null Sun 23 Dec 22:22:40 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 2etd-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2etd-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2etd-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2etd-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/2etd-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2etd-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 22:22:49 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/2etd-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2etd-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 117 and 0 Target number of residues in the AU: 117 Target solvent content: 0.6539 Checking the provided sequence file Detected sequence length: 171 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 171 Adjusted target solvent content: 0.49 Input MTZ file: 2etd-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: 21 Cell parameters: 80.417 85.225 53.388 90.000 90.000 90.000 Input sequence file: 2etd-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 1368 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: 58.489 3.601 Wilson plot Bfac: 79.17 1930 reflections ( 92.65 % complete ) and 0 restraints for refining 1515 atoms. Observations/parameters ratio is 0.32 ------------------------------------------------------ Starting model: R = 0.3732 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.4264 (Rfree = 0.000) for 1515 atoms. Found 2 (9 requested) and removed 32 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.83 3.88 Search for helices and strands: 0 residues in 0 chains, 1524 seeds are put forward Round 1: 33 peptides, 7 chains. Longest chain 7 peptides. Score 0.231 Round 2: 50 peptides, 10 chains. Longest chain 9 peptides. Score 0.278 Round 3: 59 peptides, 10 chains. Longest chain 9 peptides. Score 0.367 Round 4: 63 peptides, 10 chains. Longest chain 10 peptides. Score 0.404 Round 5: 58 peptides, 9 chains. Longest chain 10 peptides. Score 0.399 Taking the results from Round 4 Chains 10, Residues 53, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1930 reflections ( 92.65 % complete ) and 2841 restraints for refining 1167 atoms. 2639 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3727 (Rfree = 0.000) for 1167 atoms. Found 6 (7 requested) and removed 40 (3 requested) atoms. Cycle 2: After refmac, R = 0.3683 (Rfree = 0.000) for 1107 atoms. Found 3 (7 requested) and removed 12 (3 requested) atoms. Cycle 3: After refmac, R = 0.3306 (Rfree = 0.000) for 1077 atoms. Found 7 (7 requested) and removed 32 (3 requested) atoms. Cycle 4: After refmac, R = 0.3325 (Rfree = 0.000) for 1032 atoms. Found 5 (6 requested) and removed 10 (3 requested) atoms. Cycle 5: After refmac, R = 0.3357 (Rfree = 0.000) for 1012 atoms. Found 6 (6 requested) and removed 14 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.69 3.74 Search for helices and strands: 0 residues in 0 chains, 1084 seeds are put forward Round 1: 39 peptides, 9 chains. Longest chain 5 peptides. Score 0.203 Round 2: 49 peptides, 9 chains. Longest chain 10 peptides. Score 0.312 Round 3: 54 peptides, 8 chains. Longest chain 11 peptides. Score 0.403 Round 4: 54 peptides, 8 chains. Longest chain 10 peptides. Score 0.403 Round 5: 49 peptides, 7 chains. Longest chain 9 peptides. Score 0.400 Taking the results from Round 4 Chains 8, Residues 46, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1930 reflections ( 92.65 % complete ) and 2123 restraints for refining 987 atoms. 1947 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3454 (Rfree = 0.000) for 987 atoms. Found 5 (6 requested) and removed 25 (3 requested) atoms. Cycle 7: After refmac, R = 0.3437 (Rfree = 0.000) for 954 atoms. Found 2 (6 requested) and removed 28 (3 requested) atoms. Cycle 8: After refmac, R = 0.3492 (Rfree = 0.000) for 912 atoms. Found 5 (5 requested) and removed 22 (2 requested) atoms. Cycle 9: After refmac, R = 0.3676 (Rfree = 0.000) for 891 atoms. Found 5 (5 requested) and removed 16 (2 requested) atoms. Cycle 10: After refmac, R = 0.3688 (Rfree = 0.000) for 874 atoms. Found 2 (5 requested) and removed 10 (2 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.68 3.73 Search for helices and strands: 0 residues in 0 chains, 934 seeds are put forward Round 1: 52 peptides, 10 chains. Longest chain 8 peptides. Score 0.299 Round 2: 59 peptides, 11 chains. Longest chain 9 peptides. Score 0.325 Round 3: 59 peptides, 9 chains. Longest chain 10 peptides. Score 0.408 Round 4: 65 peptides, 9 chains. Longest chain 12 peptides. Score 0.460 Round 5: 63 peptides, 8 chains. Longest chain 11 peptides. Score 0.482 Taking the results from Round 5 Chains 8, Residues 55, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1930 reflections ( 92.65 % complete ) and 1946 restraints for refining 941 atoms. 1734 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3512 (Rfree = 0.000) for 941 atoms. Found 5 (6 requested) and removed 16 (3 requested) atoms. Cycle 12: After refmac, R = 0.3576 (Rfree = 0.000) for 918 atoms. Found 4 (5 requested) and removed 19 (2 requested) atoms. Cycle 13: After refmac, R = 0.3406 (Rfree = 0.000) for 897 atoms. Found 4 (5 requested) and removed 9 (2 requested) atoms. Cycle 14: After refmac, R = 0.3719 (Rfree = 0.000) for 890 atoms. Found 5 (5 requested) and removed 17 (2 requested) atoms. Cycle 15: After refmac, R = 0.3074 (Rfree = 0.000) for 870 atoms. Found 3 (5 requested) and removed 8 (2 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.58 3.63 Search for helices and strands: 0 residues in 0 chains, 917 seeds are put forward Round 1: 53 peptides, 10 chains. Longest chain 10 peptides. Score 0.309 Round 2: 58 peptides, 10 chains. Longest chain 10 peptides. Score 0.358 Round 3: 53 peptides, 6 chains. Longest chain 19 peptides. Score 0.477 Round 4: 56 peptides, 7 chains. Longest chain 17 peptides. Score 0.462 Round 5: 61 peptides, 9 chains. Longest chain 12 peptides. Score 0.426 Taking the results from Round 3 Chains 6, Residues 47, Estimated correctness of the model 0.0 % 1 chains (18 residues) have been docked in sequence ------------------------------------------------------ 1930 reflections ( 92.65 % complete ) and 1761 restraints for refining 973 atoms. 1501 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3592 (Rfree = 0.000) for 973 atoms. Found 6 (6 requested) and removed 34 (3 requested) atoms. Cycle 17: After refmac, R = 0.3616 (Rfree = 0.000) for 933 atoms. Found 6 (6 requested) and removed 28 (3 requested) atoms. Cycle 18: After refmac, R = 0.3739 (Rfree = 0.000) for 901 atoms. Found 3 (5 requested) and removed 14 (2 requested) atoms. Cycle 19: After refmac, R = 0.3403 (Rfree = 0.000) for 881 atoms. Found 5 (5 requested) and removed 26 (2 requested) atoms. Cycle 20: After refmac, R = 0.3511 (Rfree = 0.000) for 854 atoms. Found 5 (5 requested) and removed 8 (2 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 4.66 4.72 Search for helices and strands: 0 residues in 0 chains, 888 seeds are put forward Round 1: 51 peptides, 8 chains. Longest chain 12 peptides. Score 0.375 Round 2: 64 peptides, 11 chains. Longest chain 15 peptides. Score 0.373 Round 3: 60 peptides, 9 chains. Longest chain 9 peptides. Score 0.417 Round 4: 60 peptides, 9 chains. Longest chain 13 peptides. Score 0.417 Round 5: 58 peptides, 8 chains. Longest chain 11 peptides. Score 0.439 Taking the results from Round 5 Chains 8, Residues 50, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1930 reflections ( 92.65 % complete ) and 2058 restraints for refining 975 atoms. 1866 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3194 (Rfree = 0.000) for 975 atoms. Found 4 (6 requested) and removed 8 (3 requested) atoms. Cycle 22: After refmac, R = 0.3297 (Rfree = 0.000) for 967 atoms. Found 3 (6 requested) and removed 12 (3 requested) atoms. Cycle 23: After refmac, R = 0.3093 (Rfree = 0.000) for 948 atoms. Found 6 (6 requested) and removed 11 (3 requested) atoms. Cycle 24: After refmac, R = 0.3073 (Rfree = 0.000) for 938 atoms. Found 6 (6 requested) and removed 13 (3 requested) atoms. Cycle 25: After refmac, R = 0.3006 (Rfree = 0.000) for 924 atoms. Found 5 (5 requested) and removed 6 (2 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 5.65 5.73 Search for helices and strands: 0 residues in 0 chains, 975 seeds are put forward Round 1: 40 peptides, 7 chains. Longest chain 10 peptides. Score 0.310 Round 2: 59 peptides, 11 chains. Longest chain 8 peptides. Score 0.325 Round 3: 58 peptides, 10 chains. Longest chain 11 peptides. Score 0.358 Round 4: 61 peptides, 9 chains. Longest chain 13 peptides. Score 0.426 Round 5: 58 peptides, 9 chains. Longest chain 11 peptides. Score 0.399 Taking the results from Round 4 Chains 9, Residues 52, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1930 reflections ( 92.65 % complete ) and 2390 restraints for refining 1052 atoms. 2191 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3531 (Rfree = 0.000) for 1052 atoms. Found 6 (6 requested) and removed 60 (3 requested) atoms. Cycle 27: After refmac, R = 0.3309 (Rfree = 0.000) for 987 atoms. Found 5 (6 requested) and removed 14 (3 requested) atoms. Cycle 28: After refmac, R = 0.3268 (Rfree = 0.000) for 970 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. Cycle 29: After refmac, R = 0.3136 (Rfree = 0.000) for 965 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Cycle 30: After refmac, R = 0.3215 (Rfree = 0.000) for 956 atoms. Found 6 (6 requested) and removed 10 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.69 3.74 Search for helices and strands: 0 residues in 0 chains, 1003 seeds are put forward Round 1: 55 peptides, 13 chains. Longest chain 5 peptides. Score 0.199 Round 2: 64 peptides, 12 chains. Longest chain 12 peptides. Score 0.332 Round 3: 65 peptides, 11 chains. Longest chain 11 peptides. Score 0.382 Round 4: 53 peptides, 9 chains. Longest chain 10 peptides. Score 0.352 Round 5: 53 peptides, 9 chains. Longest chain 13 peptides. Score 0.352 Taking the results from Round 3 Chains 11, Residues 54, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1930 reflections ( 92.65 % complete ) and 2440 restraints for refining 1077 atoms. 2235 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3625 (Rfree = 0.000) for 1077 atoms. Found 6 (6 requested) and removed 11 (3 requested) atoms. Cycle 32: After refmac, R = 0.3698 (Rfree = 0.000) for 1057 atoms. Found 6 (6 requested) and removed 17 (3 requested) atoms. Cycle 33: After refmac, R = 0.3198 (Rfree = 0.000) for 1026 atoms. Found 6 (6 requested) and removed 30 (3 requested) atoms. Cycle 34: After refmac, R = 0.3277 (Rfree = 0.000) for 986 atoms. Found 4 (6 requested) and removed 11 (3 requested) atoms. Cycle 35: After refmac, R = 0.2961 (Rfree = 0.000) for 970 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.61 3.66 Search for helices and strands: 0 residues in 0 chains, 1017 seeds are put forward Round 1: 49 peptides, 10 chains. Longest chain 8 peptides. Score 0.268 Round 2: 50 peptides, 9 chains. Longest chain 9 peptides. Score 0.322 Round 3: 61 peptides, 11 chains. Longest chain 9 peptides. Score 0.345 Round 4: 50 peptides, 9 chains. Longest chain 8 peptides. Score 0.322 Round 5: 50 peptides, 9 chains. Longest chain 7 peptides. Score 0.322 Taking the results from Round 3 Chains 11, Residues 50, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1930 reflections ( 92.65 % complete ) and 2111 restraints for refining 1011 atoms. 1922 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3159 (Rfree = 0.000) for 1011 atoms. Found 5 (6 requested) and removed 11 (3 requested) atoms. Cycle 37: After refmac, R = 0.3055 (Rfree = 0.000) for 996 atoms. Found 3 (6 requested) and removed 6 (3 requested) atoms. Cycle 38: After refmac, R = 0.3028 (Rfree = 0.000) for 986 atoms. Found 5 (6 requested) and removed 5 (3 requested) atoms. Cycle 39: After refmac, R = 0.3392 (Rfree = 0.000) for 983 atoms. Found 6 (6 requested) and removed 11 (3 requested) atoms. Cycle 40: After refmac, R = 0.3222 (Rfree = 0.000) for 970 atoms. Found 2 (6 requested) and removed 7 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.72 3.77 Search for helices and strands: 0 residues in 0 chains, 1016 seeds are put forward Round 1: 37 peptides, 8 chains. Longest chain 6 peptides. Score 0.228 Round 2: 52 peptides, 9 chains. Longest chain 13 peptides. Score 0.342 Round 3: 48 peptides, 8 chains. Longest chain 13 peptides. Score 0.346 Round 4: 42 peptides, 7 chains. Longest chain 9 peptides. Score 0.331 Round 5: 39 peptides, 6 chains. Longest chain 12 peptides. Score 0.347 Taking the results from Round 5 Chains 6, Residues 33, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1930 reflections ( 92.65 % complete ) and 2211 restraints for refining 1025 atoms. 2085 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3273 (Rfree = 0.000) for 1025 atoms. Found 4 (6 requested) and removed 8 (3 requested) atoms. Cycle 42: After refmac, R = 0.3363 (Rfree = 0.000) for 1016 atoms. Found 3 (6 requested) and removed 13 (3 requested) atoms. Cycle 43: After refmac, R = 0.3178 (Rfree = 0.000) for 998 atoms. Found 5 (6 requested) and removed 6 (3 requested) atoms. Cycle 44: After refmac, R = 0.3308 (Rfree = 0.000) for 995 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 45: After refmac, R = 0.3337 (Rfree = 0.000) for 993 atoms. Found 1 (6 requested) and removed 10 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.70 3.75 Search for helices and strands: 0 residues in 0 chains, 1021 seeds are put forward Round 1: 38 peptides, 9 chains. Longest chain 6 peptides. Score 0.191 Round 2: 50 peptides, 9 chains. Longest chain 12 peptides. Score 0.322 Round 3: 49 peptides, 11 chains. Longest chain 8 peptides. Score 0.223 Round 4: 52 peptides, 9 chains. Longest chain 10 peptides. Score 0.342 Round 5: 42 peptides, 7 chains. Longest chain 12 peptides. Score 0.331 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 9, Residues 43, 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 2etd-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 1930 reflections ( 92.65 % complete ) and 2110 restraints for refining 1000 atoms. 1947 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3506 (Rfree = 0.000) for 1000 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.3261 (Rfree = 0.000) for 992 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.3191 (Rfree = 0.000) for 985 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.2867 (Rfree = 0.000) for 979 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:47:19 GMT 2018 Job finished. TimeTaking 24.65 Used memory is bytes: 18409840