null Sun 23 Dec 22:23:10 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 2b8m-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2b8m-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2b8m-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2b8m-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/2b8m-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2b8m-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 22:23:20 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/2b8m-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2b8m-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 77 and 0 Target number of residues in the AU: 77 Target solvent content: 0.6348 Checking the provided sequence file Detected sequence length: 117 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 117 Adjusted target solvent content: 0.45 Input MTZ file: 2b8m-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: 152 Cell parameters: 50.280 50.280 78.170 90.000 90.000 120.000 Input sequence file: 2b8m-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 936 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 Loops will be built when appropriate and at the last cycle Resolution range: 29.086 4.001 Wilson plot Bfac: 66.70 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 1087 reflections ( 99.09 % complete ) and 0 restraints for refining 1044 atoms. Observations/parameters ratio is 0.26 ------------------------------------------------------ Starting model: R = 0.3140 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2999 (Rfree = 0.000) for 1044 atoms. Found 4 (4 requested) and removed 7 (2 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.44 3.68 Search for helices and strands: 0 residues in 0 chains, 1051 seeds are put forward Round 1: 40 peptides, 8 chains. Longest chain 7 peptides. Score 0.300 Round 2: 55 peptides, 9 chains. Longest chain 9 peptides. Score 0.454 Round 3: 65 peptides, 11 chains. Longest chain 11 peptides. Score 0.472 Round 4: 69 peptides, 9 chains. Longest chain 15 peptides. Score 0.615 Round 5: 69 peptides, 8 chains. Longest chain 16 peptides. Score 0.658 Taking the results from Round 5 Chains 8, Residues 61, Estimated correctness of the model 10.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1087 reflections ( 99.09 % complete ) and 1945 restraints for refining 845 atoms. 1709 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2623 (Rfree = 0.000) for 845 atoms. Found 3 (4 requested) and removed 5 (2 requested) atoms. Cycle 2: After refmac, R = 0.2998 (Rfree = 0.000) for 828 atoms. Found 4 (4 requested) and removed 5 (2 requested) atoms. Cycle 3: After refmac, R = 0.3018 (Rfree = 0.000) for 822 atoms. Found 1 (3 requested) and removed 2 (1 requested) atoms. Cycle 4: After refmac, R = 0.2324 (Rfree = 0.000) for 820 atoms. Found 1 (3 requested) and removed 5 (1 requested) atoms. Cycle 5: After refmac, R = 0.2825 (Rfree = 0.000) for 815 atoms. Found 0 (3 requested) and removed 2 (1 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.68 3.93 Search for helices and strands: 0 residues in 0 chains, 845 seeds are put forward Round 1: 52 peptides, 10 chains. Longest chain 8 peptides. Score 0.354 Round 2: 67 peptides, 9 chains. Longest chain 12 peptides. Score 0.595 Round 3: 64 peptides, 9 chains. Longest chain 13 peptides. Score 0.562 Round 4: 69 peptides, 5 chains. Longest chain 28 peptides. Score 0.770 Round 5: 70 peptides, 7 chains. Longest chain 27 peptides. Score 0.707 Taking the results from Round 4 Chains 5, Residues 64, Estimated correctness of the model 56.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1087 reflections ( 99.09 % complete ) and 1884 restraints for refining 846 atoms. 1633 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2583 (Rfree = 0.000) for 846 atoms. Found 3 (4 requested) and removed 6 (2 requested) atoms. Cycle 7: After refmac, R = 0.2262 (Rfree = 0.000) for 837 atoms. Found 0 (4 requested) and removed 3 (2 requested) atoms. Cycle 8: After refmac, R = 0.2265 (Rfree = 0.000) for 828 atoms. Found 0 (3 requested) and removed 2 (1 requested) atoms. Cycle 9: After refmac, R = 0.2252 (Rfree = 0.000) for 824 atoms. Found 1 (3 requested) and removed 1 (1 requested) atoms. Cycle 10: After refmac, R = 0.2311 (Rfree = 0.000) for 823 atoms. Found 1 (3 requested) and removed 3 (1 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.59 3.84 Search for helices and strands: 0 residues in 0 chains, 838 seeds are put forward Round 1: 65 peptides, 10 chains. Longest chain 15 peptides. Score 0.524 Round 2: 73 peptides, 9 chains. Longest chain 15 peptides. Score 0.653 Round 3: 72 peptides, 9 chains. Longest chain 18 peptides. Score 0.644 Round 4: 73 peptides, 8 chains. Longest chain 15 peptides. Score 0.693 Round 5: 66 peptides, 9 chains. Longest chain 15 peptides. Score 0.584 Taking the results from Round 4 Chains 8, Residues 65, Estimated correctness of the model 26.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1087 reflections ( 99.09 % complete ) and 1999 restraints for refining 846 atoms. 1747 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2527 (Rfree = 0.000) for 846 atoms. Found 4 (4 requested) and removed 9 (2 requested) atoms. Cycle 12: After refmac, R = 0.2253 (Rfree = 0.000) for 831 atoms. Found 0 (3 requested) and removed 8 (1 requested) atoms. Cycle 13: After refmac, R = 0.1829 (Rfree = 0.000) for 817 atoms. Found 0 (3 requested) and removed 4 (1 requested) atoms. Cycle 14: After refmac, R = 0.1876 (Rfree = 0.000) for 811 atoms. Found 0 (3 requested) and removed 3 (1 requested) atoms. Cycle 15: After refmac, R = 0.1976 (Rfree = 0.000) for 806 atoms. Found 0 (3 requested) and removed 3 (1 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.52 3.76 Search for helices and strands: 0 residues in 0 chains, 821 seeds are put forward Round 1: 43 peptides, 9 chains. Longest chain 6 peptides. Score 0.281 Round 2: 53 peptides, 9 chains. Longest chain 12 peptides. Score 0.427 Round 3: 55 peptides, 9 chains. Longest chain 9 peptides. Score 0.454 Round 4: 54 peptides, 7 chains. Longest chain 15 peptides. Score 0.550 Round 5: 61 peptides, 10 chains. Longest chain 10 peptides. Score 0.475 Taking the results from Round 4 Chains 7, Residues 47, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1087 reflections ( 99.09 % complete ) and 2049 restraints for refining 829 atoms. 1868 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2408 (Rfree = 0.000) for 829 atoms. Found 3 (3 requested) and removed 7 (1 requested) atoms. Cycle 17: After refmac, R = 0.2424 (Rfree = 0.000) for 824 atoms. Found 2 (3 requested) and removed 5 (1 requested) atoms. Cycle 18: After refmac, R = 0.2521 (Rfree = 0.000) for 819 atoms. Found 1 (3 requested) and removed 2 (1 requested) atoms. Cycle 19: After refmac, R = 0.2446 (Rfree = 0.000) for 817 atoms. Found 3 (3 requested) and removed 17 (1 requested) atoms. Cycle 20: After refmac, R = 0.1816 (Rfree = 0.000) for 802 atoms. Found 1 (3 requested) and removed 6 (1 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.59 3.84 Search for helices and strands: 0 residues in 0 chains, 817 seeds are put forward Round 1: 38 peptides, 6 chains. Longest chain 10 peptides. Score 0.400 Round 2: 44 peptides, 7 chains. Longest chain 14 peptides. Score 0.423 Round 3: 50 peptides, 7 chains. Longest chain 17 peptides. Score 0.502 Round 4: 48 peptides, 6 chains. Longest chain 18 peptides. Score 0.533 Round 5: 52 peptides, 5 chains. Longest chain 18 peptides. Score 0.629 Taking the results from Round 5 Chains 5, Residues 47, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1087 reflections ( 99.09 % complete ) and 1996 restraints for refining 840 atoms. 1813 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1786 (Rfree = 0.000) for 840 atoms. Found 1 (3 requested) and removed 5 (1 requested) atoms. Cycle 22: After refmac, R = 0.1701 (Rfree = 0.000) for 829 atoms. Found 0 (3 requested) and removed 9 (1 requested) atoms. Cycle 23: After refmac, R = 0.1763 (Rfree = 0.000) for 819 atoms. Found 0 (3 requested) and removed 5 (1 requested) atoms. Cycle 24: After refmac, R = 0.2066 (Rfree = 0.000) for 814 atoms. Found 3 (3 requested) and removed 5 (1 requested) atoms. Cycle 25: After refmac, R = 0.1555 (Rfree = 0.000) for 812 atoms. Found 2 (3 requested) and removed 2 (1 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.52 3.76 Search for helices and strands: 0 residues in 0 chains, 828 seeds are put forward Round 1: 50 peptides, 10 chains. Longest chain 8 peptides. Score 0.324 Round 2: 59 peptides, 10 chains. Longest chain 14 peptides. Score 0.450 Round 3: 53 peptides, 8 chains. Longest chain 13 peptides. Score 0.484 Round 4: 55 peptides, 8 chains. Longest chain 10 peptides. Score 0.509 Round 5: 68 peptides, 10 chains. Longest chain 13 peptides. Score 0.558 Taking the results from Round 5 Chains 10, Residues 58, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1087 reflections ( 99.09 % complete ) and 2030 restraints for refining 846 atoms. 1808 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1921 (Rfree = 0.000) for 846 atoms. Found 4 (4 requested) and removed 5 (2 requested) atoms. Cycle 27: After refmac, R = 0.1834 (Rfree = 0.000) for 841 atoms. Found 2 (4 requested) and removed 6 (2 requested) atoms. Cycle 28: After refmac, R = 0.1525 (Rfree = 0.000) for 836 atoms. Found 2 (3 requested) and removed 1 (1 requested) atoms. Cycle 29: After refmac, R = 0.1447 (Rfree = 0.000) for 836 atoms. Found 0 (3 requested) and removed 2 (1 requested) atoms. Cycle 30: After refmac, R = 0.1488 (Rfree = 0.000) for 834 atoms. Found 0 (3 requested) and removed 3 (1 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.54 3.78 Search for helices and strands: 0 residues in 0 chains, 838 seeds are put forward Round 1: 48 peptides, 9 chains. Longest chain 10 peptides. Score 0.357 Round 2: 48 peptides, 8 chains. Longest chain 9 peptides. Score 0.418 Round 3: 43 peptides, 6 chains. Longest chain 12 peptides. Score 0.470 Round 4: 43 peptides, 8 chains. Longest chain 8 peptides. Score 0.346 Round 5: 58 peptides, 10 chains. Longest chain 9 peptides. Score 0.436 Taking the results from Round 3 Chains 6, Residues 37, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1087 reflections ( 99.09 % complete ) and 2093 restraints for refining 846 atoms. 1951 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1781 (Rfree = 0.000) for 846 atoms. Found 1 (4 requested) and removed 4 (2 requested) atoms. Cycle 32: After refmac, R = 0.1615 (Rfree = 0.000) for 839 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 33: After refmac, R = 0.1627 (Rfree = 0.000) for 834 atoms. Found 3 (3 requested) and removed 1 (1 requested) atoms. Cycle 34: After refmac, R = 0.1623 (Rfree = 0.000) for 835 atoms. Found 3 (3 requested) and removed 1 (1 requested) atoms. Cycle 35: After refmac, R = 0.1523 (Rfree = 0.000) for 836 atoms. Found 1 (3 requested) and removed 1 (1 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.56 3.81 Search for helices and strands: 0 residues in 0 chains, 862 seeds are put forward Round 1: 42 peptides, 10 chains. Longest chain 5 peptides. Score 0.200 Round 2: 47 peptides, 11 chains. Longest chain 6 peptides. Score 0.215 Round 3: 53 peptides, 11 chains. Longest chain 8 peptides. Score 0.307 Round 4: 44 peptides, 9 chains. Longest chain 7 peptides. Score 0.297 Round 5: 45 peptides, 9 chains. Longest chain 9 peptides. Score 0.312 Taking the results from Round 5 Chains 9, Residues 36, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1087 reflections ( 99.09 % complete ) and 2119 restraints for refining 846 atoms. 1984 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2115 (Rfree = 0.000) for 846 atoms. Found 4 (4 requested) and removed 5 (2 requested) atoms. Cycle 37: After refmac, R = 0.1493 (Rfree = 0.000) for 835 atoms. Found 2 (4 requested) and removed 3 (2 requested) atoms. Cycle 38: After refmac, R = 0.1454 (Rfree = 0.000) for 831 atoms. Found 2 (3 requested) and removed 2 (1 requested) atoms. Cycle 39: After refmac, R = 0.1246 (Rfree = 0.000) for 828 atoms. Found 3 (3 requested) and removed 1 (1 requested) atoms. Cycle 40: After refmac, R = 0.1116 (Rfree = 0.000) for 829 atoms. Found 2 (3 requested) and removed 1 (1 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.48 3.72 Search for helices and strands: 0 residues in 0 chains, 859 seeds are put forward Round 1: 29 peptides, 7 chains. Longest chain 5 peptides. Score 0.185 Round 2: 41 peptides, 8 chains. Longest chain 9 peptides. Score 0.315 Round 3: 41 peptides, 8 chains. Longest chain 10 peptides. Score 0.315 Round 4: 40 peptides, 7 chains. Longest chain 10 peptides. Score 0.365 Round 5: 37 peptides, 6 chains. Longest chain 10 peptides. Score 0.386 Taking the results from Round 5 Chains 6, Residues 31, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1087 reflections ( 99.09 % complete ) and 1987 restraints for refining 834 atoms. 1869 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1774 (Rfree = 0.000) for 834 atoms. Found 3 (3 requested) and removed 2 (1 requested) atoms. Cycle 42: After refmac, R = 0.1409 (Rfree = 0.000) for 829 atoms. Found 1 (3 requested) and removed 2 (1 requested) atoms. Cycle 43: After refmac, R = 0.1303 (Rfree = 0.000) for 827 atoms. Found 0 (3 requested) and removed 2 (1 requested) atoms. Cycle 44: After refmac, R = 0.1250 (Rfree = 0.000) for 825 atoms. Found 0 (3 requested) and removed 1 (1 requested) atoms. Cycle 45: After refmac, R = 0.1204 (Rfree = 0.000) for 823 atoms. Found 0 (3 requested) and removed 1 (1 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.51 3.75 Search for helices and strands: 0 residues in 0 chains, 850 seeds are put forward Round 1: 29 peptides, 7 chains. Longest chain 5 peptides. Score 0.185 Round 2: 35 peptides, 7 chains. Longest chain 8 peptides. Score 0.288 Round 3: 32 peptides, 6 chains. Longest chain 7 peptides. Score 0.308 Round 4: 36 peptides, 8 chains. Longest chain 6 peptides. Score 0.235 Round 5: 38 peptides, 7 chains. Longest chain 10 peptides. Score 0.335 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 7, Residues 31, 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 2b8m-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 1087 reflections ( 99.09 % complete ) and 2011 restraints for refining 835 atoms. 1894 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1493 (Rfree = 0.000) for 835 atoms. Found 0 (3 requested) and removed 1 (1 requested) atoms. Cycle 47: After refmac, R = 0.1481 (Rfree = 0.000) for 831 atoms. Found 0 (3 requested) and removed 1 (1 requested) atoms. Cycle 48: After refmac, R = 0.1386 (Rfree = 0.000) for 828 atoms. Found 0 (3 requested) and removed 1 (1 requested) atoms. Cycle 49: After refmac, R = 0.1317 (Rfree = 0.000) for 826 atoms. Found 0 (3 requested) and removed 1 (1 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:45:45 GMT 2018 Job finished. TimeTaking 22.58 Used memory is bytes: 9240944