Mon 24 Dec 00:15:18 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vl4-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vl4-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vl4-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vl4-3.8-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/1vl4-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vl4-3.8-parrot-mrncs ############### 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 00:15:23 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/mrncs/ArpWArp/wArpResults/WorkingDir/1vl4-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vl4-3.8-parrot-mrncs/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-mrncs.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-mrncs.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 7933 atoms. Observations/parameters ratio is 0.33 ------------------------------------------------------ Starting model: R = 0.3137 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3097 (Rfree = 0.000) for 7933 atoms. Found 43 (43 requested) and removed 46 (21 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.38 3.25 Search for helices and strands: 0 residues in 0 chains, 8023 seeds are put forward NCS extension: 0 residues added, 8023 seeds are put forward Round 1: 335 peptides, 67 chains. Longest chain 10 peptides. Score 0.293 Round 2: 447 peptides, 74 chains. Longest chain 15 peptides. Score 0.427 Round 3: 530 peptides, 77 chains. Longest chain 21 peptides. Score 0.525 Round 4: 542 peptides, 72 chains. Longest chain 22 peptides. Score 0.569 Round 5: 555 peptides, 71 chains. Longest chain 25 peptides. Score 0.590 Taking the results from Round 5 Chains 75, Residues 484, Estimated correctness of the model 0.0 % 10 chains (71 residues) have been docked in sequence ------------------------------------------------------ 10562 reflections ( 99.28 % complete ) and 13865 restraints for refining 6466 atoms. 11778 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2814 (Rfree = 0.000) for 6466 atoms. Found 35 (35 requested) and removed 62 (17 requested) atoms. Cycle 2: After refmac, R = 0.2606 (Rfree = 0.000) for 6309 atoms. Found 26 (35 requested) and removed 39 (17 requested) atoms. Cycle 3: After refmac, R = 0.2679 (Rfree = 0.000) for 6193 atoms. Found 30 (34 requested) and removed 35 (17 requested) atoms. Cycle 4: After refmac, R = 0.2568 (Rfree = 0.000) for 6135 atoms. Found 34 (34 requested) and removed 37 (17 requested) atoms. Cycle 5: After refmac, R = 0.2444 (Rfree = 0.000) for 6079 atoms. Found 28 (33 requested) and removed 43 (16 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.37 3.24 Search for helices and strands: 0 residues in 0 chains, 6243 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 6258 seeds are put forward Round 1: 428 peptides, 81 chains. Longest chain 13 peptides. Score 0.350 Round 2: 505 peptides, 78 chains. Longest chain 17 peptides. Score 0.486 Round 3: 525 peptides, 80 chains. Longest chain 20 peptides. Score 0.501 Round 4: 529 peptides, 74 chains. Longest chain 24 peptides. Score 0.541 Round 5: 508 peptides, 72 chains. Longest chain 17 peptides. Score 0.525 Taking the results from Round 4 Chains 77, Residues 455, Estimated correctness of the model 0.0 % 5 chains (42 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 10562 reflections ( 99.28 % complete ) and 14074 restraints for refining 6297 atoms. 12197 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2409 (Rfree = 0.000) for 6297 atoms. Found 27 (34 requested) and removed 80 (17 requested) atoms. Cycle 7: After refmac, R = 0.2239 (Rfree = 0.000) for 6162 atoms. Found 19 (34 requested) and removed 38 (17 requested) atoms. Cycle 8: After refmac, R = 0.2184 (Rfree = 0.000) for 6103 atoms. Found 16 (33 requested) and removed 33 (16 requested) atoms. Cycle 9: After refmac, R = 0.2220 (Rfree = 0.000) for 6066 atoms. Found 25 (33 requested) and removed 29 (16 requested) atoms. Cycle 10: After refmac, R = 0.2120 (Rfree = 0.000) for 6043 atoms. Found 20 (33 requested) and removed 26 (16 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.33 3.20 Search for helices and strands: 0 residues in 0 chains, 6210 seeds are put forward NCS extension: 21 residues added (3 deleted due to clashes), 6231 seeds are put forward Round 1: 434 peptides, 80 chains. Longest chain 17 peptides. Score 0.366 Round 2: 506 peptides, 76 chains. Longest chain 16 peptides. Score 0.499 Round 3: 497 peptides, 75 chains. Longest chain 18 peptides. Score 0.493 Round 4: 492 peptides, 66 chains. Longest chain 22 peptides. Score 0.539 Round 5: 508 peptides, 75 chains. Longest chain 24 peptides. Score 0.508 Taking the results from Round 4 Chains 67, Residues 426, Estimated correctness of the model 0.0 % 3 chains (35 residues) have been docked in sequence ------------------------------------------------------ 10562 reflections ( 99.28 % complete ) and 14404 restraints for refining 6423 atoms. 12650 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2277 (Rfree = 0.000) for 6423 atoms. Found 30 (35 requested) and removed 53 (17 requested) atoms. Cycle 12: After refmac, R = 0.2136 (Rfree = 0.000) for 6351 atoms. Found 20 (35 requested) and removed 41 (17 requested) atoms. Cycle 13: After refmac, R = 0.2027 (Rfree = 0.000) for 6293 atoms. Found 20 (34 requested) and removed 32 (17 requested) atoms. Cycle 14: After refmac, R = 0.1999 (Rfree = 0.000) for 6262 atoms. Found 13 (34 requested) and removed 25 (17 requested) atoms. Cycle 15: After refmac, R = 0.1821 (Rfree = 0.000) for 6233 atoms. Found 7 (34 requested) and removed 22 (17 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.41 3.28 Search for helices and strands: 0 residues in 0 chains, 6380 seeds are put forward NCS extension: 16 residues added (4 deleted due to clashes), 6396 seeds are put forward Round 1: 434 peptides, 76 chains. Longest chain 15 peptides. Score 0.393 Round 2: 463 peptides, 70 chains. Longest chain 20 peptides. Score 0.476 Round 3: 463 peptides, 70 chains. Longest chain 28 peptides. Score 0.476 Round 4: 479 peptides, 68 chains. Longest chain 18 peptides. Score 0.510 Round 5: 471 peptides, 64 chains. Longest chain 20 peptides. Score 0.524 Taking the results from Round 5 Chains 65, Residues 407, Estimated correctness of the model 0.0 % 5 chains (33 residues) have been docked in sequence ------------------------------------------------------ 10562 reflections ( 99.28 % complete ) and 14597 restraints for refining 6468 atoms. 12935 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2220 (Rfree = 0.000) for 6468 atoms. Found 32 (35 requested) and removed 48 (17 requested) atoms. Cycle 17: After refmac, R = 0.2143 (Rfree = 0.000) for 6404 atoms. Found 27 (35 requested) and removed 27 (17 requested) atoms. Cycle 18: After refmac, R = 0.2205 (Rfree = 0.000) for 6378 atoms. Found 35 (35 requested) and removed 29 (17 requested) atoms. Cycle 19: After refmac, R = 0.2159 (Rfree = 0.000) for 6360 atoms. Found 35 (35 requested) and removed 24 (17 requested) atoms. Cycle 20: After refmac, R = 0.2093 (Rfree = 0.000) for 6336 atoms. Found 35 (35 requested) and removed 27 (17 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.38 3.25 Search for helices and strands: 0 residues in 0 chains, 6514 seeds are put forward NCS extension: 21 residues added (3 deleted due to clashes), 6535 seeds are put forward Round 1: 411 peptides, 82 chains. Longest chain 10 peptides. Score 0.315 Round 2: 478 peptides, 79 chains. Longest chain 17 peptides. Score 0.441 Round 3: 468 peptides, 70 chains. Longest chain 19 peptides. Score 0.483 Round 4: 485 peptides, 67 chains. Longest chain 22 peptides. Score 0.524 Round 5: 472 peptides, 72 chains. Longest chain 15 peptides. Score 0.476 Taking the results from Round 4 Chains 71, Residues 418, Estimated correctness of the model 0.0 % 6 chains (54 residues) have been docked in sequence ------------------------------------------------------ 10562 reflections ( 99.28 % complete ) and 14008 restraints for refining 6469 atoms. 12221 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2366 (Rfree = 0.000) for 6469 atoms. Found 35 (35 requested) and removed 51 (17 requested) atoms. Cycle 22: After refmac, R = 0.2081 (Rfree = 0.000) for 6396 atoms. Found 22 (35 requested) and removed 30 (17 requested) atoms. Cycle 23: After refmac, R = 0.1954 (Rfree = 0.000) for 6365 atoms. Found 16 (35 requested) and removed 25 (17 requested) atoms. Cycle 24: After refmac, R = 0.1945 (Rfree = 0.000) for 6335 atoms. Found 15 (34 requested) and removed 27 (17 requested) atoms. Cycle 25: After refmac, R = 0.1896 (Rfree = 0.000) for 6310 atoms. Found 12 (34 requested) and removed 26 (17 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.41 3.28 Search for helices and strands: 0 residues in 0 chains, 6459 seeds are put forward NCS extension: 39 residues added (3 deleted due to clashes), 6498 seeds are put forward Round 1: 395 peptides, 77 chains. Longest chain 13 peptides. Score 0.323 Round 2: 461 peptides, 76 chains. Longest chain 18 peptides. Score 0.435 Round 3: 465 peptides, 76 chains. Longest chain 13 peptides. Score 0.441 Round 4: 452 peptides, 69 chains. Longest chain 15 peptides. Score 0.466 Round 5: 447 peptides, 68 chains. Longest chain 22 peptides. Score 0.465 Taking the results from Round 4 Chains 69, Residues 383, Estimated correctness of the model 0.0 % 5 chains (36 residues) have been docked in sequence ------------------------------------------------------ 10562 reflections ( 99.28 % complete ) and 14756 restraints for refining 6469 atoms. 13173 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2221 (Rfree = 0.000) for 6469 atoms. Found 25 (35 requested) and removed 35 (17 requested) atoms. Cycle 27: After refmac, R = 0.2071 (Rfree = 0.000) for 6415 atoms. Found 17 (35 requested) and removed 32 (17 requested) atoms. Cycle 28: After refmac, R = 0.2041 (Rfree = 0.000) for 6387 atoms. Found 10 (35 requested) and removed 22 (17 requested) atoms. Cycle 29: After refmac, R = 0.2037 (Rfree = 0.000) for 6365 atoms. Found 11 (35 requested) and removed 22 (17 requested) atoms. Cycle 30: After refmac, R = 0.2058 (Rfree = 0.000) for 6344 atoms. Found 19 (34 requested) and removed 29 (17 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.43 3.30 Search for helices and strands: 0 residues in 0 chains, 6501 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 6519 seeds are put forward Round 1: 416 peptides, 83 chains. Longest chain 10 peptides. Score 0.316 Round 2: 438 peptides, 68 chains. Longest chain 15 peptides. Score 0.452 Round 3: 441 peptides, 71 chains. Longest chain 18 peptides. Score 0.437 Round 4: 450 peptides, 67 chains. Longest chain 15 peptides. Score 0.476 Round 5: 484 peptides, 72 chains. Longest chain 17 peptides. Score 0.493 Taking the results from Round 5 Chains 74, Residues 412, Estimated correctness of the model 0.0 % 9 chains (58 residues) have been docked in sequence ------------------------------------------------------ 10562 reflections ( 99.28 % complete ) and 14240 restraints for refining 6468 atoms. 12457 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2463 (Rfree = 0.000) for 6468 atoms. Found 35 (35 requested) and removed 55 (17 requested) atoms. Cycle 32: After refmac, R = 0.2308 (Rfree = 0.000) for 6389 atoms. Found 35 (35 requested) and removed 30 (17 requested) atoms. Cycle 33: After refmac, R = 0.2188 (Rfree = 0.000) for 6350 atoms. Found 28 (35 requested) and removed 29 (17 requested) atoms. Cycle 34: After refmac, R = 0.2023 (Rfree = 0.000) for 6326 atoms. Found 22 (34 requested) and removed 24 (17 requested) atoms. Cycle 35: After refmac, R = 0.1816 (Rfree = 0.000) for 6313 atoms. Found 9 (34 requested) and removed 20 (17 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.37 3.24 Search for helices and strands: 0 residues in 0 chains, 6419 seeds are put forward NCS extension: 13 residues added (3 deleted due to clashes), 6432 seeds are put forward Round 1: 327 peptides, 69 chains. Longest chain 9 peptides. Score 0.263 Round 2: 416 peptides, 76 chains. Longest chain 17 peptides. Score 0.365 Round 3: 400 peptides, 65 chains. Longest chain 17 peptides. Score 0.415 Round 4: 402 peptides, 65 chains. Longest chain 17 peptides. Score 0.418 Round 5: 413 peptides, 72 chains. Longest chain 14 peptides. Score 0.387 Taking the results from Round 4 Chains 67, Residues 337, Estimated correctness of the model 0.0 % 5 chains (45 residues) have been docked in sequence ------------------------------------------------------ 10562 reflections ( 99.28 % complete ) and 14826 restraints for refining 6468 atoms. 13380 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2295 (Rfree = 0.000) for 6468 atoms. Found 29 (35 requested) and removed 34 (17 requested) atoms. Cycle 37: After refmac, R = 0.2356 (Rfree = 0.000) for 6411 atoms. Found 35 (35 requested) and removed 32 (17 requested) atoms. Cycle 38: After refmac, R = 0.2133 (Rfree = 0.000) for 6375 atoms. Found 35 (35 requested) and removed 29 (17 requested) atoms. Cycle 39: After refmac, R = 0.1819 (Rfree = 0.000) for 6357 atoms. Found 11 (35 requested) and removed 21 (17 requested) atoms. Cycle 40: After refmac, R = 0.1796 (Rfree = 0.000) for 6335 atoms. Found 19 (34 requested) and removed 19 (17 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.40 3.27 Search for helices and strands: 0 residues in 0 chains, 6475 seeds are put forward NCS extension: 19 residues added (3 deleted due to clashes), 6494 seeds are put forward Round 1: 321 peptides, 64 chains. Longest chain 13 peptides. Score 0.290 Round 2: 379 peptides, 67 chains. Longest chain 16 peptides. Score 0.367 Round 3: 360 peptides, 63 chains. Longest chain 15 peptides. Score 0.365 Round 4: 352 peptides, 61 chains. Longest chain 17 peptides. Score 0.366 Round 5: 359 peptides, 60 chains. Longest chain 15 peptides. Score 0.384 Taking the results from Round 5 Chains 61, Residues 299, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 10562 reflections ( 99.28 % complete ) and 15169 restraints for refining 6469 atoms. 13986 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2319 (Rfree = 0.000) for 6469 atoms. Found 35 (35 requested) and removed 46 (17 requested) atoms. Cycle 42: After refmac, R = 0.2317 (Rfree = 0.000) for 6423 atoms. Found 35 (35 requested) and removed 44 (17 requested) atoms. Cycle 43: After refmac, R = 0.1902 (Rfree = 0.000) for 6378 atoms. Found 20 (35 requested) and removed 22 (17 requested) atoms. Cycle 44: After refmac, R = 0.1856 (Rfree = 0.000) for 6359 atoms. Found 22 (35 requested) and removed 25 (17 requested) atoms. Failed to save intermediate PDBFailed to save intermediate PDB Cycle 45: After refmac, R = 0.1787 (Rfree = 0.000) for 6348 atoms. Found 12 (34 requested) and removed 21 (17 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.41 3.28 Search for helices and strands: 0 residues in 0 chains, 6448 seeds are put forward NCS extension: 20 residues added (4 deleted due to clashes), 6468 seeds are put forward Round 1: 277 peptides, 59 chains. Longest chain 9 peptides. Score 0.248 Round 2: 324 peptides, 64 chains. Longest chain 12 peptides. Score 0.296 Round 3: 352 peptides, 60 chains. Longest chain 12 peptides. Score 0.373 Round 4: 344 peptides, 63 chains. Longest chain 14 peptides. Score 0.338 Round 5: 338 peptides, 58 chains. Longest chain 12 peptides. Score 0.364 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 60, Residues 292, Estimated correctness of the model 0.0 % 3 chains (13 residues) have been docked in sequence Sequence coverage is 4 % Consider running further cycles of model building using 1vl4-3_warpNtrace.pdb as input Building loops using Loopy2018 60 chains (292 residues) following loop building 3 chains (13 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 10562 reflections ( 99.28 % complete ) and 15026 restraints for refining 6389 atoms. 13892 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2398 (Rfree = 0.000) for 6389 atoms. Found 0 (35 requested) and removed 17 (17 requested) atoms. Cycle 47: After refmac, R = 0.2384 (Rfree = 0.000) for 6342 atoms. Found 0 (35 requested) and removed 17 (17 requested) atoms. Cycle 48: After refmac, R = 0.2341 (Rfree = 0.000) for 6298 atoms. Found 0 (34 requested) and removed 17 (17 requested) atoms. Cycle 49: After refmac, R = 0.2572 (Rfree = 0.000) for 6259 atoms. TimeTaking 75.15