Mon 24 Dec 00:12:19 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-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2o1q-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2o1q-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2o1q-3.8-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-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2o1q-3.8-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 00:12:24 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-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2o1q-3.8-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 169 and 0 Target number of residues in the AU: 169 Target solvent content: 0.6421 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-3.8-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-3.8-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 3.801 Wilson plot Bfac: 72.44 2845 reflections ( 99.65 % complete ) and 0 restraints for refining 2560 atoms. Observations/parameters ratio is 0.28 ------------------------------------------------------ Starting model: R = 0.3436 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3191 (Rfree = 0.000) for 2560 atoms. Found 14 (14 requested) and removed 31 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.45 4.00 Search for helices and strands: 0 residues in 0 chains, 2577 seeds are put forward NCS extension: 0 residues added, 2577 seeds are put forward Round 1: 86 peptides, 18 chains. Longest chain 7 peptides. Score 0.272 Round 2: 123 peptides, 21 chains. Longest chain 18 peptides. Score 0.431 Round 3: 120 peptides, 19 chains. Longest chain 12 peptides. Score 0.464 Round 4: 132 peptides, 20 chains. Longest chain 16 peptides. Score 0.506 Round 5: 128 peptides, 21 chains. Longest chain 10 peptides. Score 0.460 Taking the results from Round 4 Chains 21, Residues 112, Estimated correctness of the model 0.0 % 7 chains (39 residues) have been docked in sequence ------------------------------------------------------ 2845 reflections ( 99.65 % complete ) and 4502 restraints for refining 2096 atoms. 3959 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2730 (Rfree = 0.000) for 2096 atoms. Found 7 (11 requested) and removed 20 (5 requested) atoms. Cycle 2: After refmac, R = 0.2605 (Rfree = 0.000) for 2044 atoms. Found 10 (11 requested) and removed 13 (5 requested) atoms. Cycle 3: After refmac, R = 0.1924 (Rfree = 0.000) for 2025 atoms. Found 3 (11 requested) and removed 10 (5 requested) atoms. Cycle 4: After refmac, R = 0.2188 (Rfree = 0.000) for 2010 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 5: After refmac, R = 0.1752 (Rfree = 0.000) for 2003 atoms. Found 6 (11 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.41 3.96 Search for helices and strands: 0 residues in 0 chains, 2040 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 2051 seeds are put forward Round 1: 112 peptides, 22 chains. Longest chain 8 peptides. Score 0.335 Round 2: 123 peptides, 22 chains. Longest chain 9 peptides. Score 0.405 Round 3: 116 peptides, 20 chains. Longest chain 11 peptides. Score 0.414 Round 4: 115 peptides, 21 chains. Longest chain 13 peptides. Score 0.381 Round 5: 113 peptides, 19 chains. Longest chain 12 peptides. Score 0.422 Taking the results from Round 5 Chains 19, Residues 94, Estimated correctness of the model 0.0 % 4 chains (24 residues) have been docked in sequence ------------------------------------------------------ 2845 reflections ( 99.65 % complete ) and 4621 restraints for refining 2054 atoms. 4180 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2327 (Rfree = 0.000) for 2054 atoms. Found 11 (11 requested) and removed 17 (5 requested) atoms. Cycle 7: After refmac, R = 0.2374 (Rfree = 0.000) for 2027 atoms. Found 11 (11 requested) and removed 15 (5 requested) atoms. Cycle 8: After refmac, R = 0.1988 (Rfree = 0.000) for 2003 atoms. Found 11 (11 requested) and removed 7 (5 requested) atoms. Cycle 9: After refmac, R = 0.2122 (Rfree = 0.000) for 2003 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 10: After refmac, R = 0.2034 (Rfree = 0.000) for 2001 atoms. Found 11 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.42 3.97 Search for helices and strands: 0 residues in 0 chains, 2049 seeds are put forward NCS extension: 0 residues added, 2049 seeds are put forward Round 1: 88 peptides, 19 chains. Longest chain 8 peptides. Score 0.256 Round 2: 108 peptides, 19 chains. Longest chain 10 peptides. Score 0.391 Round 3: 117 peptides, 22 chains. Longest chain 10 peptides. Score 0.367 Round 4: 123 peptides, 18 chains. Longest chain 14 peptides. Score 0.505 Round 5: 123 peptides, 16 chains. Longest chain 14 peptides. Score 0.552 Taking the results from Round 5 Chains 16, Residues 107, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2845 reflections ( 99.65 % complete ) and 4504 restraints for refining 1983 atoms. 4092 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1948 (Rfree = 0.000) for 1983 atoms. Found 10 (10 requested) and removed 16 (5 requested) atoms. Cycle 12: After refmac, R = 0.2347 (Rfree = 0.000) for 1966 atoms. Found 10 (10 requested) and removed 15 (5 requested) atoms. Cycle 13: After refmac, R = 0.2048 (Rfree = 0.000) for 1951 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. Cycle 14: After refmac, R = 0.2343 (Rfree = 0.000) for 1940 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. Cycle 15: After refmac, R = 0.2016 (Rfree = 0.000) for 1933 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.47 4.03 Search for helices and strands: 0 residues in 0 chains, 1988 seeds are put forward NCS extension: 0 residues added, 1988 seeds are put forward Round 1: 118 peptides, 24 chains. Longest chain 8 peptides. Score 0.320 Round 2: 124 peptides, 23 chains. Longest chain 12 peptides. Score 0.385 Round 3: 116 peptides, 20 chains. Longest chain 10 peptides. Score 0.414 Round 4: 128 peptides, 19 chains. Longest chain 17 peptides. Score 0.508 Round 5: 120 peptides, 20 chains. Longest chain 9 peptides. Score 0.438 Taking the results from Round 4 Chains 21, Residues 109, Estimated correctness of the model 0.0 % 3 chains (19 residues) have been docked in sequence ------------------------------------------------------ 2845 reflections ( 99.65 % complete ) and 4370 restraints for refining 2042 atoms. 3903 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2001 (Rfree = 0.000) for 2042 atoms. Found 11 (11 requested) and removed 19 (5 requested) atoms. Cycle 17: After refmac, R = 0.1664 (Rfree = 0.000) for 2020 atoms. Found 2 (11 requested) and removed 8 (5 requested) atoms. Cycle 18: After refmac, R = 0.1564 (Rfree = 0.000) for 1999 atoms. Found 2 (11 requested) and removed 8 (5 requested) atoms. Cycle 19: After refmac, R = 0.1549 (Rfree = 0.000) for 1990 atoms. Found 2 (10 requested) and removed 5 (5 requested) atoms. Cycle 20: After refmac, R = 0.1528 (Rfree = 0.000) for 1984 atoms. Found 1 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.43 3.98 Search for helices and strands: 0 residues in 0 chains, 2023 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 2035 seeds are put forward Round 1: 95 peptides, 21 chains. Longest chain 8 peptides. Score 0.247 Round 2: 113 peptides, 22 chains. Longest chain 9 peptides. Score 0.342 Round 3: 117 peptides, 21 chains. Longest chain 12 peptides. Score 0.394 Round 4: 106 peptides, 17 chains. Longest chain 14 peptides. Score 0.432 Round 5: 108 peptides, 16 chains. Longest chain 12 peptides. Score 0.470 Taking the results from Round 5 Chains 16, Residues 92, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 2845 reflections ( 99.65 % complete ) and 4832 restraints for refining 2092 atoms. 4452 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2117 (Rfree = 0.000) for 2092 atoms. Found 11 (11 requested) and removed 15 (5 requested) atoms. Cycle 22: After refmac, R = 0.2362 (Rfree = 0.000) for 2069 atoms. Found 11 (11 requested) and removed 19 (5 requested) atoms. Cycle 23: After refmac, R = 0.2264 (Rfree = 0.000) for 2045 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. Cycle 24: After refmac, R = 0.2254 (Rfree = 0.000) for 2032 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 25: After refmac, R = 0.1612 (Rfree = 0.000) for 2020 atoms. Found 9 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.47 4.03 Search for helices and strands: 0 residues in 0 chains, 2055 seeds are put forward NCS extension: 0 residues added, 2055 seeds are put forward Round 1: 70 peptides, 14 chains. Longest chain 9 peptides. Score 0.278 Round 2: 95 peptides, 20 chains. Longest chain 8 peptides. Score 0.277 Round 3: 101 peptides, 20 chains. Longest chain 7 peptides. Score 0.318 Round 4: 107 peptides, 20 chains. Longest chain 8 peptides. Score 0.357 Round 5: 106 peptides, 19 chains. Longest chain 9 peptides. Score 0.378 Taking the results from Round 5 Chains 19, Residues 87, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2845 reflections ( 99.65 % complete ) and 4551 restraints for refining 1965 atoms. 4222 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2177 (Rfree = 0.000) for 1965 atoms. Found 10 (10 requested) and removed 19 (5 requested) atoms. Cycle 27: After refmac, R = 0.2365 (Rfree = 0.000) for 1943 atoms. Found 10 (10 requested) and removed 18 (5 requested) atoms. Cycle 28: After refmac, R = 0.1971 (Rfree = 0.000) for 1931 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. Cycle 29: After refmac, R = 0.2200 (Rfree = 0.000) for 1928 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. Cycle 30: After refmac, R = 0.2065 (Rfree = 0.000) for 1927 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.50 4.06 Search for helices and strands: 0 residues in 0 chains, 1963 seeds are put forward NCS extension: 0 residues added, 1963 seeds are put forward Round 1: 83 peptides, 17 chains. Longest chain 11 peptides. Score 0.280 Round 2: 102 peptides, 21 chains. Longest chain 8 peptides. Score 0.296 Round 3: 107 peptides, 19 chains. Longest chain 12 peptides. Score 0.385 Round 4: 101 peptides, 19 chains. Longest chain 11 peptides. Score 0.346 Round 5: 100 peptides, 19 chains. Longest chain 10 peptides. Score 0.339 Taking the results from Round 3 Chains 19, Residues 88, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2845 reflections ( 99.65 % complete ) and 4516 restraints for refining 1948 atoms. 4183 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1776 (Rfree = 0.000) for 1948 atoms. Found 5 (10 requested) and removed 15 (5 requested) atoms. Cycle 32: After refmac, R = 0.1619 (Rfree = 0.000) for 1931 atoms. Found 4 (10 requested) and removed 8 (5 requested) atoms. Cycle 33: After refmac, R = 0.1436 (Rfree = 0.000) for 1924 atoms. Found 1 (10 requested) and removed 5 (5 requested) atoms. Cycle 34: After refmac, R = 0.1407 (Rfree = 0.000) for 1914 atoms. Found 2 (10 requested) and removed 5 (5 requested) atoms. Cycle 35: After refmac, R = 0.1320 (Rfree = 0.000) for 1911 atoms. Found 2 (10 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.52 4.09 Search for helices and strands: 0 residues in 0 chains, 1938 seeds are put forward NCS extension: 0 residues added, 1938 seeds are put forward Round 1: 80 peptides, 18 chains. Longest chain 7 peptides. Score 0.228 Round 2: 95 peptides, 18 chains. Longest chain 9 peptides. Score 0.334 Round 3: 97 peptides, 19 chains. Longest chain 7 peptides. Score 0.319 Round 4: 95 peptides, 18 chains. Longest chain 9 peptides. Score 0.334 Round 5: 98 peptides, 18 chains. Longest chain 10 peptides. Score 0.354 Taking the results from Round 5 Chains 18, Residues 80, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2845 reflections ( 99.65 % complete ) and 4862 restraints for refining 2048 atoms. 4560 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2171 (Rfree = 0.000) for 2048 atoms. Found 11 (11 requested) and removed 16 (5 requested) atoms. Cycle 37: After refmac, R = 0.2115 (Rfree = 0.000) for 2034 atoms. Found 11 (11 requested) and removed 14 (5 requested) atoms. Cycle 38: After refmac, R = 0.2262 (Rfree = 0.000) for 2016 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. Cycle 39: After refmac, R = 0.2314 (Rfree = 0.000) for 2005 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 40: After refmac, R = 0.2242 (Rfree = 0.000) for 2001 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.45 4.00 Search for helices and strands: 0 residues in 0 chains, 2055 seeds are put forward NCS extension: 0 residues added, 2055 seeds are put forward Round 1: 49 peptides, 11 chains. Longest chain 6 peptides. Score 0.212 Round 2: 68 peptides, 14 chains. Longest chain 7 peptides. Score 0.263 Round 3: 79 peptides, 16 chains. Longest chain 8 peptides. Score 0.282 Round 4: 66 peptides, 14 chains. Longest chain 9 peptides. Score 0.248 Round 5: 70 peptides, 13 chains. Longest chain 8 peptides. Score 0.310 Taking the results from Round 5 Chains 13, Residues 57, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2845 reflections ( 99.65 % complete ) and 4512 restraints for refining 1901 atoms. 4297 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2296 (Rfree = 0.000) for 1901 atoms. Found 10 (10 requested) and removed 15 (5 requested) atoms. Cycle 42: After refmac, R = 0.2285 (Rfree = 0.000) for 1887 atoms. Found 10 (10 requested) and removed 13 (5 requested) atoms. Cycle 43: After refmac, R = 0.2082 (Rfree = 0.000) for 1876 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. Cycle 44: After refmac, R = 0.2170 (Rfree = 0.000) for 1870 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 45: After refmac, R = 0.2214 (Rfree = 0.000) for 1865 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.34 3.88 Search for helices and strands: 0 residues in 0 chains, 1891 seeds are put forward NCS extension: 0 residues added, 1891 seeds are put forward Round 1: 55 peptides, 11 chains. Longest chain 9 peptides. Score 0.261 Round 2: 61 peptides, 10 chains. Longest chain 13 peptides. Score 0.341 Round 3: 63 peptides, 10 chains. Longest chain 13 peptides. Score 0.355 Round 4: 59 peptides, 11 chains. Longest chain 7 peptides. Score 0.293 Round 5: 59 peptides, 10 chains. Longest chain 10 peptides. Score 0.326 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 10, Residues 53, 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-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2845 reflections ( 99.65 % complete ) and 3778 restraints for refining 1732 atoms. 3576 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2179 (Rfree = 0.000) for 1732 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.2282 (Rfree = 0.000) for 1724 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.2115 (Rfree = 0.000) for 1712 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.2169 (Rfree = 0.000) for 1707 atoms. TimeTaking 31.13