Sun 23 Dec 22:23:10 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 2prx-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2prx-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2prx-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2prx-3.2-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/2prx-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2prx-3.2-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 22:23:20 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/2prx-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2prx-3.2-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 223 and 0 Target number of residues in the AU: 223 Target solvent content: 0.5895 Checking the provided sequence file Detected sequence length: 160 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 320 Adjusted target solvent content: 0.41 Input MTZ file: 2prx-3.2-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: 144 Cell parameters: 38.520 38.520 171.590 90.000 90.000 120.000 Input sequence file: 2prx-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 2560 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: 28.816 3.201 Wilson plot Bfac: 47.95 4648 reflections ( 99.64 % complete ) and 0 restraints for refining 2823 atoms. Observations/parameters ratio is 0.41 ------------------------------------------------------ Starting model: R = 0.3236 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2360 (Rfree = 0.000) for 2823 atoms. Found 12 (25 requested) and removed 45 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.98 3.36 Search for helices and strands: 0 residues in 0 chains, 2801 seeds are put forward NCS extension: 0 residues added, 2801 seeds are put forward Round 1: 73 peptides, 16 chains. Longest chain 6 peptides. Score 0.231 Round 2: 89 peptides, 19 chains. Longest chain 8 peptides. Score 0.254 Round 3: 102 peptides, 21 chains. Longest chain 10 peptides. Score 0.283 Round 4: 108 peptides, 22 chains. Longest chain 10 peptides. Score 0.295 Round 5: 114 peptides, 24 chains. Longest chain 10 peptides. Score 0.280 Taking the results from Round 4 Chains 22, Residues 86, Estimated correctness of the model 0.0 % 6 chains (30 residues) have been docked in sequence ------------------------------------------------------ 4648 reflections ( 99.64 % complete ) and 5177 restraints for refining 2337 atoms. 4789 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2230 (Rfree = 0.000) for 2337 atoms. Found 9 (20 requested) and removed 18 (10 requested) atoms. Cycle 2: After refmac, R = 0.2444 (Rfree = 0.000) for 2322 atoms. Found 10 (20 requested) and removed 19 (10 requested) atoms. Cycle 3: After refmac, R = 0.2136 (Rfree = 0.000) for 2301 atoms. Found 6 (20 requested) and removed 16 (10 requested) atoms. Cycle 4: After refmac, R = 0.1915 (Rfree = 0.000) for 2291 atoms. Found 5 (20 requested) and removed 16 (10 requested) atoms. Cycle 5: After refmac, R = 0.1968 (Rfree = 0.000) for 2279 atoms. Found 7 (20 requested) and removed 12 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.95 3.33 Search for helices and strands: 0 residues in 0 chains, 2331 seeds are put forward NCS extension: 0 residues added, 2331 seeds are put forward Round 1: 114 peptides, 24 chains. Longest chain 10 peptides. Score 0.280 Round 2: 127 peptides, 23 chains. Longest chain 9 peptides. Score 0.380 Round 3: 139 peptides, 23 chains. Longest chain 11 peptides. Score 0.444 Round 4: 119 peptides, 22 chains. Longest chain 8 peptides. Score 0.359 Round 5: 131 peptides, 24 chains. Longest chain 11 peptides. Score 0.378 Taking the results from Round 3 Chains 23, Residues 116, Estimated correctness of the model 0.0 % 4 chains (21 residues) have been docked in sequence ------------------------------------------------------ 4648 reflections ( 99.64 % complete ) and 5089 restraints for refining 2330 atoms. 4599 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2303 (Rfree = 0.000) for 2330 atoms. Found 20 (20 requested) and removed 20 (10 requested) atoms. Cycle 7: After refmac, R = 0.1896 (Rfree = 0.000) for 2330 atoms. Found 7 (20 requested) and removed 17 (10 requested) atoms. Cycle 8: After refmac, R = 0.1839 (Rfree = 0.000) for 2311 atoms. Found 4 (20 requested) and removed 11 (10 requested) atoms. Cycle 9: After refmac, R = 0.1866 (Rfree = 0.000) for 2300 atoms. Found 5 (20 requested) and removed 12 (10 requested) atoms. Cycle 10: After refmac, R = 0.2196 (Rfree = 0.000) for 2288 atoms. Found 20 (20 requested) and removed 16 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.96 3.34 Search for helices and strands: 0 residues in 0 chains, 2318 seeds are put forward NCS extension: 3 residues added (0 deleted due to clashes), 2321 seeds are put forward Round 1: 91 peptides, 18 chains. Longest chain 13 peptides. Score 0.294 Round 2: 113 peptides, 20 chains. Longest chain 10 peptides. Score 0.373 Round 3: 121 peptides, 19 chains. Longest chain 12 peptides. Score 0.441 Round 4: 120 peptides, 19 chains. Longest chain 14 peptides. Score 0.435 Round 5: 123 peptides, 21 chains. Longest chain 11 peptides. Score 0.405 Taking the results from Round 3 Chains 19, Residues 102, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4648 reflections ( 99.64 % complete ) and 5148 restraints for refining 2297 atoms. 4759 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2478 (Rfree = 0.000) for 2297 atoms. Found 20 (20 requested) and removed 31 (10 requested) atoms. Cycle 12: After refmac, R = 0.1925 (Rfree = 0.000) for 2279 atoms. Found 12 (20 requested) and removed 15 (10 requested) atoms. Cycle 13: After refmac, R = 0.1688 (Rfree = 0.000) for 2265 atoms. Found 7 (20 requested) and removed 11 (10 requested) atoms. Cycle 14: After refmac, R = 0.1696 (Rfree = 0.000) for 2257 atoms. Found 6 (20 requested) and removed 13 (10 requested) atoms. Cycle 15: After refmac, R = 0.1607 (Rfree = 0.000) for 2249 atoms. Found 6 (20 requested) and removed 14 (10 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.00 3.39 Search for helices and strands: 0 residues in 0 chains, 2267 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 2283 seeds are put forward Round 1: 114 peptides, 23 chains. Longest chain 8 peptides. Score 0.305 Round 2: 126 peptides, 21 chains. Longest chain 13 peptides. Score 0.421 Round 3: 132 peptides, 21 chains. Longest chain 15 peptides. Score 0.452 Round 4: 126 peptides, 21 chains. Longest chain 11 peptides. Score 0.421 Round 5: 119 peptides, 22 chains. Longest chain 9 peptides. Score 0.359 Taking the results from Round 3 Chains 22, Residues 111, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 4648 reflections ( 99.64 % complete ) and 4945 restraints for refining 2275 atoms. 4474 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2113 (Rfree = 0.000) for 2275 atoms. Found 20 (20 requested) and removed 18 (10 requested) atoms. Cycle 17: After refmac, R = 0.1861 (Rfree = 0.000) for 2276 atoms. Found 9 (20 requested) and removed 14 (10 requested) atoms. Cycle 18: After refmac, R = 0.1903 (Rfree = 0.000) for 2265 atoms. Found 10 (20 requested) and removed 15 (10 requested) atoms. Cycle 19: After refmac, R = 0.1742 (Rfree = 0.000) for 2255 atoms. Found 1 (20 requested) and removed 12 (10 requested) atoms. Cycle 20: After refmac, R = 0.1757 (Rfree = 0.000) for 2241 atoms. Found 7 (20 requested) and removed 13 (10 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.96 3.34 Search for helices and strands: 0 residues in 0 chains, 2262 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 2281 seeds are put forward Round 1: 105 peptides, 24 chains. Longest chain 6 peptides. Score 0.225 Round 2: 127 peptides, 23 chains. Longest chain 11 peptides. Score 0.380 Round 3: 123 peptides, 23 chains. Longest chain 9 peptides. Score 0.358 Round 4: 110 peptides, 21 chains. Longest chain 8 peptides. Score 0.332 Round 5: 115 peptides, 21 chains. Longest chain 8 peptides. Score 0.360 Taking the results from Round 2 Chains 23, Residues 104, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4648 reflections ( 99.64 % complete ) and 5213 restraints for refining 2274 atoms. 4820 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1998 (Rfree = 0.000) for 2274 atoms. Found 19 (20 requested) and removed 17 (10 requested) atoms. Cycle 22: After refmac, R = 0.1854 (Rfree = 0.000) for 2274 atoms. Found 5 (20 requested) and removed 15 (10 requested) atoms. Cycle 23: After refmac, R = 0.2057 (Rfree = 0.000) for 2263 atoms. Found 20 (20 requested) and removed 10 (10 requested) atoms. Cycle 24: After refmac, R = 0.2074 (Rfree = 0.000) for 2270 atoms. Found 20 (20 requested) and removed 12 (10 requested) atoms. Cycle 25: After refmac, R = 0.1696 (Rfree = 0.000) for 2273 atoms. Found 8 (20 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.94 3.32 Search for helices and strands: 0 residues in 0 chains, 2298 seeds are put forward NCS extension: 0 residues added, 2298 seeds are put forward Round 1: 97 peptides, 21 chains. Longest chain 7 peptides. Score 0.252 Round 2: 111 peptides, 20 chains. Longest chain 10 peptides. Score 0.362 Round 3: 110 peptides, 20 chains. Longest chain 11 peptides. Score 0.356 Round 4: 118 peptides, 22 chains. Longest chain 12 peptides. Score 0.353 Round 5: 109 peptides, 20 chains. Longest chain 8 peptides. Score 0.351 Taking the results from Round 2 Chains 20, Residues 91, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4648 reflections ( 99.64 % complete ) and 5221 restraints for refining 2244 atoms. 4877 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2364 (Rfree = 0.000) for 2244 atoms. Found 20 (20 requested) and removed 18 (10 requested) atoms. Cycle 27: After refmac, R = 0.1699 (Rfree = 0.000) for 2239 atoms. Found 11 (20 requested) and removed 11 (10 requested) atoms. Cycle 28: After refmac, R = 0.1674 (Rfree = 0.000) for 2236 atoms. Found 8 (20 requested) and removed 11 (10 requested) atoms. Cycle 29: After refmac, R = 0.1641 (Rfree = 0.000) for 2232 atoms. Found 11 (20 requested) and removed 11 (10 requested) atoms. Cycle 30: After refmac, R = 0.1617 (Rfree = 0.000) for 2226 atoms. Found 10 (20 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.03 3.42 Search for helices and strands: 0 residues in 0 chains, 2243 seeds are put forward NCS extension: 0 residues added, 2243 seeds are put forward Round 1: 97 peptides, 21 chains. Longest chain 7 peptides. Score 0.252 Round 2: 94 peptides, 17 chains. Longest chain 11 peptides. Score 0.338 Round 3: 106 peptides, 19 chains. Longest chain 13 peptides. Score 0.358 Round 4: 115 peptides, 19 chains. Longest chain 12 peptides. Score 0.409 Round 5: 109 peptides, 19 chains. Longest chain 11 peptides. Score 0.375 Taking the results from Round 4 Chains 19, Residues 96, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 4648 reflections ( 99.64 % complete ) and 4869 restraints for refining 2220 atoms. 4487 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2011 (Rfree = 0.000) for 2220 atoms. Found 19 (19 requested) and removed 11 (9 requested) atoms. Cycle 32: After refmac, R = 0.1689 (Rfree = 0.000) for 2222 atoms. Found 11 (19 requested) and removed 10 (9 requested) atoms. Cycle 33: After refmac, R = 0.1693 (Rfree = 0.000) for 2223 atoms. Found 18 (19 requested) and removed 13 (9 requested) atoms. Cycle 34: After refmac, R = 0.1626 (Rfree = 0.000) for 2227 atoms. Found 15 (19 requested) and removed 11 (9 requested) atoms. Cycle 35: After refmac, R = 0.1683 (Rfree = 0.000) for 2231 atoms. Found 18 (20 requested) and removed 17 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.01 3.40 Search for helices and strands: 0 residues in 0 chains, 2250 seeds are put forward NCS extension: 0 residues added, 2250 seeds are put forward Round 1: 89 peptides, 18 chains. Longest chain 9 peptides. Score 0.281 Round 2: 103 peptides, 19 chains. Longest chain 9 peptides. Score 0.341 Round 3: 115 peptides, 20 chains. Longest chain 14 peptides. Score 0.385 Round 4: 104 peptides, 20 chains. Longest chain 8 peptides. Score 0.321 Round 5: 122 peptides, 21 chains. Longest chain 10 peptides. Score 0.399 Taking the results from Round 5 Chains 21, Residues 101, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4648 reflections ( 99.64 % complete ) and 5283 restraints for refining 2295 atoms. 4900 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1703 (Rfree = 0.000) for 2295 atoms. Found 15 (20 requested) and removed 18 (10 requested) atoms. Cycle 37: After refmac, R = 0.1687 (Rfree = 0.000) for 2288 atoms. Found 13 (20 requested) and removed 13 (10 requested) atoms. Cycle 38: After refmac, R = 0.1651 (Rfree = 0.000) for 2288 atoms. Found 14 (20 requested) and removed 11 (10 requested) atoms. Cycle 39: After refmac, R = 0.1621 (Rfree = 0.000) for 2291 atoms. Found 7 (20 requested) and removed 11 (10 requested) atoms. Cycle 40: After refmac, R = 0.1604 (Rfree = 0.000) for 2286 atoms. Found 12 (20 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.91 3.28 Search for helices and strands: 0 residues in 0 chains, 2331 seeds are put forward NCS extension: 0 residues added, 2331 seeds are put forward Round 1: 93 peptides, 19 chains. Longest chain 7 peptides. Score 0.280 Round 2: 115 peptides, 21 chains. Longest chain 12 peptides. Score 0.360 Round 3: 116 peptides, 20 chains. Longest chain 10 peptides. Score 0.390 Round 4: 108 peptides, 17 chains. Longest chain 10 peptides. Score 0.418 Round 5: 105 peptides, 18 chains. Longest chain 10 peptides. Score 0.377 Taking the results from Round 4 Chains 17, Residues 91, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 4648 reflections ( 99.64 % complete ) and 5359 restraints for refining 2337 atoms. 4991 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1814 (Rfree = 0.000) for 2337 atoms. Found 17 (20 requested) and removed 13 (10 requested) atoms. Cycle 42: After refmac, R = 0.1748 (Rfree = 0.000) for 2340 atoms. Found 18 (20 requested) and removed 12 (10 requested) atoms. Cycle 43: After refmac, R = 0.1662 (Rfree = 0.000) for 2342 atoms. Found 12 (21 requested) and removed 11 (10 requested) atoms. Cycle 44: After refmac, R = 0.1658 (Rfree = 0.000) for 2340 atoms. Found 11 (21 requested) and removed 16 (10 requested) atoms. Cycle 45: After refmac, R = 0.1562 (Rfree = 0.000) for 2333 atoms. Found 11 (20 requested) and removed 17 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.95 3.33 Search for helices and strands: 0 residues in 0 chains, 2353 seeds are put forward NCS extension: 0 residues added, 2353 seeds are put forward Round 1: 103 peptides, 22 chains. Longest chain 6 peptides. Score 0.264 Round 2: 111 peptides, 19 chains. Longest chain 11 peptides. Score 0.387 Round 3: 118 peptides, 20 chains. Longest chain 9 peptides. Score 0.401 Round 4: 122 peptides, 22 chains. Longest chain 8 peptides. Score 0.376 Round 5: 106 peptides, 20 chains. Longest chain 8 peptides. Score 0.333 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 20, Residues 98, 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 2prx-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4648 reflections ( 99.64 % complete ) and 5309 restraints for refining 2337 atoms. 4937 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1667 (Rfree = 0.000) for 2337 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 47: After refmac, R = 0.1600 (Rfree = 0.000) for 2325 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 48: After refmac, R = 0.1645 (Rfree = 0.000) for 2315 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 49: After refmac, R = 0.2074 (Rfree = 0.000) for 2304 atoms. TimeTaking 43.15