Mon 24 Dec 00:43:28 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 1vr0-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vr0-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vr0-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vr0-3.6-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/1vr0-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vr0-3.6-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 00:43:34 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/1vr0-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vr0-3.6-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 495 and 0 Target number of residues in the AU: 495 Target solvent content: 0.6343 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: 1vr0-3.6-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: 20 Cell parameters: 46.686 69.193 453.518 90.000 90.000 90.000 Input sequence file: 1vr0-3.6-parrot-mrncs.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 3.600 Wilson plot Bfac: 68.71 9023 reflections ( 99.64 % complete ) and 0 restraints for refining 6588 atoms. Observations/parameters ratio is 0.34 ------------------------------------------------------ Starting model: R = 0.3199 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3120 (Rfree = 0.000) for 6588 atoms. Found 42 (42 requested) and removed 51 (21 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.41 3.65 Search for helices and strands: 0 residues in 0 chains, 6717 seeds are put forward NCS extension: 0 residues added, 6717 seeds are put forward Round 1: 231 peptides, 46 chains. Longest chain 8 peptides. Score 0.292 Round 2: 342 peptides, 63 chains. Longest chain 11 peptides. Score 0.383 Round 3: 373 peptides, 62 chains. Longest chain 14 peptides. Score 0.457 Round 4: 403 peptides, 56 chains. Longest chain 17 peptides. Score 0.562 Round 5: 409 peptides, 59 chains. Longest chain 16 peptides. Score 0.549 Taking the results from Round 4 Chains 56, Residues 347, Estimated correctness of the model 0.0 % 2 chains (10 residues) have been docked in sequence ------------------------------------------------------ 9023 reflections ( 99.64 % complete ) and 12253 restraints for refining 5371 atoms. 10896 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2527 (Rfree = 0.000) for 5371 atoms. Found 24 (34 requested) and removed 42 (17 requested) atoms. Cycle 2: After refmac, R = 0.2442 (Rfree = 0.000) for 5289 atoms. Found 15 (34 requested) and removed 32 (17 requested) atoms. Cycle 3: After refmac, R = 0.2394 (Rfree = 0.000) for 5224 atoms. Found 30 (33 requested) and removed 33 (16 requested) atoms. Cycle 4: After refmac, R = 0.1976 (Rfree = 0.000) for 5200 atoms. Found 7 (33 requested) and removed 25 (16 requested) atoms. Cycle 5: After refmac, R = 0.1840 (Rfree = 0.000) for 5166 atoms. Found 7 (33 requested) and removed 25 (16 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.38 3.61 Search for helices and strands: 0 residues in 0 chains, 5390 seeds are put forward NCS extension: 18 residues added (6 deleted due to clashes), 5408 seeds are put forward Round 1: 352 peptides, 61 chains. Longest chain 13 peptides. Score 0.422 Round 2: 395 peptides, 59 chains. Longest chain 20 peptides. Score 0.524 Round 3: 396 peptides, 58 chains. Longest chain 20 peptides. Score 0.534 Round 4: 432 peptides, 60 chains. Longest chain 18 peptides. Score 0.581 Round 5: 402 peptides, 56 chains. Longest chain 18 peptides. Score 0.560 Taking the results from Round 4 Chains 60, Residues 372, Estimated correctness of the model 7.1 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 9023 reflections ( 99.64 % complete ) and 12150 restraints for refining 5284 atoms. 10708 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2148 (Rfree = 0.000) for 5284 atoms. Found 19 (33 requested) and removed 45 (16 requested) atoms. Cycle 7: After refmac, R = 0.2071 (Rfree = 0.000) for 5232 atoms. Found 21 (33 requested) and removed 37 (16 requested) atoms. Cycle 8: After refmac, R = 0.2098 (Rfree = 0.000) for 5201 atoms. Found 27 (33 requested) and removed 29 (16 requested) atoms. Cycle 9: After refmac, R = 0.2109 (Rfree = 0.000) for 5188 atoms. Found 27 (33 requested) and removed 26 (16 requested) atoms. Cycle 10: After refmac, R = 0.2087 (Rfree = 0.000) for 5180 atoms. Found 27 (33 requested) and removed 26 (16 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.35 3.58 Search for helices and strands: 0 residues in 0 chains, 5409 seeds are put forward NCS extension: 8 residues added (6 deleted due to clashes), 5417 seeds are put forward Round 1: 323 peptides, 57 chains. Longest chain 17 peptides. Score 0.397 Round 2: 357 peptides, 57 chains. Longest chain 15 peptides. Score 0.468 Round 3: 375 peptides, 55 chains. Longest chain 20 peptides. Score 0.520 Round 4: 383 peptides, 54 chains. Longest chain 22 peptides. Score 0.542 Round 5: 380 peptides, 50 chains. Longest chain 39 peptides. Score 0.568 Taking the results from Round 5 Chains 50, Residues 330, Estimated correctness of the model 1.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9023 reflections ( 99.64 % complete ) and 12605 restraints for refining 5373 atoms. 11335 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2324 (Rfree = 0.000) for 5373 atoms. Found 24 (34 requested) and removed 90 (17 requested) atoms. Cycle 12: After refmac, R = 0.2280 (Rfree = 0.000) for 5278 atoms. Found 34 (34 requested) and removed 34 (17 requested) atoms. Cycle 13: After refmac, R = 0.2280 (Rfree = 0.000) for 5256 atoms. Found 33 (33 requested) and removed 27 (16 requested) atoms. Cycle 14: After refmac, R = 0.2119 (Rfree = 0.000) for 5250 atoms. Found 33 (33 requested) and removed 29 (16 requested) atoms. Cycle 15: After refmac, R = 0.2131 (Rfree = 0.000) for 5246 atoms. Found 30 (33 requested) and removed 31 (16 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.35 3.58 Search for helices and strands: 0 residues in 0 chains, 5449 seeds are put forward NCS extension: 20 residues added (7 deleted due to clashes), 5469 seeds are put forward Round 1: 316 peptides, 59 chains. Longest chain 11 peptides. Score 0.363 Round 2: 370 peptides, 59 chains. Longest chain 15 peptides. Score 0.477 Round 3: 369 peptides, 54 chains. Longest chain 19 peptides. Score 0.517 Round 4: 352 peptides, 51 chains. Longest chain 15 peptides. Score 0.510 Round 5: 366 peptides, 54 chains. Longest chain 16 peptides. Score 0.511 Taking the results from Round 3 Chains 54, Residues 315, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9023 reflections ( 99.64 % complete ) and 12654 restraints for refining 5372 atoms. 11448 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2178 (Rfree = 0.000) for 5372 atoms. Found 34 (34 requested) and removed 42 (17 requested) atoms. Cycle 17: After refmac, R = 0.2093 (Rfree = 0.000) for 5343 atoms. Found 34 (34 requested) and removed 38 (17 requested) atoms. Cycle 18: After refmac, R = 0.1992 (Rfree = 0.000) for 5325 atoms. Found 33 (34 requested) and removed 33 (17 requested) atoms. Cycle 19: After refmac, R = 0.2022 (Rfree = 0.000) for 5312 atoms. Found 34 (34 requested) and removed 26 (17 requested) atoms. Cycle 20: After refmac, R = 0.1969 (Rfree = 0.000) for 5307 atoms. Found 34 (34 requested) and removed 26 (17 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.37 3.60 Search for helices and strands: 0 residues in 0 chains, 5515 seeds are put forward NCS extension: 16 residues added (4 deleted due to clashes), 5531 seeds are put forward Round 1: 310 peptides, 56 chains. Longest chain 14 peptides. Score 0.378 Round 2: 335 peptides, 50 chains. Longest chain 20 peptides. Score 0.485 Round 3: 361 peptides, 56 chains. Longest chain 21 peptides. Score 0.485 Round 4: 347 peptides, 50 chains. Longest chain 17 peptides. Score 0.508 Round 5: 355 peptides, 49 chains. Longest chain 23 peptides. Score 0.532 Taking the results from Round 5 Chains 49, Residues 306, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9023 reflections ( 99.64 % complete ) and 12843 restraints for refining 5371 atoms. 11668 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2192 (Rfree = 0.000) for 5371 atoms. Found 34 (34 requested) and removed 37 (17 requested) atoms. Cycle 22: After refmac, R = 0.2038 (Rfree = 0.000) for 5347 atoms. Found 34 (34 requested) and removed 28 (17 requested) atoms. Cycle 23: After refmac, R = 0.1969 (Rfree = 0.000) for 5342 atoms. Found 34 (34 requested) and removed 25 (17 requested) atoms. Cycle 24: After refmac, R = 0.1940 (Rfree = 0.000) for 5339 atoms. Found 34 (34 requested) and removed 19 (17 requested) atoms. Cycle 25: After refmac, R = 0.1908 (Rfree = 0.000) for 5353 atoms. Found 34 (34 requested) and removed 28 (17 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.40 3.63 Search for helices and strands: 0 residues in 0 chains, 5560 seeds are put forward NCS extension: 13 residues added (4 deleted due to clashes), 5573 seeds are put forward Round 1: 306 peptides, 55 chains. Longest chain 13 peptides. Score 0.378 Round 2: 345 peptides, 58 chains. Longest chain 19 peptides. Score 0.435 Round 3: 346 peptides, 55 chains. Longest chain 15 peptides. Score 0.463 Round 4: 353 peptides, 56 chains. Longest chain 18 peptides. Score 0.469 Round 5: 342 peptides, 53 chains. Longest chain 22 peptides. Score 0.473 Taking the results from Round 5 Chains 53, Residues 289, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9023 reflections ( 99.64 % complete ) and 12647 restraints for refining 5371 atoms. 11544 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2191 (Rfree = 0.000) for 5371 atoms. Found 34 (34 requested) and removed 31 (17 requested) atoms. Cycle 27: After refmac, R = 0.2076 (Rfree = 0.000) for 5350 atoms. Found 34 (34 requested) and removed 24 (17 requested) atoms. Cycle 28: After refmac, R = 0.1727 (Rfree = 0.000) for 5346 atoms. Found 18 (34 requested) and removed 19 (17 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.1625 (Rfree = 0.000) for 5338 atoms. Found 2 (34 requested) and removed 19 (17 requested) atoms. Cycle 30: After refmac, R = 0.1624 (Rfree = 0.000) for 5320 atoms. Found 3 (34 requested) and removed 20 (17 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.39 3.62 Search for helices and strands: 0 residues in 0 chains, 5503 seeds are put forward NCS extension: 34 residues added (2 deleted due to clashes), 5537 seeds are put forward Round 1: 250 peptides, 46 chains. Longest chain 15 peptides. Score 0.338 Round 2: 290 peptides, 46 chains. Longest chain 15 peptides. Score 0.429 Round 3: 308 peptides, 48 chains. Longest chain 15 peptides. Score 0.448 Round 4: 331 peptides, 50 chains. Longest chain 17 peptides. Score 0.477 Round 5: 332 peptides, 48 chains. Longest chain 19 peptides. Score 0.497 Taking the results from Round 5 Chains 48, Residues 284, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9023 reflections ( 99.64 % complete ) and 12699 restraints for refining 5370 atoms. 11611 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2089 (Rfree = 0.000) for 5370 atoms. Found 34 (34 requested) and removed 24 (17 requested) atoms. Cycle 32: After refmac, R = 0.2140 (Rfree = 0.000) for 5356 atoms. Found 34 (34 requested) and removed 25 (17 requested) atoms. Cycle 33: After refmac, R = 0.2133 (Rfree = 0.000) for 5346 atoms. Found 34 (34 requested) and removed 29 (17 requested) atoms. Cycle 34: After refmac, R = 0.1700 (Rfree = 0.000) for 5342 atoms. Found 14 (34 requested) and removed 25 (17 requested) atoms. Cycle 35: After refmac, R = 0.1673 (Rfree = 0.000) for 5320 atoms. Found 5 (34 requested) and removed 22 (17 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.36 3.59 Search for helices and strands: 0 residues in 0 chains, 5526 seeds are put forward NCS extension: 14 residues added (8 deleted due to clashes), 5540 seeds are put forward Round 1: 259 peptides, 53 chains. Longest chain 9 peptides. Score 0.288 Round 2: 302 peptides, 53 chains. Longest chain 16 peptides. Score 0.389 Round 3: 296 peptides, 49 chains. Longest chain 17 peptides. Score 0.413 Round 4: 298 peptides, 46 chains. Longest chain 17 peptides. Score 0.446 Round 5: 306 peptides, 48 chains. Longest chain 18 peptides. Score 0.444 Taking the results from Round 4 Chains 46, Residues 252, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9023 reflections ( 99.64 % complete ) and 12817 restraints for refining 5373 atoms. 11855 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2093 (Rfree = 0.000) for 5373 atoms. Found 22 (34 requested) and removed 30 (17 requested) atoms. Cycle 37: After refmac, R = 0.2157 (Rfree = 0.000) for 5351 atoms. Found 34 (34 requested) and removed 30 (17 requested) atoms. Cycle 38: After refmac, R = 0.2081 (Rfree = 0.000) for 5344 atoms. Found 34 (34 requested) and removed 29 (17 requested) atoms. Cycle 39: After refmac, R = 0.2138 (Rfree = 0.000) for 5339 atoms. Found 34 (34 requested) and removed 28 (17 requested) atoms. Cycle 40: After refmac, R = 0.1693 (Rfree = 0.000) for 5341 atoms. Found 12 (34 requested) and removed 23 (17 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.35 3.58 Search for helices and strands: 0 residues in 0 chains, 5533 seeds are put forward NCS extension: 27 residues added (1 deleted due to clashes), 5560 seeds are put forward Round 1: 253 peptides, 51 chains. Longest chain 10 peptides. Score 0.294 Round 2: 287 peptides, 51 chains. Longest chain 16 peptides. Score 0.374 Round 3: 275 peptides, 47 chains. Longest chain 13 peptides. Score 0.386 Round 4: 295 peptides, 48 chains. Longest chain 17 peptides. Score 0.421 Round 5: 284 peptides, 52 chains. Longest chain 12 peptides. Score 0.358 Taking the results from Round 4 Chains 49, Residues 247, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 9023 reflections ( 99.64 % complete ) and 12442 restraints for refining 5372 atoms. 11475 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1977 (Rfree = 0.000) for 5372 atoms. Found 29 (34 requested) and removed 52 (17 requested) atoms. Cycle 42: After refmac, R = 0.1963 (Rfree = 0.000) for 5337 atoms. Found 34 (34 requested) and removed 50 (17 requested) atoms. Cycle 43: After refmac, R = 0.1959 (Rfree = 0.000) for 5312 atoms. Found 32 (34 requested) and removed 28 (17 requested) atoms. Cycle 44: After refmac, R = 0.1911 (Rfree = 0.000) for 5308 atoms. Found 34 (34 requested) and removed 25 (17 requested) atoms. Cycle 45: After refmac, R = 0.1561 (Rfree = 0.000) for 5313 atoms. Found 3 (34 requested) and removed 19 (17 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.35 3.58 Search for helices and strands: 0 residues in 0 chains, 5455 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 5469 seeds are put forward Round 1: 259 peptides, 52 chains. Longest chain 10 peptides. Score 0.299 Round 2: 273 peptides, 51 chains. Longest chain 10 peptides. Score 0.342 Round 3: 287 peptides, 48 chains. Longest chain 13 peptides. Score 0.403 Round 4: 302 peptides, 49 chains. Longest chain 14 peptides. Score 0.426 Round 5: 308 peptides, 51 chains. Longest chain 20 peptides. Score 0.420 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 49, Residues 253, 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. 9023 reflections ( 99.64 % complete ) and 12633 restraints for refining 5373 atoms. 11670 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1925 (Rfree = 0.000) for 5373 atoms. Found 0 (34 requested) and removed 17 (17 requested) atoms. Cycle 47: After refmac, R = 0.1982 (Rfree = 0.000) for 5345 atoms. Found 0 (34 requested) and removed 17 (17 requested) atoms. Cycle 48: After refmac, R = 0.1927 (Rfree = 0.000) for 5319 atoms. Found 0 (34 requested) and removed 17 (17 requested) atoms. Cycle 49: After refmac, R = 0.1914 (Rfree = 0.000) for 5298 atoms. TimeTaking 70.68