Mon 24 Dec 01:08:37 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-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2p1a-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2p1a-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p1a-3.4-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-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p1a-3.4-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 01:08:42 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-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p1a-3.4-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 201 and 0 Target number of residues in the AU: 201 Target solvent content: 0.6456 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-3.4-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-3.4-parrot-mrncs.fasta_lf Building free atoms model in initial map for 2464 target number of atoms Had to go as low as 0.60 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 3.400 Wilson plot Bfac: 75.28 4531 reflections ( 99.47 % complete ) and 0 restraints for refining 2740 atoms. Observations/parameters ratio is 0.41 ------------------------------------------------------ Starting model: R = 0.3375 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3041 (Rfree = 0.000) for 2740 atoms. Found 20 (20 requested) and removed 30 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.48 3.67 Search for helices and strands: 0 residues in 0 chains, 2818 seeds are put forward NCS extension: 0 residues added, 2818 seeds are put forward Round 1: 98 peptides, 22 chains. Longest chain 6 peptides. Score 0.230 Round 2: 133 peptides, 26 chains. Longest chain 8 peptides. Score 0.336 Round 3: 133 peptides, 26 chains. Longest chain 8 peptides. Score 0.336 Round 4: 147 peptides, 26 chains. Longest chain 10 peptides. Score 0.410 Round 5: 152 peptides, 24 chains. Longest chain 14 peptides. Score 0.477 Taking the results from Round 5 Chains 24, Residues 128, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4531 reflections ( 99.47 % complete ) and 5220 restraints for refining 2239 atoms. 4732 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2304 (Rfree = 0.000) for 2239 atoms. Found 15 (16 requested) and removed 19 (8 requested) atoms. Cycle 2: After refmac, R = 0.2088 (Rfree = 0.000) for 2219 atoms. Found 6 (16 requested) and removed 12 (8 requested) atoms. Cycle 3: After refmac, R = 0.2105 (Rfree = 0.000) for 2200 atoms. Found 2 (16 requested) and removed 11 (8 requested) atoms. Cycle 4: After refmac, R = 0.2120 (Rfree = 0.000) for 2183 atoms. Found 6 (16 requested) and removed 10 (8 requested) atoms. Cycle 5: After refmac, R = 0.2040 (Rfree = 0.000) for 2175 atoms. Found 6 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.39 3.58 Search for helices and strands: 0 residues in 0 chains, 2312 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 2335 seeds are put forward Round 1: 120 peptides, 24 chains. Longest chain 11 peptides. Score 0.311 Round 2: 141 peptides, 24 chains. Longest chain 11 peptides. Score 0.423 Round 3: 148 peptides, 24 chains. Longest chain 13 peptides. Score 0.458 Round 4: 143 peptides, 22 chains. Longest chain 13 peptides. Score 0.475 Round 5: 137 peptides, 22 chains. Longest chain 12 peptides. Score 0.446 Taking the results from Round 4 Chains 22, Residues 121, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4531 reflections ( 99.47 % complete ) and 5275 restraints for refining 2220 atoms. 4813 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2072 (Rfree = 0.000) for 2220 atoms. Found 11 (16 requested) and removed 11 (8 requested) atoms. Cycle 7: After refmac, R = 0.1941 (Rfree = 0.000) for 2210 atoms. Found 2 (16 requested) and removed 12 (8 requested) atoms. Cycle 8: After refmac, R = 0.2084 (Rfree = 0.000) for 2196 atoms. Found 11 (16 requested) and removed 12 (8 requested) atoms. Cycle 9: After refmac, R = 0.2148 (Rfree = 0.000) for 2191 atoms. Found 7 (16 requested) and removed 10 (8 requested) atoms. Cycle 10: After refmac, R = 0.1910 (Rfree = 0.000) for 2180 atoms. Found 2 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.37 3.55 Search for helices and strands: 0 residues in 0 chains, 2284 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 2295 seeds are put forward Round 1: 118 peptides, 23 chains. Longest chain 9 peptides. Score 0.323 Round 2: 132 peptides, 22 chains. Longest chain 11 peptides. Score 0.421 Round 3: 121 peptides, 22 chains. Longest chain 13 peptides. Score 0.363 Round 4: 140 peptides, 22 chains. Longest chain 11 peptides. Score 0.461 Round 5: 149 peptides, 24 chains. Longest chain 11 peptides. Score 0.462 Taking the results from Round 5 Chains 24, Residues 125, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4531 reflections ( 99.47 % complete ) and 5154 restraints for refining 2240 atoms. 4678 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2104 (Rfree = 0.000) for 2240 atoms. Found 10 (16 requested) and removed 14 (8 requested) atoms. Cycle 12: After refmac, R = 0.2037 (Rfree = 0.000) for 2224 atoms. Found 4 (16 requested) and removed 10 (8 requested) atoms. Cycle 13: After refmac, R = 0.2022 (Rfree = 0.000) for 2215 atoms. Found 6 (16 requested) and removed 11 (8 requested) atoms. Cycle 14: After refmac, R = 0.2025 (Rfree = 0.000) for 2208 atoms. Found 3 (16 requested) and removed 10 (8 requested) atoms. Cycle 15: After refmac, R = 0.2009 (Rfree = 0.000) for 2200 atoms. Found 4 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.40 3.59 Search for helices and strands: 0 residues in 0 chains, 2309 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 2325 seeds are put forward Round 1: 120 peptides, 25 chains. Longest chain 8 peptides. Score 0.287 Round 2: 131 peptides, 21 chains. Longest chain 13 peptides. Score 0.438 Round 3: 121 peptides, 18 chains. Longest chain 12 peptides. Score 0.454 Round 4: 127 peptides, 18 chains. Longest chain 12 peptides. Score 0.483 Round 5: 132 peptides, 18 chains. Longest chain 13 peptides. Score 0.507 Taking the results from Round 5 Chains 18, Residues 114, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4531 reflections ( 99.47 % complete ) and 5283 restraints for refining 2241 atoms. 4845 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2230 (Rfree = 0.000) for 2241 atoms. Found 11 (16 requested) and removed 12 (8 requested) atoms. Cycle 17: After refmac, R = 0.2079 (Rfree = 0.000) for 2239 atoms. Found 4 (16 requested) and removed 9 (8 requested) atoms. Cycle 18: After refmac, R = 0.2050 (Rfree = 0.000) for 2233 atoms. Found 1 (16 requested) and removed 10 (8 requested) atoms. Cycle 19: After refmac, R = 0.1971 (Rfree = 0.000) for 2224 atoms. Found 4 (16 requested) and removed 8 (8 requested) atoms. Cycle 20: After refmac, R = 0.2128 (Rfree = 0.000) for 2218 atoms. Found 8 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.40 3.59 Search for helices and strands: 0 residues in 0 chains, 2313 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 2324 seeds are put forward Round 1: 105 peptides, 22 chains. Longest chain 9 peptides. Score 0.273 Round 2: 133 peptides, 25 chains. Longest chain 11 peptides. Score 0.359 Round 3: 125 peptides, 22 chains. Longest chain 10 peptides. Score 0.385 Round 4: 121 peptides, 20 chains. Longest chain 13 peptides. Score 0.409 Round 5: 128 peptides, 22 chains. Longest chain 14 peptides. Score 0.400 Taking the results from Round 4 Chains 20, Residues 101, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4531 reflections ( 99.47 % complete ) and 5401 restraints for refining 2241 atoms. 5017 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2118 (Rfree = 0.000) for 2241 atoms. Found 9 (16 requested) and removed 13 (8 requested) atoms. Cycle 22: After refmac, R = 0.2008 (Rfree = 0.000) for 2234 atoms. Found 6 (16 requested) and removed 9 (8 requested) atoms. Cycle 23: After refmac, R = 0.2322 (Rfree = 0.000) for 2224 atoms. Found 16 (16 requested) and removed 13 (8 requested) atoms. Cycle 24: After refmac, R = 0.2000 (Rfree = 0.000) for 2223 atoms. Found 6 (16 requested) and removed 9 (8 requested) atoms. Cycle 25: After refmac, R = 0.2026 (Rfree = 0.000) for 2219 atoms. Found 6 (16 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.37 3.55 Search for helices and strands: 0 residues in 0 chains, 2303 seeds are put forward NCS extension: 0 residues added, 2303 seeds are put forward Round 1: 102 peptides, 21 chains. Longest chain 8 peptides. Score 0.280 Round 2: 124 peptides, 24 chains. Longest chain 10 peptides. Score 0.333 Round 3: 111 peptides, 19 chains. Longest chain 11 peptides. Score 0.379 Round 4: 113 peptides, 20 chains. Longest chain 11 peptides. Score 0.367 Round 5: 103 peptides, 17 chains. Longest chain 10 peptides. Score 0.383 Taking the results from Round 5 Chains 17, Residues 86, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4531 reflections ( 99.47 % complete ) and 5484 restraints for refining 2241 atoms. 5157 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2071 (Rfree = 0.000) for 2241 atoms. Found 8 (16 requested) and removed 12 (8 requested) atoms. Cycle 27: After refmac, R = 0.1978 (Rfree = 0.000) for 2234 atoms. Found 8 (16 requested) and removed 8 (8 requested) atoms. Cycle 28: After refmac, R = 0.2089 (Rfree = 0.000) for 2232 atoms. Found 9 (16 requested) and removed 9 (8 requested) atoms. Cycle 29: After refmac, R = 0.1793 (Rfree = 0.000) for 2228 atoms. Found 1 (16 requested) and removed 11 (8 requested) atoms. Cycle 30: After refmac, R = 0.1998 (Rfree = 0.000) for 2216 atoms. Found 10 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.40 3.59 Search for helices and strands: 0 residues in 0 chains, 2317 seeds are put forward NCS extension: 0 residues added, 2317 seeds are put forward Round 1: 112 peptides, 24 chains. Longest chain 7 peptides. Score 0.265 Round 2: 115 peptides, 21 chains. Longest chain 11 peptides. Score 0.354 Round 3: 117 peptides, 20 chains. Longest chain 10 peptides. Score 0.388 Round 4: 109 peptides, 19 chains. Longest chain 9 peptides. Score 0.368 Round 5: 106 peptides, 18 chains. Longest chain 10 peptides. Score 0.376 Taking the results from Round 3 Chains 20, Residues 97, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4531 reflections ( 99.47 % complete ) and 5290 restraints for refining 2236 atoms. 4922 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2064 (Rfree = 0.000) for 2236 atoms. Found 13 (16 requested) and removed 12 (8 requested) atoms. Cycle 32: After refmac, R = 0.1954 (Rfree = 0.000) for 2236 atoms. Found 4 (16 requested) and removed 8 (8 requested) atoms. Cycle 33: After refmac, R = 0.1925 (Rfree = 0.000) for 2227 atoms. Found 4 (16 requested) and removed 9 (8 requested) atoms. Cycle 34: After refmac, R = 0.1805 (Rfree = 0.000) for 2221 atoms. Found 4 (16 requested) and removed 10 (8 requested) atoms. Cycle 35: After refmac, R = 0.1746 (Rfree = 0.000) for 2210 atoms. Found 1 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.36 3.54 Search for helices and strands: 0 residues in 0 chains, 2291 seeds are put forward NCS extension: 0 residues added, 2291 seeds are put forward Round 1: 86 peptides, 21 chains. Longest chain 5 peptides. Score 0.180 Round 2: 84 peptides, 17 chains. Longest chain 8 peptides. Score 0.273 Round 3: 90 peptides, 18 chains. Longest chain 7 peptides. Score 0.283 Round 4: 91 peptides, 18 chains. Longest chain 8 peptides. Score 0.290 Round 5: 111 peptides, 21 chains. Longest chain 10 peptides. Score 0.332 Taking the results from Round 5 Chains 21, Residues 90, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4531 reflections ( 99.47 % complete ) and 5387 restraints for refining 2240 atoms. 5048 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2022 (Rfree = 0.000) for 2240 atoms. Found 8 (16 requested) and removed 8 (8 requested) atoms. Cycle 37: After refmac, R = 0.1968 (Rfree = 0.000) for 2235 atoms. Found 2 (16 requested) and removed 8 (8 requested) atoms. Cycle 38: After refmac, R = 0.2183 (Rfree = 0.000) for 2229 atoms. Found 16 (16 requested) and removed 8 (8 requested) atoms. Cycle 39: After refmac, R = 0.1955 (Rfree = 0.000) for 2233 atoms. Found 4 (16 requested) and removed 10 (8 requested) atoms. Cycle 40: After refmac, R = 0.1713 (Rfree = 0.000) for 2227 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.34 3.52 Search for helices and strands: 0 residues in 0 chains, 2288 seeds are put forward NCS extension: 0 residues added, 2288 seeds are put forward Round 1: 85 peptides, 19 chains. Longest chain 6 peptides. Score 0.226 Round 2: 103 peptides, 20 chains. Longest chain 7 peptides. Score 0.310 Round 3: 105 peptides, 21 chains. Longest chain 8 peptides. Score 0.297 Round 4: 103 peptides, 20 chains. Longest chain 8 peptides. Score 0.310 Round 5: 97 peptides, 18 chains. Longest chain 8 peptides. Score 0.325 Taking the results from Round 5 Chains 18, Residues 79, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4531 reflections ( 99.47 % complete ) and 5426 restraints for refining 2241 atoms. 5128 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2018 (Rfree = 0.000) for 2241 atoms. Found 15 (16 requested) and removed 8 (8 requested) atoms. Cycle 42: After refmac, R = 0.2091 (Rfree = 0.000) for 2242 atoms. Found 15 (16 requested) and removed 9 (8 requested) atoms. Cycle 43: After refmac, R = 0.2010 (Rfree = 0.000) for 2238 atoms. Found 11 (16 requested) and removed 8 (8 requested) atoms. Cycle 44: After refmac, R = 0.1925 (Rfree = 0.000) for 2240 atoms. Found 12 (16 requested) and removed 10 (8 requested) atoms. Cycle 45: After refmac, R = 0.1950 (Rfree = 0.000) for 2238 atoms. Found 5 (16 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.34 3.52 Search for helices and strands: 0 residues in 0 chains, 2299 seeds are put forward NCS extension: 0 residues added, 2299 seeds are put forward Round 1: 83 peptides, 20 chains. Longest chain 5 peptides. Score 0.187 Round 2: 95 peptides, 19 chains. Longest chain 7 peptides. Score 0.288 Round 3: 87 peptides, 16 chains. Longest chain 8 peptides. Score 0.317 Round 4: 85 peptides, 16 chains. Longest chain 8 peptides. Score 0.305 Round 5: 85 peptides, 16 chains. Longest chain 9 peptides. Score 0.305 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 16, Residues 71, 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-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4531 reflections ( 99.47 % complete ) and 5488 restraints for refining 2241 atoms. 5220 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2022 (Rfree = 0.000) for 2241 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2076 (Rfree = 0.000) for 2231 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.2040 (Rfree = 0.000) for 2223 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.2015 (Rfree = 0.000) for 2214 atoms. TimeTaking 31.95