Mon 24 Dec 08:03:39 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 1vl4-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vl4-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vl4-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vl4-3.8-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/1vl4-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vl4-3.8-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 08:03:44 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/1vl4-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vl4-3.8-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 700 and 0 Target number of residues in the AU: 700 Target solvent content: 0.6319 Checking the provided sequence file Detected sequence length: 447 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 894 Adjusted target solvent content: 0.53 Input MTZ file: 1vl4-3.8-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: 19 Cell parameters: 80.171 107.117 119.834 90.000 90.000 90.000 Input sequence file: 1vl4-3.8-parrot-noncs.fasta_lf Building free atoms model in initial map for 7152 target number of atoms Had to go as low as 0.65 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: 79.862 3.800 Wilson plot Bfac: 67.53 10562 reflections ( 99.28 % complete ) and 0 restraints for refining 7902 atoms. Observations/parameters ratio is 0.33 ------------------------------------------------------ Starting model: R = 0.3165 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3248 (Rfree = 0.000) for 7902 atoms. Found 43 (43 requested) and removed 34 (21 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.41 3.28 Search for helices and strands: 0 residues in 0 chains, 8043 seeds are put forward NCS extension: 0 residues added, 8043 seeds are put forward Round 1: 300 peptides, 55 chains. Longest chain 16 peptides. Score 0.321 Round 2: 437 peptides, 73 chains. Longest chain 14 peptides. Score 0.418 Round 3: 487 peptides, 72 chains. Longest chain 19 peptides. Score 0.497 Round 4: 518 peptides, 66 chains. Longest chain 20 peptides. Score 0.572 Round 5: 530 peptides, 70 chains. Longest chain 23 peptides. Score 0.565 Taking the results from Round 4 Chains 71, Residues 452, Estimated correctness of the model 0.0 % 8 chains (86 residues) have been docked in sequence ------------------------------------------------------ 10562 reflections ( 99.28 % complete ) and 13786 restraints for refining 6466 atoms. 11743 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2659 (Rfree = 0.000) for 6466 atoms. Found 29 (35 requested) and removed 63 (17 requested) atoms. Cycle 2: After refmac, R = 0.2572 (Rfree = 0.000) for 6285 atoms. Found 22 (35 requested) and removed 49 (17 requested) atoms. Cycle 3: After refmac, R = 0.2567 (Rfree = 0.000) for 6181 atoms. Found 34 (34 requested) and removed 32 (17 requested) atoms. Cycle 4: After refmac, R = 0.2520 (Rfree = 0.000) for 6128 atoms. Found 28 (34 requested) and removed 36 (17 requested) atoms. Cycle 5: After refmac, R = 0.2188 (Rfree = 0.000) for 6071 atoms. Found 9 (33 requested) and removed 25 (16 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.40 3.27 Search for helices and strands: 0 residues in 0 chains, 6228 seeds are put forward NCS extension: 41 residues added (1 deleted due to clashes), 6269 seeds are put forward Round 1: 460 peptides, 81 chains. Longest chain 13 peptides. Score 0.400 Round 2: 506 peptides, 68 chains. Longest chain 19 peptides. Score 0.546 Round 3: 509 peptides, 69 chains. Longest chain 20 peptides. Score 0.544 Round 4: 528 peptides, 70 chains. Longest chain 25 peptides. Score 0.563 Round 5: 513 peptides, 66 chains. Longest chain 22 peptides. Score 0.566 Taking the results from Round 5 Chains 68, Residues 447, Estimated correctness of the model 0.0 % 3 chains (37 residues) have been docked in sequence ------------------------------------------------------ 10562 reflections ( 99.28 % complete ) and 14169 restraints for refining 6469 atoms. 12323 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2561 (Rfree = 0.000) for 6469 atoms. Found 26 (35 requested) and removed 63 (17 requested) atoms. Cycle 7: After refmac, R = 0.2359 (Rfree = 0.000) for 6372 atoms. Found 35 (35 requested) and removed 44 (17 requested) atoms. Cycle 8: After refmac, R = 0.2216 (Rfree = 0.000) for 6330 atoms. Found 23 (34 requested) and removed 42 (17 requested) atoms. Cycle 9: After refmac, R = 0.2123 (Rfree = 0.000) for 6296 atoms. Found 29 (34 requested) and removed 28 (17 requested) atoms. Cycle 10: After refmac, R = 0.2128 (Rfree = 0.000) for 6282 atoms. Found 34 (34 requested) and removed 33 (17 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.45 3.31 Search for helices and strands: 0 residues in 0 chains, 6451 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 6474 seeds are put forward Round 1: 430 peptides, 71 chains. Longest chain 18 peptides. Score 0.421 Round 2: 494 peptides, 66 chains. Longest chain 32 peptides. Score 0.542 Round 3: 492 peptides, 68 chains. Longest chain 23 peptides. Score 0.528 Round 4: 519 peptides, 69 chains. Longest chain 29 peptides. Score 0.557 Round 5: 526 peptides, 72 chains. Longest chain 26 peptides. Score 0.549 Taking the results from Round 4 Chains 72, Residues 450, Estimated correctness of the model 0.0 % 8 chains (50 residues) have been docked in sequence ------------------------------------------------------ 10562 reflections ( 99.28 % complete ) and 14035 restraints for refining 6469 atoms. 12137 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2616 (Rfree = 0.000) for 6469 atoms. Found 35 (35 requested) and removed 66 (17 requested) atoms. Cycle 12: After refmac, R = 0.2410 (Rfree = 0.000) for 6371 atoms. Found 35 (35 requested) and removed 40 (17 requested) atoms. Cycle 13: After refmac, R = 0.2242 (Rfree = 0.000) for 6322 atoms. Found 35 (35 requested) and removed 33 (17 requested) atoms. Cycle 14: After refmac, R = 0.2088 (Rfree = 0.000) for 6290 atoms. Found 28 (34 requested) and removed 28 (17 requested) atoms. Cycle 15: After refmac, R = 0.1844 (Rfree = 0.000) for 6271 atoms. Found 6 (34 requested) and removed 22 (17 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.38 3.25 Search for helices and strands: 0 residues in 0 chains, 6429 seeds are put forward NCS extension: 30 residues added (1 deleted due to clashes), 6459 seeds are put forward Round 1: 419 peptides, 74 chains. Longest chain 15 peptides. Score 0.383 Round 2: 475 peptides, 73 chains. Longest chain 19 peptides. Score 0.474 Round 3: 490 peptides, 70 chains. Longest chain 33 peptides. Score 0.513 Round 4: 507 peptides, 73 chains. Longest chain 31 peptides. Score 0.518 Round 5: 499 peptides, 71 chains. Longest chain 29 peptides. Score 0.519 Taking the results from Round 5 Chains 71, Residues 428, Estimated correctness of the model 0.0 % 6 chains (59 residues) have been docked in sequence ------------------------------------------------------ 10562 reflections ( 99.28 % complete ) and 14173 restraints for refining 6468 atoms. 12336 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2335 (Rfree = 0.000) for 6468 atoms. Found 35 (35 requested) and removed 45 (17 requested) atoms. Cycle 17: After refmac, R = 0.2314 (Rfree = 0.000) for 6384 atoms. Found 35 (35 requested) and removed 37 (17 requested) atoms. Cycle 18: After refmac, R = 0.2290 (Rfree = 0.000) for 6325 atoms. Found 35 (35 requested) and removed 38 (17 requested) atoms. Cycle 19: After refmac, R = 0.2230 (Rfree = 0.000) for 6285 atoms. Found 34 (34 requested) and removed 28 (17 requested) atoms. Cycle 20: After refmac, R = 0.1872 (Rfree = 0.000) for 6260 atoms. Found 11 (34 requested) and removed 20 (17 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.39 3.26 Search for helices and strands: 0 residues in 0 chains, 6403 seeds are put forward NCS extension: 40 residues added (1 deleted due to clashes), 6443 seeds are put forward Round 1: 412 peptides, 77 chains. Longest chain 17 peptides. Score 0.351 Round 2: 446 peptides, 71 chains. Longest chain 22 peptides. Score 0.445 Round 3: 460 peptides, 66 chains. Longest chain 29 peptides. Score 0.496 Round 4: 458 peptides, 72 chains. Longest chain 16 peptides. Score 0.456 Round 5: 464 peptides, 66 chains. Longest chain 27 peptides. Score 0.502 Taking the results from Round 5 Chains 69, Residues 398, Estimated correctness of the model 0.0 % 4 chains (27 residues) have been docked in sequence ------------------------------------------------------ 10562 reflections ( 99.28 % complete ) and 14611 restraints for refining 6468 atoms. 12999 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2335 (Rfree = 0.000) for 6468 atoms. Found 35 (35 requested) and removed 43 (17 requested) atoms. Failed to save intermediate PDB Cycle 22: After refmac, R = 0.2198 (Rfree = 0.000) for 6386 atoms. Found 34 (35 requested) and removed 31 (17 requested) atoms. Cycle 23: After refmac, R = 0.1826 (Rfree = 0.000) for 6344 atoms. Found 13 (35 requested) and removed 37 (17 requested) atoms. Cycle 24: After refmac, R = 0.1743 (Rfree = 0.000) for 6298 atoms. Found 15 (34 requested) and removed 32 (17 requested) atoms. Cycle 25: After refmac, R = 0.1686 (Rfree = 0.000) for 6269 atoms. Found 6 (34 requested) and removed 20 (17 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.43 3.30 Search for helices and strands: 0 residues in 0 chains, 6397 seeds are put forward NCS extension: 18 residues added (3 deleted due to clashes), 6415 seeds are put forward Round 1: 404 peptides, 79 chains. Longest chain 11 peptides. Score 0.324 Round 2: 436 peptides, 70 chains. Longest chain 15 peptides. Score 0.436 Round 3: 423 peptides, 69 chains. Longest chain 14 peptides. Score 0.423 Round 4: 443 peptides, 72 chains. Longest chain 16 peptides. Score 0.434 Round 5: 441 peptides, 68 chains. Longest chain 18 peptides. Score 0.457 Taking the results from Round 5 Chains 69, Residues 373, Estimated correctness of the model 0.0 % 5 chains (41 residues) have been docked in sequence ------------------------------------------------------ 10562 reflections ( 99.28 % complete ) and 14451 restraints for refining 6469 atoms. 12899 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2293 (Rfree = 0.000) for 6469 atoms. Found 35 (35 requested) and removed 47 (17 requested) atoms. Cycle 27: After refmac, R = 0.2134 (Rfree = 0.000) for 6386 atoms. Found 35 (35 requested) and removed 36 (17 requested) atoms. Cycle 28: After refmac, R = 0.1980 (Rfree = 0.000) for 6321 atoms. Found 19 (35 requested) and removed 28 (17 requested) atoms. Cycle 29: After refmac, R = 0.1959 (Rfree = 0.000) for 6294 atoms. Found 28 (34 requested) and removed 20 (17 requested) atoms. Cycle 30: After refmac, R = 0.1730 (Rfree = 0.000) for 6294 atoms. Found 3 (34 requested) and removed 19 (17 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.40 3.27 Search for helices and strands: 0 residues in 0 chains, 6413 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 6435 seeds are put forward Round 1: 352 peptides, 72 chains. Longest chain 10 peptides. Score 0.286 Round 2: 408 peptides, 71 chains. Longest chain 13 peptides. Score 0.386 Round 3: 403 peptides, 68 chains. Longest chain 19 peptides. Score 0.399 Round 4: 411 peptides, 63 chains. Longest chain 16 peptides. Score 0.445 Round 5: 439 peptides, 66 chains. Longest chain 27 peptides. Score 0.467 Taking the results from Round 5 Chains 69, Residues 373, Estimated correctness of the model 0.0 % 3 chains (27 residues) have been docked in sequence ------------------------------------------------------ 10562 reflections ( 99.28 % complete ) and 14470 restraints for refining 6459 atoms. 12964 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2408 (Rfree = 0.000) for 6459 atoms. Found 35 (35 requested) and removed 62 (17 requested) atoms. Cycle 32: After refmac, R = 0.2314 (Rfree = 0.000) for 6368 atoms. Found 35 (35 requested) and removed 40 (17 requested) atoms. Cycle 33: After refmac, R = 0.2039 (Rfree = 0.000) for 6338 atoms. Found 34 (34 requested) and removed 34 (17 requested) atoms. Cycle 34: After refmac, R = 0.2190 (Rfree = 0.000) for 6317 atoms. Found 34 (34 requested) and removed 41 (17 requested) atoms. Cycle 35: After refmac, R = 0.2124 (Rfree = 0.000) for 6297 atoms. Found 34 (34 requested) and removed 30 (17 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.42 3.29 Search for helices and strands: 0 residues in 0 chains, 6491 seeds are put forward NCS extension: 29 residues added (2 deleted due to clashes), 6520 seeds are put forward Round 1: 321 peptides, 67 chains. Longest chain 8 peptides. Score 0.268 Round 2: 364 peptides, 65 chains. Longest chain 12 peptides. Score 0.357 Round 3: 397 peptides, 65 chains. Longest chain 18 peptides. Score 0.410 Round 4: 394 peptides, 62 chains. Longest chain 16 peptides. Score 0.426 Round 5: 385 peptides, 62 chains. Longest chain 13 peptides. Score 0.412 Taking the results from Round 4 Chains 62, Residues 332, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10562 reflections ( 99.28 % complete ) and 15093 restraints for refining 6468 atoms. 13827 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2278 (Rfree = 0.000) for 6468 atoms. Found 35 (35 requested) and removed 81 (17 requested) atoms. Cycle 37: After refmac, R = 0.2300 (Rfree = 0.000) for 6379 atoms. Found 35 (35 requested) and removed 46 (17 requested) atoms. Cycle 38: After refmac, R = 0.2122 (Rfree = 0.000) for 6349 atoms. Found 35 (35 requested) and removed 40 (17 requested) atoms. Cycle 39: After refmac, R = 0.2198 (Rfree = 0.000) for 6321 atoms. Found 34 (34 requested) and removed 31 (17 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.2089 (Rfree = 0.000) for 6307 atoms. Found 34 (34 requested) and removed 32 (17 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.42 3.29 Search for helices and strands: 0 residues in 0 chains, 6447 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 6460 seeds are put forward Round 1: 282 peptides, 59 chains. Longest chain 10 peptides. Score 0.258 Round 2: 341 peptides, 60 chains. Longest chain 17 peptides. Score 0.355 Round 3: 346 peptides, 60 chains. Longest chain 14 peptides. Score 0.363 Round 4: 359 peptides, 60 chains. Longest chain 16 peptides. Score 0.384 Round 5: 367 peptides, 64 chains. Longest chain 18 peptides. Score 0.369 Taking the results from Round 4 Chains 61, Residues 299, Estimated correctness of the model 0.0 % 7 chains (42 residues) have been docked in sequence ------------------------------------------------------ 10562 reflections ( 99.28 % complete ) and 14559 restraints for refining 6469 atoms. 13282 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2378 (Rfree = 0.000) for 6469 atoms. Found 35 (35 requested) and removed 30 (17 requested) atoms. Cycle 42: After refmac, R = 0.2526 (Rfree = 0.000) for 6399 atoms. Found 35 (35 requested) and removed 62 (17 requested) atoms. Cycle 43: After refmac, R = 0.2398 (Rfree = 0.000) for 6335 atoms. Found 35 (35 requested) and removed 29 (17 requested) atoms. Cycle 44: After refmac, R = 0.2388 (Rfree = 0.000) for 6306 atoms. Found 34 (34 requested) and removed 26 (17 requested) atoms. Cycle 45: After refmac, R = 0.2424 (Rfree = 0.000) for 6296 atoms. Found 34 (34 requested) and removed 23 (17 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.40 3.27 Search for helices and strands: 0 residues in 0 chains, 6409 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 6432 seeds are put forward Round 1: 254 peptides, 55 chains. Longest chain 10 peptides. Score 0.236 Round 2: 307 peptides, 56 chains. Longest chain 12 peptides. Score 0.326 Round 3: 327 peptides, 62 chains. Longest chain 13 peptides. Score 0.316 Round 4: 319 peptides, 55 chains. Longest chain 13 peptides. Score 0.354 Round 5: 319 peptides, 55 chains. Longest chain 14 peptides. Score 0.354 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 55, Residues 264, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence Sequence coverage is 3 % Consider running further cycles of model building using 1vl4-3_warpNtrace.pdb as input Building loops using Loopy2018 55 chains (264 residues) following loop building 2 chains (8 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 10562 reflections ( 99.28 % complete ) and 13860 restraints for refining 6085 atoms. 12835 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2284 (Rfree = 0.000) for 6085 atoms. Found 0 (33 requested) and removed 16 (16 requested) atoms. Cycle 47: After refmac, R = 0.2318 (Rfree = 0.000) for 6046 atoms. Found 0 (33 requested) and removed 16 (16 requested) atoms. Cycle 48: After refmac, R = 0.2352 (Rfree = 0.000) for 5990 atoms. Found 0 (33 requested) and removed 16 (16 requested) atoms. Cycle 49: After refmac, R = 0.1927 (Rfree = 0.000) for 5959 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Writing output files ... TimeTaking 70.72