, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7656 reflections ( 99.57 % complete ) and 12888 restraints for refining 5358 atoms. 11815 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2130 (Rfree = 0.000) for 5358 atoms. Found 29 (29 requested) and removed 35 (14 requested) atoms. Cycle 17: After refmac, R = 0.2109 (Rfree = 0.000) for 5322 atoms. Found 29 (29 requested) and removed 30 (14 requested) atoms. Cycle 18: After refmac, R = 0.1898 (Rfree = 0.000) for 5301 atoms. Found 29 (29 requested) and removed 29 (14 requested) atoms. Cycle 19: After refmac, R = 0.1862 (Rfree = 0.000) for 5279 atoms. Found 29 (29 requested) and removed 31 (14 requested) atoms. Cycle 20: After refmac, R = 0.1788 (Rfree = 0.000) for 5269 atoms. Found 26 (29 requested) and removed 24 (14 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.50 3.74 Search for helices and strands: 0 residues in 0 chains, 5478 seeds are put forward NCS extension: 11 residues added (2 deleted due to clashes), 5489 seeds are put forward Round 1: 279 peptides, 56 chains. Longest chain 12 peptides. Score 0.306 Round 2: 328 peptides, 55 chains. Longest chain 14 peptides. Score 0.426 Round 3: 347 peptides, 57 chains. Longest chain 14 peptides. Score 0.448 Round 4: 351 peptides, 54 chains. Longest chain 15 peptides. Score 0.482 Round 5: 358 peptides, 57 chains. Longest chain 13 peptides. Score 0.470 Taking the results from Round 4 Chains 54, Residues 297, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7656 reflections ( 99.57 % complete ) and 12657 restraints for refining 5362 atoms. 11523 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2023 (Rfree = 0.000) for 5362 atoms. Found 25 (29 requested) and removed 50 (14 requested) atoms. Cycle 22: After refmac, R = 0.1964 (Rfree = 0.000) for 5316 atoms. Found 28 (29 requested) and removed 27 (14 requested) atoms. Cycle 23: After refmac, R = 0.1882 (Rfree = 0.000) for 5301 atoms. Found 25 (29 requested) and removed 25 (14 requested) atoms. Cycle 24: After refmac, R = 0.1785 (Rfree = 0.000) for 5290 atoms. Found 17 (29 requested) and removed 23 (14 requested) atoms. Cycle 25: After refmac, R = 0.1402 (Rfree = 0.000) for 5272 atoms. Found 2 (29 requested) and removed 19 (14 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.52 3.76 Search for helices and strands: 0 residues in 0 chains, 5447 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 5467 seeds are put forward Round 1: 284 peptides, 59 chains. Longest chain 9 peptides. Score 0.288 Round 2: 335 peptides, 62 chains. Longest chain 13 peptides. Score 0.377 Round 3: 340 peptides, 62 chains. Longest chain 13 peptides. Score 0.388 Round 4: 367 peptides, 60 chains. Longest chain 13 peptides. Score 0.462 Round 5: 363 peptides, 60 chains. Longest chain 12 peptides. Score 0.454 Taking the results from Round 4 Chains 60, Residues 307, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7656 reflections ( 99.57 % complete ) and 12686 restraints for refining 5362 atoms. 11518 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1913 (Rfree = 0.000) for 5362 atoms. Found 15 (29 requested) and removed 18 (14 requested) atoms. Cycle 27: After refmac, R = 0.2022 (Rfree = 0.000) for 5336 atoms. Found 29 (29 requested) and removed 21 (14 requested) atoms. Cycle 28: After refmac, R = 0.1958 (Rfree = 0.000) for 5326 atoms. Found 19 (29 requested) and removed 27 (14 requested) atoms. Cycle 29: After refmac, R = 0.1588 (Rfree = 0.000) for 5308 atoms. Found 4 (29 requested) and removed 16 (14 requested) atoms. Cycle 30: After refmac, R = 0.1493 (Rfree = 0.000) for 5283 atoms. Found 4 (29 requested) and removed 17 (14 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.54 3.78 Search for helices and strands: 0 residues in 0 chains, 5453 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 5470 seeds are put forward Round 1: 272 peptides, 57 chains. Longest chain 7 peptides. Score 0.279 Round 2: 291 peptides, 52 chains. Longest chain 14 peptides. Score 0.374 Round 3: 307 peptides, 54 chains. Longest chain 15 peptides. Score 0.390 Round 4: 305 peptides, 51 chains. Longest chain 15 peptides. Score 0.414 Round 5: 305 peptides, 51 chains. Longest chain 19 peptides. Score 0.414 Taking the results from Round 5 Chains 51, Residues 254, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7656 reflections ( 99.57 % complete ) and 12928 restraints for refining 5362 atoms. 11963 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2248 (Rfree = 0.000) for 5362 atoms. Found 29 (29 requested) and removed 33 (14 requested) atoms. Cycle 32: After refmac, R = 0.1961 (Rfree = 0.000) for 5331 atoms. Found 29 (29 requested) and removed 31 (14 requested) atoms. Cycle 33: After refmac, R = 0.1508 (Rfree = 0.000) for 5307 atoms. Found 11 (29 requested) and removed 19 (14 requested) atoms. Cycle 34: After refmac, R = 0.1400 (Rfree = 0.000) for 5290 atoms. Found 4 (29 requested) and removed 20 (14 requested) atoms. Cycle 35: After refmac, R = 0.1361 (Rfree = 0.000) for 5268 atoms. Found 4 (29 requested) and removed 15 (14 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.53 3.77 Search for helices and strands: 0 residues in 0 chains, 5415 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 5436 seeds are put forward Round 1: 224 peptides, 49 chains. Longest chain 10 peptides. Score 0.242 Round 2: 272 peptides, 53 chains. Longest chain 11 peptides. Score 0.320 Round 3: 284 peptides, 51 chains. Longest chain 12 peptides. Score 0.367 Round 4: 298 peptides, 52 chains. Longest chain 15 peptides. Score 0.389 Round 5: 296 peptides, 49 chains. Longest chain 15 peptides. Score 0.413 Taking the results from Round 5 Chains 49, Residues 247, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7656 reflections ( 99.57 % complete ) and 12709 restraints for refining 5362 atoms. 11770 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1942 (Rfree = 0.000) for 5362 atoms. Found 27 (29 requested) and removed 18 (14 requested) atoms. Cycle 37: After refmac, R = 0.1992 (Rfree = 0.000) for 5347 atoms. Found 29 (29 requested) and removed 23 (14 requested) atoms. Cycle 38: After refmac, R = 0.1858 (Rfree = 0.000) for 5346 atoms. Found 29 (29 requested) and removed 27 (14 requested) atoms. Cycle 39: After refmac, R = 0.1432 (Rfree = 0.000) for 5336 atoms. Found 6 (29 requested) and removed 18 (14 requested) atoms. Cycle 40: After refmac, R = 0.1332 (Rfree = 0.000) for 5318 atoms. Found 2 (29 requested) and removed 18 (14 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.52 3.76 Search for helices and strands: 0 residues in 0 chains, 5487 seeds are put forward NCS extension: 24 residues added (2 deleted due to clashes), 5511 seeds are put forward Round 1: 240 peptides, 51 chains. Longest chain 10 peptides. Score 0.262 Round 2: 278 peptides, 52 chains. Longest chain 14 peptides. Score 0.344 Round 3: 276 peptides, 51 chains. Longest chain 12 peptides. Score 0.349 Round 4: 287 peptides, 51 chains. Longest chain 12 peptides. Score 0.374 Round 5: 294 peptides, 49 chains. Longest chain 13 peptides. Score 0.409 Taking the results from Round 5 Chains 49, Residues 245, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7656 reflections ( 99.57 % complete ) and 12833 restraints for refining 5361 atoms. 11902 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1950 (Rfree = 0.000) for 5361 atoms. Found 27 (29 requested) and removed 26 (14 requested) atoms. Cycle 42: After refmac, R = 0.1915 (Rfree = 0.000) for 5330 atoms. Found 22 (29 requested) and removed 20 (14 requested) atoms. Cycle 43: After refmac, R = 0.1427 (Rfree = 0.000) for 5305 atoms. Found 3 (29 requested) and removed 20 (14 requested) atoms. Cycle 44: After refmac, R = 0.1363 (Rfree = 0.000) for 5274 atoms. Found 3 (29 requested) and removed 15 (14 requested) atoms. Cycle 45: After refmac, R = 0.1314 (Rfree = 0.000) for 5260 atoms. Found 3 (28 requested) and removed 15 (14 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.54 3.78 Search for helices and strands: 0 residues in 0 chains, 5410 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 5432 seeds are put forward Round 1: 213 peptides, 48 chains. Longest chain 7 peptides. Score 0.224 Round 2: 245 peptides, 47 chains. Longest chain 11 peptides. Score 0.316 Round 3: 248 peptides, 46 chains. Longest chain 12 peptides. Score 0.334 Round 4: 244 peptides, 41 chains. Longest chain 17 peptides. Score 0.375 Round 5: 245 peptides, 40 chains. Longest chain 13 peptides. Score 0.388 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 40, Residues 205, 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 1vr0-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7656 reflections ( 99.57 % complete ) and 12868 restraints for refining 5361 atoms. 12088 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1856 (Rfree = 0.000) for 5361 atoms. Found 0 (29 requested) and removed 14 (14 requested) atoms. Cycle 47: After refmac, R = 0.1835 (Rfree = 0.000) for 5333 atoms. Found 0 (29 requested) and removed 14 (14 requested) atoms. Cycle 48: After refmac, R = 0.1808 (Rfree = 0.000) for 5311 atoms. Found 0 (29 requested) and removed 14 (14 requested) atoms. Cycle 49: After refmac, R = 0.1851 (Rfree = 0.000) for 5288 atoms. Found 0 (29 requested) and removed 14 (14 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:39:22 GMT 2018 Job finished. TimeTaking 76.2 Used memory is bytes: 6764272