null Tue 25 Dec 19:27:56 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 1vqr-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vqr-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vqr-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vqr-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/1vqr-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vqr-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 19:28:11 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/1vqr-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vqr-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 844 and 0 Target number of residues in the AU: 844 Target solvent content: 0.6358 Checking the provided sequence file Detected sequence length: 297 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1188 Adjusted target solvent content: 0.49 Input MTZ file: 1vqr-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: 5 Cell parameters: 123.141 122.090 96.897 90.000 120.583 90.000 Input sequence file: 1vqr-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 9504 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: 83.418 3.800 Wilson plot Bfac: 69.50 11006 reflections ( 89.82 % complete ) and 0 restraints for refining 10466 atoms. Observations/parameters ratio is 0.26 ------------------------------------------------------ Starting model: R = 0.3732 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3318 (Rfree = 0.000) for 10466 atoms. Found 42 (57 requested) and removed 179 (28 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.41 3.46 Search for helices and strands: 0 residues in 0 chains, 10433 seeds are put forward NCS extension: 0 residues added, 10433 seeds are put forward Round 1: 219 peptides, 48 chains. Longest chain 8 peptides. Score 0.218 Round 2: 285 peptides, 59 chains. Longest chain 11 peptides. Score 0.251 Round 3: 319 peptides, 66 chains. Longest chain 8 peptides. Score 0.258 Round 4: 346 peptides, 71 chains. Longest chain 9 peptides. Score 0.267 Round 5: 353 peptides, 69 chains. Longest chain 11 peptides. Score 0.291 Taking the results from Round 5 Chains 69, Residues 284, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 11006 reflections ( 89.82 % complete ) and 21885 restraints for refining 8593 atoms. 20795 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2839 (Rfree = 0.000) for 8593 atoms. Found 26 (47 requested) and removed 57 (23 requested) atoms. Cycle 2: After refmac, R = 0.2809 (Rfree = 0.000) for 8457 atoms. Found 47 (47 requested) and removed 62 (23 requested) atoms. Cycle 3: After refmac, R = 0.2589 (Rfree = 0.000) for 8379 atoms. Found 38 (46 requested) and removed 58 (23 requested) atoms. Cycle 4: After refmac, R = 0.2087 (Rfree = 0.000) for 8308 atoms. Found 11 (45 requested) and removed 45 (22 requested) atoms. Cycle 5: After refmac, R = 0.2024 (Rfree = 0.000) for 8243 atoms. Found 10 (45 requested) and removed 36 (22 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.35 3.39 Search for helices and strands: 0 residues in 0 chains, 8394 seeds are put forward NCS extension: 10 residues added (3 deleted due to clashes), 8404 seeds are put forward Round 1: 336 peptides, 75 chains. Longest chain 8 peptides. Score 0.226 Round 2: 407 peptides, 82 chains. Longest chain 9 peptides. Score 0.289 Round 3: 404 peptides, 77 chains. Longest chain 15 peptides. Score 0.315 Round 4: 413 peptides, 80 chains. Longest chain 10 peptides. Score 0.310 Round 5: 414 peptides, 77 chains. Longest chain 13 peptides. Score 0.329 Taking the results from Round 5 Chains 77, Residues 337, Estimated correctness of the model 0.0 % 3 chains (15 residues) have been docked in sequence ------------------------------------------------------ 11006 reflections ( 89.82 % complete ) and 20103 restraints for refining 8246 atoms. 18793 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2385 (Rfree = 0.000) for 8246 atoms. Found 45 (45 requested) and removed 67 (22 requested) atoms. Cycle 7: After refmac, R = 0.2337 (Rfree = 0.000) for 8166 atoms. Found 40 (45 requested) and removed 49 (22 requested) atoms. Cycle 8: After refmac, R = 0.2287 (Rfree = 0.000) for 8108 atoms. Found 44 (44 requested) and removed 50 (22 requested) atoms. Cycle 9: After refmac, R = 0.2129 (Rfree = 0.000) for 8069 atoms. Found 33 (44 requested) and removed 40 (22 requested) atoms. Cycle 10: After refmac, R = 0.1867 (Rfree = 0.000) for 8034 atoms. Found 7 (44 requested) and removed 28 (22 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.43 3.48 Search for helices and strands: 0 residues in 0 chains, 8189 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 8205 seeds are put forward Round 1: 391 peptides, 84 chains. Longest chain 9 peptides. Score 0.253 Round 2: 428 peptides, 84 chains. Longest chain 9 peptides. Score 0.307 Round 3: 426 peptides, 80 chains. Longest chain 14 peptides. Score 0.328 Round 4: 431 peptides, 77 chains. Longest chain 14 peptides. Score 0.353 Round 5: 442 peptides, 81 chains. Longest chain 15 peptides. Score 0.344 Taking the results from Round 4 Chains 77, Residues 354, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 11006 reflections ( 89.82 % complete ) and 19560 restraints for refining 8109 atoms. 18221 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2322 (Rfree = 0.000) for 8109 atoms. Found 36 (44 requested) and removed 58 (22 requested) atoms. Cycle 12: After refmac, R = 0.2139 (Rfree = 0.000) for 8048 atoms. Found 30 (44 requested) and removed 57 (22 requested) atoms. Cycle 13: After refmac, R = 0.1817 (Rfree = 0.000) for 8002 atoms. Found 10 (44 requested) and removed 30 (22 requested) atoms. Cycle 14: After refmac, R = 0.1713 (Rfree = 0.000) for 7969 atoms. Found 5 (43 requested) and removed 36 (21 requested) atoms. Cycle 15: After refmac, R = 0.1694 (Rfree = 0.000) for 7932 atoms. Found 4 (43 requested) and removed 27 (21 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.43 3.48 Search for helices and strands: 0 residues in 0 chains, 8119 seeds are put forward NCS extension: 26 residues added (0 deleted due to clashes), 8145 seeds are put forward Round 1: 436 peptides, 91 chains. Longest chain 8 peptides. Score 0.276 Round 2: 448 peptides, 85 chains. Longest chain 11 peptides. Score 0.329 Round 3: 448 peptides, 80 chains. Longest chain 14 peptides. Score 0.358 Round 4: 451 peptides, 79 chains. Longest chain 17 peptides. Score 0.368 Round 5: 454 peptides, 80 chains. Longest chain 13 peptides. Score 0.366 Taking the results from Round 4 Chains 79, Residues 372, Estimated correctness of the model 0.0 % 2 chains (10 residues) have been docked in sequence ------------------------------------------------------ 11006 reflections ( 89.82 % complete ) and 20397 restraints for refining 8452 atoms. 18959 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2177 (Rfree = 0.000) for 8452 atoms. Found 39 (46 requested) and removed 70 (23 requested) atoms. Cycle 17: After refmac, R = 0.2150 (Rfree = 0.000) for 8369 atoms. Found 29 (46 requested) and removed 97 (23 requested) atoms. Cycle 18: After refmac, R = 0.2060 (Rfree = 0.000) for 8268 atoms. Found 37 (45 requested) and removed 54 (22 requested) atoms. Cycle 19: After refmac, R = 0.2029 (Rfree = 0.000) for 8233 atoms. Found 41 (45 requested) and removed 39 (22 requested) atoms. Cycle 20: After refmac, R = 0.1935 (Rfree = 0.000) for 8216 atoms. Found 43 (45 requested) and removed 37 (22 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.42 3.47 Search for helices and strands: 0 residues in 0 chains, 8419 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 8439 seeds are put forward Round 1: 376 peptides, 80 chains. Longest chain 9 peptides. Score 0.255 Round 2: 449 peptides, 87 chains. Longest chain 11 peptides. Score 0.319 Round 3: 441 peptides, 81 chains. Longest chain 14 peptides. Score 0.343 Round 4: 443 peptides, 78 chains. Longest chain 15 peptides. Score 0.363 Round 5: 421 peptides, 74 chains. Longest chain 15 peptides. Score 0.357 Taking the results from Round 4 Chains 79, Residues 365, Estimated correctness of the model 0.0 % 3 chains (20 residues) have been docked in sequence ------------------------------------------------------ 11006 reflections ( 89.82 % complete ) and 20401 restraints for refining 8558 atoms. 18958 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2292 (Rfree = 0.000) for 8558 atoms. Found 36 (47 requested) and removed 96 (23 requested) atoms. Cycle 22: After refmac, R = 0.2064 (Rfree = 0.000) for 8453 atoms. Found 24 (46 requested) and removed 57 (23 requested) atoms. Cycle 23: After refmac, R = 0.2037 (Rfree = 0.000) for 8386 atoms. Found 30 (46 requested) and removed 46 (23 requested) atoms. Cycle 24: After refmac, R = 0.1738 (Rfree = 0.000) for 8345 atoms. Found 8 (46 requested) and removed 31 (23 requested) atoms. Cycle 25: After refmac, R = 0.1653 (Rfree = 0.000) for 8309 atoms. Found 4 (45 requested) and removed 27 (22 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.44 3.49 Search for helices and strands: 0 residues in 0 chains, 8449 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 8463 seeds are put forward Round 1: 352 peptides, 75 chains. Longest chain 10 peptides. Score 0.251 Round 2: 410 peptides, 80 chains. Longest chain 11 peptides. Score 0.305 Round 3: 408 peptides, 76 chains. Longest chain 13 peptides. Score 0.327 Round 4: 408 peptides, 74 chains. Longest chain 12 peptides. Score 0.339 Round 5: 409 peptides, 71 chains. Longest chain 13 peptides. Score 0.358 Taking the results from Round 5 Chains 71, Residues 338, Estimated correctness of the model 0.0 % 2 chains (11 residues) have been docked in sequence ------------------------------------------------------ 11006 reflections ( 89.82 % complete ) and 20699 restraints for refining 8550 atoms. 19381 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2230 (Rfree = 0.000) for 8550 atoms. Found 38 (47 requested) and removed 61 (23 requested) atoms. Cycle 27: After refmac, R = 0.2229 (Rfree = 0.000) for 8495 atoms. Found 38 (46 requested) and removed 50 (23 requested) atoms. Cycle 28: After refmac, R = 0.2084 (Rfree = 0.000) for 8455 atoms. Found 35 (46 requested) and removed 39 (23 requested) atoms. Cycle 29: After refmac, R = 0.1728 (Rfree = 0.000) for 8436 atoms. Found 6 (46 requested) and removed 39 (23 requested) atoms. Cycle 30: After refmac, R = 0.1624 (Rfree = 0.000) for 8387 atoms. Found 5 (46 requested) and removed 29 (23 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.45 3.50 Search for helices and strands: 0 residues in 0 chains, 8519 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 8533 seeds are put forward Round 1: 381 peptides, 82 chains. Longest chain 9 peptides. Score 0.250 Round 2: 394 peptides, 74 chains. Longest chain 11 peptides. Score 0.319 Round 3: 420 peptides, 77 chains. Longest chain 13 peptides. Score 0.338 Round 4: 422 peptides, 73 chains. Longest chain 13 peptides. Score 0.364 Round 5: 415 peptides, 73 chains. Longest chain 13 peptides. Score 0.355 Taking the results from Round 4 Chains 73, Residues 349, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 11006 reflections ( 89.82 % complete ) and 20362 restraints for refining 8579 atoms. 19016 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2160 (Rfree = 0.000) for 8579 atoms. Found 47 (47 requested) and removed 55 (23 requested) atoms. Cycle 32: After refmac, R = 0.2030 (Rfree = 0.000) for 8533 atoms. Found 47 (47 requested) and removed 58 (23 requested) atoms. Cycle 33: After refmac, R = 0.1573 (Rfree = 0.000) for 8497 atoms. Found 11 (46 requested) and removed 32 (23 requested) atoms. Cycle 34: After refmac, R = 0.1492 (Rfree = 0.000) for 8463 atoms. Found 3 (46 requested) and removed 32 (23 requested) atoms. Cycle 35: After refmac, R = 0.1473 (Rfree = 0.000) for 8428 atoms. Found 2 (46 requested) and removed 26 (23 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.42 3.47 Search for helices and strands: 0 residues in 0 chains, 8560 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 8582 seeds are put forward Round 1: 329 peptides, 71 chains. Longest chain 8 peptides. Score 0.241 Round 2: 364 peptides, 67 chains. Longest chain 13 peptides. Score 0.319 Round 3: 371 peptides, 72 chains. Longest chain 11 peptides. Score 0.298 Round 4: 379 peptides, 67 chains. Longest chain 13 peptides. Score 0.341 Round 5: 362 peptides, 65 chains. Longest chain 14 peptides. Score 0.329 Taking the results from Round 4 Chains 68, Residues 312, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 11006 reflections ( 89.82 % complete ) and 20887 restraints for refining 8596 atoms. 19667 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2105 (Rfree = 0.000) for 8596 atoms. Found 45 (47 requested) and removed 69 (23 requested) atoms. Cycle 37: After refmac, R = 0.2022 (Rfree = 0.000) for 8557 atoms. Found 47 (47 requested) and removed 60 (23 requested) atoms. Cycle 38: After refmac, R = 0.1856 (Rfree = 0.000) for 8530 atoms. Found 35 (46 requested) and removed 38 (23 requested) atoms. Cycle 39: After refmac, R = 0.1890 (Rfree = 0.000) for 8514 atoms. Found 37 (46 requested) and removed 48 (23 requested) atoms. Cycle 40: After refmac, R = 0.1793 (Rfree = 0.000) for 8496 atoms. Found 33 (46 requested) and removed 34 (23 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.43 3.48 Search for helices and strands: 0 residues in 0 chains, 8640 seeds are put forward NCS extension: 14 residues added (3 deleted due to clashes), 8654 seeds are put forward Round 1: 317 peptides, 69 chains. Longest chain 8 peptides. Score 0.235 Round 2: 346 peptides, 68 chains. Longest chain 12 peptides. Score 0.286 Round 3: 361 peptides, 70 chains. Longest chain 13 peptides. Score 0.296 Round 4: 359 peptides, 69 chains. Longest chain 13 peptides. Score 0.299 Round 5: 361 peptides, 63 chains. Longest chain 12 peptides. Score 0.340 Taking the results from Round 5 Chains 63, Residues 298, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 11006 reflections ( 89.82 % complete ) and 21210 restraints for refining 8596 atoms. 20081 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2234 (Rfree = 0.000) for 8596 atoms. Found 47 (47 requested) and removed 116 (23 requested) atoms. Cycle 42: After refmac, R = 0.2074 (Rfree = 0.000) for 8512 atoms. Found 46 (46 requested) and removed 37 (23 requested) atoms. Cycle 43: After refmac, R = 0.1672 (Rfree = 0.000) for 8508 atoms. Found 11 (46 requested) and removed 27 (23 requested) atoms. Cycle 44: After refmac, R = 0.1617 (Rfree = 0.000) for 8477 atoms. Found 9 (46 requested) and removed 32 (23 requested) atoms. Cycle 45: After refmac, R = 0.1534 (Rfree = 0.000) for 8449 atoms. Found 5 (46 requested) and removed 25 (23 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.47 3.52 Search for helices and strands: 0 residues in 0 chains, 8592 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 8606 seeds are put forward Round 1: 257 peptides, 59 chains. Longest chain 7 peptides. Score 0.204 Round 2: 322 peptides, 65 chains. Longest chain 10 peptides. Score 0.269 Round 3: 347 peptides, 69 chains. Longest chain 17 peptides. Score 0.282 Round 4: 326 peptides, 61 chains. Longest chain 13 peptides. Score 0.302 Round 5: 311 peptides, 60 chains. Longest chain 11 peptides. Score 0.286 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 61, Residues 265, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence Sequence coverage is 2 % Consider running further cycles of model building using 1vqr-3_warpNtrace.pdb as input Building loops using Loopy2018 61 chains (265 residues) following loop building 2 chains (7 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 11006 reflections ( 89.82 % complete ) and 21266 restraints for refining 8596 atoms. 20246 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2322 (Rfree = 0.000) for 8596 atoms. Found 0 (47 requested) and removed 23 (23 requested) atoms. Cycle 47: After refmac, R = 0.2264 (Rfree = 0.000) for 8550 atoms. Found 0 (47 requested) and removed 23 (23 requested) atoms. Cycle 48: After refmac, R = 0.2090 (Rfree = 0.000) for 8515 atoms. Found 0 (46 requested) and removed 23 (23 requested) atoms. Cycle 49: After refmac, R = 0.1961 (Rfree = 0.000) for 8479 atoms. Found 0 (46 requested) and removed 23 (23 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 21:46:34 GMT 2018 Job finished. TimeTaking 138.64 Used memory is bytes: 20056016