null 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 2aj6-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2aj6-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2aj6-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2aj6-3.6-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/2aj6-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2aj6-3.6-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/2aj6-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2aj6-3.6-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: 0.6337 Checking the provided sequence file Detected sequence length: 159 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 159 Adjusted target solvent content: 0.37 Input MTZ file: 2aj6-3.6-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: 23 Cell parameters: 40.044 74.871 90.673 90.000 90.000 90.000 Input sequence file: 2aj6-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 1272 target number of atoms Had to go as low as 0.35 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: 28.866 3.601 Wilson plot Bfac: 66.60 1710 reflections ( 98.45 % complete ) and 0 restraints for refining 1406 atoms. Observations/parameters ratio is 0.30 ------------------------------------------------------ Starting model: R = 0.3033 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2999 (Rfree = 0.000) for 1406 atoms. Found 9 (9 requested) and removed 18 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.26 3.89 Search for helices and strands: 0 residues in 0 chains, 1420 seeds are put forward Round 1: 44 peptides, 8 chains. Longest chain 8 peptides. Score 0.338 Round 2: 56 peptides, 8 chains. Longest chain 11 peptides. Score 0.480 Round 3: 71 peptides, 11 chains. Longest chain 12 peptides. Score 0.499 Round 4: 73 peptides, 10 chains. Longest chain 13 peptides. Score 0.562 Round 5: 71 peptides, 10 chains. Longest chain 12 peptides. Score 0.543 Taking the results from Round 4 Chains 10, Residues 63, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1710 reflections ( 98.45 % complete ) and 2709 restraints for refining 1111 atoms. 2467 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2631 (Rfree = 0.000) for 1111 atoms. Found 7 (7 requested) and removed 12 (3 requested) atoms. Cycle 2: After refmac, R = 0.2424 (Rfree = 0.000) for 1067 atoms. Found 7 (7 requested) and removed 12 (3 requested) atoms. Cycle 3: After refmac, R = 0.2303 (Rfree = 0.000) for 1046 atoms. Found 1 (6 requested) and removed 6 (3 requested) atoms. Cycle 4: After refmac, R = 0.2340 (Rfree = 0.000) for 1030 atoms. Found 6 (6 requested) and removed 9 (3 requested) atoms. Cycle 5: After refmac, R = 0.2241 (Rfree = 0.000) for 1022 atoms. Found 5 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.53 4.21 Search for helices and strands: 0 residues in 0 chains, 1056 seeds are put forward Round 1: 55 peptides, 11 chains. Longest chain 8 peptides. Score 0.315 Round 2: 69 peptides, 10 chains. Longest chain 12 peptides. Score 0.524 Round 3: 74 peptides, 11 chains. Longest chain 10 peptides. Score 0.530 Round 4: 75 peptides, 9 chains. Longest chain 12 peptides. Score 0.620 Round 5: 66 peptides, 9 chains. Longest chain 11 peptides. Score 0.538 Taking the results from Round 4 Chains 9, Residues 66, Estimated correctness of the model 22.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1710 reflections ( 98.45 % complete ) and 2186 restraints for refining 946 atoms. 1931 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2362 (Rfree = 0.000) for 946 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 7: After refmac, R = 0.2131 (Rfree = 0.000) for 943 atoms. Found 4 (6 requested) and removed 5 (3 requested) atoms. Cycle 8: After refmac, R = 0.1818 (Rfree = 0.000) for 942 atoms. Found 2 (6 requested) and removed 5 (3 requested) atoms. Cycle 9: After refmac, R = 0.1822 (Rfree = 0.000) for 936 atoms. Found 1 (6 requested) and removed 3 (3 requested) atoms. Cycle 10: After refmac, R = 0.1767 (Rfree = 0.000) for 934 atoms. Found 1 (5 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.43 4.10 Search for helices and strands: 0 residues in 0 chains, 981 seeds are put forward Round 1: 67 peptides, 9 chains. Longest chain 12 peptides. Score 0.548 Round 2: 78 peptides, 9 chains. Longest chain 14 peptides. Score 0.645 Round 3: 72 peptides, 9 chains. Longest chain 13 peptides. Score 0.594 Round 4: 77 peptides, 10 chains. Longest chain 14 peptides. Score 0.599 Round 5: 82 peptides, 8 chains. Longest chain 22 peptides. Score 0.709 Taking the results from Round 5 Chains 8, Residues 74, Estimated correctness of the model 52.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1710 reflections ( 98.45 % complete ) and 2151 restraints for refining 945 atoms. 1863 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2455 (Rfree = 0.000) for 945 atoms. Found 6 (6 requested) and removed 9 (3 requested) atoms. Cycle 12: After refmac, R = 0.2141 (Rfree = 0.000) for 934 atoms. Found 1 (6 requested) and removed 6 (3 requested) atoms. Cycle 13: After refmac, R = 0.2265 (Rfree = 0.000) for 924 atoms. Found 4 (5 requested) and removed 6 (2 requested) atoms. Cycle 14: After refmac, R = 0.2047 (Rfree = 0.000) for 920 atoms. Found 3 (5 requested) and removed 4 (2 requested) atoms. Cycle 15: After refmac, R = 0.1920 (Rfree = 0.000) for 917 atoms. Found 1 (5 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.38 4.04 Search for helices and strands: 0 residues in 0 chains, 960 seeds are put forward Round 1: 52 peptides, 9 chains. Longest chain 10 peptides. Score 0.384 Round 2: 61 peptides, 9 chains. Longest chain 13 peptides. Score 0.486 Round 3: 74 peptides, 10 chains. Longest chain 15 peptides. Score 0.572 Round 4: 71 peptides, 9 chains. Longest chain 16 peptides. Score 0.585 Round 5: 72 peptides, 8 chains. Longest chain 15 peptides. Score 0.634 Taking the results from Round 5 Chains 8, Residues 64, Estimated correctness of the model 27.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1710 reflections ( 98.45 % complete ) and 2208 restraints for refining 969 atoms. 1960 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2720 (Rfree = 0.000) for 969 atoms. Found 5 (5 requested) and removed 5 (3 requested) atoms. Cycle 17: After refmac, R = 0.2349 (Rfree = 0.000) for 965 atoms. Found 5 (5 requested) and removed 8 (3 requested) atoms. Cycle 18: After refmac, R = 0.2118 (Rfree = 0.000) for 959 atoms. Found 2 (5 requested) and removed 5 (3 requested) atoms. Cycle 19: After refmac, R = 0.2114 (Rfree = 0.000) for 956 atoms. Found 2 (5 requested) and removed 3 (3 requested) atoms. Cycle 20: After refmac, R = 0.2200 (Rfree = 0.000) for 952 atoms. Found 5 (5 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.42 4.08 Search for helices and strands: 0 residues in 0 chains, 990 seeds are put forward Round 1: 58 peptides, 11 chains. Longest chain 10 peptides. Score 0.353 Round 2: 59 peptides, 9 chains. Longest chain 11 peptides. Score 0.465 Round 3: 56 peptides, 7 chains. Longest chain 19 peptides. Score 0.528 Round 4: 61 peptides, 9 chains. Longest chain 11 peptides. Score 0.486 Round 5: 58 peptides, 9 chains. Longest chain 14 peptides. Score 0.454 Taking the results from Round 3 Chains 7, Residues 49, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1710 reflections ( 98.45 % complete ) and 2323 restraints for refining 969 atoms. 2134 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2118 (Rfree = 0.000) for 969 atoms. Found 5 (5 requested) and removed 4 (3 requested) atoms. Cycle 22: After refmac, R = 0.2157 (Rfree = 0.000) for 967 atoms. Found 5 (5 requested) and removed 3 (3 requested) atoms. Cycle 23: After refmac, R = 0.1918 (Rfree = 0.000) for 968 atoms. Found 5 (5 requested) and removed 4 (3 requested) atoms. Cycle 24: After refmac, R = 0.1956 (Rfree = 0.000) for 968 atoms. Found 5 (5 requested) and removed 4 (3 requested) atoms. Cycle 25: After refmac, R = 0.1831 (Rfree = 0.000) for 969 atoms. Found 1 (5 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.39 4.05 Search for helices and strands: 0 residues in 0 chains, 1008 seeds are put forward Round 1: 47 peptides, 8 chains. Longest chain 9 peptides. Score 0.376 Round 2: 52 peptides, 9 chains. Longest chain 10 peptides. Score 0.384 Round 3: 55 peptides, 8 chains. Longest chain 10 peptides. Score 0.470 Round 4: 59 peptides, 7 chains. Longest chain 11 peptides. Score 0.558 Round 5: 58 peptides, 8 chains. Longest chain 11 peptides. Score 0.502 Taking the results from Round 4 Chains 7, Residues 52, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1710 reflections ( 98.45 % complete ) and 2306 restraints for refining 982 atoms. 2105 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2136 (Rfree = 0.000) for 982 atoms. Found 5 (5 requested) and removed 6 (3 requested) atoms. Cycle 27: After refmac, R = 0.1873 (Rfree = 0.000) for 981 atoms. Found 2 (5 requested) and removed 4 (3 requested) atoms. Cycle 28: After refmac, R = 0.1806 (Rfree = 0.000) for 978 atoms. Found 1 (5 requested) and removed 3 (3 requested) atoms. Cycle 29: After refmac, R = 0.1827 (Rfree = 0.000) for 974 atoms. Found 2 (5 requested) and removed 3 (3 requested) atoms. Cycle 30: After refmac, R = 0.1714 (Rfree = 0.000) for 973 atoms. Found 0 (5 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.40 4.06 Search for helices and strands: 0 residues in 0 chains, 1017 seeds are put forward Round 1: 56 peptides, 12 chains. Longest chain 7 peptides. Score 0.275 Round 2: 66 peptides, 10 chains. Longest chain 10 peptides. Score 0.493 Round 3: 71 peptides, 9 chains. Longest chain 16 peptides. Score 0.585 Round 4: 68 peptides, 10 chains. Longest chain 12 peptides. Score 0.513 Round 5: 63 peptides, 9 chains. Longest chain 12 peptides. Score 0.507 Taking the results from Round 3 Chains 9, Residues 62, Estimated correctness of the model 8.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1710 reflections ( 98.45 % complete ) and 2282 restraints for refining 987 atoms. 2043 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2233 (Rfree = 0.000) for 987 atoms. Found 5 (5 requested) and removed 9 (3 requested) atoms. Cycle 32: After refmac, R = 0.1858 (Rfree = 0.000) for 982 atoms. Found 2 (5 requested) and removed 3 (3 requested) atoms. Cycle 33: After refmac, R = 0.1846 (Rfree = 0.000) for 980 atoms. Found 3 (5 requested) and removed 3 (3 requested) atoms. Cycle 34: After refmac, R = 0.1888 (Rfree = 0.000) for 980 atoms. Found 3 (5 requested) and removed 5 (3 requested) atoms. Cycle 35: After refmac, R = 0.1677 (Rfree = 0.000) for 977 atoms. Found 1 (5 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.41 4.07 Search for helices and strands: 0 residues in 0 chains, 1007 seeds are put forward Round 1: 58 peptides, 10 chains. Longest chain 9 peptides. Score 0.404 Round 2: 59 peptides, 10 chains. Longest chain 10 peptides. Score 0.416 Round 3: 65 peptides, 11 chains. Longest chain 10 peptides. Score 0.435 Round 4: 66 peptides, 10 chains. Longest chain 12 peptides. Score 0.493 Round 5: 69 peptides, 10 chains. Longest chain 12 peptides. Score 0.524 Taking the results from Round 5 Chains 10, Residues 59, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1710 reflections ( 98.45 % complete ) and 2228 restraints for refining 965 atoms. 2002 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2099 (Rfree = 0.000) for 965 atoms. Found 5 (5 requested) and removed 5 (3 requested) atoms. Cycle 37: After refmac, R = 0.1944 (Rfree = 0.000) for 964 atoms. Found 1 (5 requested) and removed 4 (3 requested) atoms. Cycle 38: After refmac, R = 0.1988 (Rfree = 0.000) for 956 atoms. Found 3 (5 requested) and removed 4 (3 requested) atoms. Cycle 39: After refmac, R = 0.2012 (Rfree = 0.000) for 955 atoms. Found 2 (5 requested) and removed 5 (3 requested) atoms. Cycle 40: After refmac, R = 0.1911 (Rfree = 0.000) for 952 atoms. Found 2 (5 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.40 4.06 Search for helices and strands: 0 residues in 0 chains, 990 seeds are put forward Round 1: 61 peptides, 13 chains. Longest chain 7 peptides. Score 0.286 Round 2: 59 peptides, 9 chains. Longest chain 10 peptides. Score 0.465 Round 3: 62 peptides, 8 chains. Longest chain 14 peptides. Score 0.543 Round 4: 60 peptides, 7 chains. Longest chain 12 peptides. Score 0.568 Round 5: 65 peptides, 7 chains. Longest chain 22 peptides. Score 0.614 Taking the results from Round 5 Chains 7, Residues 58, Estimated correctness of the model 20.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1710 reflections ( 98.45 % complete ) and 2344 restraints for refining 996 atoms. 2119 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2279 (Rfree = 0.000) for 996 atoms. Found 5 (5 requested) and removed 10 (3 requested) atoms. Cycle 42: After refmac, R = 0.2115 (Rfree = 0.000) for 987 atoms. Found 4 (5 requested) and removed 3 (3 requested) atoms. Cycle 43: After refmac, R = 0.2122 (Rfree = 0.000) for 987 atoms. Found 2 (5 requested) and removed 5 (3 requested) atoms. Cycle 44: After refmac, R = 0.2094 (Rfree = 0.000) for 984 atoms. Found 2 (5 requested) and removed 7 (3 requested) atoms. Cycle 45: After refmac, R = 0.2431 (Rfree = 0.000) for 979 atoms. Found 4 (5 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.42 4.08 Search for helices and strands: 0 residues in 0 chains, 1026 seeds are put forward Round 1: 50 peptides, 11 chains. Longest chain 7 peptides. Score 0.250 Round 2: 56 peptides, 9 chains. Longest chain 14 peptides. Score 0.431 Round 3: 60 peptides, 10 chains. Longest chain 9 peptides. Score 0.427 Round 4: 67 peptides, 9 chains. Longest chain 15 peptides. Score 0.548 Round 5: 64 peptides, 10 chains. Longest chain 12 peptides. Score 0.471 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 9, Residues 58, 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 2aj6-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 1710 reflections ( 98.45 % complete ) and 2387 restraints for refining 995 atoms. 2164 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2646 (Rfree = 0.000) for 995 atoms. Found 0 (5 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.2251 (Rfree = 0.000) for 992 atoms. Found 0 (5 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.2233 (Rfree = 0.000) for 988 atoms. Found 0 (5 requested) and removed 0 (3 requested) atoms. Cycle 49: After refmac, R = 0.2210 (Rfree = 0.000) for 987 atoms. Found 0 (5 requested) and removed 2 (3 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:47:07 GMT 2018 Job finished. TimeTaking 24.34 Used memory is bytes: 20190304