Mon 24 Dec 07:32:25 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2hq7-4.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2hq7-4.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2hq7-4.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2hq7-4.0-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2hq7-4.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2hq7-4.0-parrot-noncs ############### 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 ============================================================ Mon 24 Dec 07:32:29 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/noncs/ArpWArp/wArpResults/WorkingDir/2hq7-4.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2hq7-4.0-parrot-noncs/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 183 and 0 Target number of residues in the AU: 183 Target solvent content: 0.6503 Checking the provided sequence file Detected sequence length: 146 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 292 Adjusted target solvent content: 0.44 Input MTZ file: 2hq7-4.0-parrot-noncs.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: 5 Cell parameters: 85.850 36.790 97.970 90.000 113.753 90.000 Input sequence file: 2hq7-4.0-parrot-noncs.fasta_lf Building free atoms model in initial map for 2336 target number of atoms Had to go as low as 0.80 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 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 89.671 4.000 Wilson plot Bfac: 77.90 2485 reflections ( 99.04 % complete ) and 0 restraints for refining 2585 atoms. Observations/parameters ratio is 0.24 ------------------------------------------------------ Starting model: R = 0.3522 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3270 (Rfree = 0.000) for 2585 atoms. Found 12 (12 requested) and removed 33 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.61 3.91 Search for helices and strands: 0 residues in 0 chains, 2617 seeds are put forward NCS extension: 0 residues added, 2617 seeds are put forward Round 1: 97 peptides, 19 chains. Longest chain 11 peptides. Score 0.308 Round 2: 122 peptides, 20 chains. Longest chain 15 peptides. Score 0.430 Round 3: 121 peptides, 17 chains. Longest chain 17 peptides. Score 0.495 Round 4: 124 peptides, 22 chains. Longest chain 13 peptides. Score 0.393 Round 5: 119 peptides, 16 chains. Longest chain 13 peptides. Score 0.507 Taking the results from Round 5 Chains 16, Residues 103, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2485 reflections ( 99.04 % complete ) and 5103 restraints for refining 2109 atoms. 4707 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2987 (Rfree = 0.000) for 2109 atoms. Found 10 (10 requested) and removed 23 (5 requested) atoms. Cycle 2: After refmac, R = 0.2753 (Rfree = 0.000) for 2061 atoms. Found 9 (9 requested) and removed 24 (4 requested) atoms. Cycle 3: After refmac, R = 0.2267 (Rfree = 0.000) for 2030 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 4: After refmac, R = 0.2513 (Rfree = 0.000) for 2016 atoms. Found 9 (9 requested) and removed 20 (4 requested) atoms. Cycle 5: After refmac, R = 0.1952 (Rfree = 0.000) for 1998 atoms. Found 2 (9 requested) and removed 9 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.67 3.98 Search for helices and strands: 0 residues in 0 chains, 2067 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 2081 seeds are put forward Round 1: 93 peptides, 19 chains. Longest chain 8 peptides. Score 0.283 Round 2: 103 peptides, 18 chains. Longest chain 11 peptides. Score 0.371 Round 3: 125 peptides, 21 chains. Longest chain 12 peptides. Score 0.423 Round 4: 108 peptides, 17 chains. Longest chain 16 peptides. Score 0.425 Round 5: 112 peptides, 21 chains. Longest chain 11 peptides. Score 0.348 Taking the results from Round 4 Chains 17, Residues 91, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2485 reflections ( 99.04 % complete ) and 4858 restraints for refining 1995 atoms. 4511 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2356 (Rfree = 0.000) for 1995 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 7: After refmac, R = 0.2626 (Rfree = 0.000) for 1977 atoms. Found 9 (9 requested) and removed 21 (4 requested) atoms. Cycle 8: After refmac, R = 0.2436 (Rfree = 0.000) for 1957 atoms. Found 9 (9 requested) and removed 14 (4 requested) atoms. Cycle 9: After refmac, R = 0.2444 (Rfree = 0.000) for 1940 atoms. Found 9 (9 requested) and removed 20 (4 requested) atoms. Cycle 10: After refmac, R = 0.2272 (Rfree = 0.000) for 1920 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.68 3.99 Search for helices and strands: 0 residues in 0 chains, 1997 seeds are put forward NCS extension: 0 residues added, 1997 seeds are put forward Round 1: 88 peptides, 20 chains. Longest chain 8 peptides. Score 0.222 Round 2: 95 peptides, 17 chains. Longest chain 8 peptides. Score 0.349 Round 3: 102 peptides, 18 chains. Longest chain 10 peptides. Score 0.365 Round 4: 106 peptides, 20 chains. Longest chain 12 peptides. Score 0.338 Round 5: 118 peptides, 20 chains. Longest chain 12 peptides. Score 0.408 Taking the results from Round 5 Chains 20, Residues 98, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2485 reflections ( 99.04 % complete ) and 4733 restraints for refining 1988 atoms. 4361 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2553 (Rfree = 0.000) for 1988 atoms. Found 9 (9 requested) and removed 21 (4 requested) atoms. Cycle 12: After refmac, R = 0.2344 (Rfree = 0.000) for 1962 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Cycle 13: After refmac, R = 0.2146 (Rfree = 0.000) for 1943 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 14: After refmac, R = 0.1652 (Rfree = 0.000) for 1930 atoms. Found 6 (9 requested) and removed 9 (4 requested) atoms. Cycle 15: After refmac, R = 0.1443 (Rfree = 0.000) for 1925 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.70 4.01 Search for helices and strands: 0 residues in 0 chains, 2019 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 2036 seeds are put forward Round 1: 89 peptides, 19 chains. Longest chain 11 peptides. Score 0.257 Round 2: 115 peptides, 21 chains. Longest chain 14 peptides. Score 0.366 Round 3: 125 peptides, 23 chains. Longest chain 15 peptides. Score 0.375 Round 4: 123 peptides, 21 chains. Longest chain 16 peptides. Score 0.412 Round 5: 132 peptides, 23 chains. Longest chain 12 peptides. Score 0.414 Taking the results from Round 5 Chains 23, Residues 109, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2485 reflections ( 99.04 % complete ) and 4804 restraints for refining 2063 atoms. 4391 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2410 (Rfree = 0.000) for 2063 atoms. Found 9 (9 requested) and removed 26 (4 requested) atoms. Cycle 17: After refmac, R = 0.2065 (Rfree = 0.000) for 2038 atoms. Found 9 (9 requested) and removed 16 (4 requested) atoms. Cycle 18: After refmac, R = 0.2033 (Rfree = 0.000) for 2023 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Cycle 19: After refmac, R = 0.2058 (Rfree = 0.000) for 2014 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 20: After refmac, R = 0.1917 (Rfree = 0.000) for 2008 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.66 3.97 Search for helices and strands: 0 residues in 0 chains, 2081 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 2097 seeds are put forward Round 1: 86 peptides, 19 chains. Longest chain 6 peptides. Score 0.237 Round 2: 102 peptides, 19 chains. Longest chain 9 peptides. Score 0.339 Round 3: 88 peptides, 16 chains. Longest chain 11 peptides. Score 0.332 Round 4: 88 peptides, 14 chains. Longest chain 9 peptides. Score 0.386 Round 5: 92 peptides, 16 chains. Longest chain 13 peptides. Score 0.357 Taking the results from Round 4 Chains 14, Residues 74, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2485 reflections ( 99.04 % complete ) and 5007 restraints for refining 2085 atoms. 4725 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2586 (Rfree = 0.000) for 2085 atoms. Found 9 (9 requested) and removed 124 (4 requested) atoms. Cycle 22: After refmac, R = 0.1841 (Rfree = 0.000) for 1955 atoms. Found 9 (9 requested) and removed 14 (4 requested) atoms. Cycle 23: After refmac, R = 0.2268 (Rfree = 0.000) for 1941 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 24: After refmac, R = 0.2291 (Rfree = 0.000) for 1935 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 25: After refmac, R = 0.2153 (Rfree = 0.000) for 1922 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.63 3.93 Search for helices and strands: 0 residues in 0 chains, 1991 seeds are put forward NCS extension: 0 residues added, 1991 seeds are put forward Round 1: 67 peptides, 15 chains. Longest chain 6 peptides. Score 0.220 Round 2: 84 peptides, 17 chains. Longest chain 8 peptides. Score 0.279 Round 3: 93 peptides, 20 chains. Longest chain 8 peptides. Score 0.256 Round 4: 96 peptides, 18 chains. Longest chain 10 peptides. Score 0.329 Round 5: 94 peptides, 17 chains. Longest chain 10 peptides. Score 0.343 Taking the results from Round 5 Chains 17, Residues 77, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2485 reflections ( 99.04 % complete ) and 4412 restraints for refining 1913 atoms. 4121 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2232 (Rfree = 0.000) for 1913 atoms. Found 9 (9 requested) and removed 16 (4 requested) atoms. Cycle 27: After refmac, R = 0.2086 (Rfree = 0.000) for 1892 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 28: After refmac, R = 0.2174 (Rfree = 0.000) for 1883 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 29: After refmac, R = 0.2024 (Rfree = 0.000) for 1875 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 30: After refmac, R = 0.2148 (Rfree = 0.000) for 1871 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.66 3.97 Search for helices and strands: 0 residues in 0 chains, 1932 seeds are put forward NCS extension: 0 residues added, 1932 seeds are put forward Round 1: 90 peptides, 21 chains. Longest chain 8 peptides. Score 0.208 Round 2: 95 peptides, 20 chains. Longest chain 6 peptides. Score 0.269 Round 3: 102 peptides, 19 chains. Longest chain 8 peptides. Score 0.339 Round 4: 103 peptides, 19 chains. Longest chain 8 peptides. Score 0.345 Round 5: 108 peptides, 19 chains. Longest chain 10 peptides. Score 0.375 Taking the results from Round 5 Chains 19, Residues 89, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2485 reflections ( 99.04 % complete ) and 4534 restraints for refining 1961 atoms. 4197 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2100 (Rfree = 0.000) for 1961 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 32: After refmac, R = 0.2126 (Rfree = 0.000) for 1941 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 33: After refmac, R = 0.2247 (Rfree = 0.000) for 1930 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. Cycle 34: After refmac, R = 0.2063 (Rfree = 0.000) for 1920 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 35: After refmac, R = 0.1516 (Rfree = 0.000) for 1917 atoms. Found 3 (9 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.67 3.98 Search for helices and strands: 0 residues in 0 chains, 1971 seeds are put forward NCS extension: 0 residues added, 1971 seeds are put forward Round 1: 79 peptides, 18 chains. Longest chain 6 peptides. Score 0.217 Round 2: 92 peptides, 17 chains. Longest chain 9 peptides. Score 0.330 Round 3: 96 peptides, 17 chains. Longest chain 9 peptides. Score 0.355 Round 4: 104 peptides, 17 chains. Longest chain 11 peptides. Score 0.402 Round 5: 94 peptides, 17 chains. Longest chain 13 peptides. Score 0.343 Taking the results from Round 4 Chains 17, Residues 87, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2485 reflections ( 99.04 % complete ) and 4524 restraints for refining 1965 atoms. 4193 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2349 (Rfree = 0.000) for 1965 atoms. Found 9 (9 requested) and removed 5 (4 requested) atoms. Cycle 37: After refmac, R = 0.2216 (Rfree = 0.000) for 1958 atoms. Found 9 (9 requested) and removed 5 (4 requested) atoms. Cycle 38: After refmac, R = 0.2078 (Rfree = 0.000) for 1956 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 39: After refmac, R = 0.1565 (Rfree = 0.000) for 1949 atoms. Found 2 (9 requested) and removed 7 (4 requested) atoms. Cycle 40: After refmac, R = 0.1952 (Rfree = 0.000) for 1938 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.67 3.98 Search for helices and strands: 0 residues in 0 chains, 2014 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 2027 seeds are put forward Round 1: 77 peptides, 17 chains. Longest chain 6 peptides. Score 0.232 Round 2: 85 peptides, 15 chains. Longest chain 10 peptides. Score 0.341 Round 3: 82 peptides, 16 chains. Longest chain 8 peptides. Score 0.294 Round 4: 84 peptides, 15 chains. Longest chain 8 peptides. Score 0.335 Round 5: 74 peptides, 14 chains. Longest chain 8 peptides. Score 0.298 Taking the results from Round 2 Chains 15, Residues 70, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2485 reflections ( 99.04 % complete ) and 4698 restraints for refining 1971 atoms. 4433 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2193 (Rfree = 0.000) for 1971 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 42: After refmac, R = 0.2077 (Rfree = 0.000) for 1964 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 43: After refmac, R = 0.1988 (Rfree = 0.000) for 1961 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. Cycle 44: After refmac, R = 0.1926 (Rfree = 0.000) for 1961 atoms. Found 9 (9 requested) and removed 5 (4 requested) atoms. Cycle 45: After refmac, R = 0.1331 (Rfree = 0.000) for 1963 atoms. Found 7 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.66 3.97 Search for helices and strands: 0 residues in 0 chains, 2026 seeds are put forward NCS extension: 0 residues added, 2026 seeds are put forward Round 1: 54 peptides, 13 chains. Longest chain 5 peptides. Score 0.183 Round 2: 72 peptides, 15 chains. Longest chain 7 peptides. Score 0.255 Round 3: 93 peptides, 19 chains. Longest chain 7 peptides. Score 0.283 Round 4: 88 peptides, 16 chains. Longest chain 12 peptides. Score 0.332 Round 5: 86 peptides, 15 chains. Longest chain 12 peptides. Score 0.347 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 15, Residues 71, 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 2hq7-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2485 reflections ( 99.04 % complete ) and 4509 restraints for refining 1966 atoms. 4240 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2383 (Rfree = 0.000) for 1966 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.2249 (Rfree = 0.000) for 1951 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.1911 (Rfree = 0.000) for 1939 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.1985 (Rfree = 0.000) for 1927 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Writing output files ... TimeTaking 25.9