null Tue 25 Dec 19:27:57 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 2fno-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2fno-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2fno-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fno-3.4-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/2fno-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fno-3.4-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 ============================================================ Tue 25 Dec 19:28:07 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/2fno-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fno-3.4-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 403 and 0 Target number of residues in the AU: 403 Target solvent content: 0.6285 Checking the provided sequence file Detected sequence length: 248 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 496 Adjusted target solvent content: 0.54 Input MTZ file: 2fno-3.4-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: 5 Cell parameters: 110.204 50.261 117.660 90.000 115.716 90.000 Input sequence file: 2fno-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 3968 target number of atoms Had to go as low as 0.75 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: 106.006 3.400 Wilson plot Bfac: 65.36 8176 reflections ( 99.32 % complete ) and 0 restraints for refining 4370 atoms. Observations/parameters ratio is 0.47 ------------------------------------------------------ Starting model: R = 0.3165 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3022 (Rfree = 0.000) for 4370 atoms. Found 32 (32 requested) and removed 45 (16 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.25 3.08 Search for helices and strands: 0 residues in 0 chains, 4459 seeds are put forward NCS extension: 0 residues added, 4459 seeds are put forward Round 1: 227 peptides, 44 chains. Longest chain 9 peptides. Score 0.327 Round 2: 277 peptides, 43 chains. Longest chain 15 peptides. Score 0.474 Round 3: 304 peptides, 41 chains. Longest chain 25 peptides. Score 0.558 Round 4: 297 peptides, 38 chains. Longest chain 18 peptides. Score 0.572 Round 5: 301 peptides, 39 chains. Longest chain 15 peptides. Score 0.571 Taking the results from Round 4 Chains 38, Residues 259, Estimated correctness of the model 19.3 % 2 chains (23 residues) have been docked in sequence ------------------------------------------------------ 8176 reflections ( 99.32 % complete ) and 7803 restraints for refining 3608 atoms. 6736 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2730 (Rfree = 0.000) for 3608 atoms. Found 27 (27 requested) and removed 27 (13 requested) atoms. Cycle 2: After refmac, R = 0.2594 (Rfree = 0.000) for 3550 atoms. Found 27 (27 requested) and removed 21 (13 requested) atoms. Cycle 3: After refmac, R = 0.2729 (Rfree = 0.000) for 3516 atoms. Found 26 (26 requested) and removed 24 (13 requested) atoms. Cycle 4: After refmac, R = 0.2661 (Rfree = 0.000) for 3492 atoms. Found 26 (26 requested) and removed 26 (13 requested) atoms. Cycle 5: After refmac, R = 0.2558 (Rfree = 0.000) for 3478 atoms. Found 26 (26 requested) and removed 26 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.29 3.12 Search for helices and strands: 0 residues in 0 chains, 3631 seeds are put forward NCS extension: 19 residues added (8 deleted due to clashes), 3650 seeds are put forward Round 1: 286 peptides, 41 chains. Longest chain 19 peptides. Score 0.517 Round 2: 296 peptides, 36 chains. Longest chain 34 peptides. Score 0.589 Round 3: 309 peptides, 40 chains. Longest chain 23 peptides. Score 0.579 Round 4: 292 peptides, 34 chains. Longest chain 19 peptides. Score 0.600 Round 5: 287 peptides, 35 chains. Longest chain 23 peptides. Score 0.580 Taking the results from Round 4 Chains 36, Residues 258, Estimated correctness of the model 28.7 % 4 chains (38 residues) have been docked in sequence ------------------------------------------------------ 8176 reflections ( 99.32 % complete ) and 7763 restraints for refining 3608 atoms. 6634 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2428 (Rfree = 0.000) for 3608 atoms. Found 27 (27 requested) and removed 25 (13 requested) atoms. Cycle 7: After refmac, R = 0.2750 (Rfree = 0.000) for 3597 atoms. Found 27 (27 requested) and removed 26 (13 requested) atoms. Cycle 8: After refmac, R = 0.2314 (Rfree = 0.000) for 3570 atoms. Found 24 (27 requested) and removed 18 (13 requested) atoms. Cycle 9: After refmac, R = 0.2278 (Rfree = 0.000) for 3557 atoms. Found 26 (26 requested) and removed 21 (13 requested) atoms. Cycle 10: After refmac, R = 0.2165 (Rfree = 0.000) for 3548 atoms. Found 17 (26 requested) and removed 16 (13 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.27 3.10 Search for helices and strands: 0 residues in 0 chains, 3683 seeds are put forward NCS extension: 25 residues added (6 deleted due to clashes), 3708 seeds are put forward Round 1: 276 peptides, 45 chains. Longest chain 21 peptides. Score 0.450 Round 2: 297 peptides, 41 chains. Longest chain 25 peptides. Score 0.543 Round 3: 289 peptides, 41 chains. Longest chain 22 peptides. Score 0.524 Round 4: 290 peptides, 39 chains. Longest chain 25 peptides. Score 0.547 Round 5: 289 peptides, 37 chains. Longest chain 22 peptides. Score 0.565 Taking the results from Round 5 Chains 38, Residues 252, Estimated correctness of the model 16.8 % 2 chains (21 residues) have been docked in sequence ------------------------------------------------------ 8176 reflections ( 99.32 % complete ) and 8042 restraints for refining 3608 atoms. 7007 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2429 (Rfree = 0.000) for 3608 atoms. Found 23 (27 requested) and removed 23 (13 requested) atoms. Cycle 12: After refmac, R = 0.2243 (Rfree = 0.000) for 3593 atoms. Found 22 (27 requested) and removed 14 (13 requested) atoms. Cycle 13: After refmac, R = 0.2176 (Rfree = 0.000) for 3588 atoms. Found 20 (27 requested) and removed 16 (13 requested) atoms. Cycle 14: After refmac, R = 0.2466 (Rfree = 0.000) for 3585 atoms. Found 27 (27 requested) and removed 18 (13 requested) atoms. Cycle 15: After refmac, R = 0.2403 (Rfree = 0.000) for 3581 atoms. Found 27 (27 requested) and removed 18 (13 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.29 3.12 Search for helices and strands: 0 residues in 0 chains, 3718 seeds are put forward NCS extension: 33 residues added (10 deleted due to clashes), 3751 seeds are put forward Round 1: 248 peptides, 41 chains. Longest chain 12 peptides. Score 0.422 Round 2: 269 peptides, 39 chains. Longest chain 18 peptides. Score 0.498 Round 3: 282 peptides, 39 chains. Longest chain 21 peptides. Score 0.529 Round 4: 281 peptides, 40 chains. Longest chain 15 peptides. Score 0.516 Round 5: 264 peptides, 36 chains. Longest chain 19 peptides. Score 0.518 Taking the results from Round 3 Chains 39, Residues 243, Estimated correctness of the model 3.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8176 reflections ( 99.32 % complete ) and 8242 restraints for refining 3608 atoms. 7309 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2407 (Rfree = 0.000) for 3608 atoms. Found 27 (27 requested) and removed 21 (13 requested) atoms. Cycle 17: After refmac, R = 0.2254 (Rfree = 0.000) for 3603 atoms. Found 27 (27 requested) and removed 14 (13 requested) atoms. Cycle 18: After refmac, R = 0.2317 (Rfree = 0.000) for 3604 atoms. Found 27 (27 requested) and removed 18 (13 requested) atoms. Cycle 19: After refmac, R = 0.2290 (Rfree = 0.000) for 3599 atoms. Found 27 (27 requested) and removed 15 (13 requested) atoms. Cycle 20: After refmac, R = 0.2134 (Rfree = 0.000) for 3603 atoms. Found 23 (27 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.29 3.12 Search for helices and strands: 0 residues in 0 chains, 3784 seeds are put forward NCS extension: 29 residues added (3 deleted due to clashes), 3813 seeds are put forward Round 1: 212 peptides, 39 chains. Longest chain 14 peptides. Score 0.346 Round 2: 252 peptides, 33 chains. Longest chain 19 peptides. Score 0.522 Round 3: 251 peptides, 41 chains. Longest chain 10 peptides. Score 0.430 Round 4: 253 peptides, 38 chains. Longest chain 14 peptides. Score 0.469 Round 5: 263 peptides, 36 chains. Longest chain 21 peptides. Score 0.516 Taking the results from Round 2 Chains 33, Residues 219, Estimated correctness of the model 1.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8176 reflections ( 99.32 % complete ) and 8329 restraints for refining 3607 atoms. 7486 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2416 (Rfree = 0.000) for 3607 atoms. Found 27 (27 requested) and removed 25 (13 requested) atoms. Cycle 22: After refmac, R = 0.2446 (Rfree = 0.000) for 3601 atoms. Found 27 (27 requested) and removed 16 (13 requested) atoms. Cycle 23: After refmac, R = 0.2517 (Rfree = 0.000) for 3605 atoms. Found 27 (27 requested) and removed 16 (13 requested) atoms. Cycle 24: After refmac, R = 0.2147 (Rfree = 0.000) for 3603 atoms. Found 22 (27 requested) and removed 15 (13 requested) atoms. Cycle 25: After refmac, R = 0.2414 (Rfree = 0.000) for 3606 atoms. Found 27 (27 requested) and removed 20 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.33 3.16 Search for helices and strands: 0 residues in 0 chains, 3796 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 3812 seeds are put forward Round 1: 227 peptides, 42 chains. Longest chain 12 peptides. Score 0.352 Round 2: 256 peptides, 41 chains. Longest chain 15 peptides. Score 0.443 Round 3: 269 peptides, 41 chains. Longest chain 16 peptides. Score 0.476 Round 4: 265 peptides, 40 chains. Longest chain 22 peptides. Score 0.477 Round 5: 256 peptides, 39 chains. Longest chain 14 peptides. Score 0.466 Taking the results from Round 4 Chains 41, Residues 225, Estimated correctness of the model 0.0 % 1 chains (19 residues) have been docked in sequence ------------------------------------------------------ 8176 reflections ( 99.32 % complete ) and 8167 restraints for refining 3607 atoms. 7234 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2592 (Rfree = 0.000) for 3607 atoms. Found 27 (27 requested) and removed 32 (13 requested) atoms. Cycle 27: After refmac, R = 0.2630 (Rfree = 0.000) for 3576 atoms. Found 27 (27 requested) and removed 22 (13 requested) atoms. Cycle 28: After refmac, R = 0.2405 (Rfree = 0.000) for 3567 atoms. Found 25 (27 requested) and removed 18 (13 requested) atoms. Cycle 29: After refmac, R = 0.2360 (Rfree = 0.000) for 3566 atoms. Found 16 (26 requested) and removed 16 (13 requested) atoms. Cycle 30: After refmac, R = 0.2174 (Rfree = 0.000) for 3560 atoms. Found 13 (26 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.29 3.12 Search for helices and strands: 0 residues in 0 chains, 3707 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 3726 seeds are put forward Round 1: 223 peptides, 42 chains. Longest chain 10 peptides. Score 0.340 Round 2: 250 peptides, 40 chains. Longest chain 14 peptides. Score 0.439 Round 3: 250 peptides, 37 chains. Longest chain 13 peptides. Score 0.473 Round 4: 232 peptides, 37 chains. Longest chain 12 peptides. Score 0.426 Round 5: 243 peptides, 37 chains. Longest chain 15 peptides. Score 0.455 Taking the results from Round 3 Chains 37, Residues 213, Estimated correctness of the model 0.0 % 2 chains (16 residues) have been docked in sequence ------------------------------------------------------ 8176 reflections ( 99.32 % complete ) and 8248 restraints for refining 3607 atoms. 7384 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3093 (Rfree = 0.000) for 3607 atoms. Found 27 (27 requested) and removed 29 (13 requested) atoms. Cycle 32: After refmac, R = 0.2663 (Rfree = 0.000) for 3585 atoms. Found 27 (27 requested) and removed 17 (13 requested) atoms. Cycle 33: After refmac, R = 0.2620 (Rfree = 0.000) for 3586 atoms. Found 27 (27 requested) and removed 20 (13 requested) atoms. Cycle 34: After refmac, R = 0.2589 (Rfree = 0.000) for 3581 atoms. Found 27 (27 requested) and removed 19 (13 requested) atoms. Cycle 35: After refmac, R = 0.2541 (Rfree = 0.000) for 3583 atoms. Found 27 (27 requested) and removed 20 (13 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.31 3.14 Search for helices and strands: 0 residues in 0 chains, 3749 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 3764 seeds are put forward Round 1: 207 peptides, 43 chains. Longest chain 8 peptides. Score 0.280 Round 2: 227 peptides, 40 chains. Longest chain 11 peptides. Score 0.376 Round 3: 241 peptides, 40 chains. Longest chain 12 peptides. Score 0.415 Round 4: 249 peptides, 43 chains. Longest chain 13 peptides. Score 0.401 Round 5: 235 peptides, 43 chains. Longest chain 12 peptides. Score 0.363 Taking the results from Round 3 Chains 40, Residues 201, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8176 reflections ( 99.32 % complete ) and 8414 restraints for refining 3607 atoms. 7650 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2570 (Rfree = 0.000) for 3607 atoms. Found 27 (27 requested) and removed 22 (13 requested) atoms. Cycle 37: After refmac, R = 0.2609 (Rfree = 0.000) for 3595 atoms. Found 27 (27 requested) and removed 16 (13 requested) atoms. Cycle 38: After refmac, R = 0.2522 (Rfree = 0.000) for 3595 atoms. Found 27 (27 requested) and removed 16 (13 requested) atoms. Cycle 39: After refmac, R = 0.2424 (Rfree = 0.000) for 3603 atoms. Found 27 (27 requested) and removed 17 (13 requested) atoms. Cycle 40: After refmac, R = 0.2498 (Rfree = 0.000) for 3605 atoms. Found 27 (27 requested) and removed 22 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.29 3.12 Search for helices and strands: 0 residues in 0 chains, 3771 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 3785 seeds are put forward Round 1: 180 peptides, 34 chains. Longest chain 10 peptides. Score 0.314 Round 2: 207 peptides, 39 chains. Longest chain 13 peptides. Score 0.331 Round 3: 217 peptides, 39 chains. Longest chain 13 peptides. Score 0.360 Round 4: 221 peptides, 41 chains. Longest chain 11 peptides. Score 0.347 Round 5: 222 peptides, 38 chains. Longest chain 15 peptides. Score 0.387 Taking the results from Round 5 Chains 38, Residues 184, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8176 reflections ( 99.32 % complete ) and 8604 restraints for refining 3608 atoms. 7906 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2310 (Rfree = 0.000) for 3608 atoms. Found 27 (27 requested) and removed 20 (13 requested) atoms. Cycle 42: After refmac, R = 0.2007 (Rfree = 0.000) for 3605 atoms. Found 13 (27 requested) and removed 15 (13 requested) atoms. Cycle 43: After refmac, R = 0.2114 (Rfree = 0.000) for 3594 atoms. Found 27 (27 requested) and removed 16 (13 requested) atoms. Cycle 44: After refmac, R = 0.1925 (Rfree = 0.000) for 3601 atoms. Found 19 (27 requested) and removed 21 (13 requested) atoms. Cycle 45: After refmac, R = 0.1820 (Rfree = 0.000) for 3596 atoms. Found 5 (27 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.28 3.11 Search for helices and strands: 0 residues in 0 chains, 3724 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 3737 seeds are put forward Round 1: 175 peptides, 34 chains. Longest chain 11 peptides. Score 0.298 Round 2: 191 peptides, 31 chains. Longest chain 15 peptides. Score 0.386 Round 3: 194 peptides, 34 chains. Longest chain 11 peptides. Score 0.356 Round 4: 194 peptides, 33 chains. Longest chain 13 peptides. Score 0.369 Round 5: 194 peptides, 31 chains. Longest chain 15 peptides. Score 0.394 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 31, Residues 163, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence Sequence coverage is 4 % Consider running further cycles of model building using 2fno-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8176 reflections ( 99.32 % complete ) and 8562 restraints for refining 3608 atoms. 7911 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2496 (Rfree = 0.000) for 3608 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Cycle 47: After refmac, R = 0.2420 (Rfree = 0.000) for 3586 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Cycle 48: After refmac, R = 0.2198 (Rfree = 0.000) for 3563 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Cycle 49: After refmac, R = 0.1897 (Rfree = 0.000) for 3546 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:34:21 GMT 2018 Job finished. TimeTaking 66.39 Used memory is bytes: 14185320