null Sun 23 Dec 22:22:46 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 1vl4-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vl4-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vl4-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vl4-3.8-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/1vl4-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vl4-3.8-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 ============================================================ Sun 23 Dec 22:22:56 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/1vl4-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vl4-3.8-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 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-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: 1vl4-3.8-parrot-hancs.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 7876 atoms. Observations/parameters ratio is 0.34 ------------------------------------------------------ Starting model: R = 0.3143 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3166 (Rfree = 0.000) for 7876 atoms. Found 43 (43 requested) and removed 39 (21 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.39 3.26 Search for helices and strands: 0 residues in 0 chains, 7999 seeds are put forward NCS extension: 0 residues added, 7999 seeds are put forward Round 1: 363 peptides, 66 chains. Longest chain 16 peptides. Score 0.348 Round 2: 509 peptides, 79 chains. Longest chain 20 peptides. Score 0.485 Round 3: 527 peptides, 75 chains. Longest chain 21 peptides. Score 0.533 Round 4: 535 peptides, 75 chains. Longest chain 22 peptides. Score 0.543 Round 5: 544 peptides, 74 chains. Longest chain 21 peptides. Score 0.560 Taking the results from Round 5 Chains 78, Residues 470, Estimated correctness of the model 0.0 % 6 chains (53 residues) have been docked in sequence ------------------------------------------------------ 10562 reflections ( 99.28 % complete ) and 14292 restraints for refining 6467 atoms. 12322 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2882 (Rfree = 0.000) for 6467 atoms. Found 35 (35 requested) and removed 67 (17 requested) atoms. Cycle 2: After refmac, R = 0.2697 (Rfree = 0.000) for 6311 atoms. Found 35 (35 requested) and removed 49 (17 requested) atoms. Cycle 3: After refmac, R = 0.2608 (Rfree = 0.000) for 6216 atoms. Found 34 (34 requested) and removed 40 (17 requested) atoms. Cycle 4: After refmac, R = 0.2564 (Rfree = 0.000) for 6159 atoms. Found 34 (34 requested) and removed 49 (17 requested) atoms. Cycle 5: After refmac, R = 0.2310 (Rfree = 0.000) for 6094 atoms. Found 20 (33 requested) and removed 24 (16 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.41 3.28 Search for helices and strands: 0 residues in 0 chains, 6286 seeds are put forward NCS extension: 19 residues added (4 deleted due to clashes), 6305 seeds are put forward Round 1: 440 peptides, 76 chains. Longest chain 18 peptides. Score 0.403 Round 2: 504 peptides, 75 chains. Longest chain 19 peptides. Score 0.502 Round 3: 510 peptides, 68 chains. Longest chain 22 peptides. Score 0.551 Round 4: 547 peptides, 74 chains. Longest chain 23 peptides. Score 0.564 Round 5: 542 peptides, 64 chains. Longest chain 40 peptides. Score 0.612 Taking the results from Round 5 Chains 71, Residues 478, Estimated correctness of the model 4.4 % 8 chains (78 residues) have been docked in sequence ------------------------------------------------------ 10562 reflections ( 99.28 % complete ) and 13567 restraints for refining 6466 atoms. 11431 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2472 (Rfree = 0.000) for 6466 atoms. Found 33 (35 requested) and removed 81 (17 requested) atoms. Cycle 7: After refmac, R = 0.2221 (Rfree = 0.000) for 6368 atoms. Found 12 (35 requested) and removed 43 (17 requested) atoms. Cycle 8: After refmac, R = 0.2206 (Rfree = 0.000) for 6315 atoms. Found 14 (34 requested) and removed 39 (17 requested) atoms. Cycle 9: After refmac, R = 0.2173 (Rfree = 0.000) for 6268 atoms. Found 19 (34 requested) and removed 30 (17 requested) atoms. Cycle 10: After refmac, R = 0.2141 (Rfree = 0.000) for 6241 atoms. Found 23 (34 requested) and removed 33 (17 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.37 3.24 Search for helices and strands: 0 residues in 0 chains, 6431 seeds are put forward NCS extension: 28 residues added (0 deleted due to clashes), 6459 seeds are put forward Round 1: 459 peptides, 78 chains. Longest chain 15 peptides. Score 0.419 Round 2: 505 peptides, 75 chains. Longest chain 17 peptides. Score 0.504 Round 3: 516 peptides, 70 chains. Longest chain 31 peptides. Score 0.547 Round 4: 504 peptides, 69 chains. Longest chain 18 peptides. Score 0.538 Round 5: 517 peptides, 69 chains. Longest chain 29 peptides. Score 0.554 Taking the results from Round 5 Chains 70, Residues 448, Estimated correctness of the model 0.0 % 3 chains (43 residues) have been docked in sequence ------------------------------------------------------ 10562 reflections ( 99.28 % complete ) and 14345 restraints for refining 6465 atoms. 12460 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2415 (Rfree = 0.000) for 6465 atoms. Found 24 (35 requested) and removed 48 (17 requested) atoms. Cycle 12: After refmac, R = 0.2235 (Rfree = 0.000) for 6400 atoms. Found 15 (35 requested) and removed 37 (17 requested) atoms. Cycle 13: After refmac, R = 0.2173 (Rfree = 0.000) for 6361 atoms. Found 12 (35 requested) and removed 24 (17 requested) atoms. Cycle 14: After refmac, R = 0.2172 (Rfree = 0.000) for 6345 atoms. Found 15 (34 requested) and removed 25 (17 requested) atoms. Cycle 15: After refmac, R = 0.2095 (Rfree = 0.000) for 6328 atoms. Found 3 (34 requested) and removed 19 (17 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.35 3.22 Search for helices and strands: 0 residues in 0 chains, 6503 seeds are put forward NCS extension: 40 residues added (2 deleted due to clashes), 6543 seeds are put forward Round 1: 422 peptides, 71 chains. Longest chain 15 peptides. Score 0.408 Round 2: 471 peptides, 69 chains. Longest chain 24 peptides. Score 0.493 Round 3: 469 peptides, 64 chains. Longest chain 21 peptides. Score 0.521 Round 4: 499 peptides, 67 chains. Longest chain 25 peptides. Score 0.543 Round 5: 505 peptides, 73 chains. Longest chain 17 peptides. Score 0.516 Taking the results from Round 4 Chains 71, Residues 432, Estimated correctness of the model 0.0 % 6 chains (44 residues) have been docked in sequence ------------------------------------------------------ 10562 reflections ( 99.28 % complete ) and 14576 restraints for refining 6468 atoms. 12780 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2564 (Rfree = 0.000) for 6468 atoms. Found 35 (35 requested) and removed 45 (17 requested) atoms. Cycle 17: After refmac, R = 0.2266 (Rfree = 0.000) for 6415 atoms. Found 32 (35 requested) and removed 35 (17 requested) atoms. Cycle 18: After refmac, R = 0.2305 (Rfree = 0.000) for 6369 atoms. Found 19 (35 requested) and removed 36 (17 requested) atoms. Cycle 19: After refmac, R = 0.1976 (Rfree = 0.000) for 6331 atoms. Found 9 (34 requested) and removed 27 (17 requested) atoms. Cycle 20: After refmac, R = 0.2146 (Rfree = 0.000) for 6304 atoms. Found 26 (34 requested) and removed 31 (17 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.43 3.30 Search for helices and strands provided no result - WARNING Search for helices and strands: 0 residues in 0 chains, 6321 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 6336 seeds are put forward Round 1: 411 peptides, 76 chains. Longest chain 12 peptides. Score 0.357 Round 2: 452 peptides, 73 chains. Longest chain 18 peptides. Score 0.441 Round 3: 466 peptides, 72 chains. Longest chain 18 peptides. Score 0.467 Round 4: 456 peptides, 65 chains. Longest chain 20 peptides. Score 0.497 Round 5: 455 peptides, 59 chains. Longest chain 26 peptides. Score 0.532 Taking the results from Round 5 Chains 61, Residues 396, Estimated correctness of the model 0.0 % 5 chains (43 residues) have been docked in sequence ------------------------------------------------------ 10562 reflections ( 99.28 % complete ) and 14412 restraints for refining 6468 atoms. 12729 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2509 (Rfree = 0.000) for 6468 atoms. Found 35 (35 requested) and removed 43 (17 requested) atoms. Cycle 22: After refmac, R = 0.2184 (Rfree = 0.000) for 6402 atoms. Found 13 (35 requested) and removed 36 (17 requested) atoms. Cycle 23: After refmac, R = 0.2053 (Rfree = 0.000) for 6348 atoms. Found 16 (35 requested) and removed 22 (17 requested) atoms. Cycle 24: After refmac, R = 0.1979 (Rfree = 0.000) for 6326 atoms. Found 6 (34 requested) and removed 20 (17 requested) atoms. Cycle 25: After refmac, R = 0.1925 (Rfree = 0.000) for 6304 atoms. Found 6 (34 requested) and removed 21 (17 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.45 3.31 Search for helices and strands: 0 residues in 0 chains, 6465 seeds are put forward NCS extension: 34 residues added (3 deleted due to clashes), 6499 seeds are put forward Round 1: 402 peptides, 75 chains. Longest chain 18 peptides. Score 0.349 Round 2: 438 peptides, 67 chains. Longest chain 23 peptides. Score 0.459 Round 3: 448 peptides, 64 chains. Longest chain 24 peptides. Score 0.492 Round 4: 465 peptides, 65 chains. Longest chain 22 peptides. Score 0.509 Round 5: 479 peptides, 66 chains. Longest chain 27 peptides. Score 0.522 Taking the results from Round 5 Chains 67, Residues 413, Estimated correctness of the model 0.0 % 5 chains (56 residues) have been docked in sequence ------------------------------------------------------ 10562 reflections ( 99.28 % complete ) and 14214 restraints for refining 6469 atoms. 12412 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2236 (Rfree = 0.000) for 6469 atoms. Found 26 (35 requested) and removed 37 (17 requested) atoms. Cycle 27: After refmac, R = 0.2111 (Rfree = 0.000) for 6402 atoms. Found 5 (35 requested) and removed 24 (17 requested) atoms. Cycle 28: After refmac, R = 0.2041 (Rfree = 0.000) for 6370 atoms. Found 9 (35 requested) and removed 19 (17 requested) atoms. Cycle 29: After refmac, R = 0.1998 (Rfree = 0.000) for 6348 atoms. Found 7 (34 requested) and removed 22 (17 requested) atoms. Cycle 30: After refmac, R = 0.1947 (Rfree = 0.000) for 6327 atoms. Found 6 (34 requested) and removed 21 (17 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.41 3.28 Search for helices and strands: 0 residues in 0 chains, 6438 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 6461 seeds are put forward Round 1: 409 peptides, 78 chains. Longest chain 11 peptides. Score 0.340 Round 2: 430 peptides, 66 chains. Longest chain 22 peptides. Score 0.453 Round 3: 433 peptides, 67 chains. Longest chain 22 peptides. Score 0.451 Round 4: 438 peptides, 64 chains. Longest chain 22 peptides. Score 0.478 Round 5: 432 peptides, 67 chains. Longest chain 19 peptides. Score 0.450 Taking the results from Round 4 Chains 64, Residues 374, Estimated correctness of the model 0.0 % 4 chains (34 residues) have been docked in sequence ------------------------------------------------------ 10562 reflections ( 99.28 % complete ) and 14890 restraints for refining 6468 atoms. 13342 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2404 (Rfree = 0.000) for 6468 atoms. Found 35 (35 requested) and removed 27 (17 requested) atoms. Cycle 32: After refmac, R = 0.2375 (Rfree = 0.000) for 6445 atoms. Found 35 (35 requested) and removed 31 (17 requested) atoms. Cycle 33: After refmac, R = 0.2214 (Rfree = 0.000) for 6403 atoms. Found 35 (35 requested) and removed 29 (17 requested) atoms. Cycle 34: After refmac, R = 0.1837 (Rfree = 0.000) for 6381 atoms. Found 5 (35 requested) and removed 21 (17 requested) atoms. Cycle 35: After refmac, R = 0.1731 (Rfree = 0.000) for 6352 atoms. Found 4 (35 requested) and removed 22 (17 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.46 3.32 Search for helices and strands: 0 residues in 0 chains, 6472 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 6489 seeds are put forward Round 1: 343 peptides, 69 chains. Longest chain 11 peptides. Score 0.292 Round 2: 401 peptides, 67 chains. Longest chain 15 peptides. Score 0.403 Round 3: 392 peptides, 64 chains. Longest chain 18 peptides. Score 0.409 Round 4: 411 peptides, 65 chains. Longest chain 20 peptides. Score 0.432 Round 5: 429 peptides, 66 chains. Longest chain 16 peptides. Score 0.452 Taking the results from Round 5 Chains 67, Residues 363, Estimated correctness of the model 0.0 % 6 chains (31 residues) have been docked in sequence ------------------------------------------------------ 10562 reflections ( 99.28 % complete ) and 14684 restraints for refining 6469 atoms. 13204 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2277 (Rfree = 0.000) for 6469 atoms. Found 35 (35 requested) and removed 35 (17 requested) atoms. Cycle 37: After refmac, R = 0.2215 (Rfree = 0.000) for 6436 atoms. Found 35 (35 requested) and removed 36 (17 requested) atoms. Cycle 38: After refmac, R = 0.2134 (Rfree = 0.000) for 6412 atoms. Found 35 (35 requested) and removed 28 (17 requested) atoms. Cycle 39: After refmac, R = 0.1797 (Rfree = 0.000) for 6397 atoms. Found 5 (35 requested) and removed 22 (17 requested) atoms. Cycle 40: After refmac, R = 0.1733 (Rfree = 0.000) for 6369 atoms. Found 8 (35 requested) and removed 23 (17 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.46 3.32 Search for helices and strands: 0 residues in 0 chains, 6468 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 6480 seeds are put forward Round 1: 351 peptides, 70 chains. Longest chain 12 peptides. Score 0.299 Round 2: 392 peptides, 61 chains. Longest chain 31 peptides. Score 0.429 Round 3: 389 peptides, 65 chains. Longest chain 15 peptides. Score 0.397 Round 4: 381 peptides, 57 chains. Longest chain 35 peptides. Score 0.440 Round 5: 368 peptides, 57 chains. Longest chain 16 peptides. Score 0.420 Taking the results from Round 4 Chains 60, Residues 324, Estimated correctness of the model 0.0 % 6 chains (79 residues) have been docked in sequence ------------------------------------------------------ 10562 reflections ( 99.28 % complete ) and 14342 restraints for refining 6468 atoms. 12768 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2343 (Rfree = 0.000) for 6468 atoms. Found 35 (35 requested) and removed 32 (17 requested) atoms. Cycle 42: After refmac, R = 0.2239 (Rfree = 0.000) for 6410 atoms. Found 35 (35 requested) and removed 29 (17 requested) atoms. Cycle 43: After refmac, R = 0.2219 (Rfree = 0.000) for 6386 atoms. Found 35 (35 requested) and removed 29 (17 requested) atoms. Cycle 44: After refmac, R = 0.2187 (Rfree = 0.000) for 6369 atoms. Found 35 (35 requested) and removed 23 (17 requested) atoms. Cycle 45: After refmac, R = 0.2178 (Rfree = 0.000) for 6358 atoms. Found 35 (35 requested) and removed 24 (17 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.38 3.25 Search for helices and strands: 0 residues in 0 chains, 6509 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 6525 seeds are put forward Round 1: 314 peptides, 65 chains. Longest chain 13 peptides. Score 0.270 Round 2: 362 peptides, 64 chains. Longest chain 15 peptides. Score 0.361 Round 3: 375 peptides, 64 chains. Longest chain 12 peptides. Score 0.382 Round 4: 348 peptides, 57 chains. Longest chain 13 peptides. Score 0.388 Round 5: 356 peptides, 63 chains. Longest chain 12 peptides. Score 0.358 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 57, Residues 291, Estimated correctness of the model 0.0 % 3 chains (9 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 57 chains (291 residues) following loop building 3 chains (9 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 10562 reflections ( 99.28 % complete ) and 15262 restraints for refining 6469 atoms. 14118 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2468 (Rfree = 0.000) for 6469 atoms. Found 0 (35 requested) and removed 17 (17 requested) atoms. Cycle 47: After refmac, R = 0.2242 (Rfree = 0.000) for 6405 atoms. Found 0 (35 requested) and removed 17 (17 requested) atoms. Cycle 48: After refmac, R = 0.2314 (Rfree = 0.000) for 6359 atoms. Found 0 (35 requested) and removed 17 (17 requested) atoms. Cycle 49: After refmac, R = 0.2250 (Rfree = 0.000) for 6331 atoms. Found 0 (34 requested) and removed 17 (17 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:45:38 GMT 2018 Job finished. TimeTaking 82.87 Used memory is bytes: 6524816