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 1vpm-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vpm-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vpm-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vpm-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/1vpm-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vpm-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/1vpm-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vpm-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 329 and 0 Target number of residues in the AU: 329 Target solvent content: 0.6645 Checking the provided sequence file Detected sequence length: 169 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 3 Adjusted target number of residues: 507 Adjusted target solvent content: 0.48 Input MTZ file: 1vpm-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: 24 Cell parameters: 82.941 106.484 120.177 90.000 90.000 90.000 Input sequence file: 1vpm-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 4056 target number of atoms Had to go as low as 0.60 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: 79.699 3.801 Wilson plot Bfac: 87.91 5369 reflections ( 97.71 % complete ) and 0 restraints for refining 4488 atoms. Observations/parameters ratio is 0.30 ------------------------------------------------------ Starting model: R = 0.3231 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3124 (Rfree = 0.000) for 4488 atoms. Found 24 (24 requested) and removed 34 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.77 3.87 Search for helices and strands: 0 residues in 0 chains, 4554 seeds are put forward NCS extension: 0 residues added, 4554 seeds are put forward Round 1: 202 peptides, 36 chains. Longest chain 14 peptides. Score 0.368 Round 2: 287 peptides, 38 chains. Longest chain 33 peptides. Score 0.577 Round 3: 297 peptides, 35 chains. Longest chain 28 peptides. Score 0.629 Round 4: 301 peptides, 36 chains. Longest chain 18 peptides. Score 0.628 Round 5: 305 peptides, 37 chains. Longest chain 26 peptides. Score 0.627 Taking the results from Round 3 Chains 38, Residues 262, Estimated correctness of the model 11.8 % 4 chains (47 residues) have been docked in sequence ------------------------------------------------------ 5369 reflections ( 97.71 % complete ) and 7787 restraints for refining 3668 atoms. 6606 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2529 (Rfree = 0.000) for 3668 atoms. Found 14 (20 requested) and removed 22 (10 requested) atoms. Cycle 2: After refmac, R = 0.2376 (Rfree = 0.000) for 3588 atoms. Found 12 (20 requested) and removed 15 (10 requested) atoms. Cycle 3: After refmac, R = 0.2285 (Rfree = 0.000) for 3556 atoms. Found 6 (19 requested) and removed 9 (9 requested) atoms. Cycle 4: After refmac, R = 0.2235 (Rfree = 0.000) for 3528 atoms. Found 7 (19 requested) and removed 9 (9 requested) atoms. Cycle 5: After refmac, R = 0.2222 (Rfree = 0.000) for 3513 atoms. Found 6 (19 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.75 3.85 Search for helices and strands: 0 residues in 0 chains, 3622 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 3642 seeds are put forward Round 1: 264 peptides, 42 chains. Longest chain 21 peptides. Score 0.474 Round 2: 295 peptides, 37 chains. Longest chain 30 peptides. Score 0.605 Round 3: 275 peptides, 35 chains. Longest chain 19 peptides. Score 0.580 Round 4: 286 peptides, 34 chains. Longest chain 18 peptides. Score 0.616 Round 5: 288 peptides, 33 chains. Longest chain 21 peptides. Score 0.630 Taking the results from Round 5 Chains 35, Residues 255, Estimated correctness of the model 12.3 % 2 chains (23 residues) have been docked in sequence ------------------------------------------------------ 5369 reflections ( 97.71 % complete ) and 8259 restraints for refining 3668 atoms. 7203 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2282 (Rfree = 0.000) for 3668 atoms. Found 11 (20 requested) and removed 33 (10 requested) atoms. Cycle 7: After refmac, R = 0.2477 (Rfree = 0.000) for 3591 atoms. Found 20 (20 requested) and removed 39 (10 requested) atoms. Cycle 8: After refmac, R = 0.2421 (Rfree = 0.000) for 3547 atoms. Found 19 (19 requested) and removed 59 (9 requested) atoms. Cycle 9: After refmac, R = 0.2226 (Rfree = 0.000) for 3481 atoms. Found 14 (19 requested) and removed 30 (9 requested) atoms. Cycle 10: After refmac, R = 0.2329 (Rfree = 0.000) for 3437 atoms. Found 19 (19 requested) and removed 32 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.65 3.75 Search for helices and strands: 0 residues in 0 chains, 3560 seeds are put forward NCS extension: 16 residues added (4 deleted due to clashes), 3576 seeds are put forward Round 1: 213 peptides, 35 chains. Longest chain 15 peptides. Score 0.415 Round 2: 235 peptides, 39 chains. Longest chain 15 peptides. Score 0.429 Round 3: 228 peptides, 32 chains. Longest chain 14 peptides. Score 0.496 Round 4: 248 peptides, 36 chains. Longest chain 19 peptides. Score 0.502 Round 5: 234 peptides, 31 chains. Longest chain 18 peptides. Score 0.524 Taking the results from Round 5 Chains 33, Residues 203, Estimated correctness of the model 0.0 % 2 chains (27 residues) have been docked in sequence ------------------------------------------------------ 5369 reflections ( 97.71 % complete ) and 7960 restraints for refining 3531 atoms. 7091 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2340 (Rfree = 0.000) for 3531 atoms. Found 19 (19 requested) and removed 41 (9 requested) atoms. Cycle 12: After refmac, R = 0.2193 (Rfree = 0.000) for 3481 atoms. Found 19 (19 requested) and removed 23 (9 requested) atoms. Cycle 13: After refmac, R = 0.1970 (Rfree = 0.000) for 3447 atoms. Found 19 (19 requested) and removed 14 (9 requested) atoms. Cycle 14: After refmac, R = 0.2104 (Rfree = 0.000) for 3434 atoms. Found 18 (18 requested) and removed 14 (9 requested) atoms. Cycle 15: After refmac, R = 0.1873 (Rfree = 0.000) for 3420 atoms. Found 18 (18 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.68 3.78 Search for helices and strands: 0 residues in 0 chains, 3570 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 3587 seeds are put forward Round 1: 202 peptides, 36 chains. Longest chain 11 peptides. Score 0.368 Round 2: 246 peptides, 41 chains. Longest chain 13 peptides. Score 0.436 Round 3: 259 peptides, 36 chains. Longest chain 19 peptides. Score 0.530 Round 4: 277 peptides, 39 chains. Longest chain 19 peptides. Score 0.542 Round 5: 271 peptides, 37 chains. Longest chain 18 peptides. Score 0.549 Taking the results from Round 5 Chains 38, Residues 234, Estimated correctness of the model 0.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 5369 reflections ( 97.71 % complete ) and 7973 restraints for refining 3578 atoms. 7019 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2001 (Rfree = 0.000) for 3578 atoms. Found 15 (19 requested) and removed 36 (9 requested) atoms. Cycle 17: After refmac, R = 0.2052 (Rfree = 0.000) for 3531 atoms. Found 19 (19 requested) and removed 36 (9 requested) atoms. Cycle 18: After refmac, R = 0.1841 (Rfree = 0.000) for 3500 atoms. Found 13 (19 requested) and removed 40 (9 requested) atoms. Cycle 19: After refmac, R = 0.1837 (Rfree = 0.000) for 3459 atoms. Found 19 (19 requested) and removed 27 (9 requested) atoms. Cycle 20: After refmac, R = 0.1811 (Rfree = 0.000) for 3438 atoms. Found 9 (18 requested) and removed 31 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.66 3.76 Search for helices and strands: 0 residues in 0 chains, 3535 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 3560 seeds are put forward Round 1: 226 peptides, 43 chains. Longest chain 14 peptides. Score 0.350 Round 2: 232 peptides, 38 chains. Longest chain 13 peptides. Score 0.433 Round 3: 250 peptides, 39 chains. Longest chain 14 peptides. Score 0.471 Round 4: 262 peptides, 41 chains. Longest chain 16 peptides. Score 0.480 Round 5: 257 peptides, 41 chains. Longest chain 15 peptides. Score 0.467 Taking the results from Round 4 Chains 41, Residues 221, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5369 reflections ( 97.71 % complete ) and 8312 restraints for refining 3603 atoms. 7469 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2544 (Rfree = 0.000) for 3603 atoms. Found 19 (19 requested) and removed 39 (9 requested) atoms. Cycle 22: After refmac, R = 0.2161 (Rfree = 0.000) for 3552 atoms. Found 19 (19 requested) and removed 19 (9 requested) atoms. Cycle 23: After refmac, R = 0.1907 (Rfree = 0.000) for 3538 atoms. Found 19 (19 requested) and removed 20 (9 requested) atoms. Cycle 24: After refmac, R = 0.1982 (Rfree = 0.000) for 3529 atoms. Found 19 (19 requested) and removed 13 (9 requested) atoms. Cycle 25: After refmac, R = 0.1714 (Rfree = 0.000) for 3526 atoms. Found 19 (19 requested) and removed 14 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.69 3.79 Search for helices and strands: 0 residues in 0 chains, 3668 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 3682 seeds are put forward Round 1: 214 peptides, 43 chains. Longest chain 11 peptides. Score 0.312 Round 2: 229 peptides, 38 chains. Longest chain 14 peptides. Score 0.424 Round 3: 234 peptides, 35 chains. Longest chain 14 peptides. Score 0.476 Round 4: 226 peptides, 34 chains. Longest chain 12 peptides. Score 0.466 Round 5: 239 peptides, 38 chains. Longest chain 13 peptides. Score 0.453 Taking the results from Round 3 Chains 35, Residues 199, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5369 reflections ( 97.71 % complete ) and 8690 restraints for refining 3645 atoms. 7929 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2209 (Rfree = 0.000) for 3645 atoms. Found 20 (20 requested) and removed 28 (10 requested) atoms. Cycle 27: After refmac, R = 0.2084 (Rfree = 0.000) for 3614 atoms. Found 19 (19 requested) and removed 20 (9 requested) atoms. Cycle 28: After refmac, R = 0.2029 (Rfree = 0.000) for 3588 atoms. Found 19 (19 requested) and removed 22 (9 requested) atoms. Cycle 29: After refmac, R = 0.2231 (Rfree = 0.000) for 3571 atoms. Found 19 (19 requested) and removed 13 (9 requested) atoms. Cycle 30: After refmac, R = 0.2025 (Rfree = 0.000) for 3566 atoms. Found 11 (19 requested) and removed 17 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.66 3.76 Search for helices and strands: 0 residues in 0 chains, 3643 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 3658 seeds are put forward Round 1: 178 peptides, 36 chains. Longest chain 13 peptides. Score 0.290 Round 2: 235 peptides, 37 chains. Longest chain 18 peptides. Score 0.454 Round 3: 218 peptides, 33 chains. Longest chain 18 peptides. Score 0.456 Round 4: 232 peptides, 32 chains. Longest chain 18 peptides. Score 0.507 Round 5: 218 peptides, 31 chains. Longest chain 18 peptides. Score 0.481 Taking the results from Round 4 Chains 32, Residues 200, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5369 reflections ( 97.71 % complete ) and 8021 restraints for refining 3452 atoms. 7253 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2096 (Rfree = 0.000) for 3452 atoms. Found 18 (18 requested) and removed 27 (9 requested) atoms. Cycle 32: After refmac, R = 0.2150 (Rfree = 0.000) for 3433 atoms. Found 18 (18 requested) and removed 25 (9 requested) atoms. Cycle 33: After refmac, R = 0.2208 (Rfree = 0.000) for 3419 atoms. Found 18 (18 requested) and removed 23 (9 requested) atoms. Cycle 34: After refmac, R = 0.1536 (Rfree = 0.000) for 3403 atoms. Found 4 (18 requested) and removed 15 (9 requested) atoms. Cycle 35: After refmac, R = 0.1463 (Rfree = 0.000) for 3389 atoms. Found 4 (18 requested) and removed 13 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.73 3.83 Search for helices and strands: 0 residues in 0 chains, 3493 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 3517 seeds are put forward Round 1: 184 peptides, 36 chains. Longest chain 9 peptides. Score 0.310 Round 2: 213 peptides, 38 chains. Longest chain 11 peptides. Score 0.376 Round 3: 215 peptides, 31 chains. Longest chain 25 peptides. Score 0.472 Round 4: 219 peptides, 34 chains. Longest chain 20 peptides. Score 0.446 Round 5: 203 peptides, 32 chains. Longest chain 14 peptides. Score 0.425 Taking the results from Round 3 Chains 32, Residues 184, Estimated correctness of the model 0.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 5369 reflections ( 97.71 % complete ) and 7887 restraints for refining 3478 atoms. 7137 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2152 (Rfree = 0.000) for 3478 atoms. Found 19 (19 requested) and removed 23 (9 requested) atoms. Cycle 37: After refmac, R = 0.2295 (Rfree = 0.000) for 3459 atoms. Found 19 (19 requested) and removed 17 (9 requested) atoms. Cycle 38: After refmac, R = 0.2149 (Rfree = 0.000) for 3447 atoms. Found 19 (19 requested) and removed 17 (9 requested) atoms. Cycle 39: After refmac, R = 0.1932 (Rfree = 0.000) for 3429 atoms. Found 18 (18 requested) and removed 20 (9 requested) atoms. Cycle 40: After refmac, R = 0.2144 (Rfree = 0.000) for 3417 atoms. Found 18 (18 requested) and removed 16 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.66 3.76 Search for helices and strands: 0 residues in 0 chains, 3516 seeds are put forward NCS extension: 39 residues added (1 deleted due to clashes), 3555 seeds are put forward Round 1: 134 peptides, 30 chains. Longest chain 10 peptides. Score 0.222 Round 2: 176 peptides, 35 chains. Longest chain 11 peptides. Score 0.297 Round 3: 178 peptides, 34 chains. Longest chain 12 peptides. Score 0.318 Round 4: 173 peptides, 29 chains. Longest chain 12 peptides. Score 0.373 Round 5: 182 peptides, 32 chains. Longest chain 12 peptides. Score 0.360 Taking the results from Round 4 Chains 29, Residues 144, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5369 reflections ( 97.71 % complete ) and 8385 restraints for refining 3462 atoms. 7838 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2814 (Rfree = 0.000) for 3462 atoms. Found 19 (19 requested) and removed 60 (9 requested) atoms. Cycle 42: After refmac, R = 0.2418 (Rfree = 0.000) for 3411 atoms. Found 18 (18 requested) and removed 28 (9 requested) atoms. Cycle 43: After refmac, R = 0.2131 (Rfree = 0.000) for 3390 atoms. Found 18 (18 requested) and removed 23 (9 requested) atoms. Cycle 44: After refmac, R = 0.2119 (Rfree = 0.000) for 3378 atoms. Found 18 (18 requested) and removed 18 (9 requested) atoms. Cycle 45: After refmac, R = 0.2079 (Rfree = 0.000) for 3368 atoms. Found 18 (18 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.66 3.76 Search for helices and strands: 0 residues in 0 chains, 3482 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 3500 seeds are put forward Round 1: 123 peptides, 29 chains. Longest chain 6 peptides. Score 0.195 Round 2: 165 peptides, 32 chains. Longest chain 11 peptides. Score 0.303 Round 3: 169 peptides, 34 chains. Longest chain 11 peptides. Score 0.288 Round 4: 194 peptides, 35 chains. Longest chain 11 peptides. Score 0.357 Round 5: 187 peptides, 32 chains. Longest chain 12 peptides. Score 0.376 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 33, Residues 155, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence Sequence coverage is 8 % Consider running further cycles of model building using 1vpm-3_warpNtrace.pdb as input Building loops using Loopy2018 33 chains (155 residues) following loop building 2 chains (13 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5369 reflections ( 97.71 % complete ) and 7698 restraints for refining 3380 atoms. 7074 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1921 (Rfree = 0.000) for 3380 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.2025 (Rfree = 0.000) for 3362 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.2126 (Rfree = 0.000) for 3339 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.2030 (Rfree = 0.000) for 3312 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:22:03 GMT 2018 Job finished. TimeTaking 59.29 Used memory is bytes: 5494008