Mon 24 Dec 08:06:37 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 2pr7-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2pr7-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2pr7-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pr7-3.8-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/2pr7-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pr7-3.8-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 08:06:41 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/2pr7-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pr7-3.8-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 188 and 0 Target number of residues in the AU: 188 Target solvent content: 0.6519 Checking the provided sequence file Detected sequence length: 137 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 274 Adjusted target solvent content: 0.49 Input MTZ file: 2pr7-3.8-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: 1 Cell parameters: 29.149 45.153 60.777 100.722 103.858 103.308 Input sequence file: 2pr7-3.8-parrot-noncs.fasta_lf Building free atoms model in initial map for 2192 target number of atoms Had to go as low as 0.65 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: 57.053 3.801 Wilson plot Bfac: 79.01 2688 reflections ( 96.76 % complete ) and 0 restraints for refining 2411 atoms. Observations/parameters ratio is 0.28 ------------------------------------------------------ Starting model: R = 0.3184 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2912 (Rfree = 0.000) for 2411 atoms. Found 13 (13 requested) and removed 34 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.64 3.69 Search for helices and strands: 0 residues in 0 chains, 2445 seeds are put forward NCS extension: 0 residues added, 2445 seeds are put forward Round 1: 87 peptides, 17 chains. Longest chain 9 peptides. Score 0.296 Round 2: 119 peptides, 22 chains. Longest chain 9 peptides. Score 0.359 Round 3: 123 peptides, 21 chains. Longest chain 9 peptides. Score 0.406 Round 4: 130 peptides, 22 chains. Longest chain 9 peptides. Score 0.420 Round 5: 134 peptides, 22 chains. Longest chain 11 peptides. Score 0.441 Taking the results from Round 5 Chains 22, Residues 112, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2688 reflections ( 96.76 % complete ) and 4616 restraints for refining 1982 atoms. 4190 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2544 (Rfree = 0.000) for 1982 atoms. Found 10 (10 requested) and removed 14 (5 requested) atoms. Cycle 2: After refmac, R = 0.2396 (Rfree = 0.000) for 1933 atoms. Found 10 (10 requested) and removed 16 (5 requested) atoms. Cycle 3: After refmac, R = 0.1945 (Rfree = 0.000) for 1902 atoms. Found 10 (10 requested) and removed 17 (5 requested) atoms. Cycle 4: After refmac, R = 0.2079 (Rfree = 0.000) for 1882 atoms. Found 10 (10 requested) and removed 15 (5 requested) atoms. Cycle 5: After refmac, R = 0.2025 (Rfree = 0.000) for 1867 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.57 3.62 Search for helices and strands: 0 residues in 0 chains, 1930 seeds are put forward NCS extension: 9 residues added (1 deleted due to clashes), 1939 seeds are put forward Round 1: 106 peptides, 21 chains. Longest chain 10 peptides. Score 0.308 Round 2: 117 peptides, 20 chains. Longest chain 10 peptides. Score 0.396 Round 3: 128 peptides, 20 chains. Longest chain 14 peptides. Score 0.455 Round 4: 127 peptides, 21 chains. Longest chain 10 peptides. Score 0.427 Round 5: 133 peptides, 19 chains. Longest chain 16 peptides. Score 0.502 Taking the results from Round 5 Chains 21, Residues 114, Estimated correctness of the model 0.0 % 4 chains (20 residues) have been docked in sequence ------------------------------------------------------ 2688 reflections ( 96.76 % complete ) and 4155 restraints for refining 1921 atoms. 3660 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2101 (Rfree = 0.000) for 1921 atoms. Found 10 (10 requested) and removed 19 (5 requested) atoms. Cycle 7: After refmac, R = 0.1855 (Rfree = 0.000) for 1898 atoms. Found 7 (10 requested) and removed 18 (5 requested) atoms. Cycle 8: After refmac, R = 0.1532 (Rfree = 0.000) for 1871 atoms. Found 9 (10 requested) and removed 7 (5 requested) atoms. Cycle 9: After refmac, R = 0.1580 (Rfree = 0.000) for 1866 atoms. Found 5 (10 requested) and removed 6 (5 requested) atoms. Cycle 10: After refmac, R = 0.1367 (Rfree = 0.000) for 1862 atoms. Found 2 (10 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.57 3.62 Search for helices and strands: 0 residues in 0 chains, 1914 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 1934 seeds are put forward Round 1: 110 peptides, 22 chains. Longest chain 10 peptides. Score 0.307 Round 2: 118 peptides, 16 chains. Longest chain 15 peptides. Score 0.495 Round 3: 115 peptides, 19 chains. Longest chain 11 peptides. Score 0.409 Round 4: 119 peptides, 17 chains. Longest chain 16 peptides. Score 0.477 Round 5: 121 peptides, 15 chains. Longest chain 15 peptides. Score 0.531 Taking the results from Round 5 Chains 15, Residues 106, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2688 reflections ( 96.76 % complete ) and 4637 restraints for refining 1979 atoms. 4228 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1941 (Rfree = 0.000) for 1979 atoms. Found 8 (10 requested) and removed 17 (5 requested) atoms. Cycle 12: After refmac, R = 0.1963 (Rfree = 0.000) for 1964 atoms. Found 10 (10 requested) and removed 14 (5 requested) atoms. Cycle 13: After refmac, R = 0.1896 (Rfree = 0.000) for 1954 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. Cycle 14: After refmac, R = 0.1831 (Rfree = 0.000) for 1952 atoms. Found 7 (10 requested) and removed 12 (5 requested) atoms. Cycle 15: After refmac, R = 0.1368 (Rfree = 0.000) for 1943 atoms. Found 4 (10 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.59 3.64 Search for helices and strands: 0 residues in 0 chains, 2006 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 2023 seeds are put forward Round 1: 114 peptides, 22 chains. Longest chain 8 peptides. Score 0.331 Round 2: 134 peptides, 22 chains. Longest chain 10 peptides. Score 0.441 Round 3: 132 peptides, 22 chains. Longest chain 11 peptides. Score 0.431 Round 4: 130 peptides, 20 chains. Longest chain 17 peptides. Score 0.465 Round 5: 135 peptides, 21 chains. Longest chain 11 peptides. Score 0.469 Taking the results from Round 5 Chains 21, Residues 114, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2688 reflections ( 96.76 % complete ) and 4579 restraints for refining 1982 atoms. 4144 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1851 (Rfree = 0.000) for 1982 atoms. Found 10 (10 requested) and removed 21 (5 requested) atoms. Cycle 17: After refmac, R = 0.1769 (Rfree = 0.000) for 1964 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. Cycle 18: After refmac, R = 0.1684 (Rfree = 0.000) for 1956 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 19: After refmac, R = 0.1642 (Rfree = 0.000) for 1948 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. Cycle 20: After refmac, R = 0.1555 (Rfree = 0.000) for 1946 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.57 3.62 Search for helices and strands: 0 residues in 0 chains, 2010 seeds are put forward NCS extension: 0 residues added, 2010 seeds are put forward Round 1: 100 peptides, 20 chains. Longest chain 7 peptides. Score 0.297 Round 2: 115 peptides, 20 chains. Longest chain 11 peptides. Score 0.385 Round 3: 100 peptides, 18 chains. Longest chain 11 peptides. Score 0.349 Round 4: 106 peptides, 16 chains. Longest chain 11 peptides. Score 0.432 Round 5: 116 peptides, 18 chains. Longest chain 12 peptides. Score 0.438 Taking the results from Round 5 Chains 18, Residues 98, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2688 reflections ( 96.76 % complete ) and 4573 restraints for refining 1982 atoms. 4199 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2015 (Rfree = 0.000) for 1982 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 22: After refmac, R = 0.2041 (Rfree = 0.000) for 1969 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 23: After refmac, R = 0.1853 (Rfree = 0.000) for 1957 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 24: After refmac, R = 0.1889 (Rfree = 0.000) for 1951 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 25: After refmac, R = 0.1718 (Rfree = 0.000) for 1938 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.51 3.56 Search for helices and strands: 0 residues in 0 chains, 2000 seeds are put forward NCS extension: 8 residues added (1 deleted due to clashes), 2008 seeds are put forward Round 1: 97 peptides, 20 chains. Longest chain 7 peptides. Score 0.279 Round 2: 125 peptides, 21 chains. Longest chain 14 peptides. Score 0.416 Round 3: 128 peptides, 21 chains. Longest chain 11 peptides. Score 0.432 Round 4: 118 peptides, 20 chains. Longest chain 12 peptides. Score 0.402 Round 5: 131 peptides, 20 chains. Longest chain 11 peptides. Score 0.470 Taking the results from Round 5 Chains 20, Residues 111, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2688 reflections ( 96.76 % complete ) and 4408 restraints for refining 1946 atoms. 3984 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1768 (Rfree = 0.000) for 1946 atoms. Found 9 (10 requested) and removed 20 (5 requested) atoms. Cycle 27: After refmac, R = 0.1670 (Rfree = 0.000) for 1929 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. Cycle 28: After refmac, R = 0.1540 (Rfree = 0.000) for 1922 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 29: After refmac, R = 0.1506 (Rfree = 0.000) for 1921 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. Cycle 30: After refmac, R = 0.1595 (Rfree = 0.000) for 1921 atoms. Found 10 (10 requested) and removed 16 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.60 3.65 Search for helices and strands: 0 residues in 0 chains, 1985 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 2000 seeds are put forward Round 1: 100 peptides, 21 chains. Longest chain 8 peptides. Score 0.271 Round 2: 115 peptides, 20 chains. Longest chain 9 peptides. Score 0.385 Round 3: 113 peptides, 20 chains. Longest chain 10 peptides. Score 0.374 Round 4: 123 peptides, 19 chains. Longest chain 13 peptides. Score 0.452 Round 5: 117 peptides, 20 chains. Longest chain 10 peptides. Score 0.396 Taking the results from Round 4 Chains 19, Residues 104, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2688 reflections ( 96.76 % complete ) and 4536 restraints for refining 1982 atoms. 4139 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1752 (Rfree = 0.000) for 1982 atoms. Found 10 (10 requested) and removed 29 (5 requested) atoms. Cycle 32: After refmac, R = 0.1609 (Rfree = 0.000) for 1946 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. Failed to save intermediate PDB Cycle 33: After refmac, R = 0.1572 (Rfree = 0.000) for 1941 atoms. Found 10 (10 requested) and removed 13 (5 requested) atoms. Cycle 34: After refmac, R = 0.1478 (Rfree = 0.000) for 1928 atoms. Found 10 (10 requested) and removed 14 (5 requested) atoms. Cycle 35: After refmac, R = 0.1767 (Rfree = 0.000) for 1915 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.62 3.67 Search for helices and strands: 0 residues in 0 chains, 1984 seeds are put forward NCS extension: 10 residues added (2 deleted due to clashes), 1994 seeds are put forward Round 1: 99 peptides, 22 chains. Longest chain 9 peptides. Score 0.239 Round 2: 113 peptides, 22 chains. Longest chain 9 peptides. Score 0.325 Round 3: 111 peptides, 22 chains. Longest chain 9 peptides. Score 0.313 Round 4: 107 peptides, 21 chains. Longest chain 7 peptides. Score 0.314 Round 5: 110 peptides, 22 chains. Longest chain 8 peptides. Score 0.307 Taking the results from Round 2 Chains 22, Residues 91, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 2688 reflections ( 96.76 % complete ) and 4302 restraints for refining 1917 atoms. 3944 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1549 (Rfree = 0.000) for 1917 atoms. Found 10 (10 requested) and removed 34 (5 requested) atoms. Cycle 37: After refmac, R = 0.1563 (Rfree = 0.000) for 1886 atoms. Found 10 (10 requested) and removed 22 (5 requested) atoms. Cycle 38: After refmac, R = 0.1006 (Rfree = 0.000) for 1870 atoms. Found 1 (10 requested) and removed 12 (5 requested) atoms. Cycle 39: After refmac, R = 0.1102 (Rfree = 0.000) for 1855 atoms. Found 9 (10 requested) and removed 7 (5 requested) atoms. Cycle 40: After refmac, R = 0.1558 (Rfree = 0.000) for 1853 atoms. Found 10 (10 requested) and removed 14 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.59 3.64 Search for helices and strands: 0 residues in 0 chains, 1913 seeds are put forward NCS extension: 0 residues added, 1913 seeds are put forward Round 1: 87 peptides, 18 chains. Longest chain 9 peptides. Score 0.269 Round 2: 99 peptides, 17 chains. Longest chain 14 peptides. Score 0.368 Round 3: 98 peptides, 18 chains. Longest chain 12 peptides. Score 0.337 Round 4: 96 peptides, 17 chains. Longest chain 10 peptides. Score 0.351 Round 5: 95 peptides, 16 chains. Longest chain 9 peptides. Score 0.370 Taking the results from Round 5 Chains 16, Residues 79, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 2688 reflections ( 96.76 % complete ) and 4440 restraints for refining 1919 atoms. 4122 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1719 (Rfree = 0.000) for 1919 atoms. Found 10 (10 requested) and removed 20 (5 requested) atoms. Cycle 42: After refmac, R = 0.1772 (Rfree = 0.000) for 1906 atoms. Found 10 (10 requested) and removed 13 (5 requested) atoms. Cycle 43: After refmac, R = 0.1662 (Rfree = 0.000) for 1899 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. Cycle 44: After refmac, R = 0.1142 (Rfree = 0.000) for 1893 atoms. Found 1 (10 requested) and removed 5 (5 requested) atoms. Cycle 45: After refmac, R = 0.1014 (Rfree = 0.000) for 1887 atoms. Found 3 (10 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.58 3.63 Search for helices and strands: 0 residues in 0 chains, 1939 seeds are put forward NCS extension: 0 residues added, 1939 seeds are put forward Round 1: 87 peptides, 20 chains. Longest chain 5 peptides. Score 0.214 Round 2: 106 peptides, 21 chains. Longest chain 8 peptides. Score 0.308 Round 3: 110 peptides, 21 chains. Longest chain 9 peptides. Score 0.332 Round 4: 106 peptides, 18 chains. Longest chain 13 peptides. Score 0.383 Round 5: 107 peptides, 20 chains. Longest chain 9 peptides. Score 0.339 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 18, Residues 88, 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 2pr7-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2688 reflections ( 96.76 % complete ) and 4456 restraints for refining 1950 atoms. 4122 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1740 (Rfree = 0.000) for 1950 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.1686 (Rfree = 0.000) for 1934 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.1533 (Rfree = 0.000) for 1917 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.1474 (Rfree = 0.000) for 1901 atoms. TimeTaking 25.98