Sun 23 Dec 22:23:08 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 2ia7-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ia7-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ia7-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ia7-3.4-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/2ia7-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ia7-3.4-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 ============================================================ Sun 23 Dec 22:23:18 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/2ia7-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ia7-3.4-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 78 and 0 Target number of residues in the AU: 78 Target solvent content: 0.6257 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: 2ia7-3.4-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: 19 Cell parameters: 40.240 43.350 64.660 90.000 90.000 90.000 Input sequence file: 2ia7-3.4-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 3.400 Wilson plot Bfac: 62.18 1691 reflections ( 97.80 % complete ) and 0 restraints for refining 1189 atoms. Observations/parameters ratio is 0.36 ------------------------------------------------------ Starting model: R = 0.3529 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3255 (Rfree = 0.000) for 1189 atoms. Found 4 (8 requested) and removed 12 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.20 3.88 Search for helices and strands: 0 residues in 0 chains, 1196 seeds are put forward Round 1: 35 peptides, 8 chains. Longest chain 5 peptides. Score 0.219 Round 2: 46 peptides, 10 chains. Longest chain 6 peptides. Score 0.264 Round 3: 44 peptides, 10 chains. Longest chain 6 peptides. Score 0.233 Round 4: 44 peptides, 9 chains. Longest chain 7 peptides. Score 0.298 Round 5: 48 peptides, 10 chains. Longest chain 7 peptides. Score 0.295 Taking the results from Round 4 Chains 9, Residues 35, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1691 reflections ( 97.80 % complete ) and 2395 restraints for refining 975 atoms. 2264 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2555 (Rfree = 0.000) for 975 atoms. Found 5 (7 requested) and removed 4 (3 requested) atoms. Cycle 2: After refmac, R = 0.2342 (Rfree = 0.000) for 967 atoms. Found 3 (7 requested) and removed 3 (3 requested) atoms. Cycle 3: After refmac, R = 0.2365 (Rfree = 0.000) for 963 atoms. Found 6 (7 requested) and removed 5 (3 requested) atoms. Cycle 4: After refmac, R = 0.2156 (Rfree = 0.000) for 958 atoms. Found 3 (7 requested) and removed 10 (3 requested) atoms. Cycle 5: After refmac, R = 0.2001 (Rfree = 0.000) for 948 atoms. Found 2 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.20 3.88 Search for helices and strands: 0 residues in 0 chains, 966 seeds are put forward Round 1: 25 peptides, 6 chains. Longest chain 5 peptides. Score 0.186 Round 2: 30 peptides, 7 chains. Longest chain 5 peptides. Score 0.203 Round 3: 44 peptides, 9 chains. Longest chain 8 peptides. Score 0.298 Round 4: 48 peptides, 8 chains. Longest chain 11 peptides. Score 0.419 Round 5: 45 peptides, 10 chains. Longest chain 7 peptides. Score 0.249 Taking the results from Round 4 Chains 8, Residues 40, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1691 reflections ( 97.80 % complete ) and 2020 restraints for refining 852 atoms. 1868 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2420 (Rfree = 0.000) for 852 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Cycle 7: After refmac, R = 0.1992 (Rfree = 0.000) for 852 atoms. Found 3 (6 requested) and removed 4 (3 requested) atoms. Cycle 8: After refmac, R = 0.2049 (Rfree = 0.000) for 848 atoms. Found 3 (6 requested) and removed 3 (3 requested) atoms. Cycle 9: After refmac, R = 0.1838 (Rfree = 0.000) for 848 atoms. Found 0 (6 requested) and removed 4 (3 requested) atoms. Cycle 10: After refmac, R = 0.1966 (Rfree = 0.000) for 842 atoms. Found 3 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.29 3.98 Search for helices and strands: 0 residues in 0 chains, 871 seeds are put forward Round 1: 44 peptides, 10 chains. Longest chain 6 peptides. Score 0.233 Round 2: 49 peptides, 10 chains. Longest chain 7 peptides. Score 0.310 Round 3: 53 peptides, 10 chains. Longest chain 8 peptides. Score 0.369 Round 4: 53 peptides, 9 chains. Longest chain 9 peptides. Score 0.429 Round 5: 52 peptides, 10 chains. Longest chain 11 peptides. Score 0.355 Taking the results from Round 4 Chains 9, Residues 44, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1691 reflections ( 97.80 % complete ) and 1937 restraints for refining 859 atoms. 1770 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2145 (Rfree = 0.000) for 859 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 12: After refmac, R = 0.2239 (Rfree = 0.000) for 855 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 13: After refmac, R = 0.2106 (Rfree = 0.000) for 853 atoms. Found 2 (6 requested) and removed 5 (3 requested) atoms. Cycle 14: After refmac, R = 0.2028 (Rfree = 0.000) for 848 atoms. Found 3 (6 requested) and removed 4 (3 requested) atoms. Cycle 15: After refmac, R = 0.2004 (Rfree = 0.000) for 847 atoms. Found 1 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.33 4.03 Search for helices and strands: 0 residues in 0 chains, 880 seeds are put forward Round 1: 47 peptides, 11 chains. Longest chain 6 peptides. Score 0.215 Round 2: 54 peptides, 11 chains. Longest chain 7 peptides. Score 0.323 Round 3: 51 peptides, 10 chains. Longest chain 8 peptides. Score 0.340 Round 4: 51 peptides, 8 chains. Longest chain 10 peptides. Score 0.460 Round 5: 50 peptides, 9 chains. Longest chain 9 peptides. Score 0.387 Taking the results from Round 4 Chains 8, Residues 43, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1691 reflections ( 97.80 % complete ) and 2017 restraints for refining 864 atoms. 1853 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2265 (Rfree = 0.000) for 864 atoms. Found 5 (6 requested) and removed 3 (3 requested) atoms. Cycle 17: After refmac, R = 0.2315 (Rfree = 0.000) for 866 atoms. Found 6 (6 requested) and removed 3 (3 requested) atoms. Cycle 18: After refmac, R = 0.2142 (Rfree = 0.000) for 868 atoms. Found 0 (6 requested) and removed 5 (3 requested) atoms. Cycle 19: After refmac, R = 0.2080 (Rfree = 0.000) for 860 atoms. Found 2 (6 requested) and removed 4 (3 requested) atoms. Cycle 20: After refmac, R = 0.2175 (Rfree = 0.000) for 856 atoms. Found 4 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.30 4.00 Search for helices and strands: 0 residues in 0 chains, 889 seeds are put forward Round 1: 47 peptides, 10 chains. Longest chain 7 peptides. Score 0.280 Round 2: 52 peptides, 10 chains. Longest chain 8 peptides. Score 0.355 Round 3: 46 peptides, 9 chains. Longest chain 7 peptides. Score 0.328 Round 4: 59 peptides, 11 chains. Longest chain 8 peptides. Score 0.395 Round 5: 60 peptides, 11 chains. Longest chain 9 peptides. Score 0.408 Taking the results from Round 5 Chains 11, Residues 49, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1691 reflections ( 97.80 % complete ) and 1971 restraints for refining 873 atoms. 1786 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2528 (Rfree = 0.000) for 873 atoms. Found 4 (6 requested) and removed 7 (3 requested) atoms. Cycle 22: After refmac, R = 0.2444 (Rfree = 0.000) for 869 atoms. Found 3 (6 requested) and removed 5 (3 requested) atoms. Cycle 23: After refmac, R = 0.2425 (Rfree = 0.000) for 866 atoms. Found 6 (6 requested) and removed 3 (3 requested) atoms. Cycle 24: After refmac, R = 0.2190 (Rfree = 0.000) for 869 atoms. Found 1 (6 requested) and removed 3 (3 requested) atoms. Cycle 25: After refmac, R = 0.2130 (Rfree = 0.000) for 867 atoms. Found 2 (6 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.26 3.95 Search for helices and strands: 0 residues in 0 chains, 886 seeds are put forward Round 1: 37 peptides, 8 chains. Longest chain 7 peptides. Score 0.253 Round 2: 52 peptides, 10 chains. Longest chain 8 peptides. Score 0.355 Round 3: 47 peptides, 9 chains. Longest chain 8 peptides. Score 0.343 Round 4: 39 peptides, 6 chains. Longest chain 10 peptides. Score 0.416 Round 5: 43 peptides, 9 chains. Longest chain 7 peptides. Score 0.282 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 ------------------------------------------------------ 1691 reflections ( 97.80 % complete ) and 2117 restraints for refining 900 atoms. 1991 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2280 (Rfree = 0.000) for 900 atoms. Found 5 (6 requested) and removed 5 (3 requested) atoms. Cycle 27: After refmac, R = 0.2102 (Rfree = 0.000) for 898 atoms. Found 1 (6 requested) and removed 4 (3 requested) atoms. Cycle 28: After refmac, R = 0.1953 (Rfree = 0.000) for 895 atoms. Found 0 (6 requested) and removed 4 (3 requested) atoms. Cycle 29: After refmac, R = 0.1937 (Rfree = 0.000) for 891 atoms. Found 1 (6 requested) and removed 4 (3 requested) atoms. Cycle 30: After refmac, R = 0.2308 (Rfree = 0.000) for 887 atoms. Found 1 (6 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.22 3.90 Search for helices and strands: 0 residues in 0 chains, 900 seeds are put forward Round 1: 44 peptides, 9 chains. Longest chain 7 peptides. Score 0.298 Round 2: 46 peptides, 9 chains. Longest chain 8 peptides. Score 0.328 Round 3: 46 peptides, 8 chains. Longest chain 8 peptides. Score 0.391 Round 4: 51 peptides, 9 chains. Longest chain 11 peptides. Score 0.401 Round 5: 52 peptides, 8 chains. Longest chain 12 peptides. Score 0.473 Taking the results from Round 5 Chains 8, Residues 44, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1691 reflections ( 97.80 % complete ) and 2088 restraints for refining 914 atoms. 1920 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2193 (Rfree = 0.000) for 914 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 32: After refmac, R = 0.2010 (Rfree = 0.000) for 912 atoms. Found 3 (6 requested) and removed 4 (3 requested) atoms. Cycle 33: After refmac, R = 0.2001 (Rfree = 0.000) for 908 atoms. Found 3 (6 requested) and removed 4 (3 requested) atoms. Cycle 34: After refmac, R = 0.1987 (Rfree = 0.000) for 904 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 35: After refmac, R = 0.1917 (Rfree = 0.000) for 901 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.36 4.07 Search for helices and strands: 0 residues in 0 chains, 924 seeds are put forward Round 1: 31 peptides, 7 chains. Longest chain 5 peptides. Score 0.221 Round 2: 44 peptides, 9 chains. Longest chain 6 peptides. Score 0.298 Round 3: 48 peptides, 8 chains. Longest chain 10 peptides. Score 0.419 Round 4: 48 peptides, 9 chains. Longest chain 7 peptides. Score 0.358 Round 5: 49 peptides, 8 chains. Longest chain 11 peptides. Score 0.433 Taking the results from Round 5 Chains 8, Residues 41, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1691 reflections ( 97.80 % complete ) and 2216 restraints for refining 928 atoms. 2060 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2866 (Rfree = 0.000) for 928 atoms. Found 6 (7 requested) and removed 11 (3 requested) atoms. Cycle 37: After refmac, R = 0.2047 (Rfree = 0.000) for 922 atoms. Found 2 (6 requested) and removed 6 (3 requested) atoms. Cycle 38: After refmac, R = 0.1852 (Rfree = 0.000) for 918 atoms. Found 0 (6 requested) and removed 6 (3 requested) atoms. Cycle 39: After refmac, R = 0.1742 (Rfree = 0.000) for 912 atoms. Found 1 (6 requested) and removed 7 (3 requested) atoms. Cycle 40: After refmac, R = 0.1898 (Rfree = 0.000) for 906 atoms. Found 2 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.32 4.02 Search for helices and strands: 0 residues in 0 chains, 925 seeds are put forward Round 1: 33 peptides, 8 chains. Longest chain 5 peptides. Score 0.184 Round 2: 29 peptides, 6 chains. Longest chain 6 peptides. Score 0.259 Round 3: 40 peptides, 7 chains. Longest chain 11 peptides. Score 0.366 Round 4: 37 peptides, 8 chains. Longest chain 7 peptides. Score 0.253 Round 5: 42 peptides, 9 chains. Longest chain 7 peptides. Score 0.266 Taking the results from Round 3 Chains 7, Residues 33, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1691 reflections ( 97.80 % complete ) and 2285 restraints for refining 931 atoms. 2160 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2048 (Rfree = 0.000) for 931 atoms. Found 4 (7 requested) and removed 12 (3 requested) atoms. Cycle 42: After refmac, R = 0.1794 (Rfree = 0.000) for 922 atoms. Found 2 (6 requested) and removed 4 (3 requested) atoms. Cycle 43: After refmac, R = 0.1999 (Rfree = 0.000) for 920 atoms. Found 2 (6 requested) and removed 7 (3 requested) atoms. Cycle 44: After refmac, R = 0.1918 (Rfree = 0.000) for 915 atoms. Found 4 (6 requested) and removed 22 (3 requested) atoms. Cycle 45: After refmac, R = 0.1793 (Rfree = 0.000) for 897 atoms. Found 5 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.18 3.85 Search for helices and strands: 0 residues in 0 chains, 927 seeds are put forward Round 1: 21 peptides, 5 chains. Longest chain 5 peptides. Score 0.187 Round 2: 33 peptides, 7 chains. Longest chain 7 peptides. Score 0.255 Round 3: 34 peptides, 7 chains. Longest chain 7 peptides. Score 0.272 Round 4: 30 peptides, 6 chains. Longest chain 7 peptides. Score 0.276 Round 5: 35 peptides, 7 chains. Longest chain 8 peptides. Score 0.288 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 7, Residues 28, 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. 1691 reflections ( 97.80 % complete ) and 2195 restraints for refining 915 atoms. 2090 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1806 (Rfree = 0.000) for 915 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.1670 (Rfree = 0.000) for 912 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.1612 (Rfree = 0.000) for 908 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.1611 (Rfree = 0.000) for 905 atoms. Found 0 (6 requested) and removed 1 (3 requested) atoms. Writing output files ... TimeTaking 22.07