null Mon 24 Dec 07:32:25 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 1vqs-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vqs-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vqs-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vqs-3.4-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/1vqs-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vqs-3.4-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 07:32:29 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/1vqs-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vqs-3.4-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 495 and 0 Target number of residues in the AU: 495 Target solvent content: 0.6064 Checking the provided sequence file Detected sequence length: 116 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 5 Adjusted target number of residues: 580 Adjusted target solvent content: 0.54 Input MTZ file: 1vqs-3.4-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: 97 Cell parameters: 94.778 94.778 303.043 90.000 90.000 90.000 Input sequence file: 1vqs-3.4-parrot-noncs.fasta_lf Building free atoms model in initial map for 4640 target number of atoms Had to go as low as 0.85 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: 29.971 3.400 Wilson plot Bfac: 55.24 9962 reflections ( 99.63 % complete ) and 0 restraints for refining 5167 atoms. Observations/parameters ratio is 0.48 ------------------------------------------------------ Starting model: R = 0.3283 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3008 (Rfree = 0.000) for 5167 atoms. Found 38 (38 requested) and removed 30 (19 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.17 3.01 Search for helices and strands: 0 residues in 0 chains, 5243 seeds are put forward NCS extension: 0 residues added, 5243 seeds are put forward Round 1: 261 peptides, 43 chains. Longest chain 15 peptides. Score 0.406 Round 2: 332 peptides, 44 chains. Longest chain 16 peptides. Score 0.549 Round 3: 367 peptides, 46 chains. Longest chain 24 peptides. Score 0.597 Round 4: 361 peptides, 43 chains. Longest chain 23 peptides. Score 0.611 Round 5: 381 peptides, 41 chains. Longest chain 22 peptides. Score 0.658 Taking the results from Round 5 Chains 45, Residues 340, Estimated correctness of the model 46.5 % 4 chains (55 residues) have been docked in sequence ------------------------------------------------------ 9962 reflections ( 99.63 % complete ) and 8176 restraints for refining 4219 atoms. 6619 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2701 (Rfree = 0.000) for 4219 atoms. Found 31 (31 requested) and removed 27 (15 requested) atoms. Cycle 2: After refmac, R = 0.2634 (Rfree = 0.000) for 4151 atoms. Found 22 (31 requested) and removed 19 (15 requested) atoms. Cycle 3: After refmac, R = 0.2529 (Rfree = 0.000) for 4128 atoms. Found 20 (31 requested) and removed 17 (15 requested) atoms. Cycle 4: After refmac, R = 0.2443 (Rfree = 0.000) for 4108 atoms. Found 16 (31 requested) and removed 20 (15 requested) atoms. Cycle 5: After refmac, R = 0.2375 (Rfree = 0.000) for 4093 atoms. Found 18 (30 requested) and removed 19 (15 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.13 2.97 Search for helices and strands: 0 residues in 0 chains, 4249 seeds are put forward NCS extension: 15 residues added (3 deleted due to clashes), 4264 seeds are put forward Round 1: 368 peptides, 52 chains. Longest chain 24 peptides. Score 0.550 Round 2: 363 peptides, 38 chains. Longest chain 22 peptides. Score 0.652 Round 3: 375 peptides, 41 chains. Longest chain 29 peptides. Score 0.649 Round 4: 392 peptides, 44 chains. Longest chain 24 peptides. Score 0.654 Round 5: 375 peptides, 41 chains. Longest chain 28 peptides. Score 0.649 Taking the results from Round 4 Chains 45, Residues 348, Estimated correctness of the model 45.3 % 4 chains (59 residues) have been docked in sequence ------------------------------------------------------ 9962 reflections ( 99.63 % complete ) and 8395 restraints for refining 4219 atoms. 6791 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2585 (Rfree = 0.000) for 4219 atoms. Found 31 (31 requested) and removed 25 (15 requested) atoms. Cycle 7: After refmac, R = 0.2451 (Rfree = 0.000) for 4197 atoms. Found 27 (31 requested) and removed 23 (15 requested) atoms. Cycle 8: After refmac, R = 0.2395 (Rfree = 0.000) for 4180 atoms. Found 16 (31 requested) and removed 17 (15 requested) atoms. Cycle 9: After refmac, R = 0.2295 (Rfree = 0.000) for 4162 atoms. Found 8 (31 requested) and removed 20 (15 requested) atoms. Cycle 10: After refmac, R = 0.2285 (Rfree = 0.000) for 4139 atoms. Found 12 (31 requested) and removed 20 (15 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.14 2.98 Search for helices and strands: 0 residues in 0 chains, 4261 seeds are put forward NCS extension: 14 residues added (6 deleted due to clashes), 4275 seeds are put forward Round 1: 343 peptides, 47 chains. Longest chain 23 peptides. Score 0.545 Round 2: 368 peptides, 42 chains. Longest chain 23 peptides. Score 0.630 Round 3: 393 peptides, 39 chains. Longest chain 36 peptides. Score 0.690 Round 4: 385 peptides, 45 chains. Longest chain 24 peptides. Score 0.635 Round 5: 383 peptides, 38 chains. Longest chain 23 peptides. Score 0.683 Taking the results from Round 3 Chains 46, Residues 354, Estimated correctness of the model 55.3 % 6 chains (99 residues) have been docked in sequence ------------------------------------------------------ 9962 reflections ( 99.63 % complete ) and 7906 restraints for refining 4218 atoms. 6097 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2602 (Rfree = 0.000) for 4218 atoms. Found 27 (31 requested) and removed 32 (15 requested) atoms. Cycle 12: After refmac, R = 0.2475 (Rfree = 0.000) for 4189 atoms. Found 19 (31 requested) and removed 22 (15 requested) atoms. Cycle 13: After refmac, R = 0.2433 (Rfree = 0.000) for 4175 atoms. Found 12 (31 requested) and removed 20 (15 requested) atoms. Cycle 14: After refmac, R = 0.2352 (Rfree = 0.000) for 4161 atoms. Found 18 (31 requested) and removed 19 (15 requested) atoms. Cycle 15: After refmac, R = 0.2272 (Rfree = 0.000) for 4152 atoms. Found 13 (31 requested) and removed 17 (15 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.13 2.97 Search for helices and strands: 0 residues in 0 chains, 4268 seeds are put forward NCS extension: 12 residues added (6 deleted due to clashes), 4280 seeds are put forward Round 1: 348 peptides, 45 chains. Longest chain 22 peptides. Score 0.571 Round 2: 370 peptides, 36 chains. Longest chain 24 peptides. Score 0.677 Round 3: 353 peptides, 42 chains. Longest chain 22 peptides. Score 0.605 Round 4: 357 peptides, 38 chains. Longest chain 24 peptides. Score 0.642 Round 5: 382 peptides, 42 chains. Longest chain 23 peptides. Score 0.653 Taking the results from Round 2 Chains 42, Residues 334, Estimated correctness of the model 51.8 % 3 chains (46 residues) have been docked in sequence ------------------------------------------------------ 9962 reflections ( 99.63 % complete ) and 8684 restraints for refining 4218 atoms. 7193 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2527 (Rfree = 0.000) for 4218 atoms. Found 31 (31 requested) and removed 26 (15 requested) atoms. Cycle 17: After refmac, R = 0.2424 (Rfree = 0.000) for 4208 atoms. Found 18 (31 requested) and removed 23 (15 requested) atoms. Cycle 18: After refmac, R = 0.2368 (Rfree = 0.000) for 4197 atoms. Found 15 (31 requested) and removed 19 (15 requested) atoms. Cycle 19: After refmac, R = 0.2313 (Rfree = 0.000) for 4181 atoms. Found 12 (31 requested) and removed 21 (15 requested) atoms. Cycle 20: After refmac, R = 0.2301 (Rfree = 0.000) for 4167 atoms. Found 14 (31 requested) and removed 16 (15 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.12 2.96 Search for helices and strands: 0 residues in 0 chains, 4278 seeds are put forward NCS extension: 10 residues added (14 deleted due to clashes), 4288 seeds are put forward Round 1: 336 peptides, 44 chains. Longest chain 22 peptides. Score 0.557 Round 2: 355 peptides, 39 chains. Longest chain 22 peptides. Score 0.632 Round 3: 367 peptides, 36 chains. Longest chain 25 peptides. Score 0.673 Round 4: 375 peptides, 42 chains. Longest chain 25 peptides. Score 0.642 Round 5: 367 peptides, 38 chains. Longest chain 25 peptides. Score 0.658 Taking the results from Round 3 Chains 39, Residues 331, Estimated correctness of the model 50.7 % 3 chains (46 residues) have been docked in sequence ------------------------------------------------------ 9962 reflections ( 99.63 % complete ) and 8621 restraints for refining 4219 atoms. 7123 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2445 (Rfree = 0.000) for 4219 atoms. Found 25 (31 requested) and removed 22 (15 requested) atoms. Cycle 22: After refmac, R = 0.2401 (Rfree = 0.000) for 4199 atoms. Found 24 (31 requested) and removed 19 (15 requested) atoms. Cycle 23: After refmac, R = 0.2395 (Rfree = 0.000) for 4196 atoms. Found 31 (31 requested) and removed 19 (15 requested) atoms. Cycle 24: After refmac, R = 0.2372 (Rfree = 0.000) for 4201 atoms. Found 23 (31 requested) and removed 21 (15 requested) atoms. Cycle 25: After refmac, R = 0.2342 (Rfree = 0.000) for 4194 atoms. Found 27 (31 requested) and removed 21 (15 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.13 2.97 Search for helices and strands: 0 residues in 0 chains, 4306 seeds are put forward NCS extension: 14 residues added (11 deleted due to clashes), 4320 seeds are put forward Round 1: 311 peptides, 46 chains. Longest chain 19 peptides. Score 0.489 Round 2: 348 peptides, 42 chains. Longest chain 24 peptides. Score 0.596 Round 3: 341 peptides, 44 chains. Longest chain 19 peptides. Score 0.566 Round 4: 346 peptides, 39 chains. Longest chain 26 peptides. Score 0.616 Round 5: 345 peptides, 39 chains. Longest chain 26 peptides. Score 0.615 Taking the results from Round 4 Chains 40, Residues 307, Estimated correctness of the model 33.8 % 2 chains (24 residues) have been docked in sequence ------------------------------------------------------ 9962 reflections ( 99.63 % complete ) and 9131 restraints for refining 4219 atoms. 7844 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2524 (Rfree = 0.000) for 4219 atoms. Found 22 (31 requested) and removed 24 (15 requested) atoms. Cycle 27: After refmac, R = 0.2573 (Rfree = 0.000) for 4195 atoms. Found 31 (31 requested) and removed 20 (15 requested) atoms. Cycle 28: After refmac, R = 0.2461 (Rfree = 0.000) for 4197 atoms. Found 29 (31 requested) and removed 20 (15 requested) atoms. Cycle 29: After refmac, R = 0.2479 (Rfree = 0.000) for 4196 atoms. Found 31 (31 requested) and removed 20 (15 requested) atoms. Cycle 30: After refmac, R = 0.2479 (Rfree = 0.000) for 4200 atoms. Found 31 (31 requested) and removed 21 (15 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.17 3.01 Search for helices and strands: 0 residues in 0 chains, 4294 seeds are put forward NCS extension: 16 residues added (3 deleted due to clashes), 4310 seeds are put forward Round 1: 282 peptides, 41 chains. Longest chain 18 peptides. Score 0.474 Round 2: 310 peptides, 40 chains. Longest chain 24 peptides. Score 0.542 Round 3: 303 peptides, 39 chains. Longest chain 18 peptides. Score 0.537 Round 4: 307 peptides, 38 chains. Longest chain 24 peptides. Score 0.553 Round 5: 316 peptides, 40 chains. Longest chain 24 peptides. Score 0.553 Taking the results from Round 5 Chains 43, Residues 276, Estimated correctness of the model 12.6 % 2 chains (26 residues) have been docked in sequence ------------------------------------------------------ 9962 reflections ( 99.63 % complete ) and 9084 restraints for refining 4218 atoms. 7910 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2520 (Rfree = 0.000) for 4218 atoms. Found 31 (31 requested) and removed 24 (15 requested) atoms. Cycle 32: After refmac, R = 0.2489 (Rfree = 0.000) for 4214 atoms. Found 31 (31 requested) and removed 22 (15 requested) atoms. Cycle 33: After refmac, R = 0.2499 (Rfree = 0.000) for 4208 atoms. Found 31 (31 requested) and removed 23 (15 requested) atoms. Cycle 34: After refmac, R = 0.2428 (Rfree = 0.000) for 4206 atoms. Found 28 (31 requested) and removed 18 (15 requested) atoms. Cycle 35: After refmac, R = 0.2166 (Rfree = 0.000) for 4210 atoms. Found 14 (31 requested) and removed 19 (15 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.17 3.01 Search for helices and strands: 0 residues in 0 chains, 4317 seeds are put forward NCS extension: 12 residues added (6 deleted due to clashes), 4329 seeds are put forward Round 1: 264 peptides, 41 chains. Longest chain 21 peptides. Score 0.434 Round 2: 316 peptides, 44 chains. Longest chain 19 peptides. Score 0.518 Round 3: 322 peptides, 44 chains. Longest chain 24 peptides. Score 0.530 Round 4: 322 peptides, 40 chains. Longest chain 24 peptides. Score 0.565 Round 5: 308 peptides, 41 chains. Longest chain 19 peptides. Score 0.529 Taking the results from Round 4 Chains 42, Residues 282, Estimated correctness of the model 16.8 % 2 chains (27 residues) have been docked in sequence ------------------------------------------------------ 9962 reflections ( 99.63 % complete ) and 8939 restraints for refining 4219 atoms. 7736 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2492 (Rfree = 0.000) for 4219 atoms. Found 19 (31 requested) and removed 21 (15 requested) atoms. Cycle 37: After refmac, R = 0.2476 (Rfree = 0.000) for 4209 atoms. Found 29 (31 requested) and removed 17 (15 requested) atoms. Cycle 38: After refmac, R = 0.2439 (Rfree = 0.000) for 4218 atoms. Found 26 (31 requested) and removed 21 (15 requested) atoms. Cycle 39: After refmac, R = 0.2412 (Rfree = 0.000) for 4217 atoms. Found 30 (31 requested) and removed 23 (15 requested) atoms. Cycle 40: After refmac, R = 0.2134 (Rfree = 0.000) for 4222 atoms. Found 10 (31 requested) and removed 17 (15 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.16 3.00 Search for helices and strands: 0 residues in 0 chains, 4316 seeds are put forward NCS extension: 19 residues added (4 deleted due to clashes), 4335 seeds are put forward Round 1: 292 peptides, 45 chains. Longest chain 16 peptides. Score 0.457 Round 2: 309 peptides, 39 chains. Longest chain 24 peptides. Score 0.549 Round 3: 309 peptides, 39 chains. Longest chain 23 peptides. Score 0.549 Round 4: 312 peptides, 43 chains. Longest chain 23 peptides. Score 0.519 Round 5: 314 peptides, 43 chains. Longest chain 18 peptides. Score 0.523 Taking the results from Round 3 Chains 41, Residues 270, Estimated correctness of the model 11.2 % 3 chains (45 residues) have been docked in sequence ------------------------------------------------------ 9962 reflections ( 99.63 % complete ) and 8773 restraints for refining 4218 atoms. 7510 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2517 (Rfree = 0.000) for 4218 atoms. Found 26 (31 requested) and removed 22 (15 requested) atoms. Cycle 42: After refmac, R = 0.2459 (Rfree = 0.000) for 4204 atoms. Found 24 (31 requested) and removed 19 (15 requested) atoms. Cycle 43: After refmac, R = 0.2427 (Rfree = 0.000) for 4191 atoms. Found 25 (31 requested) and removed 17 (15 requested) atoms. Cycle 44: After refmac, R = 0.2442 (Rfree = 0.000) for 4187 atoms. Found 31 (31 requested) and removed 19 (15 requested) atoms. Cycle 45: After refmac, R = 0.2161 (Rfree = 0.000) for 4195 atoms. Found 5 (31 requested) and removed 16 (15 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.15 2.99 Search for helices and strands: 0 residues in 0 chains, 4262 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 4274 seeds are put forward Round 1: 255 peptides, 43 chains. Longest chain 20 peptides. Score 0.392 Round 2: 290 peptides, 44 chains. Longest chain 17 peptides. Score 0.462 Round 3: 285 peptides, 39 chains. Longest chain 23 peptides. Score 0.500 Round 4: 291 peptides, 41 chains. Longest chain 23 peptides. Score 0.493 Round 5: 302 peptides, 44 chains. Longest chain 23 peptides. Score 0.488 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 41, Residues 246, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence Sequence coverage is 4 % Consider running further cycles of model building using 1vqs-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 9962 reflections ( 99.63 % complete ) and 9486 restraints for refining 4219 atoms. 8499 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2502 (Rfree = 0.000) for 4219 atoms. Found 0 (31 requested) and removed 15 (15 requested) atoms. Cycle 47: After refmac, R = 0.2586 (Rfree = 0.000) for 4197 atoms. Found 0 (31 requested) and removed 15 (15 requested) atoms. Cycle 48: After refmac, R = 0.2480 (Rfree = 0.000) for 4180 atoms. Found 0 (31 requested) and removed 15 (15 requested) atoms. Cycle 49: After refmac, R = 0.2373 (Rfree = 0.000) for 4155 atoms. Found 0 (31 requested) and removed 15 (15 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:27:07 GMT 2018 Job finished. TimeTaking 54.71 Used memory is bytes: 1923816