Sun 23 Dec 22:22:53 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 2p4g-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2p4g-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2p4g-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p4g-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/2p4g-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p4g-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 22:23:03 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/2p4g-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p4g-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 262 and 0 Target number of residues in the AU: 262 Target solvent content: 0.6775 Checking the provided sequence file Detected sequence length: 270 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 270 Adjusted target solvent content: 0.67 Input MTZ file: 2p4g-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: 172 Cell parameters: 115.650 115.650 56.930 90.000 90.000 120.000 Input sequence file: 2p4g-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 2160 target number of atoms Had to go as low as 1.10 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: 28.913 3.800 Wilson plot Bfac: 98.65 4387 reflections ( 99.64 % complete ) and 0 restraints for refining 2406 atoms. Observations/parameters ratio is 0.46 ------------------------------------------------------ Starting model: R = 0.3447 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3160 (Rfree = 0.000) for 2406 atoms. Found 13 (13 requested) and removed 11 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.82 3.02 Search for helices and strands: 0 residues in 0 chains, 2443 seeds are put forward Round 1: 114 peptides, 21 chains. Longest chain 10 peptides. Score 0.308 Round 2: 153 peptides, 22 chains. Longest chain 16 peptides. Score 0.443 Round 3: 165 peptides, 20 chains. Longest chain 22 peptides. Score 0.515 Round 4: 154 peptides, 19 chains. Longest chain 16 peptides. Score 0.494 Round 5: 161 peptides, 19 chains. Longest chain 29 peptides. Score 0.517 Taking the results from Round 5 Chains 19, Residues 142, Estimated correctness of the model 0.0 % 1 chains (16 residues) have been docked in sequence ------------------------------------------------------ 4387 reflections ( 99.64 % complete ) and 4169 restraints for refining 1953 atoms. 3561 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2859 (Rfree = 0.000) for 1953 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. Cycle 2: After refmac, R = 0.2674 (Rfree = 0.000) for 1920 atoms. Found 10 (10 requested) and removed 17 (5 requested) atoms. Cycle 3: After refmac, R = 0.2565 (Rfree = 0.000) for 1890 atoms. Found 6 (10 requested) and removed 8 (5 requested) atoms. Cycle 4: After refmac, R = 0.2518 (Rfree = 0.000) for 1876 atoms. Found 4 (10 requested) and removed 11 (5 requested) atoms. Cycle 5: After refmac, R = 0.2517 (Rfree = 0.000) for 1856 atoms. Found 5 (10 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.85 3.04 Search for helices and strands: 0 residues in 0 chains, 1918 seeds are put forward Round 1: 141 peptides, 23 chains. Longest chain 14 peptides. Score 0.381 Round 2: 148 peptides, 18 chains. Longest chain 16 peptides. Score 0.489 Round 3: 148 peptides, 17 chains. Longest chain 25 peptides. Score 0.505 Round 4: 149 peptides, 20 chains. Longest chain 23 peptides. Score 0.461 Round 5: 154 peptides, 17 chains. Longest chain 19 peptides. Score 0.525 Taking the results from Round 5 Chains 17, Residues 137, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4387 reflections ( 99.64 % complete ) and 4375 restraints for refining 1952 atoms. 3844 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2935 (Rfree = 0.000) for 1952 atoms. Found 10 (10 requested) and removed 41 (5 requested) atoms. Cycle 7: After refmac, R = 0.2375 (Rfree = 0.000) for 1902 atoms. Found 8 (10 requested) and removed 10 (5 requested) atoms. Cycle 8: After refmac, R = 0.2383 (Rfree = 0.000) for 1888 atoms. Found 7 (10 requested) and removed 19 (5 requested) atoms. Cycle 9: After refmac, R = 0.2141 (Rfree = 0.000) for 1870 atoms. Found 4 (10 requested) and removed 9 (5 requested) atoms. Cycle 10: After refmac, R = 0.2107 (Rfree = 0.000) for 1856 atoms. Found 5 (10 requested) and removed 11 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.76 2.97 Search for helices and strands: 0 residues in 0 chains, 1958 seeds are put forward Round 1: 141 peptides, 22 chains. Longest chain 16 peptides. Score 0.398 Round 2: 167 peptides, 18 chains. Longest chain 22 peptides. Score 0.551 Round 3: 157 peptides, 22 chains. Longest chain 16 peptides. Score 0.457 Round 4: 166 peptides, 19 chains. Longest chain 22 peptides. Score 0.533 Round 5: 158 peptides, 18 chains. Longest chain 24 peptides. Score 0.522 Taking the results from Round 2 Chains 18, Residues 149, Estimated correctness of the model 0.0 % 1 chains (21 residues) have been docked in sequence ------------------------------------------------------ 4387 reflections ( 99.64 % complete ) and 4062 restraints for refining 1951 atoms. 3403 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2303 (Rfree = 0.000) for 1951 atoms. Found 9 (10 requested) and removed 21 (5 requested) atoms. Cycle 12: After refmac, R = 0.2141 (Rfree = 0.000) for 1931 atoms. Found 7 (10 requested) and removed 14 (5 requested) atoms. Cycle 13: After refmac, R = 0.2124 (Rfree = 0.000) for 1919 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 14: After refmac, R = 0.2081 (Rfree = 0.000) for 1917 atoms. Found 7 (10 requested) and removed 10 (5 requested) atoms. Cycle 15: After refmac, R = 0.2103 (Rfree = 0.000) for 1913 atoms. Found 10 (10 requested) and removed 13 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.81 3.01 Search for helices and strands: 0 residues in 0 chains, 1994 seeds are put forward Round 1: 135 peptides, 19 chains. Longest chain 16 peptides. Score 0.427 Round 2: 162 peptides, 19 chains. Longest chain 16 peptides. Score 0.520 Round 3: 138 peptides, 16 chains. Longest chain 22 peptides. Score 0.487 Round 4: 144 peptides, 16 chains. Longest chain 22 peptides. Score 0.508 Round 5: 150 peptides, 16 chains. Longest chain 18 peptides. Score 0.527 Taking the results from Round 5 Chains 16, Residues 134, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4387 reflections ( 99.64 % complete ) and 4339 restraints for refining 1952 atoms. 3819 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2418 (Rfree = 0.000) for 1952 atoms. Found 10 (10 requested) and removed 17 (5 requested) atoms. Cycle 17: After refmac, R = 0.2263 (Rfree = 0.000) for 1930 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 18: After refmac, R = 0.2261 (Rfree = 0.000) for 1927 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 19: After refmac, R = 0.2192 (Rfree = 0.000) for 1924 atoms. Found 8 (10 requested) and removed 9 (5 requested) atoms. Cycle 20: After refmac, R = 0.2121 (Rfree = 0.000) for 1920 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.86 3.05 Search for helices and strands: 0 residues in 0 chains, 2001 seeds are put forward Round 1: 117 peptides, 22 chains. Longest chain 14 peptides. Score 0.302 Round 2: 143 peptides, 20 chains. Longest chain 19 peptides. Score 0.439 Round 3: 158 peptides, 21 chains. Longest chain 21 peptides. Score 0.476 Round 4: 147 peptides, 20 chains. Longest chain 16 peptides. Score 0.454 Round 5: 160 peptides, 20 chains. Longest chain 24 peptides. Score 0.498 Taking the results from Round 5 Chains 20, Residues 140, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4387 reflections ( 99.64 % complete ) and 4471 restraints for refining 1953 atoms. 3931 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2315 (Rfree = 0.000) for 1953 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. Cycle 22: After refmac, R = 0.2109 (Rfree = 0.000) for 1949 atoms. Found 7 (10 requested) and removed 7 (5 requested) atoms. Cycle 23: After refmac, R = 0.2037 (Rfree = 0.000) for 1945 atoms. Found 5 (10 requested) and removed 5 (5 requested) atoms. Cycle 24: After refmac, R = 0.1961 (Rfree = 0.000) for 1943 atoms. Found 1 (10 requested) and removed 7 (5 requested) atoms. Cycle 25: After refmac, R = 0.1932 (Rfree = 0.000) for 1934 atoms. Found 1 (10 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.83 3.03 Search for helices and strands: 0 residues in 0 chains, 2004 seeds are put forward Round 1: 138 peptides, 24 chains. Longest chain 14 peptides. Score 0.352 Round 2: 151 peptides, 21 chains. Longest chain 14 peptides. Score 0.452 Round 3: 153 peptides, 20 chains. Longest chain 15 peptides. Score 0.475 Round 4: 151 peptides, 20 chains. Longest chain 17 peptides. Score 0.468 Round 5: 148 peptides, 20 chains. Longest chain 17 peptides. Score 0.457 Taking the results from Round 3 Chains 20, Residues 133, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4387 reflections ( 99.64 % complete ) and 4333 restraints for refining 1953 atoms. 3821 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2166 (Rfree = 0.000) for 1953 atoms. Found 10 (10 requested) and removed 5 (5 requested) atoms. Cycle 27: After refmac, R = 0.2020 (Rfree = 0.000) for 1950 atoms. Found 3 (10 requested) and removed 8 (5 requested) atoms. Cycle 28: After refmac, R = 0.1958 (Rfree = 0.000) for 1939 atoms. Found 4 (10 requested) and removed 8 (5 requested) atoms. Cycle 29: After refmac, R = 0.1824 (Rfree = 0.000) for 1931 atoms. Found 0 (10 requested) and removed 8 (5 requested) atoms. Cycle 30: After refmac, R = 0.1801 (Rfree = 0.000) for 1923 atoms. Found 3 (10 requested) and removed 11 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.80 3.00 Search for helices and strands: 0 residues in 0 chains, 1998 seeds are put forward Round 1: 136 peptides, 23 chains. Longest chain 10 peptides. Score 0.362 Round 2: 156 peptides, 20 chains. Longest chain 20 peptides. Score 0.485 Round 3: 149 peptides, 18 chains. Longest chain 20 peptides. Score 0.493 Round 4: 161 peptides, 21 chains. Longest chain 20 peptides. Score 0.486 Round 5: 149 peptides, 21 chains. Longest chain 16 peptides. Score 0.444 Taking the results from Round 3 Chains 18, Residues 131, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4387 reflections ( 99.64 % complete ) and 4395 restraints for refining 1953 atoms. 3889 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2336 (Rfree = 0.000) for 1953 atoms. Found 8 (10 requested) and removed 11 (5 requested) atoms. Cycle 32: After refmac, R = 0.2186 (Rfree = 0.000) for 1948 atoms. Found 2 (10 requested) and removed 7 (5 requested) atoms. Cycle 33: After refmac, R = 0.2042 (Rfree = 0.000) for 1939 atoms. Found 3 (10 requested) and removed 8 (5 requested) atoms. Cycle 34: After refmac, R = 0.1947 (Rfree = 0.000) for 1928 atoms. Found 4 (10 requested) and removed 5 (5 requested) atoms. Cycle 35: After refmac, R = 0.1863 (Rfree = 0.000) for 1923 atoms. Found 2 (10 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.81 3.01 Search for helices and strands: 0 residues in 0 chains, 1994 seeds are put forward Round 1: 132 peptides, 21 chains. Longest chain 16 peptides. Score 0.381 Round 2: 144 peptides, 20 chains. Longest chain 17 peptides. Score 0.443 Round 3: 143 peptides, 20 chains. Longest chain 13 peptides. Score 0.439 Round 4: 138 peptides, 19 chains. Longest chain 20 peptides. Score 0.438 Round 5: 152 peptides, 19 chains. Longest chain 18 peptides. Score 0.487 Taking the results from Round 5 Chains 19, Residues 133, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4387 reflections ( 99.64 % complete ) and 4433 restraints for refining 1952 atoms. 3920 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2244 (Rfree = 0.000) for 1952 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 37: After refmac, R = 0.2083 (Rfree = 0.000) for 1940 atoms. Found 6 (10 requested) and removed 13 (5 requested) atoms. Cycle 38: After refmac, R = 0.1916 (Rfree = 0.000) for 1929 atoms. Found 5 (10 requested) and removed 11 (5 requested) atoms. Cycle 39: After refmac, R = 0.1858 (Rfree = 0.000) for 1915 atoms. Found 2 (10 requested) and removed 9 (5 requested) atoms. Cycle 40: After refmac, R = 0.1824 (Rfree = 0.000) for 1907 atoms. Found 3 (10 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.78 2.99 Search for helices and strands: 0 residues in 0 chains, 1966 seeds are put forward Round 1: 124 peptides, 21 chains. Longest chain 14 peptides. Score 0.349 Round 2: 126 peptides, 16 chains. Longest chain 15 peptides. Score 0.445 Round 3: 132 peptides, 18 chains. Longest chain 16 peptides. Score 0.433 Round 4: 136 peptides, 18 chains. Longest chain 17 peptides. Score 0.447 Round 5: 134 peptides, 18 chains. Longest chain 16 peptides. Score 0.440 Taking the results from Round 4 Chains 20, Residues 118, Estimated correctness of the model 0.0 % 2 chains (14 residues) have been docked in sequence ------------------------------------------------------ 4387 reflections ( 99.64 % complete ) and 4414 restraints for refining 1953 atoms. 3917 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2135 (Rfree = 0.000) for 1953 atoms. Found 9 (10 requested) and removed 18 (5 requested) atoms. Cycle 42: After refmac, R = 0.1922 (Rfree = 0.000) for 1941 atoms. Found 2 (10 requested) and removed 14 (5 requested) atoms. Cycle 43: After refmac, R = (Rfree = 0.000) for 1926 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 44: After refmac, R = 0.1907 (Rfree = 0.000) for 1925 atoms. Found 9 (10 requested) and removed 7 (5 requested) atoms. Cycle 45: After refmac, R = 0.2314 (Rfree = 0.000) for 1919 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.80 3.00 Search for helices and strands: 0 residues in 0 chains, 1978 seeds are put forward Round 1: 114 peptides, 18 chains. Longest chain 12 peptides. Score 0.363 Round 2: 121 peptides, 18 chains. Longest chain 17 peptides. Score 0.391 Round 3: 124 peptides, 16 chains. Longest chain 15 peptides. Score 0.438 Round 4: 128 peptides, 17 chains. Longest chain 22 peptides. Score 0.435 Round 5: 115 peptides, 16 chains. Longest chain 14 peptides. Score 0.403 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 16, Residues 108, 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 2p4g-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4387 reflections ( 99.64 % complete ) and 4560 restraints for refining 1952 atoms. 4144 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1950 (Rfree = 0.000) for 1952 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.1865 (Rfree = 0.000) for 1942 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.1862 (Rfree = 0.000) for 1933 atoms. Found 0 (10 requested) and removed 1 (5 requested) atoms. Cycle 49: After refmac, R = 0.1875 (Rfree = 0.000) for 1932 atoms. TimeTaking 46.45