Sun 23 Dec 22:23:05 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2prv-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2prv-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2prv-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2prv-3.6-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/2prv-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2prv-3.6-parrot-hancs ############### 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 ============================================================ Sun 23 Dec 22:23:13 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/hancs/ArpWArp/wArpResults/WorkingDir/2prv-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2prv-3.6-parrot-hancs/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 199 and 0 Target number of residues in the AU: 199 Target solvent content: 0.6503 Checking the provided sequence file Detected sequence length: 153 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 306 Adjusted target solvent content: 0.46 Input MTZ file: 2prv-3.6-parrot-hancs.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: 40.107 45.170 48.067 84.512 67.558 73.075 Input sequence file: 2prv-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 2448 target number of atoms Had to go as low as 0.75 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: 44.420 3.600 Wilson plot Bfac: 77.51 3382 reflections ( 97.72 % complete ) and 0 restraints for refining 2694 atoms. Observations/parameters ratio is 0.31 ------------------------------------------------------ Starting model: R = 0.3778 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3457 (Rfree = 0.000) for 2694 atoms. Found 12 (17 requested) and removed 83 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.42 3.61 Search for helices and strands: 0 residues in 0 chains, 2648 seeds are put forward NCS extension: 0 residues added, 2648 seeds are put forward Round 1: 66 peptides, 15 chains. Longest chain 7 peptides. Score 0.210 Round 2: 88 peptides, 19 chains. Longest chain 6 peptides. Score 0.245 Round 3: 93 peptides, 20 chains. Longest chain 6 peptides. Score 0.250 Round 4: 104 peptides, 21 chains. Longest chain 8 peptides. Score 0.291 Round 5: 106 peptides, 19 chains. Longest chain 11 peptides. Score 0.352 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 ------------------------------------------------------ 3382 reflections ( 97.72 % complete ) and 5211 restraints for refining 2219 atoms. 4882 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2590 (Rfree = 0.000) for 2219 atoms. Found 8 (14 requested) and removed 16 (7 requested) atoms. Cycle 2: After refmac, R = 0.2513 (Rfree = 0.000) for 2180 atoms. Found 12 (14 requested) and removed 9 (7 requested) atoms. Cycle 3: After refmac, R = 0.2295 (Rfree = 0.000) for 2166 atoms. Found 8 (14 requested) and removed 12 (7 requested) atoms. Cycle 4: After refmac, R = 0.2271 (Rfree = 0.000) for 2149 atoms. Found 7 (13 requested) and removed 7 (6 requested) atoms. Cycle 5: After refmac, R = 0.2368 (Rfree = 0.000) for 2140 atoms. Found 12 (13 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.43 3.62 Search for helices and strands: 0 residues in 0 chains, 2195 seeds are put forward NCS extension: 0 residues added, 2195 seeds are put forward Round 1: 74 peptides, 17 chains. Longest chain 6 peptides. Score 0.208 Round 2: 104 peptides, 22 chains. Longest chain 8 peptides. Score 0.267 Round 3: 113 peptides, 22 chains. Longest chain 9 peptides. Score 0.319 Round 4: 103 peptides, 21 chains. Longest chain 9 peptides. Score 0.285 Round 5: 106 peptides, 21 chains. Longest chain 9 peptides. Score 0.303 Taking the results from Round 3 Chains 22, Residues 91, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 3382 reflections ( 97.72 % complete ) and 4751 restraints for refining 2101 atoms. 4393 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2303 (Rfree = 0.000) for 2101 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. Cycle 7: After refmac, R = 0.2191 (Rfree = 0.000) for 2080 atoms. Found 9 (13 requested) and removed 11 (6 requested) atoms. Cycle 8: After refmac, R = 0.2150 (Rfree = 0.000) for 2071 atoms. Found 13 (13 requested) and removed 8 (6 requested) atoms. Cycle 9: After refmac, R = 0.1744 (Rfree = 0.000) for 2068 atoms. Found 5 (13 requested) and removed 9 (6 requested) atoms. Cycle 10: After refmac, R = 0.1679 (Rfree = 0.000) for 2061 atoms. Found 1 (13 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.42 3.61 Search for helices and strands: 0 residues in 0 chains, 2105 seeds are put forward NCS extension: 0 residues added, 2105 seeds are put forward Round 1: 92 peptides, 21 chains. Longest chain 8 peptides. Score 0.218 Round 2: 102 peptides, 21 chains. Longest chain 10 peptides. Score 0.280 Round 3: 102 peptides, 21 chains. Longest chain 10 peptides. Score 0.280 Round 4: 99 peptides, 19 chains. Longest chain 11 peptides. Score 0.312 Round 5: 95 peptides, 17 chains. Longest chain 13 peptides. Score 0.338 Taking the results from Round 5 Chains 17, Residues 78, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3382 reflections ( 97.72 % complete ) and 5009 restraints for refining 2125 atoms. 4714 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2200 (Rfree = 0.000) for 2125 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. Cycle 12: After refmac, R = 0.2308 (Rfree = 0.000) for 2116 atoms. Found 12 (13 requested) and removed 13 (6 requested) atoms. Cycle 13: After refmac, R = 0.2005 (Rfree = 0.000) for 2109 atoms. Found 10 (13 requested) and removed 7 (6 requested) atoms. Cycle 14: After refmac, R = 0.1959 (Rfree = 0.000) for 2108 atoms. Found 13 (13 requested) and removed 6 (6 requested) atoms. Cycle 15: After refmac, R = 0.1912 (Rfree = 0.000) for 2115 atoms. Found 6 (13 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.46 3.65 Search for helices and strands: 0 residues in 0 chains, 2168 seeds are put forward NCS extension: 0 residues added, 2168 seeds are put forward Round 1: 105 peptides, 22 chains. Longest chain 10 peptides. Score 0.273 Round 2: 115 peptides, 22 chains. Longest chain 10 peptides. Score 0.330 Round 3: 108 peptides, 23 chains. Longest chain 7 peptides. Score 0.266 Round 4: 98 peptides, 18 chains. Longest chain 10 peptides. Score 0.331 Round 5: 105 peptides, 19 chains. Longest chain 11 peptides. Score 0.346 Taking the results from Round 5 Chains 19, Residues 86, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3382 reflections ( 97.72 % complete ) and 5124 restraints for refining 2205 atoms. 4799 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1917 (Rfree = 0.000) for 2205 atoms. Found 11 (14 requested) and removed 9 (7 requested) atoms. Cycle 17: After refmac, R = 0.1715 (Rfree = 0.000) for 2196 atoms. Found 3 (14 requested) and removed 7 (7 requested) atoms. Cycle 18: After refmac, R = 0.1983 (Rfree = 0.000) for 2188 atoms. Found 13 (14 requested) and removed 10 (7 requested) atoms. Cycle 19: After refmac, R = 0.1921 (Rfree = 0.000) for 2187 atoms. Found 14 (14 requested) and removed 7 (7 requested) atoms. Cycle 20: After refmac, R = 0.1579 (Rfree = 0.000) for 2193 atoms. Found 3 (14 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.42 3.61 Search for helices and strands: 0 residues in 0 chains, 2210 seeds are put forward NCS extension: 0 residues added, 2210 seeds are put forward Round 1: 85 peptides, 20 chains. Longest chain 6 peptides. Score 0.200 Round 2: 91 peptides, 18 chains. Longest chain 8 peptides. Score 0.290 Round 3: 96 peptides, 18 chains. Longest chain 8 peptides. Score 0.319 Round 4: 102 peptides, 19 chains. Longest chain 9 peptides. Score 0.329 Round 5: 100 peptides, 15 chains. Longest chain 12 peptides. Score 0.415 Taking the results from Round 5 Chains 15, Residues 85, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3382 reflections ( 97.72 % complete ) and 5303 restraints for refining 2219 atoms. 4978 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1793 (Rfree = 0.000) for 2219 atoms. Found 6 (14 requested) and removed 8 (7 requested) atoms. Cycle 22: After refmac, R = 0.1644 (Rfree = 0.000) for 2206 atoms. Found 4 (14 requested) and removed 9 (7 requested) atoms. Cycle 23: After refmac, R = 0.1522 (Rfree = 0.000) for 2198 atoms. Found 2 (14 requested) and removed 7 (7 requested) atoms. Cycle 24: After refmac, R = 0.1489 (Rfree = 0.000) for 2192 atoms. Found 3 (14 requested) and removed 9 (7 requested) atoms. Cycle 25: After refmac, R = 0.1467 (Rfree = 0.000) for 2185 atoms. Found 2 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.43 3.62 Search for helices and strands: 0 residues in 0 chains, 2214 seeds are put forward NCS extension: 0 residues added, 2214 seeds are put forward Round 1: 85 peptides, 18 chains. Longest chain 7 peptides. Score 0.253 Round 2: 86 peptides, 18 chains. Longest chain 6 peptides. Score 0.259 Round 3: 83 peptides, 16 chains. Longest chain 8 peptides. Score 0.293 Round 4: 88 peptides, 17 chains. Longest chain 7 peptides. Score 0.297 Round 5: 101 peptides, 19 chains. Longest chain 9 peptides. Score 0.323 Taking the results from Round 5 Chains 19, Residues 82, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3382 reflections ( 97.72 % complete ) and 5249 restraints for refining 2218 atoms. 4940 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1901 (Rfree = 0.000) for 2218 atoms. Found 13 (14 requested) and removed 9 (7 requested) atoms. Cycle 27: After refmac, R = 0.1682 (Rfree = 0.000) for 2211 atoms. Found 10 (14 requested) and removed 9 (7 requested) atoms. Cycle 28: After refmac, R = 0.1421 (Rfree = 0.000) for 2202 atoms. Found 1 (14 requested) and removed 8 (7 requested) atoms. Cycle 29: After refmac, R = 0.1657 (Rfree = 0.000) for 2192 atoms. Found 12 (14 requested) and removed 8 (7 requested) atoms. Failed to save intermediate PDB Cycle 30: After refmac, R = 0.1258 (Rfree = 0.000) for 2194 atoms. Found 4 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.48 3.67 Search for helices and strands: 0 residues in 0 chains, 2228 seeds are put forward NCS extension: 0 residues added, 2228 seeds are put forward Round 1: 68 peptides, 15 chains. Longest chain 6 peptides. Score 0.224 Round 2: 93 peptides, 19 chains. Longest chain 6 peptides. Score 0.276 Round 3: 82 peptides, 16 chains. Longest chain 8 peptides. Score 0.287 Round 4: 97 peptides, 18 chains. Longest chain 13 peptides. Score 0.325 Round 5: 94 peptides, 18 chains. Longest chain 8 peptides. Score 0.307 Taking the results from Round 4 Chains 20, Residues 79, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 3382 reflections ( 97.72 % complete ) and 5072 restraints for refining 2219 atoms. 4739 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1820 (Rfree = 0.000) for 2219 atoms. Found 8 (14 requested) and removed 10 (7 requested) atoms. Cycle 32: After refmac, R = 0.1883 (Rfree = 0.000) for 2210 atoms. Found 14 (14 requested) and removed 9 (7 requested) atoms. Cycle 33: After refmac, R = 0.1652 (Rfree = 0.000) for 2208 atoms. Found 11 (14 requested) and removed 10 (7 requested) atoms. Cycle 34: After refmac, R = 0.1630 (Rfree = 0.000) for 2203 atoms. Found 8 (14 requested) and removed 8 (7 requested) atoms. Cycle 35: After refmac, R = 0.1244 (Rfree = 0.000) for 2200 atoms. Found 3 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.43 3.62 Search for helices and strands: 0 residues in 0 chains, 2233 seeds are put forward NCS extension: 0 residues added, 2233 seeds are put forward Round 1: 88 peptides, 18 chains. Longest chain 8 peptides. Score 0.271 Round 2: 101 peptides, 20 chains. Longest chain 9 peptides. Score 0.299 Round 3: 99 peptides, 19 chains. Longest chain 11 peptides. Score 0.312 Round 4: 107 peptides, 21 chains. Longest chain 11 peptides. Score 0.309 Round 5: 107 peptides, 19 chains. Longest chain 11 peptides. Score 0.357 Taking the results from Round 5 Chains 19, Residues 88, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3382 reflections ( 97.72 % complete ) and 4973 restraints for refining 2201 atoms. 4640 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1629 (Rfree = 0.000) for 2201 atoms. Found 10 (14 requested) and removed 10 (7 requested) atoms. Cycle 37: After refmac, R = 0.1689 (Rfree = 0.000) for 2191 atoms. Found 14 (14 requested) and removed 10 (7 requested) atoms. Cycle 38: After refmac, R = 0.1728 (Rfree = 0.000) for 2187 atoms. Found 14 (14 requested) and removed 11 (7 requested) atoms. Cycle 39: After refmac, R = 0.1282 (Rfree = 0.000) for 2186 atoms. Found 3 (14 requested) and removed 8 (7 requested) atoms. Cycle 40: After refmac, R = 0.1171 (Rfree = 0.000) for 2175 atoms. Found 2 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.47 3.66 Search for helices and strands: 0 residues in 0 chains, 2205 seeds are put forward NCS extension: 0 residues added, 2205 seeds are put forward Round 1: 83 peptides, 19 chains. Longest chain 8 peptides. Score 0.213 Round 2: 86 peptides, 17 chains. Longest chain 8 peptides. Score 0.285 Round 3: 90 peptides, 17 chains. Longest chain 11 peptides. Score 0.309 Round 4: 94 peptides, 18 chains. Longest chain 8 peptides. Score 0.307 Round 5: 102 peptides, 19 chains. Longest chain 9 peptides. Score 0.329 Taking the results from Round 5 Chains 19, Residues 83, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3382 reflections ( 97.72 % complete ) and 4894 restraints for refining 2179 atoms. 4581 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1654 (Rfree = 0.000) for 2179 atoms. Found 13 (13 requested) and removed 8 (6 requested) atoms. Cycle 42: After refmac, R = 0.1611 (Rfree = 0.000) for 2180 atoms. Found 12 (14 requested) and removed 8 (7 requested) atoms. Cycle 43: After refmac, R = 0.1489 (Rfree = 0.000) for 2178 atoms. Found 5 (14 requested) and removed 8 (7 requested) atoms. Cycle 44: After refmac, R = 0.1451 (Rfree = 0.000) for 2173 atoms. Found 2 (13 requested) and removed 6 (6 requested) atoms. Cycle 45: After refmac, R = 0.1330 (Rfree = 0.000) for 2168 atoms. Found 1 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.53 3.72 Search for helices and strands: 0 residues in 0 chains, 2195 seeds are put forward NCS extension: 0 residues added, 2195 seeds are put forward Round 1: 66 peptides, 15 chains. Longest chain 6 peptides. Score 0.210 Round 2: 83 peptides, 17 chains. Longest chain 8 peptides. Score 0.266 Round 3: 89 peptides, 18 chains. Longest chain 11 peptides. Score 0.277 Round 4: 95 peptides, 17 chains. Longest chain 10 peptides. Score 0.338 Round 5: 103 peptides, 18 chains. Longest chain 11 peptides. Score 0.359 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 18, Residues 85, 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 2prv-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3382 reflections ( 97.72 % complete ) and 4951 restraints for refining 2218 atoms. 4629 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1989 (Rfree = 0.000) for 2218 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.1716 (Rfree = 0.000) for 2206 atoms. Found 0 (14 requested) and removed 5 (7 requested) atoms. Cycle 48: After refmac, R = 0.1630 (Rfree = 0.000) for 2200 atoms. Found 0 (14 requested) and removed 1 (7 requested) atoms. Cycle 49: After refmac, R = 0.1626 (Rfree = 0.000) for 2199 atoms. Found 0 (14 requested) and removed 3 (7 requested) atoms. Writing output files ... Failed to save intermediate PDB TimeTaking 33.3