null Sun 23 Dec 22:22:56 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 1vmg-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vmg-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vmg-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vmg-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/1vmg-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vmg-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 22:23:06 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/1vmg-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vmg-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 92 and 0 Target number of residues in the AU: 92 Target solvent content: 0.6735 Checking the provided sequence file Detected sequence length: 95 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 95 Adjusted target solvent content: 0.66 Input MTZ file: 1vmg-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: 98 Cell parameters: 79.748 79.748 95.906 90.000 90.000 90.000 Input sequence file: 1vmg-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 760 target number of atoms Had to go as low as 0.85 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: 61.319 4.002 Wilson plot Bfac: 93.07 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 1442 reflections ( 99.45 % complete ) and 0 restraints for refining 844 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Starting model: R = 0.3444 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.4246 (Rfree = 0.000) for 844 atoms. Found 4 (4 requested) and removed 13 (2 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 5.70 4.57 Search for helices and strands: 0 residues in 0 chains, 858 seeds are put forward Round 1: 19 peptides, 3 chains. Longest chain 8 peptides. Score 0.294 Round 2: 26 peptides, 4 chains. Longest chain 10 peptides. Score 0.324 Round 3: 32 peptides, 3 chains. Longest chain 21 peptides. Score 0.454 Round 4: 33 peptides, 4 chains. Longest chain 12 peptides. Score 0.409 Round 5: 31 peptides, 4 chains. Longest chain 12 peptides. Score 0.386 Taking the results from Round 3 Chains 4, Residues 29, Estimated correctness of the model 0.0 % 1 chains (19 residues) have been docked in sequence ------------------------------------------------------ 1442 reflections ( 99.45 % complete ) and 1393 restraints for refining 686 atoms. 1183 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3701 (Rfree = 0.000) for 686 atoms. Found 3 (3 requested) and removed 6 (1 requested) atoms. Cycle 2: After refmac, R = 0.3745 (Rfree = 0.000) for 672 atoms. Found 3 (3 requested) and removed 10 (1 requested) atoms. Cycle 3: After refmac, R = 0.3849 (Rfree = 0.000) for 651 atoms. Found 3 (3 requested) and removed 9 (1 requested) atoms. Cycle 4: After refmac, R = 0.3743 (Rfree = 0.000) for 625 atoms. Found 3 (3 requested) and removed 6 (1 requested) atoms. Cycle 5: After refmac, R = 0.3674 (Rfree = 0.000) for 595 atoms. Found 2 (2 requested) and removed 2 (1 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 4.38 3.51 Search for helices and strands: 0 residues in 0 chains, 625 seeds are put forward Round 1: 31 peptides, 4 chains. Longest chain 11 peptides. Score 0.386 Round 2: 34 peptides, 4 chains. Longest chain 12 peptides. Score 0.420 Round 3: 31 peptides, 4 chains. Longest chain 15 peptides. Score 0.386 Round 4: 35 peptides, 4 chains. Longest chain 11 peptides. Score 0.431 Round 5: 39 peptides, 3 chains. Longest chain 18 peptides. Score 0.524 Taking the results from Round 5 Chains 3, Residues 36, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1442 reflections ( 99.45 % complete ) and 1580 restraints for refining 664 atoms. 1439 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3751 (Rfree = 0.000) for 664 atoms. Found 3 (3 requested) and removed 9 (1 requested) atoms. Cycle 7: After refmac, R = 0.3812 (Rfree = 0.000) for 646 atoms. Found 3 (3 requested) and removed 5 (1 requested) atoms. Cycle 8: After refmac, R = 0.3760 (Rfree = 0.000) for 624 atoms. Found 3 (3 requested) and removed 7 (1 requested) atoms. Cycle 9: After refmac, R = 0.3753 (Rfree = 0.000) for 602 atoms. Found 2 (2 requested) and removed 5 (1 requested) atoms. Cycle 10: After refmac, R = 0.3763 (Rfree = 0.000) for 578 atoms. Found 2 (2 requested) and removed 8 (1 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 4.23 3.39 Search for helices and strands: 0 residues in 0 chains, 592 seeds are put forward Round 1: 32 peptides, 5 chains. Longest chain 11 peptides. Score 0.341 Round 2: 38 peptides, 4 chains. Longest chain 22 peptides. Score 0.463 Round 3: 34 peptides, 4 chains. Longest chain 14 peptides. Score 0.420 Round 4: 35 peptides, 5 chains. Longest chain 12 peptides. Score 0.377 Round 5: 35 peptides, 3 chains. Longest chain 26 peptides. Score 0.485 Taking the results from Round 5 Chains 3, Residues 32, Estimated correctness of the model 0.0 % 1 chains (25 residues) have been docked in sequence ------------------------------------------------------ 1442 reflections ( 99.45 % complete ) and 1203 restraints for refining 686 atoms. 945 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3767 (Rfree = 0.000) for 686 atoms. Found 3 (3 requested) and removed 71 (1 requested) atoms. Cycle 12: After refmac, R = 0.3703 (Rfree = 0.000) for 597 atoms. Found 2 (2 requested) and removed 6 (1 requested) atoms. Cycle 13: After refmac, R = 0.3763 (Rfree = 0.000) for 573 atoms. Found 2 (2 requested) and removed 5 (1 requested) atoms. Cycle 14: After refmac, R = 0.3801 (Rfree = 0.000) for 555 atoms. Found 2 (2 requested) and removed 4 (1 requested) atoms. Cycle 15: After refmac, R = 0.3815 (Rfree = 0.000) for 538 atoms. Found 2 (2 requested) and removed 5 (1 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 4.20 3.37 Search for helices and strands: 0 residues in 0 chains, 566 seeds are put forward Round 1: 29 peptides, 5 chains. Longest chain 8 peptides. Score 0.302 Round 2: 34 peptides, 4 chains. Longest chain 12 peptides. Score 0.420 Round 3: 33 peptides, 4 chains. Longest chain 11 peptides. Score 0.409 Round 4: 34 peptides, 4 chains. Longest chain 12 peptides. Score 0.420 Round 5: 34 peptides, 4 chains. Longest chain 11 peptides. Score 0.420 Taking the results from Round 5 Chains 4, Residues 30, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1442 reflections ( 99.45 % complete ) and 1490 restraints for refining 631 atoms. 1374 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 16: After refmac, R = 0.4394 (Rfree = 0.000) for 631 atoms. Found 2 (2 requested) and removed 8 (1 requested) atoms. Cycle 17: After refmac, R = 0.4072 (Rfree = 0.000) for 612 atoms. Found 2 (2 requested) and removed 5 (1 requested) atoms. Cycle 18: After refmac, R = 0.3765 (Rfree = 0.000) for 595 atoms. Found 2 (2 requested) and removed 5 (1 requested) atoms. Cycle 19: After refmac, R = 0.3950 (Rfree = 0.000) for 574 atoms. Found 2 (2 requested) and removed 64 (1 requested) atoms. Cycle 20: After refmac, R = 0.3741 (Rfree = 0.000) for 501 atoms. Found 2 (2 requested) and removed 3 (1 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 4.08 3.27 Search for helices and strands: 0 residues in 0 chains, 535 seeds are put forward Round 1: 25 peptides, 4 chains. Longest chain 9 peptides. Score 0.311 Round 2: 34 peptides, 6 chains. Longest chain 9 peptides. Score 0.309 Round 3: 31 peptides, 5 chains. Longest chain 9 peptides. Score 0.328 Round 4: 31 peptides, 5 chains. Longest chain 9 peptides. Score 0.328 Round 5: 29 peptides, 4 chains. Longest chain 10 peptides. Score 0.362 Taking the results from Round 5 Chains 4, Residues 25, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1442 reflections ( 99.45 % complete ) and 1385 restraints for refining 578 atoms. 1289 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 21: After refmac, R = 0.4016 (Rfree = 0.000) for 578 atoms. Found 2 (2 requested) and removed 5 (1 requested) atoms. Cycle 22: After refmac, R = 0.3863 (Rfree = 0.000) for 565 atoms. Found 2 (2 requested) and removed 17 (1 requested) atoms. Cycle 23: After refmac, R = 0.3849 (Rfree = 0.000) for 541 atoms. Found 2 (2 requested) and removed 5 (1 requested) atoms. Cycle 24: After refmac, R = 0.3876 (Rfree = 0.000) for 534 atoms. Found 2 (2 requested) and removed 5 (1 requested) atoms. Cycle 25: After refmac, R = 0.3763 (Rfree = 0.000) for 525 atoms. Found 2 (2 requested) and removed 3 (1 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 4.25 3.41 Search for helices and strands: 0 residues in 0 chains, 551 seeds are put forward Round 1: 22 peptides, 4 chains. Longest chain 7 peptides. Score 0.268 Round 2: 28 peptides, 5 chains. Longest chain 10 peptides. Score 0.289 Round 3: 31 peptides, 5 chains. Longest chain 11 peptides. Score 0.328 Round 4: 37 peptides, 4 chains. Longest chain 16 peptides. Score 0.453 Round 5: 34 peptides, 4 chains. Longest chain 11 peptides. Score 0.420 Taking the results from Round 4 Chains 4, Residues 33, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1442 reflections ( 99.45 % complete ) and 1172 restraints for refining 551 atoms. 1044 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3821 (Rfree = 0.000) for 551 atoms. Found 2 (2 requested) and removed 1 (1 requested) atoms. Cycle 27: After refmac, R = 0.3832 (Rfree = 0.000) for 542 atoms. Found 2 (2 requested) and removed 2 (1 requested) atoms. Cycle 28: After refmac, R = 0.3735 (Rfree = 0.000) for 524 atoms. Found 2 (2 requested) and removed 3 (1 requested) atoms. Cycle 29: After refmac, R = 0.4049 (Rfree = 0.000) for 519 atoms. Found 2 (2 requested) and removed 5 (1 requested) atoms. Cycle 30: After refmac, R = 0.3841 (Rfree = 0.000) for 504 atoms. Found 2 (2 requested) and removed 3 (1 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 4.16 3.34 Search for helices and strands: 0 residues in 0 chains, 528 seeds are put forward Round 1: 25 peptides, 5 chains. Longest chain 7 peptides. Score 0.247 Round 2: 33 peptides, 4 chains. Longest chain 12 peptides. Score 0.409 Round 3: 32 peptides, 4 chains. Longest chain 11 peptides. Score 0.398 Round 4: 29 peptides, 4 chains. Longest chain 11 peptides. Score 0.362 Round 5: 27 peptides, 4 chains. Longest chain 9 peptides. Score 0.337 Taking the results from Round 2 Chains 4, Residues 29, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1442 reflections ( 99.45 % complete ) and 1126 restraints for refining 516 atoms. 1014 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 31: After refmac, R = 0.4116 (Rfree = 0.000) for 516 atoms. Found 2 (2 requested) and removed 8 (1 requested) atoms. Cycle 32: After refmac, R = 0.4137 (Rfree = 0.000) for 498 atoms. Found 2 (2 requested) and removed 10 (1 requested) atoms. Cycle 33: After refmac, R = 0.4157 (Rfree = 0.000) for 483 atoms. Found 2 (2 requested) and removed 3 (1 requested) atoms. Cycle 34: After refmac, R = 0.4031 (Rfree = 0.000) for 480 atoms. Found 2 (2 requested) and removed 9 (1 requested) atoms. Cycle 35: After refmac, R = 0.3793 (Rfree = 0.000) for 466 atoms. Found 2 (2 requested) and removed 2 (1 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.99 3.20 Search for helices and strands: 0 residues in 0 chains, 480 seeds are put forward Round 1: 29 peptides, 5 chains. Longest chain 8 peptides. Score 0.302 Round 2: 31 peptides, 3 chains. Longest chain 15 peptides. Score 0.443 Round 3: 24 peptides, 4 chains. Longest chain 7 peptides. Score 0.297 Round 4: 32 peptides, 5 chains. Longest chain 10 peptides. Score 0.341 Round 5: 31 peptides, 4 chains. Longest chain 11 peptides. Score 0.386 Taking the results from Round 2 Chains 3, Residues 28, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1442 reflections ( 99.45 % complete ) and 1147 restraints for refining 519 atoms. 1038 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 36: After refmac, R = 0.4026 (Rfree = 0.000) for 519 atoms. Found 2 (2 requested) and removed 4 (1 requested) atoms. Cycle 37: After refmac, R = 0.4015 (Rfree = 0.000) for 509 atoms. Found 2 (2 requested) and removed 6 (1 requested) atoms. Cycle 38: After refmac, R = 0.3953 (Rfree = 0.000) for 499 atoms. Found 2 (2 requested) and removed 5 (1 requested) atoms. Cycle 39: After refmac, R = 0.3718 (Rfree = 0.000) for 488 atoms. Found 2 (2 requested) and removed 6 (1 requested) atoms. Cycle 40: After refmac, R = 0.3946 (Rfree = 0.000) for 481 atoms. Found 2 (2 requested) and removed 5 (1 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 4.28 3.43 Search for helices and strands: 0 residues in 0 chains, 498 seeds are put forward Round 1: 25 peptides, 5 chains. Longest chain 6 peptides. Score 0.247 Round 2: 29 peptides, 6 chains. Longest chain 7 peptides. Score 0.242 Round 3: 22 peptides, 3 chains. Longest chain 11 peptides. Score 0.336 Round 4: 23 peptides, 4 chains. Longest chain 7 peptides. Score 0.283 Round 5: 26 peptides, 4 chains. Longest chain 8 peptides. Score 0.324 Taking the results from Round 3 Chains 3, Residues 19, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1442 reflections ( 99.45 % complete ) and 1235 restraints for refining 528 atoms. 1162 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 41: After refmac, R = 0.4127 (Rfree = 0.000) for 528 atoms. Found 2 (2 requested) and removed 2 (1 requested) atoms. Cycle 42: After refmac, R = 0.3943 (Rfree = 0.000) for 518 atoms. Found 2 (2 requested) and removed 21 (1 requested) atoms. Cycle 43: After refmac, R = 0.3917 (Rfree = 0.000) for 487 atoms. Found 2 (2 requested) and removed 5 (1 requested) atoms. Cycle 44: After refmac, R = 0.3877 (Rfree = 0.000) for 480 atoms. Found 2 (2 requested) and removed 1 (1 requested) atoms. Cycle 45: After refmac, R = 0.3917 (Rfree = 0.000) for 477 atoms. Found 2 (2 requested) and removed 2 (1 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 4.10 3.29 Search for helices and strands: 0 residues in 0 chains, 502 seeds are put forward Round 1: 27 peptides, 5 chains. Longest chain 9 peptides. Score 0.275 Round 2: 29 peptides, 4 chains. Longest chain 12 peptides. Score 0.362 Round 3: 31 peptides, 4 chains. Longest chain 13 peptides. Score 0.386 Round 4: 29 peptides, 3 chains. Longest chain 14 peptides. Score 0.421 Round 5: 30 peptides, 4 chains. Longest chain 11 peptides. Score 0.374 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 3, Residues 26, 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 1vmg-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 1442 reflections ( 99.45 % complete ) and 1156 restraints for refining 518 atoms. 1055 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 46: After refmac, R = 0.4001 (Rfree = 0.000) for 518 atoms. Found 0 (2 requested) and removed 1 (1 requested) atoms. Cycle 47: After refmac, R = 0.3842 (Rfree = 0.000) for 507 atoms. Found 0 (2 requested) and removed 1 (1 requested) atoms. Cycle 48: After refmac, R = 0.3851 (Rfree = 0.000) for 500 atoms. Found 0 (2 requested) and removed 1 (1 requested) atoms. Cycle 49: After refmac, R = 0.3813 (Rfree = 0.000) for 487 atoms. Found 0 (2 requested) and removed 1 (1 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:44:17 GMT 2018 Job finished. TimeTaking 21.35 Used memory is bytes: 3652984