Mon 24 Dec 00:37:50 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2pr7-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2pr7-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2pr7-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pr7-4.0-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2pr7-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pr7-4.0-parrot-mrncs ############### 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 00:37:54 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/mrncs/ArpWArp/wArpResults/WorkingDir/2pr7-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pr7-4.0-parrot-mrncs/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 181 and 0 Target number of residues in the AU: 181 Target solvent content: 0.6649 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: 2pr7-4.0-parrot-mrncs.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: 2pr7-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 2192 target number of atoms Had to go as low as 0.70 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 4.001 Wilson plot Bfac: 87.27 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 2313 reflections ( 96.70 % complete ) and 0 restraints for refining 2427 atoms. Observations/parameters ratio is 0.24 ------------------------------------------------------ Starting model: R = 0.3221 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2754 (Rfree = 0.000) for 2427 atoms. Found 11 (11 requested) and removed 27 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.77 3.82 Search for helices and strands: 0 residues in 0 chains, 2438 seeds are put forward NCS extension: 0 residues added, 2438 seeds are put forward Round 1: 60 peptides, 13 chains. Longest chain 7 peptides. Score 0.228 Round 2: 88 peptides, 19 chains. Longest chain 8 peptides. Score 0.248 Round 3: 104 peptides, 18 chains. Longest chain 11 peptides. Score 0.372 Round 4: 112 peptides, 20 chains. Longest chain 10 peptides. Score 0.368 Round 5: 117 peptides, 21 chains. Longest chain 10 peptides. Score 0.372 Taking the results from Round 5 Chains 21, Residues 96, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 2313 reflections ( 96.70 % complete ) and 4807 restraints for refining 1979 atoms. 4433 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2181 (Rfree = 0.000) for 1979 atoms. Found 7 (9 requested) and removed 10 (4 requested) atoms. Cycle 2: After refmac, R = 0.1941 (Rfree = 0.000) for 1945 atoms. Found 4 (9 requested) and removed 5 (4 requested) atoms. Cycle 3: After refmac, R = 0.1828 (Rfree = 0.000) for 1926 atoms. Found 2 (9 requested) and removed 4 (4 requested) atoms. Cycle 4: After refmac, R = 0.1766 (Rfree = 0.000) for 1919 atoms. Found 3 (9 requested) and removed 5 (4 requested) atoms. Cycle 5: After refmac, R = 0.1720 (Rfree = 0.000) for 1912 atoms. Found 2 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.68 3.73 Search for helices and strands: 0 residues in 0 chains, 1976 seeds are put forward NCS extension: 6 residues added (0 deleted due to clashes), 1982 seeds are put forward Round 1: 95 peptides, 21 chains. Longest chain 8 peptides. Score 0.240 Round 2: 119 peptides, 22 chains. Longest chain 9 peptides. Score 0.359 Round 3: 135 peptides, 24 chains. Longest chain 11 peptides. Score 0.401 Round 4: 130 peptides, 20 chains. Longest chain 12 peptides. Score 0.465 Round 5: 129 peptides, 22 chains. Longest chain 13 peptides. Score 0.415 Taking the results from Round 4 Chains 21, Residues 110, Estimated correctness of the model 0.0 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 2313 reflections ( 96.70 % complete ) and 4253 restraints for refining 1895 atoms. 3777 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1926 (Rfree = 0.000) for 1895 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. Cycle 7: After refmac, R = 0.1706 (Rfree = 0.000) for 1871 atoms. Found 2 (8 requested) and removed 6 (4 requested) atoms. Cycle 8: After refmac, R = 0.1684 (Rfree = 0.000) for 1861 atoms. Found 2 (8 requested) and removed 11 (4 requested) atoms. Cycle 9: After refmac, R = 0.1640 (Rfree = 0.000) for 1841 atoms. Found 2 (8 requested) and removed 5 (4 requested) atoms. Cycle 10: After refmac, R = 0.1681 (Rfree = 0.000) for 1829 atoms. Found 2 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.70 3.75 Search for helices and strands: 0 residues in 0 chains, 1897 seeds are put forward NCS extension: 0 residues added, 1897 seeds are put forward Round 1: 100 peptides, 19 chains. Longest chain 9 peptides. Score 0.323 Round 2: 123 peptides, 19 chains. Longest chain 14 peptides. Score 0.452 Round 3: 124 peptides, 18 chains. Longest chain 15 peptides. Score 0.480 Round 4: 119 peptides, 17 chains. Longest chain 18 peptides. Score 0.477 Round 5: 119 peptides, 20 chains. Longest chain 10 peptides. Score 0.407 Taking the results from Round 3 Chains 18, Residues 106, Estimated correctness of the model 0.0 % 2 chains (11 residues) have been docked in sequence ------------------------------------------------------ 2313 reflections ( 96.70 % complete ) and 4260 restraints for refining 1877 atoms. 3831 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1799 (Rfree = 0.000) for 1877 atoms. Found 5 (8 requested) and removed 13 (4 requested) atoms. Cycle 12: After refmac, R = 0.1765 (Rfree = 0.000) for 1854 atoms. Found 6 (8 requested) and removed 8 (4 requested) atoms. Cycle 13: After refmac, R = 0.1417 (Rfree = 0.000) for 1834 atoms. Found 3 (8 requested) and removed 7 (4 requested) atoms. Cycle 14: After refmac, R = 0.1558 (Rfree = 0.000) for 1828 atoms. Found 2 (8 requested) and removed 5 (4 requested) atoms. Cycle 15: After refmac, R = 0.1422 (Rfree = 0.000) for 1819 atoms. Found 2 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.75 3.80 Search for helices and strands: 0 residues in 0 chains, 1888 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 1905 seeds are put forward Round 1: 100 peptides, 19 chains. Longest chain 9 peptides. Score 0.323 Round 2: 112 peptides, 18 chains. Longest chain 11 peptides. Score 0.417 Round 3: 118 peptides, 19 chains. Longest chain 15 peptides. Score 0.426 Round 4: 121 peptides, 16 chains. Longest chain 16 peptides. Score 0.509 Round 5: 115 peptides, 18 chains. Longest chain 13 peptides. Score 0.433 Taking the results from Round 4 Chains 16, Residues 105, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2313 reflections ( 96.70 % complete ) and 4347 restraints for refining 1876 atoms. 3943 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1722 (Rfree = 0.000) for 1876 atoms. Found 5 (8 requested) and removed 15 (4 requested) atoms. Cycle 17: After refmac, R = 0.1511 (Rfree = 0.000) for 1863 atoms. Found 1 (8 requested) and removed 5 (4 requested) atoms. Cycle 18: After refmac, R = 0.1373 (Rfree = 0.000) for 1858 atoms. Found 0 (8 requested) and removed 6 (4 requested) atoms. Cycle 19: After refmac, R = 0.1330 (Rfree = 0.000) for 1850 atoms. Found 1 (8 requested) and removed 7 (4 requested) atoms. Cycle 20: After refmac, R = 0.1409 (Rfree = 0.000) for 1842 atoms. Found 4 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.64 3.69 Search for helices and strands: 0 residues in 0 chains, 1903 seeds are put forward NCS extension: 0 residues added, 1903 seeds are put forward Round 1: 112 peptides, 21 chains. Longest chain 12 peptides. Score 0.344 Round 2: 106 peptides, 17 chains. Longest chain 11 peptides. Score 0.408 Round 3: 125 peptides, 21 chains. Longest chain 10 peptides. Score 0.416 Round 4: 121 peptides, 20 chains. Longest chain 10 peptides. Score 0.418 Round 5: 128 peptides, 19 chains. Longest chain 13 peptides. Score 0.478 Taking the results from Round 5 Chains 19, Residues 109, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2313 reflections ( 96.70 % complete ) and 4443 restraints for refining 1933 atoms. 4026 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1746 (Rfree = 0.000) for 1933 atoms. Found 5 (9 requested) and removed 11 (4 requested) atoms. Cycle 22: After refmac, R = 0.1733 (Rfree = 0.000) for 1918 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. Cycle 23: After refmac, R = 0.1516 (Rfree = 0.000) for 1913 atoms. Found 1 (9 requested) and removed 6 (4 requested) atoms. Cycle 24: After refmac, R = 0.1588 (Rfree = 0.000) for 1907 atoms. Found 0 (9 requested) and removed 5 (4 requested) atoms. Cycle 25: After refmac, R = 0.1579 (Rfree = 0.000) for 1895 atoms. Found 2 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.75 3.80 Search for helices and strands: 0 residues in 0 chains, 1961 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 1982 seeds are put forward Round 1: 79 peptides, 14 chains. Longest chain 12 peptides. Score 0.327 Round 2: 104 peptides, 17 chains. Longest chain 13 peptides. Score 0.397 Round 3: 108 peptides, 15 chains. Longest chain 14 peptides. Score 0.467 Round 4: 101 peptides, 18 chains. Longest chain 11 peptides. Score 0.355 Round 5: 105 peptides, 18 chains. Longest chain 14 peptides. Score 0.378 Taking the results from Round 3 Chains 16, Residues 93, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 2313 reflections ( 96.70 % complete ) and 4561 restraints for refining 1972 atoms. 4180 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1762 (Rfree = 0.000) for 1972 atoms. Found 5 (9 requested) and removed 18 (4 requested) atoms. Cycle 27: After refmac, R = 0.1703 (Rfree = 0.000) for 1953 atoms. Found 5 (9 requested) and removed 9 (4 requested) atoms. Cycle 28: After refmac, R = 0.1550 (Rfree = 0.000) for 1946 atoms. Found 2 (9 requested) and removed 7 (4 requested) atoms. Cycle 29: After refmac, R = 0.1725 (Rfree = 0.000) for 1938 atoms. Found 5 (9 requested) and removed 11 (4 requested) atoms. Cycle 30: After refmac, R = 0.1581 (Rfree = 0.000) for 1930 atoms. Found 0 (9 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.70 3.75 Search for helices and strands: 0 residues in 0 chains, 1977 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 1995 seeds are put forward Round 1: 99 peptides, 20 chains. Longest chain 9 peptides. Score 0.291 Round 2: 110 peptides, 18 chains. Longest chain 11 peptides. Score 0.406 Round 3: 106 peptides, 16 chains. Longest chain 17 peptides. Score 0.432 Round 4: 100 peptides, 16 chains. Longest chain 10 peptides. Score 0.399 Round 5: 97 peptides, 15 chains. Longest chain 13 peptides. Score 0.407 Taking the results from Round 3 Chains 17, Residues 90, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 2313 reflections ( 96.70 % complete ) and 4497 restraints for refining 1979 atoms. 4106 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1714 (Rfree = 0.000) for 1979 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Cycle 32: After refmac, R = 0.1629 (Rfree = 0.000) for 1971 atoms. Found 2 (9 requested) and removed 6 (4 requested) atoms. Cycle 33: After refmac, R = 0.1503 (Rfree = 0.000) for 1962 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 34: After refmac, R = 0.1458 (Rfree = 0.000) for 1955 atoms. Found 1 (9 requested) and removed 8 (4 requested) atoms. Cycle 35: After refmac, R = 0.1595 (Rfree = 0.000) for 1945 atoms. Found 3 (9 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.60 3.65 Search for helices and strands: 0 residues in 0 chains, 1996 seeds are put forward NCS extension: 0 residues added, 1996 seeds are put forward Round 1: 77 peptides, 17 chains. Longest chain 7 peptides. Score 0.230 Round 2: 93 peptides, 18 chains. Longest chain 9 peptides. Score 0.306 Round 3: 100 peptides, 18 chains. Longest chain 10 peptides. Score 0.349 Round 4: 95 peptides, 17 chains. Longest chain 11 peptides. Score 0.345 Round 5: 93 peptides, 17 chains. Longest chain 11 peptides. Score 0.333 Taking the results from Round 3 Chains 18, Residues 82, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2313 reflections ( 96.70 % complete ) and 4580 restraints for refining 1964 atoms. 4270 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2060 (Rfree = 0.000) for 1964 atoms. Found 9 (9 requested) and removed 15 (4 requested) atoms. Cycle 37: After refmac, R = 0.1723 (Rfree = 0.000) for 1949 atoms. Found 3 (9 requested) and removed 11 (4 requested) atoms. Cycle 38: After refmac, R = 0.1662 (Rfree = 0.000) for 1932 atoms. Found 4 (9 requested) and removed 7 (4 requested) atoms. Cycle 39: After refmac, R = 0.1324 (Rfree = 0.000) for 1928 atoms. Found 1 (9 requested) and removed 5 (4 requested) atoms. Cycle 40: After refmac, R = 0.1371 (Rfree = 0.000) for 1922 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.67 3.72 Search for helices and strands: 0 residues in 0 chains, 1962 seeds are put forward NCS extension: 0 residues added, 1962 seeds are put forward Round 1: 78 peptides, 17 chains. Longest chain 8 peptides. Score 0.237 Round 2: 100 peptides, 17 chains. Longest chain 13 peptides. Score 0.374 Round 3: 109 peptides, 19 chains. Longest chain 10 peptides. Score 0.376 Round 4: 111 peptides, 19 chains. Longest chain 13 peptides. Score 0.387 Round 5: 111 peptides, 18 chains. Longest chain 10 peptides. Score 0.411 Taking the results from Round 5 Chains 18, Residues 93, Estimated correctness of the model 0.0 % 3 chains (18 residues) have been docked in sequence ------------------------------------------------------ 2313 reflections ( 96.70 % complete ) and 4290 restraints for refining 1970 atoms. 3893 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1664 (Rfree = 0.000) for 1970 atoms. Found 5 (9 requested) and removed 24 (4 requested) atoms. Cycle 42: After refmac, R = 0.1507 (Rfree = 0.000) for 1947 atoms. Found 3 (9 requested) and removed 9 (4 requested) atoms. Cycle 43: After refmac, R = 0.1402 (Rfree = 0.000) for 1935 atoms. Found 4 (9 requested) and removed 7 (4 requested) atoms. Cycle 44: After refmac, R = 0.1313 (Rfree = 0.000) for 1930 atoms. Found 6 (9 requested) and removed 5 (4 requested) atoms. Cycle 45: After refmac, R = 0.1220 (Rfree = 0.000) for 1923 atoms. Found 3 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.69 3.74 Search for helices and strands: 0 residues in 0 chains, 1970 seeds are put forward NCS extension: 0 residues added, 1970 seeds are put forward Round 1: 82 peptides, 17 chains. Longest chain 8 peptides. Score 0.264 Round 2: 99 peptides, 18 chains. Longest chain 9 peptides. Score 0.343 Round 3: 104 peptides, 18 chains. Longest chain 10 peptides. Score 0.372 Round 4: 105 peptides, 16 chains. Longest chain 11 peptides. Score 0.427 Round 5: 95 peptides, 15 chains. Longest chain 12 peptides. Score 0.396 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 16, Residues 89, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 2pr7-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2313 reflections ( 96.70 % complete ) and 4507 restraints for refining 1974 atoms. 4153 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1678 (Rfree = 0.000) for 1974 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.1829 (Rfree = 0.000) for 1962 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.1317 (Rfree = 0.000) for 1953 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.2025 (Rfree = 0.000) for 1947 atoms. TimeTaking 25.37