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 2huj-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2huj-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2huj-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2huj-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/2huj-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2huj-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 22:22:54 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/2huj-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2huj-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 127 and 0 Target number of residues in the AU: 127 Target solvent content: 0.6431 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: 0.61 Input MTZ file: 2huj-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: 182 Cell parameters: 100.110 100.110 66.570 90.000 90.000 120.000 Input sequence file: 2huj-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 1120 target number of atoms Had to go as low as 0.90 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: 86.698 3.803 Wilson plot Bfac: 73.63 2160 reflections ( 99.59 % complete ) and 0 restraints for refining 1244 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Starting model: R = 0.3572 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3282 (Rfree = 0.000) for 1244 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 4.17 3.59 Search for helices and strands: 0 residues in 0 chains, 1280 seeds are put forward Round 1: 52 peptides, 10 chains. Longest chain 8 peptides. Score 0.294 Round 2: 57 peptides, 9 chains. Longest chain 12 peptides. Score 0.382 Round 3: 62 peptides, 8 chains. Longest chain 14 peptides. Score 0.463 Round 4: 63 peptides, 7 chains. Longest chain 15 peptides. Score 0.507 Round 5: 64 peptides, 8 chains. Longest chain 16 peptides. Score 0.479 Taking the results from Round 4 Chains 7, Residues 56, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2160 reflections ( 99.59 % complete ) and 2481 restraints for refining 1012 atoms. 2264 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3097 (Rfree = 0.000) for 1012 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. Cycle 2: After refmac, R = 0.2964 (Rfree = 0.000) for 985 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 3: After refmac, R = 0.2935 (Rfree = 0.000) for 974 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. Cycle 4: After refmac, R = 0.2668 (Rfree = 0.000) for 960 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 5: After refmac, R = 0.2599 (Rfree = 0.000) for 952 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.49 3.01 Search for helices and strands: 0 residues in 0 chains, 1019 seeds are put forward Round 1: 61 peptides, 12 chains. Longest chain 7 peptides. Score 0.298 Round 2: 72 peptides, 11 chains. Longest chain 11 peptides. Score 0.433 Round 3: 69 peptides, 9 chains. Longest chain 14 peptides. Score 0.482 Round 4: 77 peptides, 9 chains. Longest chain 14 peptides. Score 0.541 Round 5: 71 peptides, 8 chains. Longest chain 16 peptides. Score 0.532 Taking the results from Round 4 Chains 9, Residues 68, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2160 reflections ( 99.59 % complete ) and 1935 restraints for refining 917 atoms. 1672 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2668 (Rfree = 0.000) for 917 atoms. Found 5 (5 requested) and removed 6 (2 requested) atoms. Cycle 7: After refmac, R = 0.2382 (Rfree = 0.000) for 902 atoms. Found 5 (5 requested) and removed 10 (2 requested) atoms. Cycle 8: After refmac, R = 0.2346 (Rfree = 0.000) for 890 atoms. Found 4 (4 requested) and removed 5 (2 requested) atoms. Cycle 9: After refmac, R = 0.2307 (Rfree = 0.000) for 886 atoms. Found 4 (4 requested) and removed 6 (2 requested) atoms. Cycle 10: After refmac, R = 0.2136 (Rfree = 0.000) for 881 atoms. Found 4 (4 requested) and removed 5 (2 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.43 2.96 Search for helices and strands: 0 residues in 0 chains, 949 seeds are put forward Round 1: 67 peptides, 11 chains. Longest chain 9 peptides. Score 0.392 Round 2: 73 peptides, 11 chains. Longest chain 11 peptides. Score 0.442 Round 3: 76 peptides, 11 chains. Longest chain 13 peptides. Score 0.466 Round 4: 73 peptides, 11 chains. Longest chain 9 peptides. Score 0.442 Round 5: 73 peptides, 9 chains. Longest chain 15 peptides. Score 0.512 Taking the results from Round 5 Chains 9, Residues 64, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2160 reflections ( 99.59 % complete ) and 2211 restraints for refining 986 atoms. 1964 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2390 (Rfree = 0.000) for 986 atoms. Found 5 (5 requested) and removed 17 (2 requested) atoms. Cycle 12: After refmac, R = 0.2153 (Rfree = 0.000) for 965 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 13: After refmac, R = 0.2076 (Rfree = 0.000) for 957 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. Cycle 14: After refmac, R = 0.2036 (Rfree = 0.000) for 954 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. Cycle 15: After refmac, R = 0.1855 (Rfree = 0.000) for 950 atoms. Found 4 (5 requested) and removed 8 (2 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.56 3.07 Search for helices and strands: 0 residues in 0 chains, 1007 seeds are put forward Round 1: 64 peptides, 11 chains. Longest chain 10 peptides. Score 0.365 Round 2: 71 peptides, 10 chains. Longest chain 13 peptides. Score 0.462 Round 3: 69 peptides, 11 chains. Longest chain 10 peptides. Score 0.409 Round 4: 72 peptides, 11 chains. Longest chain 11 peptides. Score 0.433 Round 5: 69 peptides, 10 chains. Longest chain 12 peptides. Score 0.445 Taking the results from Round 2 Chains 10, Residues 61, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2160 reflections ( 99.59 % complete ) and 2042 restraints for refining 960 atoms. 1808 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2326 (Rfree = 0.000) for 960 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. Cycle 17: After refmac, R = 0.2374 (Rfree = 0.000) for 951 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. Cycle 18: After refmac, R = 0.2253 (Rfree = 0.000) for 948 atoms. Found 5 (5 requested) and removed 6 (2 requested) atoms. Cycle 19: After refmac, R = 0.2070 (Rfree = 0.000) for 945 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 20: After refmac, R = 0.1993 (Rfree = 0.000) for 941 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.52 3.03 Search for helices and strands: 0 residues in 0 chains, 1007 seeds are put forward Round 1: 57 peptides, 11 chains. Longest chain 7 peptides. Score 0.301 Round 2: 65 peptides, 11 chains. Longest chain 10 peptides. Score 0.374 Round 3: 65 peptides, 11 chains. Longest chain 9 peptides. Score 0.374 Round 4: 70 peptides, 11 chains. Longest chain 10 peptides. Score 0.417 Round 5: 65 peptides, 8 chains. Longest chain 14 peptides. Score 0.487 Taking the results from Round 5 Chains 8, Residues 57, Estimated correctness of the model 0.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 2160 reflections ( 99.59 % complete ) and 2153 restraints for refining 1010 atoms. 1888 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2735 (Rfree = 0.000) for 1010 atoms. Found 5 (5 requested) and removed 9 (2 requested) atoms. Cycle 22: After refmac, R = 0.2467 (Rfree = 0.000) for 995 atoms. Found 5 (5 requested) and removed 10 (2 requested) atoms. Cycle 23: After refmac, R = 0.2360 (Rfree = 0.000) for 986 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. Cycle 24: After refmac, R = 0.2194 (Rfree = 0.000) for 982 atoms. Found 1 (5 requested) and removed 2 (2 requested) atoms. Cycle 25: After refmac, R = 0.2250 (Rfree = 0.000) for 972 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.52 3.03 Search for helices and strands: 0 residues in 0 chains, 1015 seeds are put forward Round 1: 58 peptides, 11 chains. Longest chain 8 peptides. Score 0.310 Round 2: 66 peptides, 11 chains. Longest chain 10 peptides. Score 0.383 Round 3: 64 peptides, 11 chains. Longest chain 9 peptides. Score 0.365 Round 4: 57 peptides, 9 chains. Longest chain 10 peptides. Score 0.382 Round 5: 55 peptides, 10 chains. Longest chain 9 peptides. Score 0.323 Taking the results from Round 2 Chains 11, Residues 55, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2160 reflections ( 99.59 % complete ) and 2223 restraints for refining 982 atoms. 2014 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2363 (Rfree = 0.000) for 982 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. Cycle 27: After refmac, R = 0.2171 (Rfree = 0.000) for 975 atoms. Found 3 (5 requested) and removed 5 (2 requested) atoms. Cycle 28: After refmac, R = 0.2107 (Rfree = 0.000) for 970 atoms. Found 2 (5 requested) and removed 4 (2 requested) atoms. Cycle 29: After refmac, R = 0.2151 (Rfree = 0.000) for 965 atoms. Found 2 (5 requested) and removed 5 (2 requested) atoms. Cycle 30: After refmac, R = 0.2141 (Rfree = 0.000) for 961 atoms. Found 1 (5 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.53 3.04 Search for helices and strands: 0 residues in 0 chains, 984 seeds are put forward Round 1: 63 peptides, 12 chains. Longest chain 8 peptides. Score 0.317 Round 2: 69 peptides, 10 chains. Longest chain 10 peptides. Score 0.445 Round 3: 65 peptides, 10 chains. Longest chain 12 peptides. Score 0.412 Round 4: 66 peptides, 9 chains. Longest chain 13 peptides. Score 0.458 Round 5: 70 peptides, 10 chains. Longest chain 10 peptides. Score 0.454 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 ------------------------------------------------------ 2160 reflections ( 99.59 % complete ) and 2278 restraints for refining 1013 atoms. 2059 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2435 (Rfree = 0.000) for 1013 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. Cycle 32: After refmac, R = 0.2185 (Rfree = 0.000) for 1003 atoms. Found 4 (5 requested) and removed 3 (2 requested) atoms. Cycle 33: After refmac, R = 0.2272 (Rfree = 0.000) for 1001 atoms. Found 4 (5 requested) and removed 5 (2 requested) atoms. Cycle 34: After refmac, R = 0.2344 (Rfree = 0.000) for 992 atoms. Found 4 (5 requested) and removed 6 (2 requested) atoms. Cycle 35: After refmac, R = 0.2003 (Rfree = 0.000) for 987 atoms. Found 2 (5 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.56 3.07 Search for helices and strands: 0 residues in 0 chains, 1059 seeds are put forward Round 1: 51 peptides, 10 chains. Longest chain 8 peptides. Score 0.284 Round 2: 44 peptides, 8 chains. Longest chain 9 peptides. Score 0.301 Round 3: 61 peptides, 9 chains. Longest chain 12 peptides. Score 0.416 Round 4: 60 peptides, 9 chains. Longest chain 12 peptides. Score 0.408 Round 5: 64 peptides, 11 chains. Longest chain 10 peptides. Score 0.365 Taking the results from Round 3 Chains 9, Residues 52, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2160 reflections ( 99.59 % complete ) and 2323 restraints for refining 1013 atoms. 2124 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2298 (Rfree = 0.000) for 1013 atoms. Found 3 (5 requested) and removed 3 (2 requested) atoms. Cycle 37: After refmac, R = 0.2265 (Rfree = 0.000) for 997 atoms. Found 5 (5 requested) and removed 2 (2 requested) atoms. Cycle 38: After refmac, R = 0.2022 (Rfree = 0.000) for 998 atoms. Found 0 (5 requested) and removed 3 (2 requested) atoms. Cycle 39: After refmac, R = 0.1983 (Rfree = 0.000) for 993 atoms. Found 1 (5 requested) and removed 3 (2 requested) atoms. Cycle 40: After refmac, R = 0.1975 (Rfree = 0.000) for 990 atoms. Found 0 (5 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.57 3.08 Search for helices and strands: 0 residues in 0 chains, 1041 seeds are put forward Round 1: 51 peptides, 10 chains. Longest chain 8 peptides. Score 0.284 Round 2: 62 peptides, 11 chains. Longest chain 9 peptides. Score 0.347 Round 3: 57 peptides, 10 chains. Longest chain 8 peptides. Score 0.341 Round 4: 58 peptides, 10 chains. Longest chain 9 peptides. Score 0.351 Round 5: 65 peptides, 10 chains. Longest chain 12 peptides. Score 0.412 Taking the results from Round 5 Chains 10, Residues 55, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2160 reflections ( 99.59 % complete ) and 2327 restraints for refining 1012 atoms. 2117 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2427 (Rfree = 0.000) for 1012 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 42: After refmac, R = 0.2459 (Rfree = 0.000) for 1010 atoms. Found 5 (5 requested) and removed 10 (2 requested) atoms. Cycle 43: After refmac, R = 0.2245 (Rfree = 0.000) for 999 atoms. Found 5 (5 requested) and removed 2 (2 requested) atoms. Cycle 44: After refmac, R = 0.2261 (Rfree = 0.000) for 993 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. Cycle 45: After refmac, R = 0.2238 (Rfree = 0.000) for 984 atoms. Found 4 (5 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.46 2.98 Search for helices and strands: 0 residues in 0 chains, 1034 seeds are put forward Round 1: 54 peptides, 12 chains. Longest chain 7 peptides. Score 0.230 Round 2: 57 peptides, 10 chains. Longest chain 14 peptides. Score 0.341 Round 3: 66 peptides, 11 chains. Longest chain 12 peptides. Score 0.383 Round 4: 64 peptides, 9 chains. Longest chain 15 peptides. Score 0.442 Round 5: 66 peptides, 9 chains. Longest chain 12 peptides. Score 0.458 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 9, Residues 57, 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 2huj-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2160 reflections ( 99.59 % complete ) and 2252 restraints for refining 1008 atoms. 2033 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2598 (Rfree = 0.000) for 1008 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 47: After refmac, R = 0.2356 (Rfree = 0.000) for 993 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 48: After refmac, R = 0.2388 (Rfree = 0.000) for 988 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 49: After refmac, R = 0.2239 (Rfree = 0.000) for 983 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:50:53 GMT 2018 Job finished. TimeTaking 28.12 Used memory is bytes: 12140944