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 2inb-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2inb-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2inb-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2inb-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/2inb-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2inb-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/2inb-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2inb-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 97 and 0 Target number of residues in the AU: 97 Target solvent content: 0.6412 Checking the provided sequence file Detected sequence length: 140 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 140 Adjusted target solvent content: 0.48 Input MTZ file: 2inb-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: 152 Cell parameters: 59.524 59.524 71.521 90.000 90.000 120.000 Input sequence file: 2inb-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 1120 target number of atoms Had to go as low as 0.75 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: 29.762 3.600 Wilson plot Bfac: 70.68 1858 reflections ( 99.79 % complete ) and 0 restraints for refining 1247 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Starting model: R = 0.3430 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2993 (Rfree = 0.000) for 1247 atoms. Found 8 (8 requested) and removed 14 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.36 3.45 Search for helices and strands: 0 residues in 0 chains, 1272 seeds are put forward Round 1: 55 peptides, 12 chains. Longest chain 9 peptides. Score 0.256 Round 2: 76 peptides, 13 chains. Longest chain 12 peptides. Score 0.445 Round 3: 69 peptides, 8 chains. Longest chain 18 peptides. Score 0.587 Round 4: 70 peptides, 10 chains. Longest chain 14 peptides. Score 0.515 Round 5: 81 peptides, 11 chains. Longest chain 24 peptides. Score 0.574 Taking the results from Round 3 Chains 8, Residues 61, Estimated correctness of the model 9.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1858 reflections ( 99.79 % complete ) and 2371 restraints for refining 1016 atoms. 2135 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2551 (Rfree = 0.000) for 1016 atoms. Found 3 (6 requested) and removed 4 (3 requested) atoms. Cycle 2: After refmac, R = 0.2584 (Rfree = 0.000) for 1003 atoms. Found 3 (6 requested) and removed 6 (3 requested) atoms. Cycle 3: After refmac, R = 0.2539 (Rfree = 0.000) for 991 atoms. Found 5 (6 requested) and removed 5 (3 requested) atoms. Cycle 4: After refmac, R = 0.2290 (Rfree = 0.000) for 975 atoms. Found 2 (6 requested) and removed 3 (3 requested) atoms. Cycle 5: After refmac, R = 0.2391 (Rfree = 0.000) for 965 atoms. Found 5 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.49 3.58 Search for helices and strands: 0 residues in 0 chains, 1014 seeds are put forward Round 1: 55 peptides, 11 chains. Longest chain 10 peptides. Score 0.307 Round 2: 68 peptides, 12 chains. Longest chain 13 peptides. Score 0.406 Round 3: 79 peptides, 11 chains. Longest chain 21 peptides. Score 0.556 Round 4: 79 peptides, 11 chains. Longest chain 17 peptides. Score 0.556 Round 5: 77 peptides, 11 chains. Longest chain 22 peptides. Score 0.538 Taking the results from Round 4 Chains 11, Residues 68, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1858 reflections ( 99.79 % complete ) and 2125 restraints for refining 962 atoms. 1864 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2448 (Rfree = 0.000) for 962 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 7: After refmac, R = 0.2289 (Rfree = 0.000) for 958 atoms. Found 5 (6 requested) and removed 8 (3 requested) atoms. Cycle 8: After refmac, R = 0.2280 (Rfree = 0.000) for 951 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 9: After refmac, R = 0.1992 (Rfree = 0.000) for 947 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 10: After refmac, R = 0.1919 (Rfree = 0.000) for 944 atoms. Found 0 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.42 3.51 Search for helices and strands: 0 residues in 0 chains, 971 seeds are put forward Round 1: 58 peptides, 11 chains. Longest chain 9 peptides. Score 0.342 Round 2: 63 peptides, 10 chains. Longest chain 12 peptides. Score 0.445 Round 3: 74 peptides, 11 chains. Longest chain 15 peptides. Score 0.511 Round 4: 65 peptides, 7 chains. Longest chain 15 peptides. Score 0.592 Round 5: 67 peptides, 8 chains. Longest chain 15 peptides. Score 0.569 Taking the results from Round 4 Chains 7, Residues 58, Estimated correctness of the model 11.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1858 reflections ( 99.79 % complete ) and 2242 restraints for refining 968 atoms. 2017 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2305 (Rfree = 0.000) for 968 atoms. Found 4 (6 requested) and removed 6 (3 requested) atoms. Cycle 12: After refmac, R = 0.2252 (Rfree = 0.000) for 960 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. Cycle 13: After refmac, R = 0.2419 (Rfree = 0.000) for 958 atoms. Found 5 (6 requested) and removed 12 (3 requested) atoms. Cycle 14: After refmac, R = 0.2177 (Rfree = 0.000) for 946 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. Cycle 15: After refmac, R = 0.2149 (Rfree = 0.000) for 948 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.37 3.46 Search for helices and strands: 0 residues in 0 chains, 986 seeds are put forward Round 1: 55 peptides, 11 chains. Longest chain 9 peptides. Score 0.307 Round 2: 61 peptides, 9 chains. Longest chain 15 peptides. Score 0.470 Round 3: 68 peptides, 12 chains. Longest chain 9 peptides. Score 0.406 Round 4: 66 peptides, 10 chains. Longest chain 16 peptides. Score 0.475 Round 5: 66 peptides, 11 chains. Longest chain 9 peptides. Score 0.431 Taking the results from Round 4 Chains 10, Residues 56, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1858 reflections ( 99.79 % complete ) and 2101 restraints for refining 950 atoms. 1887 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2058 (Rfree = 0.000) for 950 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. Cycle 17: After refmac, R = 0.1891 (Rfree = 0.000) for 949 atoms. Found 4 (6 requested) and removed 3 (3 requested) atoms. Cycle 18: After refmac, R = 0.1845 (Rfree = 0.000) for 949 atoms. Found 5 (6 requested) and removed 3 (3 requested) atoms. Cycle 19: After refmac, R = 0.2466 (Rfree = 0.000) for 949 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Cycle 20: After refmac, R = 0.1826 (Rfree = 0.000) for 942 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.39 3.48 Search for helices and strands: 0 residues in 0 chains, 974 seeds are put forward Round 1: 66 peptides, 12 chains. Longest chain 15 peptides. Score 0.385 Round 2: 67 peptides, 10 chains. Longest chain 14 peptides. Score 0.485 Round 3: 78 peptides, 9 chains. Longest chain 26 peptides. Score 0.623 Round 4: 76 peptides, 12 chains. Longest chain 9 peptides. Score 0.488 Round 5: 84 peptides, 9 chains. Longest chain 27 peptides. Score 0.667 Taking the results from Round 5 Chains 10, Residues 75, Estimated correctness of the model 39.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 1858 reflections ( 99.79 % complete ) and 2000 restraints for refining 978 atoms. 1677 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2331 (Rfree = 0.000) for 978 atoms. Found 4 (6 requested) and removed 7 (3 requested) atoms. Cycle 22: After refmac, R = 0.2071 (Rfree = 0.000) for 973 atoms. Found 1 (6 requested) and removed 6 (3 requested) atoms. Cycle 23: After refmac, R = 0.2037 (Rfree = 0.000) for 966 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 24: After refmac, R = 0.1948 (Rfree = 0.000) for 962 atoms. Found 1 (6 requested) and removed 4 (3 requested) atoms. Cycle 25: After refmac, R = 0.1917 (Rfree = 0.000) for 959 atoms. Found 1 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.44 3.53 Search for helices and strands: 0 residues in 0 chains, 989 seeds are put forward Round 1: 67 peptides, 11 chains. Longest chain 16 peptides. Score 0.441 Round 2: 75 peptides, 12 chains. Longest chain 11 peptides. Score 0.478 Round 3: 78 peptides, 12 chains. Longest chain 17 peptides. Score 0.507 Round 4: 68 peptides, 11 chains. Longest chain 11 peptides. Score 0.452 Round 5: 72 peptides, 9 chains. Longest chain 22 peptides. Score 0.573 Taking the results from Round 5 Chains 9, Residues 63, Estimated correctness of the model 3.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1858 reflections ( 99.79 % complete ) and 2292 restraints for refining 1010 atoms. 2049 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2396 (Rfree = 0.000) for 1010 atoms. Found 4 (6 requested) and removed 7 (3 requested) atoms. Cycle 27: After refmac, R = 0.2161 (Rfree = 0.000) for 1003 atoms. Found 3 (6 requested) and removed 5 (3 requested) atoms. Cycle 28: After refmac, R = 0.2045 (Rfree = 0.000) for 997 atoms. Found 2 (6 requested) and removed 3 (3 requested) atoms. Cycle 29: After refmac, R = 0.2021 (Rfree = 0.000) for 994 atoms. Found 1 (6 requested) and removed 5 (3 requested) atoms. Cycle 30: After refmac, R = 0.2072 (Rfree = 0.000) for 989 atoms. Found 2 (6 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.40 3.49 Search for helices and strands: 0 residues in 0 chains, 1016 seeds are put forward Round 1: 48 peptides, 10 chains. Longest chain 6 peptides. Score 0.273 Round 2: 72 peptides, 12 chains. Longest chain 18 peptides. Score 0.448 Round 3: 62 peptides, 11 chains. Longest chain 9 peptides. Score 0.388 Round 4: 66 peptides, 9 chains. Longest chain 20 peptides. Score 0.519 Round 5: 64 peptides, 11 chains. Longest chain 8 peptides. Score 0.409 Taking the results from Round 4 Chains 9, Residues 57, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1858 reflections ( 99.79 % complete ) and 2276 restraints for refining 1014 atoms. 2057 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2266 (Rfree = 0.000) for 1014 atoms. Found 3 (6 requested) and removed 4 (3 requested) atoms. Cycle 32: After refmac, R = 0.2392 (Rfree = 0.000) for 1011 atoms. Found 2 (6 requested) and removed 6 (3 requested) atoms. Cycle 33: After refmac, R = 0.2166 (Rfree = 0.000) for 1004 atoms. Found 3 (6 requested) and removed 5 (3 requested) atoms. Cycle 34: After refmac, R = 0.1889 (Rfree = 0.000) for 1001 atoms. Found 2 (6 requested) and removed 3 (3 requested) atoms. Cycle 35: After refmac, R = 0.2101 (Rfree = 0.000) for 1000 atoms. Found 1 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.38 3.47 Search for helices and strands: 0 residues in 0 chains, 1036 seeds are put forward Round 1: 53 peptides, 11 chains. Longest chain 7 peptides. Score 0.283 Round 2: 69 peptides, 10 chains. Longest chain 17 peptides. Score 0.505 Round 3: 64 peptides, 9 chains. Longest chain 15 peptides. Score 0.500 Round 4: 60 peptides, 9 chains. Longest chain 11 peptides. Score 0.459 Round 5: 58 peptides, 9 chains. Longest chain 12 peptides. Score 0.438 Taking the results from Round 2 Chains 10, Residues 59, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1858 reflections ( 99.79 % complete ) and 2222 restraints for refining 997 atoms. 1996 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2162 (Rfree = 0.000) for 997 atoms. Found 3 (6 requested) and removed 8 (3 requested) atoms. Cycle 37: After refmac, R = 0.2154 (Rfree = 0.000) for 988 atoms. Found 4 (6 requested) and removed 4 (3 requested) atoms. Cycle 38: After refmac, R = 0.2088 (Rfree = 0.000) for 980 atoms. Found 1 (6 requested) and removed 5 (3 requested) atoms. Cycle 39: After refmac, R = 0.2121 (Rfree = 0.000) for 976 atoms. Found 3 (6 requested) and removed 5 (3 requested) atoms. Cycle 40: After refmac, R = 0.1792 (Rfree = 0.000) for 972 atoms. Found 2 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.43 3.52 Search for helices and strands: 0 residues in 0 chains, 1005 seeds are put forward Round 1: 51 peptides, 8 chains. Longest chain 16 peptides. Score 0.410 Round 2: 62 peptides, 11 chains. Longest chain 11 peptides. Score 0.388 Round 3: 62 peptides, 9 chains. Longest chain 17 peptides. Score 0.480 Round 4: 67 peptides, 9 chains. Longest chain 25 peptides. Score 0.528 Round 5: 56 peptides, 9 chains. Longest chain 18 peptides. Score 0.417 Taking the results from Round 4 Chains 9, Residues 58, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1858 reflections ( 99.79 % complete ) and 2108 restraints for refining 975 atoms. 1885 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2188 (Rfree = 0.000) for 975 atoms. Found 3 (6 requested) and removed 5 (3 requested) atoms. Cycle 42: After refmac, R = 0.2338 (Rfree = 0.000) for 969 atoms. Found 6 (6 requested) and removed 3 (3 requested) atoms. Cycle 43: After refmac, R = 0.2393 (Rfree = 0.000) for 971 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. Cycle 44: After refmac, R = 0.2447 (Rfree = 0.000) for 971 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 45: After refmac, R = 0.2368 (Rfree = 0.000) for 970 atoms. Found 3 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.40 3.49 Search for helices and strands: 0 residues in 0 chains, 1009 seeds are put forward Round 1: 41 peptides, 9 chains. Longest chain 8 peptides. Score 0.236 Round 2: 43 peptides, 7 chains. Longest chain 11 peptides. Score 0.370 Round 3: 49 peptides, 9 chains. Longest chain 9 peptides. Score 0.337 Round 4: 42 peptides, 7 chains. Longest chain 9 peptides. Score 0.358 Round 5: 41 peptides, 7 chains. Longest chain 9 peptides. Score 0.345 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 7, 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 2inb-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 1858 reflections ( 99.79 % complete ) and 2221 restraints for refining 939 atoms. 2084 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2421 (Rfree = 0.000) for 939 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.2408 (Rfree = 0.000) for 936 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.2187 (Rfree = 0.000) for 931 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 49: After refmac, R = 0.2243 (Rfree = 0.000) for 928 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:47:25 GMT 2018 Job finished. TimeTaking 24.65 Used memory is bytes: 10889912