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 1vku-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vku-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vku-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vku-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/1vku-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vku-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 22:22:56 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/1vku-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vku-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 55 and 0 Target number of residues in the AU: 55 Target solvent content: 0.6643 Checking the provided sequence file Detected sequence length: 100 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 100 Adjusted target solvent content: 0.39 Input MTZ file: 1vku-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: 154 Cell parameters: 45.440 45.440 74.373 90.000 90.000 120.000 Input sequence file: 1vku-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 800 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 Loops will be built when appropriate and at the last cycle Resolution range: 39.352 4.002 Wilson plot Bfac: 87.88 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 853 reflections ( 99.07 % complete ) and 0 restraints for refining 888 atoms. Observations/parameters ratio is 0.24 ------------------------------------------------------ Starting model: R = 0.3585 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3677 (Rfree = 0.000) for 888 atoms. Found 4 (4 requested) and removed 6 (2 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.86 4.48 Search for helices and strands: 0 residues in 0 chains, 908 seeds are put forward Round 1: 18 peptides, 4 chains. Longest chain 6 peptides. Score 0.218 Round 2: 30 peptides, 6 chains. Longest chain 9 peptides. Score 0.297 Round 3: 40 peptides, 7 chains. Longest chain 8 peptides. Score 0.406 Round 4: 42 peptides, 6 chains. Longest chain 13 peptides. Score 0.513 Round 5: 40 peptides, 6 chains. Longest chain 9 peptides. Score 0.481 Taking the results from Round 4 Chains 6, Residues 36, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 853 reflections ( 99.07 % complete ) and 1496 restraints for refining 631 atoms. 1358 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3550 (Rfree = 0.000) for 631 atoms. Found 1 (3 requested) and removed 5 (1 requested) atoms. Cycle 2: After refmac, R = 0.3070 (Rfree = 0.000) for 615 atoms. Found 2 (2 requested) and removed 4 (1 requested) atoms. Cycle 3: After refmac, R = 0.3155 (Rfree = 0.000) for 601 atoms. Found 2 (2 requested) and removed 6 (1 requested) atoms. Cycle 4: After refmac, R = 0.2566 (Rfree = 0.000) for 586 atoms. Found 2 (2 requested) and removed 2 (1 requested) atoms. Cycle 5: After refmac, R = 0.2724 (Rfree = 0.000) for 574 atoms. Found 1 (2 requested) and removed 1 (1 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 4.08 4.74 Search for helices and strands: 0 residues in 0 chains, 606 seeds are put forward Round 1: 30 peptides, 7 chains. Longest chain 5 peptides. Score 0.210 Round 2: 31 peptides, 5 chains. Longest chain 8 peptides. Score 0.400 Round 3: 36 peptides, 5 chains. Longest chain 9 peptides. Score 0.488 Round 4: 40 peptides, 5 chains. Longest chain 10 peptides. Score 0.552 Round 5: 44 peptides, 8 chains. Longest chain 7 peptides. Score 0.402 Taking the results from Round 4 Chains 5, Residues 35, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 853 reflections ( 99.07 % complete ) and 1426 restraints for refining 598 atoms. 1291 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3041 (Rfree = 0.000) for 598 atoms. Found 2 (2 requested) and removed 2 (1 requested) atoms. Cycle 7: After refmac, R = 0.2541 (Rfree = 0.000) for 587 atoms. Found 2 (2 requested) and removed 1 (1 requested) atoms. Cycle 8: After refmac, R = 0.3033 (Rfree = 0.000) for 580 atoms. Found 2 (2 requested) and removed 3 (1 requested) atoms. Cycle 9: After refmac, R = 0.2564 (Rfree = 0.000) for 572 atoms. Found 2 (2 requested) and removed 3 (1 requested) atoms. Cycle 10: After refmac, R = 0.2573 (Rfree = 0.000) for 567 atoms. Found 2 (2 requested) and removed 2 (1 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 4.64 5.39 Search for helices and strands: 0 residues in 0 chains, 620 seeds are put forward Round 1: 21 peptides, 5 chains. Longest chain 5 peptides. Score 0.191 Round 2: 23 peptides, 4 chains. Longest chain 7 peptides. Score 0.330 Round 3: 27 peptides, 5 chains. Longest chain 8 peptides. Score 0.323 Round 4: 36 peptides, 6 chains. Longest chain 9 peptides. Score 0.412 Round 5: 38 peptides, 7 chains. Longest chain 8 peptides. Score 0.370 Taking the results from Round 4 Chains 6, Residues 30, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 853 reflections ( 99.07 % complete ) and 1399 restraints for refining 604 atoms. 1285 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2529 (Rfree = 0.000) for 604 atoms. Found 2 (2 requested) and removed 3 (1 requested) atoms. Cycle 12: After refmac, R = 0.2199 (Rfree = 0.000) for 595 atoms. Found 2 (2 requested) and removed 2 (1 requested) atoms. Cycle 13: After refmac, R = 0.2059 (Rfree = 0.000) for 593 atoms. Found 2 (2 requested) and removed 3 (1 requested) atoms. Cycle 14: After refmac, R = 0.2441 (Rfree = 0.000) for 587 atoms. Found 2 (2 requested) and removed 1 (1 requested) atoms. Cycle 15: After refmac, R = 0.2632 (Rfree = 0.000) for 587 atoms. Found 2 (2 requested) and removed 2 (1 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 4.00 4.64 Search for helices and strands: 0 residues in 0 chains, 633 seeds are put forward Round 1: 24 peptides, 6 chains. Longest chain 4 peptides. Score 0.167 Round 2: 30 peptides, 7 chains. Longest chain 5 peptides. Score 0.210 Round 3: 32 peptides, 7 chains. Longest chain 7 peptides. Score 0.252 Round 4: 31 peptides, 6 chains. Longest chain 7 peptides. Score 0.317 Round 5: 26 peptides, 5 chains. Longest chain 7 peptides. Score 0.302 Taking the results from Round 4 Chains 6, Residues 25, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 853 reflections ( 99.07 % complete ) and 1470 restraints for refining 616 atoms. 1376 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2460 (Rfree = 0.000) for 616 atoms. Found 2 (2 requested) and removed 1 (1 requested) atoms. Cycle 17: After refmac, R = 0.2274 (Rfree = 0.000) for 601 atoms. Found 2 (2 requested) and removed 2 (1 requested) atoms. Cycle 18: After refmac, R = 0.2081 (Rfree = 0.000) for 595 atoms. Found 2 (2 requested) and removed 1 (1 requested) atoms. Cycle 19: After refmac, R = 0.1652 (Rfree = 0.000) for 592 atoms. Found 2 (2 requested) and removed 1 (1 requested) atoms. Cycle 20: After refmac, R = 0.2168 (Rfree = 0.000) for 590 atoms. Found 2 (2 requested) and removed 1 (1 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.57 4.14 Search for helices and strands: 0 residues in 0 chains, 625 seeds are put forward Round 1: 20 peptides, 4 chains. Longest chain 8 peptides. Score 0.265 Round 2: 24 peptides, 5 chains. Longest chain 6 peptides. Score 0.259 Round 3: 29 peptides, 6 chains. Longest chain 7 peptides. Score 0.276 Round 4: 24 peptides, 5 chains. Longest chain 6 peptides. Score 0.259 Round 5: 25 peptides, 5 chains. Longest chain 7 peptides. Score 0.281 Taking the results from Round 5 Chains 5, Residues 20, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 853 reflections ( 99.07 % complete ) and 1258 restraints for refining 544 atoms. 1183 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2826 (Rfree = 0.000) for 544 atoms. Found 2 (2 requested) and removed 2 (1 requested) atoms. Cycle 22: After refmac, R = 0.1913 (Rfree = 0.000) for 540 atoms. Found 2 (2 requested) and removed 2 (1 requested) atoms. Cycle 23: After refmac, R = 0.3128 (Rfree = 0.000) for 538 atoms. Found 2 (2 requested) and removed 3 (1 requested) atoms. Cycle 24: After refmac, R = 0.2069 (Rfree = 0.000) for 536 atoms. Found 2 (2 requested) and removed 1 (1 requested) atoms. Cycle 25: After refmac, R = 0.2002 (Rfree = 0.000) for 535 atoms. Found 2 (2 requested) and removed 1 (1 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.91 4.54 Search for helices and strands: 0 residues in 0 chains, 567 seeds are put forward Round 1: 27 peptides, 6 chains. Longest chain 7 peptides. Score 0.234 Round 2: 34 peptides, 7 chains. Longest chain 8 peptides. Score 0.293 Round 3: 36 peptides, 7 chains. Longest chain 8 peptides. Score 0.332 Round 4: 31 peptides, 6 chains. Longest chain 7 peptides. Score 0.317 Round 5: 31 peptides, 6 chains. Longest chain 7 peptides. Score 0.317 Taking the results from Round 3 Chains 7, Residues 29, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 853 reflections ( 99.07 % complete ) and 1129 restraints for refining 530 atoms. 1020 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1807 (Rfree = 0.000) for 530 atoms. Found 1 (2 requested) and removed 3 (1 requested) atoms. Cycle 27: After refmac, R = 0.1907 (Rfree = 0.000) for 523 atoms. Found 2 (2 requested) and removed 2 (1 requested) atoms. Cycle 28: After refmac, R = 0.1932 (Rfree = 0.000) for 520 atoms. Found 2 (2 requested) and removed 1 (1 requested) atoms. Cycle 29: After refmac, R = 0.1864 (Rfree = 0.000) for 516 atoms. Found 2 (2 requested) and removed 1 (1 requested) atoms. Cycle 30: After refmac, R = 0.1616 (Rfree = 0.000) for 513 atoms. Found 2 (2 requested) and removed 1 (1 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.70 4.29 Search for helices and strands: 0 residues in 0 chains, 556 seeds are put forward Round 1: 29 peptides, 7 chains. Longest chain 5 peptides. Score 0.189 Round 2: 31 peptides, 7 chains. Longest chain 5 peptides. Score 0.231 Round 3: 34 peptides, 7 chains. Longest chain 7 peptides. Score 0.293 Round 4: 29 peptides, 5 chains. Longest chain 10 peptides. Score 0.362 Round 5: 31 peptides, 6 chains. Longest chain 9 peptides. Score 0.317 Taking the results from Round 4 Chains 5, Residues 24, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 853 reflections ( 99.07 % complete ) and 1280 restraints for refining 543 atoms. 1189 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2591 (Rfree = 0.000) for 543 atoms. Found 2 (2 requested) and removed 3 (1 requested) atoms. Cycle 32: After refmac, R = 0.1972 (Rfree = 0.000) for 537 atoms. Found 2 (2 requested) and removed 2 (1 requested) atoms. Cycle 33: After refmac, R = 0.2048 (Rfree = 0.000) for 535 atoms. Found 2 (2 requested) and removed 1 (1 requested) atoms. Cycle 34: After refmac, R = 0.2156 (Rfree = 0.000) for 531 atoms. Found 2 (2 requested) and removed 1 (1 requested) atoms. Cycle 35: After refmac, R = 0.2197 (Rfree = 0.000) for 531 atoms. Found 2 (2 requested) and removed 1 (1 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 4.05 4.70 Search for helices and strands: 0 residues in 0 chains, 556 seeds are put forward Round 1: 22 peptides, 5 chains. Longest chain 5 peptides. Score 0.214 Round 2: 19 peptides, 4 chains. Longest chain 6 peptides. Score 0.242 Round 3: 24 peptides, 5 chains. Longest chain 7 peptides. Score 0.259 Round 4: 26 peptides, 5 chains. Longest chain 8 peptides. Score 0.302 Round 5: 19 peptides, 4 chains. Longest chain 6 peptides. Score 0.242 Taking the results from Round 4 Chains 5, Residues 21, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 853 reflections ( 99.07 % complete ) and 1120 restraints for refining 501 atoms. 1041 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2734 (Rfree = 0.000) for 501 atoms. Found 2 (2 requested) and removed 1 (1 requested) atoms. Cycle 37: After refmac, R = 0.2054 (Rfree = 0.000) for 499 atoms. Found 2 (2 requested) and removed 1 (1 requested) atoms. Cycle 38: After refmac, R = 0.2238 (Rfree = 0.000) for 498 atoms. Found 2 (2 requested) and removed 2 (1 requested) atoms. Cycle 39: After refmac, R = 0.2910 (Rfree = 0.000) for 496 atoms. Found 2 (2 requested) and removed 1 (1 requested) atoms. Cycle 40: After refmac, R = 0.1955 (Rfree = 0.000) for 496 atoms. Found 2 (2 requested) and removed 1 (1 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.74 4.34 Search for helices and strands: 0 residues in 0 chains, 521 seeds are put forward Round 1: 18 peptides, 4 chains. Longest chain 6 peptides. Score 0.218 Round 2: 20 peptides, 5 chains. Longest chain 4 peptides. Score 0.167 Round 3: 23 peptides, 5 chains. Longest chain 7 peptides. Score 0.237 Round 4: 21 peptides, 5 chains. Longest chain 5 peptides. Score 0.191 Round 5: 19 peptides, 4 chains. Longest chain 6 peptides. Score 0.242 Taking the results from Round 5 Chains 4, Residues 15, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 853 reflections ( 99.07 % complete ) and 1115 restraints for refining 492 atoms. 1059 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2674 (Rfree = 0.000) for 492 atoms. Found 2 (2 requested) and removed 1 (1 requested) atoms. Cycle 42: After refmac, R = 0.1956 (Rfree = 0.000) for 488 atoms. Found 1 (2 requested) and removed 1 (1 requested) atoms. Cycle 43: After refmac, R = 0.2168 (Rfree = 0.000) for 485 atoms. Found 2 (2 requested) and removed 2 (1 requested) atoms. Cycle 44: After refmac, R = 0.1786 (Rfree = 0.000) for 483 atoms. Found 2 (2 requested) and removed 1 (1 requested) atoms. Cycle 45: After refmac, R = 0.2244 (Rfree = 0.000) for 482 atoms. Found 2 (2 requested) and removed 1 (1 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 4.00 4.64 Search for helices and strands: 0 residues in 0 chains, 508 seeds are put forward Round 1: 12 peptides, 3 chains. Longest chain 4 peptides. Score 0.167 Round 2: 14 peptides, 3 chains. Longest chain 5 peptides. Score 0.223 Round 3: 14 peptides, 3 chains. Longest chain 5 peptides. Score 0.223 Round 4: 14 peptides, 3 chains. Longest chain 5 peptides. Score 0.223 Round 5: 14 peptides, 3 chains. Longest chain 5 peptides. Score 0.223 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 3, Residues 11, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 1vku-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 853 reflections ( 99.07 % complete ) and 872 restraints for refining 416 atoms. 831 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2590 (Rfree = 0.000) for 416 atoms. Found 0 (2 requested) and removed 1 (1 requested) atoms. Cycle 47: After refmac, R = 0.2150 (Rfree = 0.000) for 413 atoms. Found 0 (2 requested) and removed 1 (1 requested) atoms. Cycle 48: After refmac, R = 0.2268 (Rfree = 0.000) for 411 atoms. Found 0 (2 requested) and removed 1 (1 requested) atoms. Cycle 49: After refmac, R = 0.2075 (Rfree = 0.000) for 407 atoms. Found 0 (2 requested) and removed 1 (1 requested) atoms. Writing output files ... TimeTaking 19.57