Sun 23 Dec 22:23:02 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 1vl4-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vl4-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vl4-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vl4-4.0-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/1vl4-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vl4-4.0-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 ============================================================ Sun 23 Dec 22:23:12 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/1vl4-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vl4-4.0-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 688 and 0 Target number of residues in the AU: 688 Target solvent content: 0.6382 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: 1vl4-4.0-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: 19 Cell parameters: 80.171 107.117 119.834 90.000 90.000 90.000 Input sequence file: 1vl4-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 7152 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: 79.862 4.000 Wilson plot Bfac: 70.96 9072 reflections ( 99.17 % complete ) and 0 restraints for refining 7926 atoms. Observations/parameters ratio is 0.29 ------------------------------------------------------ Starting model: R = 0.3174 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3286 (Rfree = 0.000) for 7926 atoms. Found 37 (37 requested) and removed 29 (18 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.59 3.45 Search for helices and strands: 0 residues in 0 chains, 8044 seeds are put forward NCS extension: 0 residues added, 8044 seeds are put forward Round 1: 315 peptides, 67 chains. Longest chain 9 peptides. Score 0.257 Round 2: 447 peptides, 71 chains. Longest chain 16 peptides. Score 0.446 Round 3: 479 peptides, 65 chains. Longest chain 21 peptides. Score 0.528 Round 4: 507 peptides, 66 chains. Longest chain 20 peptides. Score 0.559 Round 5: 524 peptides, 64 chains. Longest chain 27 peptides. Score 0.591 Taking the results from Round 5 Chains 66, Residues 460, Estimated correctness of the model 0.0 % 6 chains (61 residues) have been docked in sequence ------------------------------------------------------ 9072 reflections ( 99.17 % complete ) and 13867 restraints for refining 6377 atoms. 11867 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2781 (Rfree = 0.000) for 6377 atoms. Found 30 (30 requested) and removed 61 (15 requested) atoms. Cycle 2: After refmac, R = 0.2575 (Rfree = 0.000) for 6219 atoms. Found 28 (30 requested) and removed 57 (15 requested) atoms. Cycle 3: After refmac, R = 0.2377 (Rfree = 0.000) for 6138 atoms. Found 29 (29 requested) and removed 42 (14 requested) atoms. Cycle 4: After refmac, R = 0.2292 (Rfree = 0.000) for 6091 atoms. Found 22 (29 requested) and removed 30 (14 requested) atoms. Cycle 5: After refmac, R = 0.2328 (Rfree = 0.000) for 6065 atoms. Found 28 (28 requested) and removed 37 (14 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.60 3.46 Search for helices and strands: 0 residues in 0 chains, 6247 seeds are put forward NCS extension: 40 residues added (2 deleted due to clashes), 6287 seeds are put forward Round 1: 416 peptides, 72 chains. Longest chain 13 peptides. Score 0.392 Round 2: 489 peptides, 73 chains. Longest chain 15 peptides. Score 0.494 Round 3: 494 peptides, 70 chains. Longest chain 13 peptides. Score 0.519 Round 4: 504 peptides, 63 chains. Longest chain 18 peptides. Score 0.572 Round 5: 511 peptides, 65 chains. Longest chain 33 peptides. Score 0.569 Taking the results from Round 4 Chains 67, Residues 441, Estimated correctness of the model 0.0 % 5 chains (41 residues) have been docked in sequence ------------------------------------------------------ 9072 reflections ( 99.17 % complete ) and 14619 restraints for refining 6456 atoms. 12783 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2455 (Rfree = 0.000) for 6456 atoms. Found 26 (30 requested) and removed 67 (15 requested) atoms. Cycle 7: After refmac, R = 0.2221 (Rfree = 0.000) for 6345 atoms. Found 12 (30 requested) and removed 40 (15 requested) atoms. Cycle 8: After refmac, R = 0.2124 (Rfree = 0.000) for 6294 atoms. Found 9 (30 requested) and removed 21 (15 requested) atoms. Cycle 9: After refmac, R = 0.2076 (Rfree = 0.000) for 6271 atoms. Found 11 (29 requested) and removed 24 (14 requested) atoms. Cycle 10: After refmac, R = 0.2126 (Rfree = 0.000) for 6250 atoms. Found 10 (29 requested) and removed 25 (14 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.56 3.42 Search for helices and strands: 0 residues in 0 chains, 6398 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 6423 seeds are put forward Round 1: 426 peptides, 72 chains. Longest chain 13 peptides. Score 0.408 Round 2: 475 peptides, 62 chains. Longest chain 28 peptides. Score 0.541 Round 3: 481 peptides, 63 chains. Longest chain 19 peptides. Score 0.543 Round 4: 492 peptides, 63 chains. Longest chain 28 peptides. Score 0.557 Round 5: 475 peptides, 61 chains. Longest chain 28 peptides. Score 0.547 Taking the results from Round 4 Chains 66, Residues 429, Estimated correctness of the model 0.0 % 7 chains (99 residues) have been docked in sequence ------------------------------------------------------ 9072 reflections ( 99.17 % complete ) and 13687 restraints for refining 6459 atoms. 11667 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2530 (Rfree = 0.000) for 6459 atoms. Found 30 (30 requested) and removed 66 (15 requested) atoms. Cycle 12: After refmac, R = 0.2496 (Rfree = 0.000) for 6352 atoms. Found 30 (30 requested) and removed 58 (15 requested) atoms. Cycle 13: After refmac, R = 0.2225 (Rfree = 0.000) for 6281 atoms. Found 27 (30 requested) and removed 47 (15 requested) atoms. Cycle 14: After refmac, R = 0.2071 (Rfree = 0.000) for 6226 atoms. Found 11 (29 requested) and removed 29 (14 requested) atoms. Cycle 15: After refmac, R = 0.1950 (Rfree = 0.000) for 6185 atoms. Found 6 (29 requested) and removed 24 (14 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.54 3.40 Search for helices and strands: 0 residues in 0 chains, 6349 seeds are put forward NCS extension: 26 residues added (0 deleted due to clashes), 6375 seeds are put forward Round 1: 397 peptides, 61 chains. Longest chain 17 peptides. Score 0.437 Round 2: 430 peptides, 62 chains. Longest chain 16 peptides. Score 0.479 Round 3: 443 peptides, 59 chains. Longest chain 18 peptides. Score 0.516 Round 4: 469 peptides, 60 chains. Longest chain 25 peptides. Score 0.545 Round 5: 455 peptides, 61 chains. Longest chain 20 peptides. Score 0.520 Taking the results from Round 4 Chains 63, Residues 409, Estimated correctness of the model 0.0 % 6 chains (72 residues) have been docked in sequence ------------------------------------------------------ 9072 reflections ( 99.17 % complete ) and 13967 restraints for refining 6459 atoms. 12130 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2282 (Rfree = 0.000) for 6459 atoms. Found 25 (30 requested) and removed 83 (15 requested) atoms. Cycle 17: After refmac, R = 0.2170 (Rfree = 0.000) for 6358 atoms. Found 15 (30 requested) and removed 41 (15 requested) atoms. Cycle 18: After refmac, R = 0.2128 (Rfree = 0.000) for 6324 atoms. Found 10 (30 requested) and removed 34 (15 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.2070 (Rfree = 0.000) for 6290 atoms. Found 9 (29 requested) and removed 21 (14 requested) atoms. Cycle 20: After refmac, R = 0.2104 (Rfree = 0.000) for 6272 atoms. Found 8 (29 requested) and removed 31 (14 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.55 3.41 Search for helices and strands: 0 residues in 0 chains, 6412 seeds are put forward NCS extension: 30 residues added (2 deleted due to clashes), 6442 seeds are put forward Round 1: 387 peptides, 71 chains. Longest chain 10 peptides. Score 0.352 Round 2: 431 peptides, 66 chains. Longest chain 13 peptides. Score 0.455 Round 3: 436 peptides, 66 chains. Longest chain 17 peptides. Score 0.462 Round 4: 464 peptides, 65 chains. Longest chain 22 peptides. Score 0.508 Round 5: 446 peptides, 66 chains. Longest chain 21 peptides. Score 0.477 Taking the results from Round 4 Chains 67, Residues 399, Estimated correctness of the model 0.0 % 3 chains (28 residues) have been docked in sequence ------------------------------------------------------ 9072 reflections ( 99.17 % complete ) and 14740 restraints for refining 6459 atoms. 13126 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2354 (Rfree = 0.000) for 6459 atoms. Found 30 (30 requested) and removed 60 (15 requested) atoms. Cycle 22: After refmac, R = 0.2233 (Rfree = 0.000) for 6378 atoms. Found 26 (30 requested) and removed 48 (15 requested) atoms. Cycle 23: After refmac, R = 0.2163 (Rfree = 0.000) for 6334 atoms. Found 23 (30 requested) and removed 28 (15 requested) atoms. Cycle 24: After refmac, R = 0.2089 (Rfree = 0.000) for 6311 atoms. Found 14 (30 requested) and removed 32 (15 requested) atoms. Cycle 25: After refmac, R = 0.2000 (Rfree = 0.000) for 6282 atoms. Found 11 (29 requested) and removed 23 (14 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.59 3.45 Search for helices and strands: 0 residues in 0 chains, 6449 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 6473 seeds are put forward Round 1: 357 peptides, 73 chains. Longest chain 9 peptides. Score 0.287 Round 2: 388 peptides, 62 chains. Longest chain 15 peptides. Score 0.416 Round 3: 406 peptides, 64 chains. Longest chain 16 peptides. Score 0.431 Round 4: 424 peptides, 63 chains. Longest chain 20 peptides. Score 0.464 Round 5: 426 peptides, 63 chains. Longest chain 17 peptides. Score 0.467 Taking the results from Round 5 Chains 64, Residues 363, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 9072 reflections ( 99.17 % complete ) and 15285 restraints for refining 6459 atoms. 13878 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2295 (Rfree = 0.000) for 6459 atoms. Found 30 (30 requested) and removed 65 (15 requested) atoms. Cycle 27: After refmac, R = 0.2054 (Rfree = 0.000) for 6401 atoms. Found 21 (30 requested) and removed 39 (15 requested) atoms. Cycle 28: After refmac, R = 0.1974 (Rfree = 0.000) for 6362 atoms. Found 9 (30 requested) and removed 32 (15 requested) atoms. Cycle 29: After refmac, R = 0.2000 (Rfree = 0.000) for 6335 atoms. Found 15 (30 requested) and removed 25 (15 requested) atoms. Cycle 30: After refmac, R = 0.1813 (Rfree = 0.000) for 6316 atoms. Found 3 (30 requested) and removed 29 (15 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.61 3.47 Search for helices and strands: 0 residues in 0 chains, 6470 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 6490 seeds are put forward Round 1: 328 peptides, 65 chains. Longest chain 12 peptides. Score 0.295 Round 2: 380 peptides, 63 chains. Longest chain 15 peptides. Score 0.397 Round 3: 377 peptides, 57 chains. Longest chain 17 peptides. Score 0.434 Round 4: 386 peptides, 59 chains. Longest chain 15 peptides. Score 0.434 Round 5: 382 peptides, 57 chains. Longest chain 17 peptides. Score 0.441 Taking the results from Round 5 Chains 59, Residues 325, Estimated correctness of the model 0.0 % 3 chains (35 residues) have been docked in sequence ------------------------------------------------------ 9072 reflections ( 99.17 % complete ) and 15011 restraints for refining 6458 atoms. 13656 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2408 (Rfree = 0.000) for 6458 atoms. Found 30 (30 requested) and removed 46 (15 requested) atoms. Cycle 32: After refmac, R = 0.2183 (Rfree = 0.000) for 6408 atoms. Found 25 (30 requested) and removed 25 (15 requested) atoms. Cycle 33: After refmac, R = 0.2132 (Rfree = 0.000) for 6396 atoms. Found 18 (30 requested) and removed 27 (15 requested) atoms. Cycle 34: After refmac, R = 0.2078 (Rfree = 0.000) for 6368 atoms. Found 28 (30 requested) and removed 23 (15 requested) atoms. Cycle 35: After refmac, R = 0.1911 (Rfree = 0.000) for 6365 atoms. Found 4 (30 requested) and removed 20 (15 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.58 3.44 Search for helices and strands: 0 residues in 0 chains, 6478 seeds are put forward NCS extension: 22 residues added (3 deleted due to clashes), 6500 seeds are put forward Round 1: 312 peptides, 64 chains. Longest chain 11 peptides. Score 0.274 Round 2: 336 peptides, 59 chains. Longest chain 21 peptides. Score 0.354 Round 3: 362 peptides, 61 chains. Longest chain 17 peptides. Score 0.382 Round 4: 351 peptides, 58 chains. Longest chain 17 peptides. Score 0.386 Round 5: 346 peptides, 60 chains. Longest chain 17 peptides. Score 0.363 Taking the results from Round 4 Chains 58, Residues 293, Estimated correctness of the model 0.0 % 3 chains (28 residues) have been docked in sequence ------------------------------------------------------ 9072 reflections ( 99.17 % complete ) and 15306 restraints for refining 6456 atoms. 14100 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2420 (Rfree = 0.000) for 6456 atoms. Found 30 (30 requested) and removed 51 (15 requested) atoms. Cycle 37: After refmac, R = 0.2286 (Rfree = 0.000) for 6390 atoms. Found 30 (30 requested) and removed 48 (15 requested) atoms. Cycle 38: After refmac, R = 0.2044 (Rfree = 0.000) for 6343 atoms. Found 28 (30 requested) and removed 29 (15 requested) atoms. Cycle 39: After refmac, R = 0.1826 (Rfree = 0.000) for 6317 atoms. Found 8 (30 requested) and removed 21 (15 requested) atoms. Cycle 40: After refmac, R = 0.1798 (Rfree = 0.000) for 6291 atoms. Found 5 (29 requested) and removed 19 (14 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.64 3.50 Search for helices and strands: 0 residues in 0 chains, 6392 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 6417 seeds are put forward Round 1: 281 peptides, 61 chains. Longest chain 9 peptides. Score 0.240 Round 2: 347 peptides, 64 chains. Longest chain 15 peptides. Score 0.336 Round 3: 363 peptides, 68 chains. Longest chain 11 peptides. Score 0.334 Round 4: 350 peptides, 64 chains. Longest chain 15 peptides. Score 0.341 Round 5: 376 peptides, 67 chains. Longest chain 16 peptides. Score 0.362 Taking the results from Round 5 Chains 67, Residues 309, Estimated correctness of the model 0.0 % 2 chains (10 residues) have been docked in sequence ------------------------------------------------------ 9072 reflections ( 99.17 % complete ) and 15201 restraints for refining 6405 atoms. 14000 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2499 (Rfree = 0.000) for 6405 atoms. Found 30 (30 requested) and removed 54 (15 requested) atoms. Cycle 42: After refmac, R = 0.2386 (Rfree = 0.000) for 6342 atoms. Found 30 (30 requested) and removed 38 (15 requested) atoms. Cycle 43: After refmac, R = 0.1946 (Rfree = 0.000) for 6307 atoms. Found 11 (30 requested) and removed 26 (15 requested) atoms. Cycle 44: After refmac, R = 0.2006 (Rfree = 0.000) for 6276 atoms. Found 16 (29 requested) and removed 22 (14 requested) atoms. Cycle 45: After refmac, R = 0.1843 (Rfree = 0.000) for 6263 atoms. Found 5 (29 requested) and removed 19 (14 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.58 3.44 Search for helices and strands: 0 residues in 0 chains, 6380 seeds are put forward NCS extension: 26 residues added (0 deleted due to clashes), 6406 seeds are put forward Round 1: 243 peptides, 54 chains. Longest chain 9 peptides. Score 0.223 Round 2: 301 peptides, 59 chains. Longest chain 9 peptides. Score 0.293 Round 3: 307 peptides, 57 chains. Longest chain 14 peptides. Score 0.319 Round 4: 310 peptides, 56 chains. Longest chain 12 peptides. Score 0.331 Round 5: 314 peptides, 54 chains. Longest chain 14 peptides. Score 0.353 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 54, Residues 260, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence Sequence coverage is 3 % Consider running further cycles of model building using 1vl4-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 9072 reflections ( 99.17 % complete ) and 15469 restraints for refining 6384 atoms. 14453 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2169 (Rfree = 0.000) for 6384 atoms. Found 0 (30 requested) and removed 15 (15 requested) atoms. Cycle 47: After refmac, R = 0.2243 (Rfree = 0.000) for 6349 atoms. Found 0 (30 requested) and removed 15 (15 requested) atoms. Cycle 48: After refmac, R = 0.2243 (Rfree = 0.000) for 6314 atoms. Found 0 (30 requested) and removed 15 (15 requested) atoms. Cycle 49: After refmac, R = 0.1846 (Rfree = 0.000) for 6282 atoms. TimeTaking 80.4