null Sun 23 Dec 22:22:49 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 2etj-1.7-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2etj-1.7-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2etj-1.7-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2etj-1.7-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/2etj-1.7-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2etj-1.7-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 22:22:59 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/2etj-1.7-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2etj-1.7-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 224 and 0 Target number of residues in the AU: 224 Target solvent content: 0.4876 Checking the provided sequence file Detected sequence length: 250 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 250 Adjusted target solvent content: 0.43 Input MTZ file: 2etj-1.7-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: 144 Cell parameters: 51.821 51.821 76.293 90.000 90.000 120.000 Input sequence file: 2etj-1.7-parrot-hancs.fasta_lf Building free atoms model in initial map for 2000 target number of atoms Had to go as low as 0.45 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 1 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: 24.534 1.700 Wilson plot Bfac: 20.65 25218 reflections ( 99.95 % complete ) and 0 restraints for refining 2212 atoms. Observations/parameters ratio is 2.85 ------------------------------------------------------ Starting model: R = 0.3635 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3143 (Rfree = 0.000) for 2212 atoms. Found 78 (120 requested) and removed 71 (60 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.90 2.09 Round 1: 150 peptides, 19 chains. Longest chain 23 peptides. Score 0.640 Round 2: 166 peptides, 12 chains. Longest chain 27 peptides. Score 0.812 Round 3: 177 peptides, 12 chains. Longest chain 35 peptides. Score 0.838 Round 4: 188 peptides, 4 chains. Longest chain 155 peptides. Score 0.930 Round 5: 184 peptides, 5 chains. Longest chain 83 peptides. Score 0.918 Taking the results from Round 4 Chains 4, Residues 184, Estimated correctness of the model 99.7 % 2 chains (177 residues) have been docked in sequence Building loops using Loopy2018 4 chains (184 residues) following loop building 2 chains (177 residues) in sequence following loop building ------------------------------------------------------ 25218 reflections ( 99.95 % complete ) and 2219 restraints for refining 1993 atoms. 798 conditional restraints added. Observations/parameters ratio is 3.16 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3330 (Rfree = 0.000) for 1993 atoms. Found 54 (108 requested) and removed 59 (54 requested) atoms. Cycle 2: After refmac, R = 0.3068 (Rfree = 0.000) for 1979 atoms. Found 48 (106 requested) and removed 35 (54 requested) atoms. Cycle 3: After refmac, R = 0.2728 (Rfree = 0.000) for 1977 atoms. Found 56 (104 requested) and removed 29 (54 requested) atoms. Cycle 4: After refmac, R = 0.2530 (Rfree = 0.000) for 1964 atoms. Found 55 (102 requested) and removed 30 (54 requested) atoms. Cycle 5: After refmac, R = 0.2410 (Rfree = 0.000) for 1972 atoms. Found 47 (99 requested) and removed 23 (54 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.84 2.02 Round 1: 187 peptides, 4 chains. Longest chain 98 peptides. Score 0.929 Round 2: 193 peptides, 3 chains. Longest chain 103 peptides. Score 0.942 Round 3: 194 peptides, 4 chains. Longest chain 67 peptides. Score 0.936 Round 4: 196 peptides, 3 chains. Longest chain 83 peptides. Score 0.944 Round 5: 193 peptides, 4 chains. Longest chain 67 peptides. Score 0.935 Taking the results from Round 4 Chains 3, Residues 193, Estimated correctness of the model 99.8 % 3 chains (193 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 147 A and 150 A 2 chains (195 residues) following loop building 2 chains (195 residues) in sequence following loop building ------------------------------------------------------ 25218 reflections ( 99.95 % complete ) and 2011 restraints for refining 1974 atoms. 470 conditional restraints added. Observations/parameters ratio is 3.19 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2425 (Rfree = 0.000) for 1974 atoms. Found 67 (98 requested) and removed 54 (53 requested) atoms. Cycle 7: After refmac, R = 0.2289 (Rfree = 0.000) for 1978 atoms. Found 51 (97 requested) and removed 23 (54 requested) atoms. Cycle 8: After refmac, R = 0.2180 (Rfree = 0.000) for 2004 atoms. Found 42 (98 requested) and removed 18 (54 requested) atoms. Cycle 9: After refmac, R = 0.2127 (Rfree = 0.000) for 2024 atoms. Found 36 (99 requested) and removed 15 (55 requested) atoms. Cycle 10: After refmac, R = 0.2073 (Rfree = 0.000) for 2037 atoms. Found 39 (100 requested) and removed 14 (55 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.83 2.01 Round 1: 197 peptides, 3 chains. Longest chain 104 peptides. Score 0.945 Round 2: 198 peptides, 4 chains. Longest chain 84 peptides. Score 0.940 Round 3: 198 peptides, 4 chains. Longest chain 104 peptides. Score 0.940 Round 4: 200 peptides, 3 chains. Longest chain 104 peptides. Score 0.948 Round 5: 195 peptides, 5 chains. Longest chain 81 peptides. Score 0.930 Taking the results from Round 4 Chains 3, Residues 197, Estimated correctness of the model 99.8 % 3 chains (197 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 127 A and 130 A 2 chains (199 residues) following loop building 2 chains (199 residues) in sequence following loop building ------------------------------------------------------ 25218 reflections ( 99.95 % complete ) and 1966 restraints for refining 1994 atoms. 395 conditional restraints added. Observations/parameters ratio is 3.16 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2188 (Rfree = 0.000) for 1994 atoms. Found 78 (97 requested) and removed 44 (54 requested) atoms. Cycle 12: After refmac, R = 0.2099 (Rfree = 0.000) for 2025 atoms. Found 57 (97 requested) and removed 35 (55 requested) atoms. Cycle 13: After refmac, R = 0.2027 (Rfree = 0.000) for 2044 atoms. Found 44 (95 requested) and removed 16 (55 requested) atoms. Cycle 14: After refmac, R = 0.1983 (Rfree = 0.000) for 2068 atoms. Found 48 (96 requested) and removed 20 (56 requested) atoms. Cycle 15: After refmac, R = 0.1954 (Rfree = 0.000) for 2089 atoms. Found 45 (98 requested) and removed 25 (57 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.83 2.01 Round 1: 201 peptides, 2 chains. Longest chain 164 peptides. Score 0.955 Round 2: 200 peptides, 3 chains. Longest chain 164 peptides. Score 0.948 Round 3: 200 peptides, 3 chains. Longest chain 84 peptides. Score 0.948 Round 4: 198 peptides, 4 chains. Longest chain 95 peptides. Score 0.940 Round 5: 200 peptides, 3 chains. Longest chain 84 peptides. Score 0.948 Taking the results from Round 1 Chains 2, Residues 199, Estimated correctness of the model 99.9 % 2 chains (199 residues) have been docked in sequence Building loops using Loopy2018 2 chains (199 residues) following loop building 2 chains (199 residues) in sequence following loop building ------------------------------------------------------ 25218 reflections ( 99.95 % complete ) and 1992 restraints for refining 1994 atoms. 421 conditional restraints added. Observations/parameters ratio is 3.16 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2130 (Rfree = 0.000) for 1994 atoms. Found 74 (91 requested) and removed 39 (54 requested) atoms. Cycle 17: After refmac, R = 0.2047 (Rfree = 0.000) for 2027 atoms. Found 49 (90 requested) and removed 14 (55 requested) atoms. Cycle 18: After refmac, R = 0.1983 (Rfree = 0.000) for 2059 atoms. Found 36 (92 requested) and removed 11 (56 requested) atoms. Cycle 19: After refmac, R = 0.1947 (Rfree = 0.000) for 2080 atoms. Found 36 (93 requested) and removed 14 (56 requested) atoms. Cycle 20: After refmac, R = 0.1918 (Rfree = 0.000) for 2098 atoms. Found 43 (93 requested) and removed 21 (57 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.83 2.01 Round 1: 200 peptides, 2 chains. Longest chain 164 peptides. Score 0.954 Round 2: 200 peptides, 2 chains. Longest chain 164 peptides. Score 0.954 Round 3: 199 peptides, 3 chains. Longest chain 164 peptides. Score 0.947 Round 4: 198 peptides, 4 chains. Longest chain 104 peptides. Score 0.940 Round 5: 196 peptides, 5 chains. Longest chain 60 peptides. Score 0.931 Taking the results from Round 2 Chains 2, Residues 198, Estimated correctness of the model 99.9 % 2 chains (198 residues) have been docked in sequence Building loops using Loopy2018 2 chains (198 residues) following loop building 2 chains (198 residues) in sequence following loop building ------------------------------------------------------ 25218 reflections ( 99.95 % complete ) and 1993 restraints for refining 1994 atoms. 430 conditional restraints added. Observations/parameters ratio is 3.16 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2091 (Rfree = 0.000) for 1994 atoms. Found 78 (89 requested) and removed 41 (54 requested) atoms. Cycle 22: After refmac, R = 0.2016 (Rfree = 0.000) for 2029 atoms. Found 55 (88 requested) and removed 14 (55 requested) atoms. Cycle 23: After refmac, R = 0.1945 (Rfree = 0.000) for 2068 atoms. Found 36 (90 requested) and removed 13 (56 requested) atoms. Cycle 24: After refmac, R = 0.1906 (Rfree = 0.000) for 2087 atoms. Found 42 (90 requested) and removed 17 (56 requested) atoms. Cycle 25: After refmac, R = 0.1886 (Rfree = 0.000) for 2110 atoms. Found 33 (91 requested) and removed 27 (57 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.83 2.01 Round 1: 199 peptides, 3 chains. Longest chain 104 peptides. Score 0.947 Round 2: 200 peptides, 2 chains. Longest chain 164 peptides. Score 0.954 Round 3: 199 peptides, 3 chains. Longest chain 132 peptides. Score 0.947 Round 4: 197 peptides, 5 chains. Longest chain 80 peptides. Score 0.932 Round 5: 199 peptides, 2 chains. Longest chain 163 peptides. Score 0.953 Taking the results from Round 2 Chains 2, Residues 198, Estimated correctness of the model 99.9 % 2 chains (198 residues) have been docked in sequence Building loops using Loopy2018 2 chains (198 residues) following loop building 2 chains (198 residues) in sequence following loop building ------------------------------------------------------ 25218 reflections ( 99.95 % complete ) and 2009 restraints for refining 1994 atoms. 446 conditional restraints added. Observations/parameters ratio is 3.16 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2081 (Rfree = 0.000) for 1994 atoms. Found 75 (84 requested) and removed 35 (54 requested) atoms. Cycle 27: After refmac, R = 0.2008 (Rfree = 0.000) for 2032 atoms. Found 41 (86 requested) and removed 12 (55 requested) atoms. Cycle 28: After refmac, R = 0.1945 (Rfree = 0.000) for 2057 atoms. Found 33 (87 requested) and removed 7 (56 requested) atoms. Cycle 29: After refmac, R = 0.1918 (Rfree = 0.000) for 2077 atoms. Found 34 (88 requested) and removed 11 (56 requested) atoms. Cycle 30: After refmac, R = 0.1885 (Rfree = 0.000) for 2098 atoms. Found 41 (89 requested) and removed 19 (57 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.83 2.01 Round 1: 200 peptides, 2 chains. Longest chain 164 peptides. Score 0.954 Round 2: 200 peptides, 2 chains. Longest chain 164 peptides. Score 0.954 Round 3: 198 peptides, 4 chains. Longest chain 80 peptides. Score 0.940 Round 4: 199 peptides, 3 chains. Longest chain 96 peptides. Score 0.947 Round 5: 200 peptides, 2 chains. Longest chain 164 peptides. Score 0.954 Taking the results from Round 5 Chains 2, Residues 198, Estimated correctness of the model 99.9 % 2 chains (198 residues) have been docked in sequence Building loops using Loopy2018 2 chains (198 residues) following loop building 2 chains (198 residues) in sequence following loop building ------------------------------------------------------ 25218 reflections ( 99.95 % complete ) and 2021 restraints for refining 1994 atoms. 458 conditional restraints added. Observations/parameters ratio is 3.16 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2072 (Rfree = 0.000) for 1994 atoms. Found 74 (84 requested) and removed 32 (54 requested) atoms. Cycle 32: After refmac, R = 0.1994 (Rfree = 0.000) for 2033 atoms. Found 45 (86 requested) and removed 13 (55 requested) atoms. Cycle 33: After refmac, R = 0.1943 (Rfree = 0.000) for 2064 atoms. Found 34 (87 requested) and removed 21 (56 requested) atoms. Cycle 34: After refmac, R = 0.1903 (Rfree = 0.000) for 2075 atoms. Found 40 (86 requested) and removed 12 (56 requested) atoms. Cycle 35: After refmac, R = 0.1869 (Rfree = 0.000) for 2102 atoms. Found 30 (87 requested) and removed 25 (57 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.82 2.00 Round 1: 200 peptides, 2 chains. Longest chain 164 peptides. Score 0.954 Round 2: 199 peptides, 3 chains. Longest chain 132 peptides. Score 0.947 Round 3: 197 peptides, 4 chains. Longest chain 155 peptides. Score 0.939 Round 4: 198 peptides, 4 chains. Longest chain 84 peptides. Score 0.940 Round 5: 195 peptides, 3 chains. Longest chain 154 peptides. Score 0.944 Taking the results from Round 1 Chains 2, Residues 198, Estimated correctness of the model 99.9 % 2 chains (198 residues) have been docked in sequence Building loops using Loopy2018 2 chains (198 residues) following loop building 2 chains (198 residues) in sequence following loop building ------------------------------------------------------ 25218 reflections ( 99.95 % complete ) and 1991 restraints for refining 1994 atoms. 428 conditional restraints added. Observations/parameters ratio is 3.16 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2053 (Rfree = 0.000) for 1994 atoms. Found 80 (80 requested) and removed 35 (54 requested) atoms. Cycle 37: After refmac, R = 0.1981 (Rfree = 0.000) for 2036 atoms. Found 51 (82 requested) and removed 19 (55 requested) atoms. Cycle 38: After refmac, R = 0.1937 (Rfree = 0.000) for 2065 atoms. Found 40 (83 requested) and removed 18 (56 requested) atoms. Cycle 39: After refmac, R = 0.1895 (Rfree = 0.000) for 2086 atoms. Found 41 (84 requested) and removed 23 (56 requested) atoms. Cycle 40: After refmac, R = 0.1873 (Rfree = 0.000) for 2096 atoms. Found 50 (82 requested) and removed 26 (57 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.82 2.00 Round 1: 201 peptides, 2 chains. Longest chain 165 peptides. Score 0.955 Round 2: 198 peptides, 4 chains. Longest chain 80 peptides. Score 0.940 Round 3: 198 peptides, 4 chains. Longest chain 104 peptides. Score 0.940 Round 4: 196 peptides, 6 chains. Longest chain 60 peptides. Score 0.924 Round 5: 199 peptides, 3 chains. Longest chain 84 peptides. Score 0.947 Taking the results from Round 1 Chains 2, Residues 199, Estimated correctness of the model 99.9 % 2 chains (199 residues) have been docked in sequence Building loops using Loopy2018 2 chains (199 residues) following loop building 2 chains (199 residues) in sequence following loop building ------------------------------------------------------ 25218 reflections ( 99.95 % complete ) and 1974 restraints for refining 2009 atoms. 403 conditional restraints added. Observations/parameters ratio is 3.14 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2050 (Rfree = 0.000) for 2009 atoms. Found 75 (76 requested) and removed 41 (54 requested) atoms. Cycle 42: After refmac, R = 0.1978 (Rfree = 0.000) for 2036 atoms. Found 60 (75 requested) and removed 10 (55 requested) atoms. Cycle 43: After refmac, R = 0.1914 (Rfree = 0.000) for 2083 atoms. Found 41 (77 requested) and removed 24 (56 requested) atoms. Cycle 44: After refmac, R = 0.1873 (Rfree = 0.000) for 2098 atoms. Found 44 (75 requested) and removed 20 (57 requested) atoms. Cycle 45: After refmac, R = 0.1853 (Rfree = 0.000) for 2117 atoms. Found 35 (76 requested) and removed 30 (57 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.83 2.01 Round 1: 199 peptides, 3 chains. Longest chain 104 peptides. Score 0.947 Round 2: 198 peptides, 4 chains. Longest chain 74 peptides. Score 0.940 Round 3: 196 peptides, 5 chains. Longest chain 84 peptides. Score 0.931 Round 4: 198 peptides, 4 chains. Longest chain 96 peptides. Score 0.940 Round 5: 193 peptides, 7 chains. Longest chain 51 peptides. Score 0.913 Taking the results from Round 1 Last building cycle: Chain fragments will be rearranged Chains 3, Residues 196, Estimated correctness of the model 99.8 % 3 chains (196 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 127 A and 130 A 2 chains (198 residues) following loop building 2 chains (198 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 25218 reflections ( 99.95 % complete ) and 1563 restraints for refining 1538 atoms. Observations/parameters ratio is 4.10 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2563 (Rfree = 0.000) for 1538 atoms. Found 32 (53 requested) and removed 0 (53 requested) atoms. Cycle 47: After refmac, R = 0.2406 (Rfree = 0.000) for 1538 atoms. Found 13 (54 requested) and removed 0 (42 requested) atoms. Cycle 48: After refmac, R = 0.2310 (Rfree = 0.000) for 1538 atoms. Found 10 (55 requested) and removed 1 (43 requested) atoms. Cycle 49: After refmac, R = 0.2261 (Rfree = 0.000) for 1538 atoms. Found 4 (55 requested) and removed 0 (43 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:09:35 GMT 2018 Job finished. TimeTaking 46.75 Used memory is bytes: 13923064