Mon 24 Dec 00:04:01 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 2p1a-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2p1a-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2p1a-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p1a-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/2p1a-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p1a-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 00:04:06 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/2p1a-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p1a-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 183 and 0 Target number of residues in the AU: 183 Target solvent content: 0.6774 Checking the provided sequence file Detected sequence length: 154 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 308 Adjusted target solvent content: 0.46 Input MTZ file: 2p1a-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: 19 Cell parameters: 45.470 77.850 86.720 90.000 90.000 90.000 Input sequence file: 2p1a-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 2464 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: 29.570 4.001 Wilson plot Bfac: 98.76 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 2832 reflections ( 99.33 % complete ) and 0 restraints for refining 2731 atoms. Observations/parameters ratio is 0.26 ------------------------------------------------------ Starting model: R = 0.3630 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3521 (Rfree = 0.000) for 2731 atoms. Found 12 (12 requested) and removed 32 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 4.32 4.56 Search for helices and strands: 0 residues in 0 chains, 2786 seeds are put forward NCS extension: 0 residues added, 2786 seeds are put forward Round 1: 61 peptides, 12 chains. Longest chain 7 peptides. Score 0.263 Round 2: 78 peptides, 13 chains. Longest chain 11 peptides. Score 0.342 Round 3: 89 peptides, 16 chains. Longest chain 8 peptides. Score 0.329 Round 4: 95 peptides, 16 chains. Longest chain 9 peptides. Score 0.363 Round 5: 105 peptides, 16 chains. Longest chain 12 peptides. Score 0.418 Taking the results from Round 5 Chains 16, Residues 89, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2832 reflections ( 99.33 % complete ) and 5694 restraints for refining 2225 atoms. 5354 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2689 (Rfree = 0.000) for 2225 atoms. Found 5 (10 requested) and removed 16 (5 requested) atoms. Cycle 2: After refmac, R = 0.2331 (Rfree = 0.000) for 2178 atoms. Found 3 (10 requested) and removed 13 (5 requested) atoms. Cycle 3: After refmac, R = 0.2369 (Rfree = 0.000) for 2148 atoms. Found 2 (10 requested) and removed 8 (5 requested) atoms. Cycle 4: After refmac, R = 0.2311 (Rfree = 0.000) for 2130 atoms. Found 3 (10 requested) and removed 7 (5 requested) atoms. Cycle 5: After refmac, R = 0.2167 (Rfree = 0.000) for 2118 atoms. Found 1 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 4.10 4.32 Search for helices and strands: 0 residues in 0 chains, 2197 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 2210 seeds are put forward Round 1: 79 peptides, 17 chains. Longest chain 8 peptides. Score 0.241 Round 2: 87 peptides, 16 chains. Longest chain 11 peptides. Score 0.317 Round 3: 99 peptides, 16 chains. Longest chain 14 peptides. Score 0.386 Round 4: 95 peptides, 15 chains. Longest chain 13 peptides. Score 0.388 Round 5: 95 peptides, 15 chains. Longest chain 16 peptides. Score 0.388 Taking the results from Round 5 Chains 15, Residues 80, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2832 reflections ( 99.33 % complete ) and 4933 restraints for refining 2000 atoms. 4628 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2705 (Rfree = 0.000) for 2000 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. Cycle 7: After refmac, R = 0.2488 (Rfree = 0.000) for 1985 atoms. Found 1 (9 requested) and removed 8 (4 requested) atoms. Cycle 8: After refmac, R = 0.2399 (Rfree = 0.000) for 1974 atoms. Found 1 (9 requested) and removed 6 (4 requested) atoms. Cycle 9: After refmac, R = 0.2357 (Rfree = 0.000) for 1968 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. Cycle 10: After refmac, R = 0.2357 (Rfree = 0.000) for 1964 atoms. Found 0 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 4.05 4.27 Search for helices and strands: 0 residues in 0 chains, 2051 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 2075 seeds are put forward Round 1: 86 peptides, 18 chains. Longest chain 9 peptides. Score 0.259 Round 2: 91 peptides, 16 chains. Longest chain 10 peptides. Score 0.341 Round 3: 94 peptides, 16 chains. Longest chain 13 peptides. Score 0.358 Round 4: 98 peptides, 16 chains. Longest chain 13 peptides. Score 0.380 Round 5: 107 peptides, 16 chains. Longest chain 11 peptides. Score 0.428 Taking the results from Round 5 Chains 16, Residues 91, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2832 reflections ( 99.33 % complete ) and 5086 restraints for refining 2057 atoms. 4738 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2544 (Rfree = 0.000) for 2057 atoms. Found 4 (9 requested) and removed 6 (4 requested) atoms. Cycle 12: After refmac, R = 0.2445 (Rfree = 0.000) for 2045 atoms. Found 3 (9 requested) and removed 6 (4 requested) atoms. Cycle 13: After refmac, R = 0.2378 (Rfree = 0.000) for 2037 atoms. Found 1 (9 requested) and removed 6 (4 requested) atoms. Cycle 14: After refmac, R = 0.2325 (Rfree = 0.000) for 2031 atoms. Found 0 (9 requested) and removed 5 (4 requested) atoms. Cycle 15: After refmac, R = 0.2292 (Rfree = 0.000) for 2026 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 4.13 4.36 Search for helices and strands: 0 residues in 0 chains, 2145 seeds are put forward NCS extension: 0 residues added, 2145 seeds are put forward Round 1: 83 peptides, 16 chains. Longest chain 10 peptides. Score 0.293 Round 2: 96 peptides, 14 chains. Longest chain 17 peptides. Score 0.418 Round 3: 93 peptides, 14 chains. Longest chain 16 peptides. Score 0.402 Round 4: 94 peptides, 14 chains. Longest chain 16 peptides. Score 0.407 Round 5: 97 peptides, 12 chains. Longest chain 17 peptides. Score 0.471 Taking the results from Round 5 Chains 12, Residues 85, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2832 reflections ( 99.33 % complete ) and 5076 restraints for refining 2073 atoms. 4748 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2536 (Rfree = 0.000) for 2073 atoms. Found 5 (9 requested) and removed 14 (4 requested) atoms. Cycle 17: After refmac, R = 0.2434 (Rfree = 0.000) for 2059 atoms. Found 3 (9 requested) and removed 7 (4 requested) atoms. Cycle 18: After refmac, R = 0.2382 (Rfree = 0.000) for 2051 atoms. Found 4 (9 requested) and removed 6 (4 requested) atoms. Cycle 19: After refmac, R = 0.2324 (Rfree = 0.000) for 2048 atoms. Found 3 (9 requested) and removed 6 (4 requested) atoms. Cycle 20: After refmac, R = 0.2284 (Rfree = 0.000) for 2045 atoms. Found 1 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 4.13 4.36 Search for helices and strands: 0 residues in 0 chains, 2141 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 2162 seeds are put forward Round 1: 82 peptides, 15 chains. Longest chain 11 peptides. Score 0.313 Round 2: 84 peptides, 14 chains. Longest chain 12 peptides. Score 0.351 Round 3: 81 peptides, 11 chains. Longest chain 14 peptides. Score 0.412 Round 4: 96 peptides, 17 chains. Longest chain 10 peptides. Score 0.344 Round 5: 96 peptides, 16 chains. Longest chain 16 peptides. Score 0.369 Taking the results from Round 3 Chains 11, Residues 70, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2832 reflections ( 99.33 % complete ) and 4988 restraints for refining 2045 atoms. 4719 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2237 (Rfree = 0.000) for 2045 atoms. Found 3 (9 requested) and removed 10 (4 requested) atoms. Cycle 22: After refmac, R = 0.2073 (Rfree = 0.000) for 2033 atoms. Found 2 (9 requested) and removed 6 (4 requested) atoms. Cycle 23: After refmac, R = 0.2148 (Rfree = 0.000) for 2024 atoms. Found 3 (9 requested) and removed 9 (4 requested) atoms. Cycle 24: After refmac, R = 0.2054 (Rfree = 0.000) for 2014 atoms. Found 3 (9 requested) and removed 8 (4 requested) atoms. Cycle 25: After refmac, R = 0.1908 (Rfree = 0.000) for 2008 atoms. Found 2 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 4.06 4.28 Search for helices and strands: 0 residues in 0 chains, 2124 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 2141 seeds are put forward Round 1: 76 peptides, 15 chains. Longest chain 10 peptides. Score 0.276 Round 2: 74 peptides, 13 chains. Longest chain 10 peptides. Score 0.318 Round 3: 88 peptides, 15 chains. Longest chain 12 peptides. Score 0.349 Round 4: 84 peptides, 14 chains. Longest chain 12 peptides. Score 0.351 Round 5: 79 peptides, 13 chains. Longest chain 10 peptides. Score 0.348 Taking the results from Round 4 Chains 14, Residues 70, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2832 reflections ( 99.33 % complete ) and 4974 restraints for refining 2015 atoms. 4708 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2170 (Rfree = 0.000) for 2015 atoms. Found 5 (9 requested) and removed 22 (4 requested) atoms. Cycle 27: After refmac, R = 0.2152 (Rfree = 0.000) for 1994 atoms. Found 3 (9 requested) and removed 11 (4 requested) atoms. Cycle 28: After refmac, R = 0.2086 (Rfree = 0.000) for 1983 atoms. Found 1 (9 requested) and removed 9 (4 requested) atoms. Cycle 29: After refmac, R = 0.1965 (Rfree = 0.000) for 1973 atoms. Found 4 (9 requested) and removed 8 (4 requested) atoms. Cycle 30: After refmac, R = 0.1873 (Rfree = 0.000) for 1966 atoms. Found 1 (9 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.94 4.16 Search for helices and strands: 0 residues in 0 chains, 2067 seeds are put forward NCS extension: 8 residues added (2 deleted due to clashes), 2075 seeds are put forward Round 1: 89 peptides, 20 chains. Longest chain 7 peptides. Score 0.225 Round 2: 88 peptides, 16 chains. Longest chain 12 peptides. Score 0.323 Round 3: 85 peptides, 18 chains. Longest chain 9 peptides. Score 0.253 Round 4: 87 peptides, 15 chains. Longest chain 10 peptides. Score 0.343 Round 5: 86 peptides, 15 chains. Longest chain 10 peptides. Score 0.337 Taking the results from Round 4 Chains 15, Residues 72, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2832 reflections ( 99.33 % complete ) and 4944 restraints for refining 2044 atoms. 4671 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2280 (Rfree = 0.000) for 2044 atoms. Found 7 (9 requested) and removed 17 (4 requested) atoms. Cycle 32: After refmac, R = 0.2288 (Rfree = 0.000) for 2026 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 33: After refmac, R = 0.2420 (Rfree = 0.000) for 2020 atoms. Found 9 (9 requested) and removed 19 (4 requested) atoms. Cycle 34: After refmac, R = 0.2494 (Rfree = 0.000) for 1999 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 35: After refmac, R = 0.2113 (Rfree = 0.000) for 1986 atoms. Found 8 (9 requested) and removed 10 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.87 4.08 Search for helices and strands: 0 residues in 0 chains, 2088 seeds are put forward NCS extension: 6 residues added (0 deleted due to clashes), 2094 seeds are put forward Round 1: 54 peptides, 12 chains. Longest chain 7 peptides. Score 0.213 Round 2: 72 peptides, 15 chains. Longest chain 9 peptides. Score 0.250 Round 3: 76 peptides, 16 chains. Longest chain 8 peptides. Score 0.249 Round 4: 73 peptides, 14 chains. Longest chain 8 peptides. Score 0.284 Round 5: 66 peptides, 13 chains. Longest chain 9 peptides. Score 0.267 Taking the results from Round 4 Chains 14, Residues 59, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2832 reflections ( 99.33 % complete ) and 4395 restraints for refining 1846 atoms. 4173 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2386 (Rfree = 0.000) for 1846 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 37: After refmac, R = 0.2285 (Rfree = 0.000) for 1841 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 38: After refmac, R = 0.2232 (Rfree = 0.000) for 1834 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. Cycle 39: After refmac, R = 0.2116 (Rfree = 0.000) for 1820 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 40: After refmac, R = 0.2381 (Rfree = 0.000) for 1815 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.83 4.04 Search for helices and strands: 0 residues in 0 chains, 1921 seeds are put forward NCS extension: 0 residues added, 1921 seeds are put forward Round 1: 51 peptides, 12 chains. Longest chain 6 peptides. Score 0.190 Round 2: 61 peptides, 13 chains. Longest chain 6 peptides. Score 0.233 Round 3: 64 peptides, 12 chains. Longest chain 7 peptides. Score 0.283 Round 4: 68 peptides, 12 chains. Longest chain 8 peptides. Score 0.308 Round 5: 67 peptides, 12 chains. Longest chain 8 peptides. Score 0.302 Taking the results from Round 4 Chains 12, Residues 56, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2832 reflections ( 99.33 % complete ) and 3943 restraints for refining 1729 atoms. 3731 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2336 (Rfree = 0.000) for 1729 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 42: After refmac, R = 0.2161 (Rfree = 0.000) for 1721 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 43: After refmac, R = 0.2331 (Rfree = 0.000) for 1716 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 44: After refmac, R = 0.2103 (Rfree = 0.000) for 1712 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 45: After refmac, R = 0.2213 (Rfree = 0.000) for 1711 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.93 4.15 Search for helices and strands: 0 residues in 0 chains, 1786 seeds are put forward NCS extension: 0 residues added, 1786 seeds are put forward Round 1: 63 peptides, 14 chains. Longest chain 7 peptides. Score 0.218 Round 2: 74 peptides, 14 chains. Longest chain 8 peptides. Score 0.291 Round 3: 71 peptides, 13 chains. Longest chain 13 peptides. Score 0.299 Round 4: 73 peptides, 14 chains. Longest chain 8 peptides. Score 0.284 Round 5: 75 peptides, 13 chains. Longest chain 14 peptides. Score 0.324 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 13, Residues 62, 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 2p1a-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2832 reflections ( 99.33 % complete ) and 3980 restraints for refining 1728 atoms. 3745 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2525 (Rfree = 0.000) for 1728 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.2164 (Rfree = 0.000) for 1720 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.2253 (Rfree = 0.000) for 1708 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.2248 (Rfree = 0.000) for 1690 atoms. TimeTaking 28.75