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 2ia7-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ia7-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ia7-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ia7-3.8-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/2ia7-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ia7-3.8-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/2ia7-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ia7-3.8-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 76 and 0 Target number of residues in the AU: 76 Target solvent content: 0.6353 Checking the provided sequence file Detected sequence length: 134 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 134 Adjusted target solvent content: 0.36 Input MTZ file: 2ia7-3.8-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: 19 Cell parameters: 40.240 43.350 64.660 90.000 90.000 90.000 Input sequence file: 2ia7-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 1072 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: 26.833 3.802 Wilson plot Bfac: 67.44 1225 reflections ( 97.07 % complete ) and 0 restraints for refining 1184 atoms. Observations/parameters ratio is 0.26 ------------------------------------------------------ Starting model: R = 0.3547 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2384 (Rfree = 0.000) for 1184 atoms. Found 5 (6 requested) and removed 9 (3 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.32 4.02 Search for helices and strands: 0 residues in 0 chains, 1208 seeds are put forward Round 1: 36 peptides, 8 chains. Longest chain 8 peptides. Score 0.236 Round 2: 40 peptides, 8 chains. Longest chain 9 peptides. Score 0.301 Round 3: 45 peptides, 9 chains. Longest chain 9 peptides. Score 0.313 Round 4: 42 peptides, 9 chains. Longest chain 8 peptides. Score 0.266 Round 5: 46 peptides, 9 chains. Longest chain 9 peptides. Score 0.328 Taking the results from Round 5 Chains 9, Residues 37, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1225 reflections ( 97.07 % complete ) and 2476 restraints for refining 970 atoms. 2337 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2515 (Rfree = 0.000) for 970 atoms. Found 4 (5 requested) and removed 7 (2 requested) atoms. Cycle 2: After refmac, R = 0.2359 (Rfree = 0.000) for 965 atoms. Found 0 (5 requested) and removed 6 (2 requested) atoms. Cycle 3: After refmac, R = 0.2296 (Rfree = 0.000) for 957 atoms. Found 0 (5 requested) and removed 4 (2 requested) atoms. Cycle 4: After refmac, R = 0.2279 (Rfree = 0.000) for 947 atoms. Found 0 (5 requested) and removed 3 (2 requested) atoms. Cycle 5: After refmac, R = 0.2232 (Rfree = 0.000) for 942 atoms. Found 0 (5 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.45 4.18 Search for helices and strands: 0 residues in 0 chains, 956 seeds are put forward Round 1: 32 peptides, 7 chains. Longest chain 7 peptides. Score 0.238 Round 2: 45 peptides, 8 chains. Longest chain 9 peptides. Score 0.377 Round 3: 44 peptides, 7 chains. Longest chain 8 peptides. Score 0.424 Round 4: 37 peptides, 7 chains. Longest chain 8 peptides. Score 0.320 Round 5: 46 peptides, 8 chains. Longest chain 12 peptides. Score 0.391 Taking the results from Round 3 Chains 7, Residues 37, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1225 reflections ( 97.07 % complete ) and 2243 restraints for refining 918 atoms. 2102 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2332 (Rfree = 0.000) for 918 atoms. Found 3 (5 requested) and removed 4 (2 requested) atoms. Cycle 7: After refmac, R = 0.2208 (Rfree = 0.000) for 912 atoms. Found 1 (5 requested) and removed 4 (2 requested) atoms. Cycle 8: After refmac, R = 0.2180 (Rfree = 0.000) for 905 atoms. Found 1 (4 requested) and removed 4 (2 requested) atoms. Cycle 9: After refmac, R = 0.2171 (Rfree = 0.000) for 899 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 10: After refmac, R = 0.2165 (Rfree = 0.000) for 896 atoms. Found 1 (4 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.50 4.24 Search for helices and strands: 0 residues in 0 chains, 918 seeds are put forward Round 1: 36 peptides, 8 chains. Longest chain 6 peptides. Score 0.236 Round 2: 40 peptides, 8 chains. Longest chain 7 peptides. Score 0.301 Round 3: 46 peptides, 9 chains. Longest chain 7 peptides. Score 0.328 Round 4: 52 peptides, 10 chains. Longest chain 8 peptides. Score 0.355 Round 5: 55 peptides, 10 chains. Longest chain 9 peptides. Score 0.398 Taking the results from Round 5 Chains 10, Residues 45, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1225 reflections ( 97.07 % complete ) and 1927 restraints for refining 837 atoms. 1757 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2438 (Rfree = 0.000) for 837 atoms. Found 4 (4 requested) and removed 4 (2 requested) atoms. Cycle 12: After refmac, R = 0.2214 (Rfree = 0.000) for 833 atoms. Found 3 (4 requested) and removed 4 (2 requested) atoms. Cycle 13: After refmac, R = 0.2131 (Rfree = 0.000) for 826 atoms. Found 1 (4 requested) and removed 2 (2 requested) atoms. Cycle 14: After refmac, R = 0.2063 (Rfree = 0.000) for 823 atoms. Found 1 (4 requested) and removed 2 (2 requested) atoms. Cycle 15: After refmac, R = 0.2103 (Rfree = 0.000) for 820 atoms. Found 2 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.45 4.18 Search for helices and strands: 0 residues in 0 chains, 854 seeds are put forward Round 1: 37 peptides, 8 chains. Longest chain 6 peptides. Score 0.253 Round 2: 31 peptides, 6 chains. Longest chain 8 peptides. Score 0.293 Round 3: 38 peptides, 7 chains. Longest chain 7 peptides. Score 0.336 Round 4: 40 peptides, 7 chains. Longest chain 11 peptides. Score 0.366 Round 5: 35 peptides, 7 chains. Longest chain 6 peptides. Score 0.288 Taking the results from Round 4 Chains 8, Residues 33, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 1225 reflections ( 97.07 % complete ) and 1886 restraints for refining 835 atoms. 1722 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2388 (Rfree = 0.000) for 835 atoms. Found 4 (4 requested) and removed 4 (2 requested) atoms. Cycle 17: After refmac, R = 0.2052 (Rfree = 0.000) for 834 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 18: After refmac, R = 0.2002 (Rfree = 0.000) for 829 atoms. Found 3 (4 requested) and removed 2 (2 requested) atoms. Cycle 19: After refmac, R = 0.1963 (Rfree = 0.000) for 827 atoms. Found 2 (4 requested) and removed 3 (2 requested) atoms. Cycle 20: After refmac, R = 0.1855 (Rfree = 0.000) for 826 atoms. Found 1 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.41 4.13 Search for helices and strands: 0 residues in 0 chains, 838 seeds are put forward Round 1: 44 peptides, 9 chains. Longest chain 10 peptides. Score 0.298 Round 2: 52 peptides, 8 chains. Longest chain 12 peptides. Score 0.473 Round 3: 45 peptides, 7 chains. Longest chain 13 peptides. Score 0.438 Round 4: 43 peptides, 7 chains. Longest chain 9 peptides. Score 0.410 Round 5: 44 peptides, 7 chains. Longest chain 9 peptides. Score 0.424 Taking the results from Round 2 Chains 8, Residues 44, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 1225 reflections ( 97.07 % complete ) and 1884 restraints for refining 825 atoms. 1709 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2151 (Rfree = 0.000) for 825 atoms. Found 3 (4 requested) and removed 4 (2 requested) atoms. Cycle 22: After refmac, R = 0.2001 (Rfree = 0.000) for 823 atoms. Found 1 (4 requested) and removed 4 (2 requested) atoms. Cycle 23: After refmac, R = 0.1855 (Rfree = 0.000) for 819 atoms. Found 1 (4 requested) and removed 3 (2 requested) atoms. Cycle 24: After refmac, R = 0.1798 (Rfree = 0.000) for 817 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 25: After refmac, R = 0.1711 (Rfree = 0.000) for 814 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.37 4.08 Search for helices and strands: 0 residues in 0 chains, 848 seeds are put forward Round 1: 33 peptides, 6 chains. Longest chain 8 peptides. Score 0.325 Round 2: 53 peptides, 10 chains. Longest chain 7 peptides. Score 0.369 Round 3: 60 peptides, 10 chains. Longest chain 10 peptides. Score 0.465 Round 4: 60 peptides, 10 chains. Longest chain 10 peptides. Score 0.465 Round 5: 60 peptides, 10 chains. Longest chain 11 peptides. Score 0.465 Taking the results from Round 5 Chains 10, Residues 50, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1225 reflections ( 97.07 % complete ) and 1949 restraints for refining 861 atoms. 1759 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2107 (Rfree = 0.000) for 861 atoms. Found 4 (4 requested) and removed 5 (2 requested) atoms. Cycle 27: After refmac, R = 0.1873 (Rfree = 0.000) for 858 atoms. Found 1 (4 requested) and removed 2 (2 requested) atoms. Cycle 28: After refmac, R = 0.1776 (Rfree = 0.000) for 857 atoms. Found 0 (4 requested) and removed 3 (2 requested) atoms. Cycle 29: After refmac, R = 0.1790 (Rfree = 0.000) for 854 atoms. Found 2 (4 requested) and removed 2 (2 requested) atoms. Cycle 30: After refmac, R = 0.1724 (Rfree = 0.000) for 853 atoms. Found 1 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.36 4.07 Search for helices and strands: 0 residues in 0 chains, 885 seeds are put forward Round 1: 42 peptides, 8 chains. Longest chain 8 peptides. Score 0.332 Round 2: 40 peptides, 7 chains. Longest chain 9 peptides. Score 0.366 Round 3: 45 peptides, 8 chains. Longest chain 9 peptides. Score 0.377 Round 4: 48 peptides, 8 chains. Longest chain 9 peptides. Score 0.419 Round 5: 46 peptides, 8 chains. Longest chain 10 peptides. Score 0.391 Taking the results from Round 4 Chains 8, Residues 40, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 1225 reflections ( 97.07 % complete ) and 1932 restraints for refining 874 atoms. 1757 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1858 (Rfree = 0.000) for 874 atoms. Found 4 (4 requested) and removed 6 (2 requested) atoms. Cycle 32: After refmac, R = 0.1646 (Rfree = 0.000) for 867 atoms. Found 2 (4 requested) and removed 2 (2 requested) atoms. Cycle 33: After refmac, R = 0.1592 (Rfree = 0.000) for 867 atoms. Found 3 (4 requested) and removed 2 (2 requested) atoms. Cycle 34: After refmac, R = 0.1489 (Rfree = 0.000) for 866 atoms. Found 1 (4 requested) and removed 2 (2 requested) atoms. Cycle 35: After refmac, R = 0.1409 (Rfree = 0.000) for 864 atoms. Found 1 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.50 4.24 Search for helices and strands: 0 residues in 0 chains, 902 seeds are put forward Round 1: 30 peptides, 6 chains. Longest chain 8 peptides. Score 0.276 Round 2: 46 peptides, 8 chains. Longest chain 9 peptides. Score 0.391 Round 3: 44 peptides, 8 chains. Longest chain 10 peptides. Score 0.362 Round 4: 43 peptides, 7 chains. Longest chain 9 peptides. Score 0.410 Round 5: 44 peptides, 8 chains. Longest chain 10 peptides. Score 0.362 Taking the results from Round 4 Chains 7, Residues 36, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1225 reflections ( 97.07 % complete ) and 2079 restraints for refining 875 atoms. 1942 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1938 (Rfree = 0.000) for 875 atoms. Found 4 (4 requested) and removed 4 (2 requested) atoms. Cycle 37: After refmac, R = 0.1680 (Rfree = 0.000) for 875 atoms. Found 1 (4 requested) and removed 2 (2 requested) atoms. Cycle 38: After refmac, R = 0.1599 (Rfree = 0.000) for 873 atoms. Found 1 (4 requested) and removed 2 (2 requested) atoms. Cycle 39: After refmac, R = 0.1541 (Rfree = 0.000) for 872 atoms. Found 1 (4 requested) and removed 3 (2 requested) atoms. Cycle 40: After refmac, R = 0.1507 (Rfree = 0.000) for 870 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.46 4.19 Search for helices and strands: 0 residues in 0 chains, 898 seeds are put forward Round 1: 28 peptides, 6 chains. Longest chain 8 peptides. Score 0.241 Round 2: 35 peptides, 7 chains. Longest chain 9 peptides. Score 0.288 Round 3: 37 peptides, 6 chains. Longest chain 14 peptides. Score 0.387 Round 4: 39 peptides, 6 chains. Longest chain 15 peptides. Score 0.416 Round 5: 36 peptides, 7 chains. Longest chain 7 peptides. Score 0.304 Taking the results from Round 4 Chains 6, Residues 33, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1225 reflections ( 97.07 % complete ) and 2062 restraints for refining 883 atoms. 1936 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1784 (Rfree = 0.000) for 883 atoms. Found 4 (4 requested) and removed 5 (2 requested) atoms. Cycle 42: After refmac, R = 0.1594 (Rfree = 0.000) for 882 atoms. Found 1 (4 requested) and removed 3 (2 requested) atoms. Cycle 43: After refmac, R = 0.1713 (Rfree = 0.000) for 880 atoms. Found 2 (4 requested) and removed 5 (2 requested) atoms. Cycle 44: After refmac, R = 0.1500 (Rfree = 0.000) for 876 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 45: After refmac, R = 0.1439 (Rfree = 0.000) for 874 atoms. Found 1 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.48 4.21 Search for helices and strands: 0 residues in 0 chains, 914 seeds are put forward Round 1: 30 peptides, 6 chains. Longest chain 8 peptides. Score 0.276 Round 2: 42 peptides, 7 chains. Longest chain 14 peptides. Score 0.396 Round 3: 39 peptides, 6 chains. Longest chain 17 peptides. Score 0.416 Round 4: 41 peptides, 6 chains. Longest chain 11 peptides. Score 0.444 Round 5: 42 peptides, 6 chains. Longest chain 11 peptides. Score 0.458 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 6, Residues 36, 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 2ia7-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 1225 reflections ( 97.07 % complete ) and 2067 restraints for refining 889 atoms. 1929 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1376 (Rfree = 0.000) for 889 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 47: After refmac, R = 0.1537 (Rfree = 0.000) for 887 atoms. Found 0 (4 requested) and removed 1 (2 requested) atoms. Cycle 48: After refmac, R = 0.1253 (Rfree = 0.000) for 883 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 49: After refmac, R = 0.1887 (Rfree = 0.000) for 881 atoms. TimeTaking 21.4