null Tue 25 Dec 19:27:57 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-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2p4g-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2p4g-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p4g-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/2p4g-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p4g-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 ============================================================ Tue 25 Dec 19:28:06 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-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p4g-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 270 and 0 Target number of residues in the AU: 270 Target solvent content: 0.6676 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-3.6-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: 172 Cell parameters: 115.650 115.650 56.930 90.000 90.000 120.000 Input sequence file: 2p4g-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 2160 target number of atoms Had to go as low as 1.15 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 3.601 Wilson plot Bfac: 89.97 5143 reflections ( 99.67 % complete ) and 0 restraints for refining 2380 atoms. Observations/parameters ratio is 0.54 ------------------------------------------------------ Starting model: R = 0.3465 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3443 (Rfree = 0.000) for 2380 atoms. Found 15 (15 requested) and removed 33 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.86 3.05 Search for helices and strands: 0 residues in 0 chains, 2411 seeds are put forward Round 1: 128 peptides, 24 chains. Longest chain 9 peptides. Score 0.312 Round 2: 144 peptides, 21 chains. Longest chain 15 peptides. Score 0.426 Round 3: 164 peptides, 24 chains. Longest chain 12 peptides. Score 0.450 Round 4: 162 peptides, 19 chains. Longest chain 16 peptides. Score 0.520 Round 5: 159 peptides, 18 chains. Longest chain 22 peptides. Score 0.526 Taking the results from Round 5 Chains 18, Residues 141, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5143 reflections ( 99.67 % complete ) and 4520 restraints for refining 1958 atoms. 3974 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3355 (Rfree = 0.000) for 1958 atoms. Found 12 (12 requested) and removed 25 (6 requested) atoms. Cycle 2: After refmac, R = 0.2589 (Rfree = 0.000) for 1915 atoms. Found 10 (12 requested) and removed 15 (6 requested) atoms. Cycle 3: After refmac, R = 0.2474 (Rfree = 0.000) for 1899 atoms. Found 3 (12 requested) and removed 10 (6 requested) atoms. Cycle 4: After refmac, R = 0.2659 (Rfree = 0.000) for 1887 atoms. Found 3 (12 requested) and removed 9 (6 requested) atoms. Cycle 5: After refmac, R = 0.2696 (Rfree = 0.000) for 1879 atoms. Found 1 (12 requested) and removed 11 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.74 2.95 Search for helices and strands: 0 residues in 0 chains, 1931 seeds are put forward Round 1: 153 peptides, 23 chains. Longest chain 21 peptides. Score 0.426 Round 2: 167 peptides, 21 chains. Longest chain 31 peptides. Score 0.506 Round 3: 171 peptides, 23 chains. Longest chain 21 peptides. Score 0.489 Round 4: 168 peptides, 20 chains. Longest chain 21 peptides. Score 0.524 Round 5: 170 peptides, 20 chains. Longest chain 27 peptides. Score 0.531 Taking the results from Round 5 Chains 20, Residues 150, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5143 reflections ( 99.67 % complete ) and 4399 restraints for refining 1957 atoms. 3819 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2615 (Rfree = 0.000) for 1957 atoms. Found 9 (12 requested) and removed 17 (6 requested) atoms. Cycle 7: After refmac, R = 0.2418 (Rfree = 0.000) for 1923 atoms. Found 8 (12 requested) and removed 16 (6 requested) atoms. Cycle 8: After refmac, R = 0.2260 (Rfree = 0.000) for 1902 atoms. Found 8 (12 requested) and removed 10 (6 requested) atoms. Cycle 9: After refmac, R = 0.2323 (Rfree = 0.000) for 1893 atoms. Found 3 (12 requested) and removed 18 (6 requested) atoms. Cycle 10: After refmac, R = 0.2372 (Rfree = 0.000) for 1872 atoms. Found 12 (12 requested) and removed 22 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.66 2.89 Search for helices and strands: 0 residues in 0 chains, 1949 seeds are put forward Round 1: 146 peptides, 23 chains. Longest chain 13 peptides. Score 0.400 Round 2: 163 peptides, 21 chains. Longest chain 20 peptides. Score 0.493 Round 3: 157 peptides, 21 chains. Longest chain 20 peptides. Score 0.472 Round 4: 161 peptides, 19 chains. Longest chain 21 peptides. Score 0.517 Round 5: 158 peptides, 20 chains. Longest chain 16 peptides. Score 0.492 Taking the results from Round 4 Chains 20, Residues 142, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 5143 reflections ( 99.67 % complete ) and 4308 restraints for refining 1958 atoms. 3720 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2456 (Rfree = 0.000) for 1958 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 12: After refmac, R = 0.2376 (Rfree = 0.000) for 1941 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 13: After refmac, R = 0.2035 (Rfree = 0.000) for 1934 atoms. Found 12 (12 requested) and removed 7 (6 requested) atoms. Cycle 14: After refmac, R = 0.1946 (Rfree = 0.000) for 1932 atoms. Found 3 (12 requested) and removed 7 (6 requested) atoms. Cycle 15: After refmac, R = 0.1891 (Rfree = 0.000) for 1921 atoms. Found 2 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.59 2.84 Search for helices and strands: 0 residues in 0 chains, 1996 seeds are put forward Round 1: 150 peptides, 23 chains. Longest chain 14 peptides. Score 0.415 Round 2: 166 peptides, 21 chains. Longest chain 16 peptides. Score 0.503 Round 3: 142 peptides, 17 chains. Longest chain 20 peptides. Score 0.485 Round 4: 146 peptides, 18 chains. Longest chain 18 peptides. Score 0.482 Round 5: 152 peptides, 19 chains. Longest chain 19 peptides. Score 0.487 Taking the results from Round 2 Chains 21, Residues 145, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5143 reflections ( 99.67 % complete ) and 4260 restraints for refining 1958 atoms. 3701 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2161 (Rfree = 0.000) for 1958 atoms. Found 8 (12 requested) and removed 7 (6 requested) atoms. Cycle 17: After refmac, R = 0.1962 (Rfree = 0.000) for 1943 atoms. Found 3 (12 requested) and removed 8 (6 requested) atoms. Cycle 18: After refmac, R = 0.1864 (Rfree = 0.000) for 1932 atoms. Found 1 (12 requested) and removed 7 (6 requested) atoms. Cycle 19: After refmac, R = 0.1827 (Rfree = 0.000) for 1922 atoms. Found 1 (12 requested) and removed 7 (6 requested) atoms. Cycle 20: After refmac, R = 0.1811 (Rfree = 0.000) for 1916 atoms. Found 2 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.63 2.87 Search for helices and strands: 0 residues in 0 chains, 1996 seeds are put forward Round 1: 144 peptides, 24 chains. Longest chain 16 peptides. Score 0.376 Round 2: 158 peptides, 20 chains. Longest chain 16 peptides. Score 0.492 Round 3: 159 peptides, 16 chains. Longest chain 38 peptides. Score 0.555 Round 4: 153 peptides, 21 chains. Longest chain 18 peptides. Score 0.459 Round 5: 149 peptides, 18 chains. Longest chain 31 peptides. Score 0.493 Taking the results from Round 3 Chains 18, Residues 143, Estimated correctness of the model 0.0 % 3 chains (51 residues) have been docked in sequence ------------------------------------------------------ 5143 reflections ( 99.67 % complete ) and 3756 restraints for refining 1956 atoms. 3019 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2225 (Rfree = 0.000) for 1956 atoms. Found 12 (12 requested) and removed 19 (6 requested) atoms. Cycle 22: After refmac, R = 0.2031 (Rfree = 0.000) for 1936 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 23: After refmac, R = 0.1889 (Rfree = 0.000) for 1924 atoms. Found 3 (12 requested) and removed 12 (6 requested) atoms. Cycle 24: After refmac, R = 0.1825 (Rfree = 0.000) for 1912 atoms. Found 4 (12 requested) and removed 12 (6 requested) atoms. Cycle 25: After refmac, R = 0.1720 (Rfree = 0.000) for 1902 atoms. Found 7 (12 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.56 2.81 Search for helices and strands: 0 residues in 0 chains, 1970 seeds are put forward Round 1: 149 peptides, 23 chains. Longest chain 20 peptides. Score 0.412 Round 2: 169 peptides, 22 chains. Longest chain 20 peptides. Score 0.498 Round 3: 157 peptides, 22 chains. Longest chain 20 peptides. Score 0.457 Round 4: 155 peptides, 21 chains. Longest chain 20 peptides. Score 0.466 Round 5: 164 peptides, 21 chains. Longest chain 16 peptides. Score 0.496 Taking the results from Round 2 Chains 22, Residues 147, Estimated correctness of the model 0.0 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 5143 reflections ( 99.67 % complete ) and 3984 restraints for refining 1958 atoms. 3348 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2199 (Rfree = 0.000) for 1958 atoms. Found 9 (12 requested) and removed 8 (6 requested) atoms. Cycle 27: After refmac, R = 0.1990 (Rfree = 0.000) for 1934 atoms. Found 6 (12 requested) and removed 7 (6 requested) atoms. Cycle 28: After refmac, R = 0.1898 (Rfree = 0.000) for 1923 atoms. Found 2 (12 requested) and removed 9 (6 requested) atoms. Cycle 29: After refmac, R = 0.1855 (Rfree = 0.000) for 1915 atoms. Found 2 (12 requested) and removed 6 (6 requested) atoms. Cycle 30: After refmac, R = 0.1797 (Rfree = 0.000) for 1908 atoms. Found 3 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.64 2.88 Search for helices and strands: 0 residues in 0 chains, 1978 seeds are put forward Round 1: 148 peptides, 25 chains. Longest chain 15 peptides. Score 0.374 Round 2: 150 peptides, 23 chains. Longest chain 17 peptides. Score 0.415 Round 3: 159 peptides, 24 chains. Longest chain 18 peptides. Score 0.432 Round 4: 146 peptides, 21 chains. Longest chain 18 peptides. Score 0.434 Round 5: 149 peptides, 23 chains. Longest chain 14 peptides. Score 0.412 Taking the results from Round 4 Chains 21, Residues 125, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5143 reflections ( 99.67 % complete ) and 4415 restraints for refining 1958 atoms. 3936 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2164 (Rfree = 0.000) for 1958 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. Cycle 32: After refmac, R = 0.1869 (Rfree = 0.000) for 1948 atoms. Found 4 (12 requested) and removed 7 (6 requested) atoms. Cycle 33: After refmac, R = 0.1778 (Rfree = 0.000) for 1944 atoms. Found 4 (12 requested) and removed 11 (6 requested) atoms. Cycle 34: After refmac, R = 0.1698 (Rfree = 0.000) for 1934 atoms. Found 2 (12 requested) and removed 7 (6 requested) atoms. Cycle 35: After refmac, R = 0.1718 (Rfree = 0.000) for 1928 atoms. Found 2 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.61 2.85 Search for helices and strands: 0 residues in 0 chains, 2010 seeds are put forward Round 1: 119 peptides, 22 chains. Longest chain 12 peptides. Score 0.310 Round 2: 133 peptides, 20 chains. Longest chain 15 peptides. Score 0.402 Round 3: 143 peptides, 20 chains. Longest chain 14 peptides. Score 0.439 Round 4: 142 peptides, 20 chains. Longest chain 11 peptides. Score 0.436 Round 5: 148 peptides, 21 chains. Longest chain 15 peptides. Score 0.441 Taking the results from Round 5 Chains 21, Residues 127, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5143 reflections ( 99.67 % complete ) and 4472 restraints for refining 1958 atoms. 3985 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2255 (Rfree = 0.000) for 1958 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 37: After refmac, R = 0.2212 (Rfree = 0.000) for 1946 atoms. Found 6 (12 requested) and removed 11 (6 requested) atoms. Cycle 38: After refmac, R = 0.2015 (Rfree = 0.000) for 1934 atoms. Found 6 (12 requested) and removed 12 (6 requested) atoms. Cycle 39: After refmac, R = 0.2039 (Rfree = 0.000) for 1926 atoms. Found 5 (12 requested) and removed 10 (6 requested) atoms. Cycle 40: After refmac, R = 0.1792 (Rfree = 0.000) for 1918 atoms. Found 2 (12 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.61 2.85 Search for helices and strands: 0 residues in 0 chains, 2009 seeds are put forward Round 1: 118 peptides, 20 chains. Longest chain 10 peptides. Score 0.343 Round 2: 144 peptides, 21 chains. Longest chain 15 peptides. Score 0.426 Round 3: 135 peptides, 20 chains. Longest chain 17 peptides. Score 0.410 Round 4: 142 peptides, 20 chains. Longest chain 17 peptides. Score 0.436 Round 5: 135 peptides, 18 chains. Longest chain 14 peptides. Score 0.444 Taking the results from Round 5 Chains 18, Residues 117, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5143 reflections ( 99.67 % complete ) and 4438 restraints for refining 1958 atoms. 3988 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2177 (Rfree = 0.000) for 1958 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 42: After refmac, R = 0.2047 (Rfree = 0.000) for 1952 atoms. Found 12 (12 requested) and removed 6 (6 requested) atoms. Cycle 43: After refmac, R = 0.1953 (Rfree = 0.000) for 1950 atoms. Found 10 (12 requested) and removed 7 (6 requested) atoms. Cycle 44: After refmac, R = 0.1969 (Rfree = 0.000) for 1949 atoms. Found 12 (12 requested) and removed 7 (6 requested) atoms. Cycle 45: After refmac, R = 0.1690 (Rfree = 0.000) for 1954 atoms. Found 1 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.65 2.88 Search for helices and strands: 0 residues in 0 chains, 2037 seeds are put forward Round 1: 138 peptides, 26 chains. Longest chain 9 peptides. Score 0.318 Round 2: 165 peptides, 27 chains. Longest chain 13 peptides. Score 0.405 Round 3: 150 peptides, 24 chains. Longest chain 18 peptides. Score 0.399 Round 4: 148 peptides, 22 chains. Longest chain 15 peptides. Score 0.424 Round 5: 130 peptides, 19 chains. Longest chain 14 peptides. Score 0.408 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 22, Residues 126, 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. 5143 reflections ( 99.67 % complete ) and 4310 restraints for refining 1956 atoms. 3828 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2109 (Rfree = 0.000) for 1956 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.2096 (Rfree = 0.000) for 1939 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.1968 (Rfree = 0.000) for 1929 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.1963 (Rfree = 0.000) for 1923 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:16:06 GMT 2018 Job finished. TimeTaking 48.16 Used memory is bytes: 1291560