Mon 24 Dec 00:38:45 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 2o1q-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2o1q-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2o1q-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2o1q-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/2o1q-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2o1q-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 00:38:51 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/2o1q-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2o1q-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 166 and 0 Target number of residues in the AU: 166 Target solvent content: 0.6485 Checking the provided sequence file Detected sequence length: 145 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 290 Adjusted target solvent content: 0.39 Input MTZ file: 2o1q-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: 92 Cell parameters: 61.883 61.883 133.475 90.000 90.000 90.000 Input sequence file: 2o1q-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 2320 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: 56.142 4.002 Wilson plot Bfac: 76.90 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 2457 reflections ( 99.59 % complete ) and 0 restraints for refining 2569 atoms. Observations/parameters ratio is 0.24 ------------------------------------------------------ Starting model: R = 0.3613 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3398 (Rfree = 0.000) for 2569 atoms. Found 12 (12 requested) and removed 28 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.60 4.18 Search for helices and strands: 0 residues in 0 chains, 2573 seeds are put forward NCS extension: 0 residues added, 2573 seeds are put forward Round 1: 70 peptides, 16 chains. Longest chain 7 peptides. Score 0.215 Round 2: 96 peptides, 21 chains. Longest chain 7 peptides. Score 0.255 Round 3: 107 peptides, 23 chains. Longest chain 8 peptides. Score 0.274 Round 4: 107 peptides, 19 chains. Longest chain 8 peptides. Score 0.385 Round 5: 101 peptides, 19 chains. Longest chain 8 peptides. Score 0.346 Taking the results from Round 4 Chains 19, Residues 88, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 2457 reflections ( 99.59 % complete ) and 5063 restraints for refining 2094 atoms. 4717 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2803 (Rfree = 0.000) for 2094 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Cycle 2: After refmac, R = 0.2569 (Rfree = 0.000) for 2054 atoms. Found 9 (9 requested) and removed 16 (4 requested) atoms. Cycle 3: After refmac, R = 0.1980 (Rfree = 0.000) for 2033 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. Cycle 4: After refmac, R = 0.2419 (Rfree = 0.000) for 2022 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. Cycle 5: After refmac, R = 0.2377 (Rfree = 0.000) for 2019 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.54 4.11 Search for helices and strands: 0 residues in 0 chains, 2052 seeds are put forward NCS extension: 0 residues added, 2052 seeds are put forward Round 1: 108 peptides, 24 chains. Longest chain 7 peptides. Score 0.252 Round 2: 120 peptides, 25 chains. Longest chain 9 peptides. Score 0.305 Round 3: 122 peptides, 24 chains. Longest chain 9 peptides. Score 0.346 Round 4: 122 peptides, 23 chains. Longest chain 11 peptides. Score 0.372 Round 5: 118 peptides, 20 chains. Longest chain 11 peptides. Score 0.426 Taking the results from Round 5 Chains 21, Residues 98, Estimated correctness of the model 0.0 % 4 chains (25 residues) have been docked in sequence ------------------------------------------------------ 2457 reflections ( 99.59 % complete ) and 4686 restraints for refining 2051 atoms. 4248 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2423 (Rfree = 0.000) for 2051 atoms. Found 9 (9 requested) and removed 18 (4 requested) atoms. Cycle 7: After refmac, R = 0.2381 (Rfree = 0.000) for 2022 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. Cycle 8: After refmac, R = 0.2170 (Rfree = 0.000) for 1999 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Cycle 9: After refmac, R = 0.2205 (Rfree = 0.000) for 1980 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 10: After refmac, R = 0.2081 (Rfree = 0.000) for 1973 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.59 4.17 Search for helices and strands: 0 residues in 0 chains, 2009 seeds are put forward NCS extension: 3 residues added (0 deleted due to clashes), 2012 seeds are put forward Round 1: 73 peptides, 17 chains. Longest chain 6 peptides. Score 0.206 Round 2: 92 peptides, 16 chains. Longest chain 16 peptides. Score 0.371 Round 3: 96 peptides, 17 chains. Longest chain 11 peptides. Score 0.369 Round 4: 99 peptides, 15 chains. Longest chain 18 peptides. Score 0.443 Round 5: 111 peptides, 17 chains. Longest chain 16 peptides. Score 0.462 Taking the results from Round 5 Chains 17, Residues 94, Estimated correctness of the model 0.0 % 2 chains (10 residues) have been docked in sequence ------------------------------------------------------ 2457 reflections ( 99.59 % complete ) and 4732 restraints for refining 2000 atoms. 4340 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2432 (Rfree = 0.000) for 2000 atoms. Found 9 (9 requested) and removed 24 (4 requested) atoms. Cycle 12: After refmac, R = 0.2250 (Rfree = 0.000) for 1970 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 13: After refmac, R = 0.2301 (Rfree = 0.000) for 1951 atoms. Found 9 (9 requested) and removed 14 (4 requested) atoms. Cycle 14: After refmac, R = 0.2119 (Rfree = 0.000) for 1936 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. Cycle 15: After refmac, R = 0.2071 (Rfree = 0.000) for 1926 atoms. Found 9 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.65 4.24 Search for helices and strands: 0 residues in 0 chains, 1969 seeds are put forward NCS extension: 30 residues added (2 deleted due to clashes), 1999 seeds are put forward Round 1: 77 peptides, 17 chains. Longest chain 7 peptides. Score 0.236 Round 2: 101 peptides, 17 chains. Longest chain 12 peptides. Score 0.401 Round 3: 98 peptides, 17 chains. Longest chain 12 peptides. Score 0.382 Round 4: 114 peptides, 19 chains. Longest chain 20 peptides. Score 0.428 Round 5: 111 peptides, 19 chains. Longest chain 12 peptides. Score 0.410 Taking the results from Round 4 Chains 21, Residues 95, Estimated correctness of the model 0.0 % 3 chains (22 residues) have been docked in sequence ------------------------------------------------------ 2457 reflections ( 99.59 % complete ) and 4215 restraints for refining 1906 atoms. 3809 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2169 (Rfree = 0.000) for 1906 atoms. Found 9 (9 requested) and removed 20 (4 requested) atoms. Cycle 17: After refmac, R = 0.2088 (Rfree = 0.000) for 1881 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 18: After refmac, R = 0.1909 (Rfree = 0.000) for 1871 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. Cycle 19: After refmac, R = 0.2051 (Rfree = 0.000) for 1860 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 20: After refmac, R = 0.1341 (Rfree = 0.000) for 1856 atoms. Found 4 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.63 4.21 Search for helices and strands: 0 residues in 0 chains, 1886 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 1898 seeds are put forward Round 1: 67 peptides, 15 chains. Longest chain 6 peptides. Score 0.223 Round 2: 71 peptides, 14 chains. Longest chain 8 peptides. Score 0.285 Round 3: 85 peptides, 14 chains. Longest chain 12 peptides. Score 0.383 Round 4: 87 peptides, 13 chains. Longest chain 12 peptides. Score 0.424 Round 5: 93 peptides, 14 chains. Longest chain 12 peptides. Score 0.434 Taking the results from Round 5 Chains 14, Residues 79, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2457 reflections ( 99.59 % complete ) and 4491 restraints for refining 1895 atoms. 4189 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2046 (Rfree = 0.000) for 1895 atoms. Found 8 (8 requested) and removed 14 (4 requested) atoms. Cycle 22: After refmac, R = 0.1991 (Rfree = 0.000) for 1881 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. Cycle 23: After refmac, R = 0.2110 (Rfree = 0.000) for 1873 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 24: After refmac, R = 0.2028 (Rfree = 0.000) for 1865 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. Cycle 25: After refmac, R = 0.1484 (Rfree = 0.000) for 1862 atoms. Found 1 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.58 4.16 Search for helices and strands: 0 residues in 0 chains, 1893 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 1908 seeds are put forward Round 1: 79 peptides, 19 chains. Longest chain 5 peptides. Score 0.190 Round 2: 94 peptides, 18 chains. Longest chain 11 peptides. Score 0.328 Round 3: 96 peptides, 18 chains. Longest chain 11 peptides. Score 0.341 Round 4: 94 peptides, 17 chains. Longest chain 10 peptides. Score 0.356 Round 5: 94 peptides, 16 chains. Longest chain 11 peptides. Score 0.384 Taking the results from Round 5 Chains 16, Residues 78, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 2457 reflections ( 99.59 % complete ) and 4280 restraints for refining 1873 atoms. 3972 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2133 (Rfree = 0.000) for 1873 atoms. Found 8 (8 requested) and removed 19 (4 requested) atoms. Cycle 27: After refmac, R = 0.1962 (Rfree = 0.000) for 1852 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 28: After refmac, R = 0.2368 (Rfree = 0.000) for 1837 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 29: After refmac, R = 0.2205 (Rfree = 0.000) for 1830 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 30: After refmac, R = 0.2113 (Rfree = 0.000) for 1823 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.52 4.09 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: 71 peptides, 15 chains. Longest chain 7 peptides. Score 0.254 Round 2: 90 peptides, 19 chains. Longest chain 9 peptides. Score 0.271 Round 3: 92 peptides, 19 chains. Longest chain 7 peptides. Score 0.285 Round 4: 96 peptides, 18 chains. Longest chain 9 peptides. Score 0.341 Round 5: 98 peptides, 20 chains. Longest chain 9 peptides. Score 0.297 Taking the results from Round 4 Chains 18, Residues 78, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 2457 reflections ( 99.59 % complete ) and 4033 restraints for refining 1850 atoms. 3720 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2033 (Rfree = 0.000) for 1850 atoms. Found 8 (8 requested) and removed 17 (4 requested) atoms. Cycle 32: After refmac, R = 0.2411 (Rfree = 0.000) for 1824 atoms. Found 8 (8 requested) and removed 14 (4 requested) atoms. Cycle 33: After refmac, R = 0.2084 (Rfree = 0.000) for 1804 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 34: After refmac, R = 0.1968 (Rfree = 0.000) for 1794 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. Cycle 35: After refmac, R = 0.2128 (Rfree = 0.000) for 1787 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.52 4.09 Search for helices and strands: 0 residues in 0 chains, 1830 seeds are put forward NCS extension: 0 residues added, 1830 seeds are put forward Round 1: 88 peptides, 21 chains. Longest chain 6 peptides. Score 0.197 Round 2: 94 peptides, 20 chains. Longest chain 6 peptides. Score 0.270 Round 3: 93 peptides, 19 chains. Longest chain 8 peptides. Score 0.292 Round 4: 96 peptides, 18 chains. Longest chain 11 peptides. Score 0.341 Round 5: 88 peptides, 19 chains. Longest chain 8 peptides. Score 0.256 Taking the results from Round 4 Chains 18, Residues 78, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 2457 reflections ( 99.59 % complete ) and 4166 restraints for refining 1867 atoms. 3865 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2259 (Rfree = 0.000) for 1867 atoms. Found 8 (8 requested) and removed 16 (4 requested) atoms. Cycle 37: After refmac, R = 0.2008 (Rfree = 0.000) for 1849 atoms. Found 8 (8 requested) and removed 17 (4 requested) atoms. Cycle 38: After refmac, R = 0.2034 (Rfree = 0.000) for 1833 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. Cycle 39: After refmac, R = 0.2104 (Rfree = 0.000) for 1828 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. Cycle 40: After refmac, R = 0.1927 (Rfree = 0.000) for 1818 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.52 4.09 Search for helices and strands: 0 residues in 0 chains, 1859 seeds are put forward NCS extension: 0 residues added, 1859 seeds are put forward Round 1: 57 peptides, 13 chains. Longest chain 6 peptides. Score 0.209 Round 2: 71 peptides, 14 chains. Longest chain 7 peptides. Score 0.285 Round 3: 80 peptides, 16 chains. Longest chain 8 peptides. Score 0.289 Round 4: 83 peptides, 16 chains. Longest chain 7 peptides. Score 0.310 Round 5: 71 peptides, 15 chains. Longest chain 8 peptides. Score 0.254 Taking the results from Round 4 Chains 16, Residues 67, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2457 reflections ( 99.59 % complete ) and 3934 restraints for refining 1779 atoms. 3682 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2347 (Rfree = 0.000) for 1779 atoms. Found 8 (8 requested) and removed 17 (4 requested) atoms. Cycle 42: After refmac, R = 0.2093 (Rfree = 0.000) for 1757 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. Cycle 43: After refmac, R = 0.1965 (Rfree = 0.000) for 1745 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. Cycle 44: After refmac, R = 0.1966 (Rfree = 0.000) for 1743 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. Cycle 45: After refmac, R = 0.1990 (Rfree = 0.000) for 1739 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.53 4.10 Search for helices and strands: 0 residues in 0 chains, 1769 seeds are put forward NCS extension: 0 residues added, 1769 seeds are put forward Round 1: 51 peptides, 12 chains. Longest chain 5 peptides. Score 0.193 Round 2: 57 peptides, 11 chains. Longest chain 6 peptides. Score 0.277 Round 3: 66 peptides, 11 chains. Longest chain 9 peptides. Score 0.344 Round 4: 58 peptides, 10 chains. Longest chain 8 peptides. Score 0.318 Round 5: 60 peptides, 12 chains. Longest chain 7 peptides. Score 0.267 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 11, Residues 55, 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 2o1q-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2457 reflections ( 99.59 % complete ) and 3637 restraints for refining 1673 atoms. 3428 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2233 (Rfree = 0.000) for 1673 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.2266 (Rfree = 0.000) for 1662 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.2142 (Rfree = 0.000) for 1650 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.1893 (Rfree = 0.000) for 1643 atoms. TimeTaking 28.75