Sun 23 Dec 22:22:59 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 2fg0-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2fg0-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2fg0-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fg0-3.8-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/2fg0-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fg0-3.8-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 22:23:08 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/2fg0-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fg0-3.8-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 493 and 0 Target number of residues in the AU: 493 Target solvent content: 0.6493 Checking the provided sequence file Detected sequence length: 246 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 492 Adjusted target solvent content: 0.65 Input MTZ file: 2fg0-3.8-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: 92 Cell parameters: 124.890 124.890 97.540 90.000 90.000 90.000 Input sequence file: 2fg0-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 3936 target number of atoms Had to go as low as 0.80 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: 88.311 3.800 Wilson plot Bfac: 77.32 7991 reflections ( 99.65 % complete ) and 0 restraints for refining 4366 atoms. Observations/parameters ratio is 0.46 ------------------------------------------------------ Starting model: R = 0.3059 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3051 (Rfree = 0.000) for 4366 atoms. Found 24 (24 requested) and removed 18 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.59 2.92 Search for helices and strands: 0 residues in 0 chains, 4465 seeds are put forward NCS extension: 0 residues added, 4465 seeds are put forward Round 1: 258 peptides, 38 chains. Longest chain 17 peptides. Score 0.429 Round 2: 314 peptides, 34 chains. Longest chain 31 peptides. Score 0.571 Round 3: 328 peptides, 30 chains. Longest chain 33 peptides. Score 0.625 Round 4: 306 peptides, 29 chains. Longest chain 27 peptides. Score 0.598 Round 5: 310 peptides, 28 chains. Longest chain 28 peptides. Score 0.612 Taking the results from Round 3 Chains 35, Residues 298, Estimated correctness of the model 10.2 % 4 chains (68 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.65 % complete ) and 7024 restraints for refining 3560 atoms. 5588 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2612 (Rfree = 0.000) for 3560 atoms. Found 19 (19 requested) and removed 31 (9 requested) atoms. Cycle 2: After refmac, R = 0.2549 (Rfree = 0.000) for 3450 atoms. Found 19 (19 requested) and removed 16 (9 requested) atoms. Cycle 3: After refmac, R = 0.2497 (Rfree = 0.000) for 3401 atoms. Found 18 (18 requested) and removed 16 (9 requested) atoms. Cycle 4: After refmac, R = 0.2416 (Rfree = 0.000) for 3378 atoms. Found 18 (18 requested) and removed 13 (9 requested) atoms. Cycle 5: After refmac, R = 0.2361 (Rfree = 0.000) for 3357 atoms. Found 12 (18 requested) and removed 13 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.60 2.93 Search for helices and strands: 0 residues in 0 chains, 3454 seeds are put forward NCS extension: 29 residues added (1 deleted due to clashes), 3483 seeds are put forward Round 1: 296 peptides, 36 chains. Longest chain 34 peptides. Score 0.522 Round 2: 314 peptides, 31 chains. Longest chain 39 peptides. Score 0.595 Round 3: 305 peptides, 33 chains. Longest chain 30 peptides. Score 0.564 Round 4: 309 peptides, 32 chains. Longest chain 26 peptides. Score 0.579 Round 5: 305 peptides, 31 chains. Longest chain 29 peptides. Score 0.580 Taking the results from Round 2 Chains 36, Residues 283, Estimated correctness of the model 0.0 % 4 chains (53 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.65 % complete ) and 7036 restraints for refining 3467 atoms. 5764 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2605 (Rfree = 0.000) for 3467 atoms. Found 19 (19 requested) and removed 39 (9 requested) atoms. Cycle 7: After refmac, R = 0.2486 (Rfree = 0.000) for 3410 atoms. Found 15 (18 requested) and removed 19 (9 requested) atoms. Cycle 8: After refmac, R = 0.2348 (Rfree = 0.000) for 3387 atoms. Found 14 (18 requested) and removed 16 (9 requested) atoms. Cycle 9: After refmac, R = 0.2283 (Rfree = 0.000) for 3368 atoms. Found 7 (18 requested) and removed 16 (9 requested) atoms. Cycle 10: After refmac, R = 0.2242 (Rfree = 0.000) for 3346 atoms. Found 2 (18 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.59 2.92 Search for helices and strands: 0 residues in 0 chains, 3433 seeds are put forward NCS extension: 18 residues added (9 deleted due to clashes), 3451 seeds are put forward Round 1: 279 peptides, 35 chains. Longest chain 29 peptides. Score 0.499 Round 2: 293 peptides, 27 chains. Longest chain 29 peptides. Score 0.592 Round 3: 299 peptides, 33 chains. Longest chain 27 peptides. Score 0.553 Round 4: 289 peptides, 32 chains. Longest chain 25 peptides. Score 0.544 Round 5: 293 peptides, 30 chains. Longest chain 28 peptides. Score 0.568 Taking the results from Round 2 Chains 34, Residues 266, Estimated correctness of the model 0.0 % 6 chains (72 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.65 % complete ) and 7084 restraints for refining 3559 atoms. 5766 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2554 (Rfree = 0.000) for 3559 atoms. Found 19 (19 requested) and removed 26 (9 requested) atoms. Cycle 12: After refmac, R = 0.2355 (Rfree = 0.000) for 3525 atoms. Found 11 (19 requested) and removed 15 (9 requested) atoms. Cycle 13: After refmac, R = 0.2337 (Rfree = 0.000) for 3506 atoms. Found 9 (19 requested) and removed 14 (9 requested) atoms. Cycle 14: After refmac, R = 0.2340 (Rfree = 0.000) for 3487 atoms. Found 5 (19 requested) and removed 16 (9 requested) atoms. Cycle 15: After refmac, R = 0.2359 (Rfree = 0.000) for 3467 atoms. Found 7 (19 requested) and removed 15 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.58 2.91 Search for helices and strands: 0 residues in 0 chains, 3575 seeds are put forward NCS extension: 30 residues added (0 deleted due to clashes), 3605 seeds are put forward Round 1: 269 peptides, 41 chains. Longest chain 14 peptides. Score 0.424 Round 2: 303 peptides, 37 chains. Longest chain 19 peptides. Score 0.527 Round 3: 288 peptides, 32 chains. Longest chain 26 peptides. Score 0.542 Round 4: 310 peptides, 30 chains. Longest chain 29 peptides. Score 0.596 Round 5: 306 peptides, 28 chains. Longest chain 26 peptides. Score 0.605 Taking the results from Round 5 Chains 36, Residues 278, Estimated correctness of the model 1.2 % 5 chains (62 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.65 % complete ) and 7166 restraints for refining 3560 atoms. 5853 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2841 (Rfree = 0.000) for 3560 atoms. Found 19 (19 requested) and removed 37 (9 requested) atoms. Cycle 17: After refmac, R = 0.2558 (Rfree = 0.000) for 3509 atoms. Found 19 (19 requested) and removed 24 (9 requested) atoms. Cycle 18: After refmac, R = 0.2765 (Rfree = 0.000) for 3494 atoms. Found 19 (19 requested) and removed 21 (9 requested) atoms. Cycle 19: After refmac, R = 0.2584 (Rfree = 0.000) for 3483 atoms. Found 6 (19 requested) and removed 22 (9 requested) atoms. Cycle 20: After refmac, R = 0.2607 (Rfree = 0.000) for 3456 atoms. Found 7 (19 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.58 2.91 Search for helices and strands: 0 residues in 0 chains, 3568 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 3589 seeds are put forward Round 1: 280 peptides, 36 chains. Longest chain 20 peptides. Score 0.492 Round 2: 302 peptides, 34 chains. Longest chain 24 peptides. Score 0.550 Round 3: 291 peptides, 33 chains. Longest chain 20 peptides. Score 0.539 Round 4: 299 peptides, 36 chains. Longest chain 18 peptides. Score 0.528 Round 5: 306 peptides, 36 chains. Longest chain 26 peptides. Score 0.541 Taking the results from Round 2 Chains 34, Residues 268, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.65 % complete ) and 7859 restraints for refining 3560 atoms. 6821 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2732 (Rfree = 0.000) for 3560 atoms. Found 19 (19 requested) and removed 37 (9 requested) atoms. Cycle 22: After refmac, R = 0.2748 (Rfree = 0.000) for 3521 atoms. Found 19 (19 requested) and removed 31 (9 requested) atoms. Cycle 23: After refmac, R = 0.2687 (Rfree = 0.000) for 3498 atoms. Found 19 (19 requested) and removed 34 (9 requested) atoms. Cycle 24: After refmac, R = 0.2430 (Rfree = 0.000) for 3470 atoms. Found 19 (19 requested) and removed 22 (9 requested) atoms. Failed to save intermediate PDB Cycle 25: After refmac, R = 0.2412 (Rfree = 0.000) for 3455 atoms. Found 19 (19 requested) and removed 17 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.57 2.90 Search for helices and strands: 0 residues in 0 chains, 3564 seeds are put forward NCS extension: 33 residues added (2 deleted due to clashes), 3597 seeds are put forward Round 1: 271 peptides, 44 chains. Longest chain 14 peptides. Score 0.400 Round 2: 290 peptides, 36 chains. Longest chain 30 peptides. Score 0.511 Round 3: 301 peptides, 37 chains. Longest chain 20 peptides. Score 0.523 Round 4: 290 peptides, 37 chains. Longest chain 21 peptides. Score 0.503 Round 5: 288 peptides, 37 chains. Longest chain 21 peptides. Score 0.499 Taking the results from Round 3 Chains 42, Residues 264, Estimated correctness of the model 0.0 % 5 chains (50 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.65 % complete ) and 7345 restraints for refining 3559 atoms. 6129 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2541 (Rfree = 0.000) for 3559 atoms. Found 19 (19 requested) and removed 20 (9 requested) atoms. Cycle 27: After refmac, R = 0.2444 (Rfree = 0.000) for 3503 atoms. Found 16 (19 requested) and removed 13 (9 requested) atoms. Cycle 28: After refmac, R = 0.2399 (Rfree = 0.000) for 3470 atoms. Found 17 (19 requested) and removed 14 (9 requested) atoms. Cycle 29: After refmac, R = 0.2287 (Rfree = 0.000) for 3456 atoms. Found 19 (19 requested) and removed 16 (9 requested) atoms. Cycle 30: After refmac, R = 0.2231 (Rfree = 0.000) for 3440 atoms. Found 10 (19 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.55 2.89 Search for helices and strands: 0 residues in 0 chains, 3570 seeds are put forward NCS extension: 10 residues added (5 deleted due to clashes), 3580 seeds are put forward Round 1: 276 peptides, 44 chains. Longest chain 16 peptides. Score 0.411 Round 2: 279 peptides, 34 chains. Longest chain 19 peptides. Score 0.508 Round 3: 288 peptides, 32 chains. Longest chain 29 peptides. Score 0.542 Round 4: 294 peptides, 34 chains. Longest chain 20 peptides. Score 0.536 Round 5: 293 peptides, 33 chains. Longest chain 19 peptides. Score 0.542 Taking the results from Round 5 Chains 35, Residues 260, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.65 % complete ) and 7900 restraints for refining 3560 atoms. 6838 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2768 (Rfree = 0.000) for 3560 atoms. Found 19 (19 requested) and removed 20 (9 requested) atoms. Cycle 32: After refmac, R = 0.2550 (Rfree = 0.000) for 3535 atoms. Found 19 (19 requested) and removed 17 (9 requested) atoms. Cycle 33: After refmac, R = 0.2454 (Rfree = 0.000) for 3518 atoms. Found 19 (19 requested) and removed 10 (9 requested) atoms. Cycle 34: After refmac, R = 0.2320 (Rfree = 0.000) for 3503 atoms. Found 19 (19 requested) and removed 14 (9 requested) atoms. Cycle 35: After refmac, R = 0.2283 (Rfree = 0.000) for 3489 atoms. Found 19 (19 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.58 2.91 Search for helices and strands: 0 residues in 0 chains, 3621 seeds are put forward NCS extension: 31 residues added (0 deleted due to clashes), 3652 seeds are put forward Round 1: 266 peptides, 42 chains. Longest chain 15 peptides. Score 0.408 Round 2: 289 peptides, 36 chains. Longest chain 25 peptides. Score 0.509 Round 3: 300 peptides, 36 chains. Longest chain 20 peptides. Score 0.530 Round 4: 300 peptides, 37 chains. Longest chain 19 peptides. Score 0.521 Round 5: 307 peptides, 41 chains. Longest chain 18 peptides. Score 0.500 Taking the results from Round 3 Chains 37, Residues 264, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.65 % complete ) and 7902 restraints for refining 3559 atoms. 6857 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2608 (Rfree = 0.000) for 3559 atoms. Found 18 (19 requested) and removed 16 (9 requested) atoms. Cycle 37: After refmac, R = 0.2306 (Rfree = 0.000) for 3534 atoms. Found 13 (19 requested) and removed 15 (9 requested) atoms. Cycle 38: After refmac, R = 0.2235 (Rfree = 0.000) for 3521 atoms. Found 7 (19 requested) and removed 12 (9 requested) atoms. Cycle 39: After refmac, R = 0.2351 (Rfree = 0.000) for 3511 atoms. Found 6 (19 requested) and removed 10 (9 requested) atoms. Cycle 40: After refmac, R = 0.2224 (Rfree = 0.000) for 3501 atoms. Found 2 (19 requested) and removed 13 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.59 2.92 Search for helices and strands: 0 residues in 0 chains, 3627 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 3648 seeds are put forward Round 1: 251 peptides, 41 chains. Longest chain 16 peptides. Score 0.385 Round 2: 271 peptides, 35 chains. Longest chain 22 peptides. Score 0.484 Round 3: 275 peptides, 32 chains. Longest chain 22 peptides. Score 0.518 Round 4: 279 peptides, 37 chains. Longest chain 23 peptides. Score 0.481 Round 5: 277 peptides, 34 chains. Longest chain 22 peptides. Score 0.504 Taking the results from Round 3 Chains 35, Residues 243, Estimated correctness of the model 0.0 % 5 chains (47 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.65 % complete ) and 7585 restraints for refining 3560 atoms. 6471 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2571 (Rfree = 0.000) for 3560 atoms. Found 19 (19 requested) and removed 11 (9 requested) atoms. Cycle 42: After refmac, R = 0.2314 (Rfree = 0.000) for 3540 atoms. Found 11 (19 requested) and removed 14 (9 requested) atoms. Cycle 43: After refmac, R = 0.2252 (Rfree = 0.000) for 3525 atoms. Found 16 (19 requested) and removed 11 (9 requested) atoms. Cycle 44: After refmac, R = 0.2188 (Rfree = 0.000) for 3520 atoms. Found 9 (19 requested) and removed 15 (9 requested) atoms. Cycle 45: After refmac, R = 0.2201 (Rfree = 0.000) for 3503 atoms. Found 14 (19 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.56 2.90 Search for helices and strands: 0 residues in 0 chains, 3606 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 3630 seeds are put forward Round 1: 253 peptides, 41 chains. Longest chain 13 peptides. Score 0.390 Round 2: 263 peptides, 33 chains. Longest chain 24 peptides. Score 0.486 Round 3: 261 peptides, 33 chains. Longest chain 24 peptides. Score 0.482 Round 4: 259 peptides, 31 chains. Longest chain 24 peptides. Score 0.496 Round 5: 265 peptides, 30 chains. Longest chain 24 peptides. Score 0.517 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 31, Residues 235, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence Sequence coverage is 3 % Consider running further cycles of model building using 2fg0-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7991 reflections ( 99.65 % complete ) and 8271 restraints for refining 3559 atoms. 7336 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2509 (Rfree = 0.000) for 3559 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.2708 (Rfree = 0.000) for 3534 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.2368 (Rfree = 0.000) for 3504 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.2329 (Rfree = 0.000) for 3482 atoms. TimeTaking 60.42