null Mon 24 Dec 07:34:41 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 2pr7-4.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2pr7-4.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2pr7-4.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pr7-4.0-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/2pr7-4.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pr7-4.0-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 07:34:45 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/2pr7-4.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pr7-4.0-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 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-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: 2pr7-4.0-parrot-noncs.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 2433 atoms. Observations/parameters ratio is 0.24 ------------------------------------------------------ Starting model: R = 0.3303 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3102 (Rfree = 0.000) for 2433 atoms. Found 11 (11 requested) and removed 34 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.77 3.82 Search for helices and strands: 0 residues in 0 chains, 2451 seeds are put forward NCS extension: 0 residues added, 2451 seeds are put forward Round 1: 60 peptides, 12 chains. Longest chain 10 peptides. Score 0.259 Round 2: 98 peptides, 19 chains. Longest chain 10 peptides. Score 0.311 Round 3: 112 peptides, 20 chains. Longest chain 11 peptides. Score 0.368 Round 4: 121 peptides, 22 chains. Longest chain 10 peptides. Score 0.371 Round 5: 116 peptides, 21 chains. Longest chain 11 peptides. Score 0.367 Taking the results from Round 4 Chains 22, Residues 99, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 2313 reflections ( 96.70 % complete ) and 4740 restraints for refining 1980 atoms. 4346 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2408 (Rfree = 0.000) for 1980 atoms. Found 5 (9 requested) and removed 13 (4 requested) atoms. Cycle 2: After refmac, R = 0.2143 (Rfree = 0.000) for 1938 atoms. Found 4 (9 requested) and removed 10 (4 requested) atoms. Cycle 3: After refmac, R = 0.2148 (Rfree = 0.000) for 1911 atoms. Found 3 (9 requested) and removed 13 (4 requested) atoms. Cycle 4: After refmac, R = 0.2369 (Rfree = 0.000) for 1886 atoms. Found 5 (9 requested) and removed 8 (4 requested) atoms. Cycle 5: After refmac, R = 0.2169 (Rfree = 0.000) for 1865 atoms. Found 5 (8 requested) and removed 9 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.65 3.70 Search for helices and strands: 0 residues in 0 chains, 1929 seeds are put forward NCS extension: 0 residues added, 1929 seeds are put forward Round 1: 90 peptides, 20 chains. Longest chain 6 peptides. Score 0.234 Round 2: 114 peptides, 21 chains. Longest chain 9 peptides. Score 0.355 Round 3: 105 peptides, 18 chains. Longest chain 11 peptides. Score 0.378 Round 4: 107 peptides, 19 chains. Longest chain 10 peptides. Score 0.364 Round 5: 105 peptides, 18 chains. Longest chain 11 peptides. Score 0.378 Taking the results from Round 5 Chains 18, Residues 87, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 2313 reflections ( 96.70 % complete ) and 3954 restraints for refining 1738 atoms. 3601 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1977 (Rfree = 0.000) for 1738 atoms. Found 5 (8 requested) and removed 17 (4 requested) atoms. Cycle 7: After refmac, R = 0.1794 (Rfree = 0.000) for 1711 atoms. Found 6 (8 requested) and removed 8 (4 requested) atoms. Cycle 8: After refmac, R = 0.1589 (Rfree = 0.000) for 1705 atoms. Found 2 (8 requested) and removed 6 (4 requested) atoms. Cycle 9: After refmac, R = 0.1466 (Rfree = 0.000) for 1699 atoms. Found 4 (8 requested) and removed 6 (4 requested) atoms. Cycle 10: After refmac, R = 0.1427 (Rfree = 0.000) for 1689 atoms. Found 4 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.73 3.78 Search for helices and strands: 0 residues in 0 chains, 1756 seeds are put forward NCS extension: 0 residues added, 1756 seeds are put forward Round 1: 99 peptides, 21 chains. Longest chain 7 peptides. Score 0.265 Round 2: 115 peptides, 19 chains. Longest chain 13 peptides. Score 0.409 Round 3: 114 peptides, 21 chains. Longest chain 11 peptides. Score 0.355 Round 4: 120 peptides, 21 chains. Longest chain 10 peptides. Score 0.389 Round 5: 119 peptides, 19 chains. Longest chain 15 peptides. Score 0.431 Taking the results from Round 5 Chains 20, Residues 100, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 2313 reflections ( 96.70 % complete ) and 3878 restraints for refining 1798 atoms. 3453 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1878 (Rfree = 0.000) for 1798 atoms. Found 7 (8 requested) and removed 12 (4 requested) atoms. Cycle 12: After refmac, R = 0.1648 (Rfree = 0.000) for 1777 atoms. Found 7 (8 requested) and removed 7 (4 requested) atoms. Cycle 13: After refmac, R = 0.1451 (Rfree = 0.000) for 1771 atoms. Found 3 (8 requested) and removed 6 (4 requested) atoms. Cycle 14: After refmac, R = 0.1474 (Rfree = 0.000) for 1765 atoms. Found 6 (8 requested) and removed 7 (4 requested) atoms. Cycle 15: After refmac, R = 0.1461 (Rfree = 0.000) for 1762 atoms. Found 1 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.76 3.81 Search for helices and strands: 0 residues in 0 chains, 1824 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 1838 seeds are put forward Round 1: 86 peptides, 17 chains. Longest chain 10 peptides. Score 0.289 Round 2: 100 peptides, 18 chains. Longest chain 12 peptides. Score 0.349 Round 3: 95 peptides, 16 chains. Longest chain 12 peptides. Score 0.370 Round 4: 97 peptides, 15 chains. Longest chain 16 peptides. Score 0.407 Round 5: 105 peptides, 17 chains. Longest chain 16 peptides. Score 0.402 Taking the results from Round 4 Chains 15, Residues 82, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2313 reflections ( 96.70 % complete ) and 4267 restraints for refining 1835 atoms. 3954 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1580 (Rfree = 0.000) for 1835 atoms. Found 5 (8 requested) and removed 41 (4 requested) atoms. Cycle 17: After refmac, R = 0.1582 (Rfree = 0.000) for 1793 atoms. Found 5 (8 requested) and removed 9 (4 requested) atoms. Cycle 18: After refmac, R = 0.1536 (Rfree = 0.000) for 1784 atoms. Found 3 (8 requested) and removed 6 (4 requested) atoms. Cycle 19: After refmac, R = 0.1351 (Rfree = 0.000) for 1780 atoms. Found 0 (8 requested) and removed 7 (4 requested) atoms. Cycle 20: After refmac, R = 0.1380 (Rfree = 0.000) for 1772 atoms. Found 1 (8 requested) and removed 9 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.75 3.80 Search for helices and strands: 0 residues in 0 chains, 1817 seeds are put forward NCS extension: 26 residues added (0 deleted due to clashes), 1843 seeds are put forward Round 1: 81 peptides, 16 chains. Longest chain 10 peptides. Score 0.285 Round 2: 94 peptides, 17 chains. Longest chain 12 peptides. Score 0.339 Round 3: 86 peptides, 15 chains. Longest chain 11 peptides. Score 0.343 Round 4: 87 peptides, 15 chains. Longest chain 12 peptides. Score 0.349 Round 5: 87 peptides, 15 chains. Longest chain 11 peptides. Score 0.349 Taking the results from Round 5 Chains 15, Residues 72, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 2313 reflections ( 96.70 % complete ) and 4419 restraints for refining 1845 atoms. 4139 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1736 (Rfree = 0.000) for 1845 atoms. Found 7 (8 requested) and removed 5 (4 requested) atoms. Cycle 22: After refmac, R = 0.1647 (Rfree = 0.000) for 1842 atoms. Found 6 (8 requested) and removed 8 (4 requested) atoms. Cycle 23: After refmac, R = 0.1635 (Rfree = 0.000) for 1834 atoms. Found 5 (8 requested) and removed 5 (4 requested) atoms. Cycle 24: After refmac, R = 0.1460 (Rfree = 0.000) for 1828 atoms. Found 3 (8 requested) and removed 6 (4 requested) atoms. Cycle 25: After refmac, R = 0.1435 (Rfree = 0.000) for 1823 atoms. Found 1 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.66 3.71 Search for helices and strands: 0 residues in 0 chains, 1862 seeds are put forward NCS extension: 0 residues added, 1862 seeds are put forward Round 1: 101 peptides, 20 chains. Longest chain 9 peptides. Score 0.303 Round 2: 115 peptides, 20 chains. Longest chain 10 peptides. Score 0.385 Round 3: 118 peptides, 21 chains. Longest chain 11 peptides. Score 0.378 Round 4: 112 peptides, 21 chains. Longest chain 11 peptides. Score 0.344 Round 5: 117 peptides, 22 chains. Longest chain 11 peptides. Score 0.348 Taking the results from Round 2 Chains 20, Residues 95, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2313 reflections ( 96.70 % complete ) and 4333 restraints for refining 1879 atoms. 3973 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1703 (Rfree = 0.000) for 1879 atoms. Found 6 (8 requested) and removed 11 (4 requested) atoms. Cycle 27: After refmac, R = 0.1560 (Rfree = 0.000) for 1864 atoms. Found 5 (8 requested) and removed 5 (4 requested) atoms. Cycle 28: After refmac, R = 0.1529 (Rfree = 0.000) for 1859 atoms. Found 2 (8 requested) and removed 9 (4 requested) atoms. Cycle 29: After refmac, R = 0.1515 (Rfree = 0.000) for 1852 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 30: After refmac, R = 0.1349 (Rfree = 0.000) for 1845 atoms. Found 2 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.68 3.73 Search for helices and strands: 0 residues in 0 chains, 1908 seeds are put forward NCS extension: 0 residues added, 1908 seeds are put forward Round 1: 84 peptides, 18 chains. Longest chain 7 peptides. Score 0.249 Round 2: 93 peptides, 19 chains. Longest chain 9 peptides. Score 0.280 Round 3: 88 peptides, 16 chains. Longest chain 9 peptides. Score 0.329 Round 4: 101 peptides, 17 chains. Longest chain 13 peptides. Score 0.380 Round 5: 89 peptides, 16 chains. Longest chain 9 peptides. Score 0.335 Taking the results from Round 4 Chains 17, Residues 84, Estimated correctness of the model 0.0 % 5 chains (24 residues) have been docked in sequence ------------------------------------------------------ 2313 reflections ( 96.70 % complete ) and 4323 restraints for refining 1950 atoms. 3945 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2024 (Rfree = 0.000) for 1950 atoms. Found 9 (9 requested) and removed 24 (4 requested) atoms. Cycle 32: After refmac, R = 0.1763 (Rfree = 0.000) for 1913 atoms. Found 8 (9 requested) and removed 16 (4 requested) atoms. Cycle 33: After refmac, R = 0.1465 (Rfree = 0.000) for 1900 atoms. Found 1 (9 requested) and removed 8 (4 requested) atoms. Cycle 34: After refmac, R = 0.1512 (Rfree = 0.000) for 1889 atoms. Found 2 (8 requested) and removed 5 (4 requested) atoms. Cycle 35: After refmac, R = 0.1475 (Rfree = 0.000) for 1881 atoms. Found 5 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.65 3.70 Search for helices and strands: 0 residues in 0 chains, 1943 seeds are put forward NCS extension: 0 residues added, 1943 seeds are put forward Round 1: 81 peptides, 19 chains. Longest chain 6 peptides. Score 0.201 Round 2: 105 peptides, 21 chains. Longest chain 11 peptides. Score 0.302 Round 3: 99 peptides, 19 chains. Longest chain 8 peptides. Score 0.317 Round 4: 102 peptides, 20 chains. Longest chain 8 peptides. Score 0.310 Round 5: 101 peptides, 20 chains. Longest chain 8 peptides. Score 0.303 Taking the results from Round 3 Chains 19, Residues 80, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 2313 reflections ( 96.70 % complete ) and 4345 restraints for refining 1855 atoms. 4023 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1972 (Rfree = 0.000) for 1855 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. Cycle 37: After refmac, R = 0.1856 (Rfree = 0.000) for 1844 atoms. Found 4 (8 requested) and removed 10 (4 requested) atoms. Cycle 38: After refmac, R = 0.1887 (Rfree = 0.000) for 1836 atoms. Found 1 (8 requested) and removed 7 (4 requested) atoms. Cycle 39: After refmac, R = 0.1610 (Rfree = 0.000) for 1829 atoms. Found 1 (8 requested) and removed 5 (4 requested) atoms. Cycle 40: After refmac, R = 0.1485 (Rfree = 0.000) for 1825 atoms. Found 2 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.69 3.74 Search for helices and strands: 0 residues in 0 chains, 1876 seeds are put forward NCS extension: 0 residues added, 1876 seeds are put forward Round 1: 78 peptides, 17 chains. Longest chain 10 peptides. Score 0.237 Round 2: 67 peptides, 12 chains. Longest chain 12 peptides. Score 0.306 Round 3: 77 peptides, 14 chains. Longest chain 12 peptides. Score 0.314 Round 4: 66 peptides, 12 chains. Longest chain 10 peptides. Score 0.300 Round 5: 73 peptides, 14 chains. Longest chain 10 peptides. Score 0.288 Taking the results from Round 3 Chains 14, Residues 63, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 2313 reflections ( 96.70 % complete ) and 4605 restraints for refining 1901 atoms. 4359 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1998 (Rfree = 0.000) for 1901 atoms. Found 9 (9 requested) and removed 22 (4 requested) atoms. Cycle 42: After refmac, R = 0.1584 (Rfree = 0.000) for 1881 atoms. Found 5 (8 requested) and removed 7 (4 requested) atoms. Cycle 43: After refmac, R = 0.1475 (Rfree = 0.000) for 1876 atoms. Found 3 (8 requested) and removed 6 (4 requested) atoms. Cycle 44: After refmac, R = 0.1668 (Rfree = 0.000) for 1873 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 45: After refmac, R = 0.1487 (Rfree = 0.000) for 1873 atoms. Found 2 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.67 3.72 Search for helices and strands: 0 residues in 0 chains, 1922 seeds are put forward NCS extension: 0 residues added, 1922 seeds are put forward Round 1: 75 peptides, 16 chains. Longest chain 8 peptides. Score 0.245 Round 2: 96 peptides, 19 chains. Longest chain 12 peptides. Score 0.299 Round 3: 85 peptides, 16 chains. Longest chain 9 peptides. Score 0.310 Round 4: 81 peptides, 16 chains. Longest chain 6 peptides. Score 0.285 Round 5: 81 peptides, 17 chains. Longest chain 7 peptides. Score 0.257 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 16, Residues 69, 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 2pr7-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2313 reflections ( 96.70 % complete ) and 4657 restraints for refining 1910 atoms. 4397 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1809 (Rfree = 0.000) for 1910 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.1962 (Rfree = 0.000) for 1899 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.1562 (Rfree = 0.000) for 1894 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.2051 (Rfree = 0.000) for 1886 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 07:57:59 GMT 2018 Job finished. TimeTaking 23.3 Used memory is bytes: 10218080