Sun 23 Dec 22:22:43 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 2hq7-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2hq7-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2hq7-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hq7-4.0-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/2hq7-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hq7-4.0-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 22:22:53 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/2hq7-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hq7-4.0-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 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-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: 5 Cell parameters: 85.850 36.790 97.970 90.000 113.753 90.000 Input sequence file: 2hq7-4.0-parrot-hancs.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 2607 atoms. Observations/parameters ratio is 0.24 ------------------------------------------------------ Starting model: R = 0.3418 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3336 (Rfree = 0.000) for 2607 atoms. Found 12 (12 requested) and removed 42 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.61 3.91 Search for helices and strands: 0 residues in 0 chains, 2626 seeds are put forward NCS extension: 0 residues added, 2626 seeds are put forward Round 1: 85 peptides, 17 chains. Longest chain 7 peptides. Score 0.286 Round 2: 100 peptides, 16 chains. Longest chain 10 peptides. Score 0.405 Round 3: 118 peptides, 18 chains. Longest chain 12 peptides. Score 0.456 Round 4: 118 peptides, 18 chains. Longest chain 12 peptides. Score 0.456 Round 5: 129 peptides, 19 chains. Longest chain 13 peptides. Score 0.490 Taking the results from Round 5 Chains 19, Residues 110, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2485 reflections ( 99.04 % complete ) and 4996 restraints for refining 2108 atoms. 4575 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3020 (Rfree = 0.000) for 2108 atoms. Found 10 (10 requested) and removed 13 (5 requested) atoms. Cycle 2: After refmac, R = 0.2880 (Rfree = 0.000) for 2066 atoms. Found 7 (10 requested) and removed 28 (5 requested) atoms. Cycle 3: After refmac, R = 0.2622 (Rfree = 0.000) for 2030 atoms. Found 5 (9 requested) and removed 19 (4 requested) atoms. Cycle 4: After refmac, R = 0.2497 (Rfree = 0.000) for 2014 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. Cycle 5: After refmac, R = 0.2567 (Rfree = 0.000) for 1993 atoms. Found 9 (9 requested) and removed 18 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.68 3.99 Search for helices and strands: 0 residues in 0 chains, 2051 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 2067 seeds are put forward Round 1: 89 peptides, 18 chains. Longest chain 7 peptides. Score 0.284 Round 2: 110 peptides, 17 chains. Longest chain 10 peptides. Score 0.436 Round 3: 111 peptides, 18 chains. Longest chain 11 peptides. Score 0.417 Round 4: 101 peptides, 16 chains. Longest chain 12 peptides. Score 0.411 Round 5: 106 peptides, 16 chains. Longest chain 13 peptides. Score 0.439 Taking the results from Round 5 Chains 16, Residues 90, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2485 reflections ( 99.04 % complete ) and 4930 restraints for refining 2051 atoms. 4586 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2515 (Rfree = 0.000) for 2051 atoms. Found 9 (9 requested) and removed 23 (4 requested) atoms. Cycle 7: After refmac, R = 0.2332 (Rfree = 0.000) for 2016 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Cycle 8: After refmac, R = 0.2121 (Rfree = 0.000) for 1999 atoms. Found 9 (9 requested) and removed 15 (4 requested) atoms. Cycle 9: After refmac, R = 0.2173 (Rfree = 0.000) for 1985 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 10: After refmac, R = 0.2032 (Rfree = 0.000) for 1978 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.60 3.90 Search for helices and strands: 0 residues in 0 chains, 2036 seeds are put forward NCS extension: 0 residues added, 2036 seeds are put forward Round 1: 91 peptides, 21 chains. Longest chain 6 peptides. Score 0.215 Round 2: 117 peptides, 23 chains. Longest chain 9 peptides. Score 0.328 Round 3: 117 peptides, 19 chains. Longest chain 18 peptides. Score 0.426 Round 4: 110 peptides, 18 chains. Longest chain 11 peptides. Score 0.412 Round 5: 111 peptides, 18 chains. Longest chain 11 peptides. Score 0.417 Taking the results from Round 3 Chains 19, Residues 98, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2485 reflections ( 99.04 % complete ) and 4747 restraints for refining 1997 atoms. 4374 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2236 (Rfree = 0.000) for 1997 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. Cycle 12: After refmac, R = 0.1999 (Rfree = 0.000) for 1984 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 13: After refmac, R = 0.1993 (Rfree = 0.000) for 1974 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 14: After refmac, R = 0.2112 (Rfree = 0.000) for 1964 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. Cycle 15: After refmac, R = 0.1861 (Rfree = 0.000) for 1951 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.61 3.91 Search for helices and strands: 0 residues in 0 chains, 2037 seeds are put forward NCS extension: 32 residues added (2 deleted due to clashes), 2069 seeds are put forward Round 1: 90 peptides, 18 chains. Longest chain 13 peptides. Score 0.291 Round 2: 117 peptides, 22 chains. Longest chain 14 peptides. Score 0.353 Round 3: 110 peptides, 18 chains. Longest chain 17 peptides. Score 0.412 Round 4: 104 peptides, 19 chains. Longest chain 14 peptides. Score 0.351 Round 5: 113 peptides, 16 chains. Longest chain 18 peptides. Score 0.476 Taking the results from Round 5 Chains 16, Residues 97, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2485 reflections ( 99.04 % complete ) and 4738 restraints for refining 1995 atoms. 4366 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2320 (Rfree = 0.000) for 1995 atoms. Found 9 (9 requested) and removed 20 (4 requested) atoms. Cycle 17: After refmac, R = 0.2221 (Rfree = 0.000) for 1967 atoms. Found 9 (9 requested) and removed 18 (4 requested) atoms. Cycle 18: After refmac, R = 0.2125 (Rfree = 0.000) for 1944 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 19: After refmac, R = 0.1968 (Rfree = 0.000) for 1935 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Cycle 20: After refmac, R = 0.1887 (Rfree = 0.000) for 1927 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.63 3.93 Search for helices and strands: 0 residues in 0 chains, 2010 seeds are put forward NCS extension: 26 residues added (2 deleted due to clashes), 2036 seeds are put forward Round 1: 81 peptides, 17 chains. Longest chain 8 peptides. Score 0.259 Round 2: 98 peptides, 19 chains. Longest chain 9 peptides. Score 0.315 Round 3: 109 peptides, 19 chains. Longest chain 10 peptides. Score 0.381 Round 4: 113 peptides, 20 chains. Longest chain 12 peptides. Score 0.379 Round 5: 112 peptides, 18 chains. Longest chain 11 peptides. Score 0.423 Taking the results from Round 5 Chains 18, Residues 94, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2485 reflections ( 99.04 % complete ) and 4628 restraints for refining 2013 atoms. 4270 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2240 (Rfree = 0.000) for 2013 atoms. Found 9 (9 requested) and removed 17 (4 requested) atoms. Cycle 22: After refmac, R = 0.1994 (Rfree = 0.000) for 1992 atoms. Found 8 (9 requested) and removed 17 (4 requested) atoms. Cycle 23: After refmac, R = 0.2117 (Rfree = 0.000) for 1977 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 24: After refmac, R = 0.1877 (Rfree = 0.000) for 1966 atoms. Found 9 (9 requested) and removed 4 (4 requested) atoms. Cycle 25: After refmac, R = 0.2183 (Rfree = 0.000) for 1966 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.66 3.97 Search for helices and strands: 0 residues in 0 chains, 2036 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 2050 seeds are put forward Round 1: 84 peptides, 17 chains. Longest chain 8 peptides. Score 0.279 Round 2: 107 peptides, 20 chains. Longest chain 9 peptides. Score 0.344 Round 3: 113 peptides, 19 chains. Longest chain 15 peptides. Score 0.404 Round 4: 104 peptides, 19 chains. Longest chain 9 peptides. Score 0.351 Round 5: 114 peptides, 21 chains. Longest chain 10 peptides. Score 0.360 Taking the results from Round 3 Chains 19, Residues 94, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2485 reflections ( 99.04 % complete ) and 4572 restraints for refining 1963 atoms. 4215 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2151 (Rfree = 0.000) for 1963 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 27: After refmac, R = 0.1849 (Rfree = 0.000) for 1958 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 28: After refmac, R = 0.2010 (Rfree = 0.000) for 1948 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 29: After refmac, R = 0.2007 (Rfree = 0.000) for 1941 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. Cycle 30: After refmac, R = 0.1970 (Rfree = 0.000) for 1938 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.63 3.93 Search for helices and strands: 0 residues in 0 chains, 2006 seeds are put forward NCS extension: 0 residues added, 2006 seeds are put forward Round 1: 82 peptides, 19 chains. Longest chain 6 peptides. Score 0.209 Round 2: 107 peptides, 21 chains. Longest chain 9 peptides. Score 0.318 Round 3: 99 peptides, 18 chains. Longest chain 9 peptides. Score 0.347 Round 4: 100 peptides, 18 chains. Longest chain 10 peptides. Score 0.353 Round 5: 92 peptides, 18 chains. Longest chain 9 peptides. Score 0.304 Taking the results from Round 4 Chains 18, Residues 82, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2485 reflections ( 99.04 % complete ) and 4618 restraints for refining 1952 atoms. 4308 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2179 (Rfree = 0.000) for 1952 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 32: After refmac, R = 0.1864 (Rfree = 0.000) for 1945 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 33: After refmac, R = 0.2023 (Rfree = 0.000) for 1940 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. Cycle 34: After refmac, R = 0.1879 (Rfree = 0.000) for 1927 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 35: After refmac, R = 0.1854 (Rfree = 0.000) for 1923 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.59 3.89 Search for helices and strands: 0 residues in 0 chains, 1999 seeds are put forward NCS extension: 0 residues added, 1999 seeds are put forward Round 1: 57 peptides, 13 chains. Longest chain 5 peptides. Score 0.207 Round 2: 70 peptides, 14 chains. Longest chain 7 peptides. Score 0.271 Round 3: 76 peptides, 15 chains. Longest chain 7 peptides. Score 0.282 Round 4: 68 peptides, 14 chains. Longest chain 7 peptides. Score 0.257 Round 5: 66 peptides, 13 chains. Longest chain 8 peptides. Score 0.273 Taking the results from Round 3 Chains 15, Residues 61, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2485 reflections ( 99.04 % complete ) and 4436 restraints for refining 1910 atoms. 4207 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2410 (Rfree = 0.000) for 1910 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 37: After refmac, R = 0.2458 (Rfree = 0.000) for 1899 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 38: After refmac, R = 0.1920 (Rfree = 0.000) for 1894 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. Cycle 39: After refmac, R = 0.2240 (Rfree = 0.000) for 1895 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Cycle 40: After refmac, R = 0.1879 (Rfree = 0.000) for 1892 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.69 4.00 Search for helices and strands: 0 residues in 0 chains, 1955 seeds are put forward NCS extension: 0 residues added, 1955 seeds are put forward Round 1: 64 peptides, 14 chains. Longest chain 8 peptides. Score 0.228 Round 2: 86 peptides, 18 chains. Longest chain 8 peptides. Score 0.265 Round 3: 82 peptides, 16 chains. Longest chain 9 peptides. Score 0.294 Round 4: 82 peptides, 18 chains. Longest chain 6 peptides. Score 0.238 Round 5: 86 peptides, 16 chains. Longest chain 9 peptides. Score 0.320 Taking the results from Round 5 Chains 16, Residues 70, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2485 reflections ( 99.04 % complete ) and 4373 restraints for refining 1878 atoms. 4109 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2264 (Rfree = 0.000) for 1878 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 42: After refmac, R = 0.1986 (Rfree = 0.000) for 1872 atoms. Found 8 (8 requested) and removed 15 (4 requested) atoms. Cycle 43: After refmac, R = 0.2100 (Rfree = 0.000) for 1858 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 44: After refmac, R = 0.2238 (Rfree = 0.000) for 1851 atoms. Found 8 (8 requested) and removed 27 (4 requested) atoms. Cycle 45: After refmac, R = 0.2041 (Rfree = 0.000) for 1824 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.65 3.96 Search for helices and strands: 0 residues in 0 chains, 1891 seeds are put forward NCS extension: 0 residues added, 1891 seeds are put forward Round 1: 75 peptides, 18 chains. Longest chain 6 peptides. Score 0.189 Round 2: 90 peptides, 19 chains. Longest chain 8 peptides. Score 0.263 Round 3: 99 peptides, 18 chains. Longest chain 11 peptides. Score 0.347 Round 4: 103 peptides, 20 chains. Longest chain 11 peptides. Score 0.319 Round 5: 94 peptides, 18 chains. Longest chain 9 peptides. Score 0.316 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 18, Residues 81, 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 4266 restraints for refining 1866 atoms. 3960 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2044 (Rfree = 0.000) for 1866 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.2263 (Rfree = 0.000) for 1853 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.2124 (Rfree = 0.000) for 1841 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.2235 (Rfree = 0.000) for 1836 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Writing output files ... Failed to save intermediate PDB TimeTaking 33.4