null Sun 23 Dec 22:23:14 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 2aj6-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2aj6-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2aj6-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2aj6-3.8-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/2aj6-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2aj6-3.8-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 22:23:22 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/2aj6-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2aj6-3.8-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 89 and 0 Target number of residues in the AU: 89 Target solvent content: 0.6456 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: 2aj6-3.8-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: 23 Cell parameters: 40.044 74.871 90.673 90.000 90.000 90.000 Input sequence file: 2aj6-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 1272 target number of atoms Had to go as low as 0.40 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 3.801 Wilson plot Bfac: 74.98 1460 reflections ( 98.25 % complete ) and 0 restraints for refining 1414 atoms. Observations/parameters ratio is 0.26 ------------------------------------------------------ Starting model: R = 0.3163 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3162 (Rfree = 0.000) for 1414 atoms. Found 7 (7 requested) and removed 17 (3 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.62 4.32 Search for helices and strands: 0 residues in 0 chains, 1416 seeds are put forward Round 1: 39 peptides, 7 chains. Longest chain 11 peptides. Score 0.329 Round 2: 58 peptides, 9 chains. Longest chain 13 peptides. Score 0.454 Round 3: 70 peptides, 10 chains. Longest chain 12 peptides. Score 0.534 Round 4: 68 peptides, 9 chains. Longest chain 20 peptides. Score 0.557 Round 5: 75 peptides, 9 chains. Longest chain 14 peptides. Score 0.620 Taking the results from Round 5 Chains 9, Residues 66, Estimated correctness of the model 7.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1460 reflections ( 98.25 % complete ) and 2466 restraints for refining 1040 atoms. 2211 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3070 (Rfree = 0.000) for 1040 atoms. Found 2 (5 requested) and removed 15 (2 requested) atoms. Cycle 2: After refmac, R = 0.2409 (Rfree = 0.000) for 1005 atoms. Found 2 (5 requested) and removed 16 (2 requested) atoms. Cycle 3: After refmac, R = 0.2115 (Rfree = 0.000) for 983 atoms. Found 0 (5 requested) and removed 6 (2 requested) atoms. Cycle 4: After refmac, R = 0.2432 (Rfree = 0.000) for 975 atoms. Found 1 (5 requested) and removed 5 (2 requested) atoms. Cycle 5: After refmac, R = 0.2458 (Rfree = 0.000) for 966 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.63 4.33 Search for helices and strands: 0 residues in 0 chains, 993 seeds are put forward Round 1: 64 peptides, 12 chains. Longest chain 8 peptides. Score 0.374 Round 2: 58 peptides, 8 chains. Longest chain 13 peptides. Score 0.502 Round 3: 65 peptides, 10 chains. Longest chain 13 peptides. Score 0.482 Round 4: 65 peptides, 10 chains. Longest chain 13 peptides. Score 0.482 Round 5: 63 peptides, 10 chains. Longest chain 12 peptides. Score 0.461 Taking the results from Round 2 Chains 8, Residues 50, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1460 reflections ( 98.25 % complete ) and 2257 restraints for refining 955 atoms. 2065 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2344 (Rfree = 0.000) for 955 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. Cycle 7: After refmac, R = 0.2713 (Rfree = 0.000) for 953 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. Cycle 8: After refmac, R = 0.2664 (Rfree = 0.000) for 953 atoms. Found 1 (5 requested) and removed 3 (2 requested) atoms. Cycle 9: After refmac, R = 0.2280 (Rfree = 0.000) for 950 atoms. Found 2 (5 requested) and removed 6 (2 requested) atoms. Cycle 10: After refmac, R = 0.2387 (Rfree = 0.000) for 946 atoms. Found 5 (5 requested) and removed 6 (2 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.55 4.24 Search for helices and strands: 0 residues in 0 chains, 987 seeds are put forward Round 1: 52 peptides, 9 chains. Longest chain 9 peptides. Score 0.384 Round 2: 58 peptides, 8 chains. Longest chain 10 peptides. Score 0.502 Round 3: 70 peptides, 11 chains. Longest chain 12 peptides. Score 0.489 Round 4: 62 peptides, 8 chains. Longest chain 15 peptides. Score 0.543 Round 5: 69 peptides, 10 chains. Longest chain 15 peptides. Score 0.524 Taking the results from Round 4 Chains 8, Residues 54, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1460 reflections ( 98.25 % complete ) and 2380 restraints for refining 994 atoms. 2172 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2670 (Rfree = 0.000) for 994 atoms. Found 5 (5 requested) and removed 8 (2 requested) atoms. Cycle 12: After refmac, R = 0.1965 (Rfree = 0.000) for 971 atoms. Found 5 (5 requested) and removed 6 (2 requested) atoms. Cycle 13: After refmac, R = 0.2089 (Rfree = 0.000) for 966 atoms. Found 4 (5 requested) and removed 4 (2 requested) atoms. Cycle 14: After refmac, R = 0.2284 (Rfree = 0.000) for 958 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. Cycle 15: After refmac, R = 0.2313 (Rfree = 0.000) for 951 atoms. Found 3 (5 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.58 4.27 Search for helices and strands: 0 residues in 0 chains, 1002 seeds are put forward Round 1: 51 peptides, 11 chains. Longest chain 6 peptides. Score 0.263 Round 2: 69 peptides, 13 chains. Longest chain 9 peptides. Score 0.383 Round 3: 63 peptides, 10 chains. Longest chain 11 peptides. Score 0.461 Round 4: 72 peptides, 12 chains. Longest chain 11 peptides. Score 0.465 Round 5: 74 peptides, 11 chains. Longest chain 11 peptides. Score 0.530 Taking the results from Round 5 Chains 11, Residues 63, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 1460 reflections ( 98.25 % complete ) and 1917 restraints for refining 916 atoms. 1645 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2449 (Rfree = 0.000) for 916 atoms. Found 0 (5 requested) and removed 13 (2 requested) atoms. Cycle 17: After refmac, R = 0.2482 (Rfree = 0.000) for 896 atoms. Found 3 (4 requested) and removed 5 (2 requested) atoms. Cycle 18: After refmac, R = 0.2327 (Rfree = 0.000) for 893 atoms. Found 1 (4 requested) and removed 7 (2 requested) atoms. Cycle 19: After refmac, R = 0.2326 (Rfree = 0.000) for 886 atoms. Found 2 (4 requested) and removed 7 (2 requested) atoms. Cycle 20: After refmac, R = 0.2178 (Rfree = 0.000) for 880 atoms. Found 1 (4 requested) and removed 6 (2 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.57 4.26 Search for helices and strands: 0 residues in 0 chains, 919 seeds are put forward Round 1: 52 peptides, 10 chains. Longest chain 9 peptides. Score 0.331 Round 2: 63 peptides, 11 chains. Longest chain 9 peptides. Score 0.412 Round 3: 67 peptides, 11 chains. Longest chain 10 peptides. Score 0.457 Round 4: 57 peptides, 8 chains. Longest chain 13 peptides. Score 0.491 Round 5: 58 peptides, 9 chains. Longest chain 13 peptides. Score 0.454 Taking the results from Round 4 Chains 8, Residues 49, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1460 reflections ( 98.25 % complete ) and 2123 restraints for refining 908 atoms. 1935 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2414 (Rfree = 0.000) for 908 atoms. Found 4 (4 requested) and removed 4 (2 requested) atoms. Cycle 22: After refmac, R = 0.2327 (Rfree = 0.000) for 902 atoms. Found 1 (4 requested) and removed 4 (2 requested) atoms. Cycle 23: After refmac, R = 0.2029 (Rfree = 0.000) for 897 atoms. Found 4 (4 requested) and removed 2 (2 requested) atoms. Cycle 24: After refmac, R = 0.2128 (Rfree = 0.000) for 897 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 25: After refmac, R = 0.2066 (Rfree = 0.000) for 894 atoms. Found 1 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.63 4.33 Search for helices and strands: 0 residues in 0 chains, 942 seeds are put forward Round 1: 54 peptides, 11 chains. Longest chain 9 peptides. Score 0.302 Round 2: 56 peptides, 9 chains. Longest chain 8 peptides. Score 0.431 Round 3: 62 peptides, 9 chains. Longest chain 10 peptides. Score 0.497 Round 4: 48 peptides, 8 chains. Longest chain 8 peptides. Score 0.388 Round 5: 57 peptides, 8 chains. Longest chain 13 peptides. Score 0.491 Taking the results from Round 3 Chains 9, Residues 53, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1460 reflections ( 98.25 % complete ) and 2153 restraints for refining 946 atoms. 1950 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2293 (Rfree = 0.000) for 946 atoms. Found 3 (5 requested) and removed 4 (2 requested) atoms. Cycle 27: After refmac, R = 0.2198 (Rfree = 0.000) for 940 atoms. Found 3 (5 requested) and removed 4 (2 requested) atoms. Cycle 28: After refmac, R = 0.2054 (Rfree = 0.000) for 939 atoms. Found 0 (5 requested) and removed 4 (2 requested) atoms. Cycle 29: After refmac, R = 0.2215 (Rfree = 0.000) for 933 atoms. Found 2 (5 requested) and removed 3 (2 requested) atoms. Cycle 30: After refmac, R = 0.2063 (Rfree = 0.000) for 931 atoms. Found 1 (5 requested) and removed 7 (2 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.59 4.29 Search for helices and strands: 0 residues in 0 chains, 957 seeds are put forward Round 1: 46 peptides, 9 chains. Longest chain 9 peptides. Score 0.308 Round 2: 55 peptides, 10 chains. Longest chain 11 peptides. Score 0.368 Round 3: 49 peptides, 7 chains. Longest chain 15 peptides. Score 0.452 Round 4: 47 peptides, 9 chains. Longest chain 7 peptides. Score 0.321 Round 5: 55 peptides, 8 chains. Longest chain 13 peptides. Score 0.470 Taking the results from Round 5 Chains 8, Residues 47, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1460 reflections ( 98.25 % complete ) and 2244 restraints for refining 965 atoms. 2064 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2222 (Rfree = 0.000) for 965 atoms. Found 2 (5 requested) and removed 7 (2 requested) atoms. Cycle 32: After refmac, R = 0.1946 (Rfree = 0.000) for 955 atoms. Found 0 (5 requested) and removed 5 (2 requested) atoms. Cycle 33: After refmac, R = 0.1944 (Rfree = 0.000) for 948 atoms. Found 1 (5 requested) and removed 5 (2 requested) atoms. Cycle 34: After refmac, R = 0.1960 (Rfree = 0.000) for 942 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 35: After refmac, R = 0.1879 (Rfree = 0.000) for 938 atoms. Found 0 (5 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.62 4.32 Search for helices and strands: 0 residues in 0 chains, 964 seeds are put forward Round 1: 45 peptides, 9 chains. Longest chain 10 peptides. Score 0.295 Round 2: 51 peptides, 8 chains. Longest chain 16 peptides. Score 0.424 Round 3: 60 peptides, 8 chains. Longest chain 23 peptides. Score 0.523 Round 4: 55 peptides, 8 chains. Longest chain 13 peptides. Score 0.470 Round 5: 46 peptides, 5 chains. Longest chain 23 peptides. Score 0.521 Taking the results from Round 3 Chains 10, Residues 52, Estimated correctness of the model 0.0 % 1 chains (18 residues) have been docked in sequence ------------------------------------------------------ 1460 reflections ( 98.25 % complete ) and 2142 restraints for refining 1000 atoms. 1874 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2515 (Rfree = 0.000) for 1000 atoms. Found 4 (5 requested) and removed 9 (2 requested) atoms. Cycle 37: After refmac, R = 0.2251 (Rfree = 0.000) for 987 atoms. Found 2 (5 requested) and removed 6 (2 requested) atoms. Cycle 38: After refmac, R = 0.2273 (Rfree = 0.000) for 977 atoms. Found 1 (5 requested) and removed 8 (2 requested) atoms. Cycle 39: After refmac, R = 0.1921 (Rfree = 0.000) for 966 atoms. Found 1 (5 requested) and removed 2 (2 requested) atoms. Cycle 40: After refmac, R = 0.2122 (Rfree = 0.000) for 965 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.57 4.26 Search for helices and strands: 0 residues in 0 chains, 993 seeds are put forward Round 1: 41 peptides, 9 chains. Longest chain 7 peptides. Score 0.240 Round 2: 47 peptides, 9 chains. Longest chain 8 peptides. Score 0.321 Round 3: 52 peptides, 9 chains. Longest chain 12 peptides. Score 0.384 Round 4: 45 peptides, 8 chains. Longest chain 12 peptides. Score 0.350 Round 5: 49 peptides, 8 chains. Longest chain 12 peptides. Score 0.400 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 ------------------------------------------------------ 1460 reflections ( 98.25 % complete ) and 2256 restraints for refining 959 atoms. 2100 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2467 (Rfree = 0.000) for 959 atoms. Found 5 (5 requested) and removed 9 (2 requested) atoms. Cycle 42: After refmac, R = 0.2295 (Rfree = 0.000) for 951 atoms. Found 4 (5 requested) and removed 2 (2 requested) atoms. Cycle 43: After refmac, R = 0.2028 (Rfree = 0.000) for 953 atoms. Found 1 (5 requested) and removed 6 (2 requested) atoms. Cycle 44: After refmac, R = 0.1995 (Rfree = 0.000) for 945 atoms. Found 1 (5 requested) and removed 6 (2 requested) atoms. Cycle 45: After refmac, R = 0.1922 (Rfree = 0.000) for 939 atoms. Found 1 (5 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.59 4.29 Search for helices and strands: 0 residues in 0 chains, 965 seeds are put forward Round 1: 24 peptides, 5 chains. Longest chain 7 peptides. Score 0.237 Round 2: 36 peptides, 7 chains. Longest chain 6 peptides. Score 0.288 Round 3: 42 peptides, 7 chains. Longest chain 8 peptides. Score 0.368 Round 4: 38 peptides, 7 chains. Longest chain 7 peptides. Score 0.315 Round 5: 39 peptides, 8 chains. Longest chain 7 peptides. Score 0.270 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 7, Residues 35, 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. 1460 reflections ( 98.25 % complete ) and 2168 restraints for refining 908 atoms. 2035 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2677 (Rfree = 0.000) for 908 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 47: After refmac, R = 0.1999 (Rfree = 0.000) for 905 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 48: After refmac, R = 0.2010 (Rfree = 0.000) for 902 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 49: After refmac, R = 0.1955 (Rfree = 0.000) for 900 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:46:11 GMT 2018 Job finished. TimeTaking 22.95 Used memory is bytes: 15023992