Mon 24 Dec 07:47:40 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1z82-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1z82-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1z82-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1z82-3.4-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/1z82-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1z82-3.4-parrot-noncs ############### 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 07:47:44 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/noncs/ArpWArp/wArpResults/WorkingDir/1z82-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1z82-3.4-parrot-noncs/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 410 and 0 Target number of residues in the AU: 410 Target solvent content: 0.6357 Checking the provided sequence file Detected sequence length: 335 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 670 Adjusted target solvent content: 0.40 Input MTZ file: 1z82-3.4-parrot-noncs.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: 4 Cell parameters: 65.170 67.461 75.617 90.000 113.643 90.000 Input sequence file: 1z82-3.4-parrot-noncs.fasta_lf Building free atoms model in initial map for 5360 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: 29.850 3.400 Wilson plot Bfac: 69.58 8387 reflections ( 99.63 % complete ) and 0 restraints for refining 5943 atoms. Observations/parameters ratio is 0.35 ------------------------------------------------------ Starting model: R = 0.3189 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2861 (Rfree = 0.000) for 5943 atoms. Found 43 (44 requested) and removed 38 (22 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.35 3.83 Search for helices and strands: 0 residues in 0 chains, 6080 seeds are put forward NCS extension: 0 residues added, 6080 seeds are put forward Round 1: 202 peptides, 43 chains. Longest chain 8 peptides. Score 0.262 Round 2: 253 peptides, 50 chains. Longest chain 9 peptides. Score 0.325 Round 3: 288 peptides, 49 chains. Longest chain 17 peptides. Score 0.429 Round 4: 293 peptides, 48 chains. Longest chain 20 peptides. Score 0.452 Round 5: 305 peptides, 48 chains. Longest chain 16 peptides. Score 0.481 Taking the results from Round 5 Chains 48, Residues 257, Estimated correctness of the model 0.0 % 6 chains (31 residues) have been docked in sequence ------------------------------------------------------ 8387 reflections ( 99.63 % complete ) and 11166 restraints for refining 4867 atoms. 10106 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2316 (Rfree = 0.000) for 4867 atoms. Found 24 (36 requested) and removed 35 (18 requested) atoms. Cycle 2: After refmac, R = 0.2174 (Rfree = 0.000) for 4800 atoms. Found 11 (36 requested) and removed 28 (18 requested) atoms. Cycle 3: After refmac, R = 0.2076 (Rfree = 0.000) for 4755 atoms. Found 14 (36 requested) and removed 25 (18 requested) atoms. Cycle 4: After refmac, R = 0.2032 (Rfree = 0.000) for 4727 atoms. Found 11 (35 requested) and removed 21 (17 requested) atoms. Cycle 5: After refmac, R = 0.1951 (Rfree = 0.000) for 4708 atoms. Found 14 (35 requested) and removed 23 (17 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.34 3.82 Search for helices and strands: 0 residues in 0 chains, 4912 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 4937 seeds are put forward Round 1: 267 peptides, 53 chains. Longest chain 10 peptides. Score 0.329 Round 2: 329 peptides, 51 chains. Longest chain 22 peptides. Score 0.507 Round 3: 327 peptides, 52 chains. Longest chain 18 peptides. Score 0.492 Round 4: 321 peptides, 48 chains. Longest chain 19 peptides. Score 0.518 Round 5: 331 peptides, 52 chains. Longest chain 14 peptides. Score 0.501 Taking the results from Round 4 Chains 51, Residues 273, Estimated correctness of the model 0.0 % 3 chains (24 residues) have been docked in sequence ------------------------------------------------------ 8387 reflections ( 99.63 % complete ) and 10854 restraints for refining 4717 atoms. 9750 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2075 (Rfree = 0.000) for 4717 atoms. Found 26 (35 requested) and removed 32 (17 requested) atoms. Cycle 7: After refmac, R = 0.1900 (Rfree = 0.000) for 4689 atoms. Found 13 (35 requested) and removed 25 (17 requested) atoms. Cycle 8: After refmac, R = 0.1907 (Rfree = 0.000) for 4670 atoms. Found 16 (35 requested) and removed 24 (17 requested) atoms. Cycle 9: After refmac, R = 0.1874 (Rfree = 0.000) for 4658 atoms. Found 18 (35 requested) and removed 19 (17 requested) atoms. Cycle 10: After refmac, R = 0.1905 (Rfree = 0.000) for 4647 atoms. Found 18 (35 requested) and removed 20 (17 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.34 3.82 Search for helices and strands: 0 residues in 0 chains, 4835 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 4851 seeds are put forward Round 1: 282 peptides, 53 chains. Longest chain 14 peptides. Score 0.370 Round 2: 306 peptides, 50 chains. Longest chain 20 peptides. Score 0.463 Round 3: 318 peptides, 49 chains. Longest chain 18 peptides. Score 0.501 Round 4: 317 peptides, 47 chains. Longest chain 16 peptides. Score 0.519 Round 5: 316 peptides, 48 chains. Longest chain 18 peptides. Score 0.507 Taking the results from Round 4 Chains 47, Residues 270, Estimated correctness of the model 0.0 % 4 chains (25 residues) have been docked in sequence ------------------------------------------------------ 8387 reflections ( 99.63 % complete ) and 11010 restraints for refining 4754 atoms. 9906 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2142 (Rfree = 0.000) for 4754 atoms. Found 28 (35 requested) and removed 39 (17 requested) atoms. Cycle 12: After refmac, R = 0.2032 (Rfree = 0.000) for 4713 atoms. Found 28 (35 requested) and removed 30 (17 requested) atoms. Cycle 13: After refmac, R = 0.1945 (Rfree = 0.000) for 4703 atoms. Found 24 (35 requested) and removed 22 (17 requested) atoms. Cycle 14: After refmac, R = 0.1880 (Rfree = 0.000) for 4699 atoms. Found 20 (35 requested) and removed 22 (17 requested) atoms. Cycle 15: After refmac, R = 0.1920 (Rfree = 0.000) for 4684 atoms. Found 24 (35 requested) and removed 25 (17 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.35 3.83 Search for helices and strands: 0 residues in 0 chains, 4874 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 4892 seeds are put forward Round 1: 250 peptides, 47 chains. Longest chain 13 peptides. Score 0.352 Round 2: 283 peptides, 47 chains. Longest chain 13 peptides. Score 0.438 Round 3: 285 peptides, 45 chains. Longest chain 15 peptides. Score 0.465 Round 4: 301 peptides, 48 chains. Longest chain 16 peptides. Score 0.472 Round 5: 309 peptides, 50 chains. Longest chain 16 peptides. Score 0.470 Taking the results from Round 4 Chains 48, Residues 253, Estimated correctness of the model 0.0 % 4 chains (18 residues) have been docked in sequence ------------------------------------------------------ 8387 reflections ( 99.63 % complete ) and 10825 restraints for refining 4702 atoms. 9819 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1995 (Rfree = 0.000) for 4702 atoms. Found 24 (35 requested) and removed 28 (17 requested) atoms. Cycle 17: After refmac, R = 0.1888 (Rfree = 0.000) for 4689 atoms. Found 19 (35 requested) and removed 27 (17 requested) atoms. Cycle 18: After refmac, R = 0.1834 (Rfree = 0.000) for 4677 atoms. Found 18 (35 requested) and removed 22 (17 requested) atoms. Cycle 19: After refmac, R = 0.1791 (Rfree = 0.000) for 4668 atoms. Found 8 (35 requested) and removed 20 (17 requested) atoms. Cycle 20: After refmac, R = 0.1724 (Rfree = 0.000) for 4649 atoms. Found 14 (35 requested) and removed 19 (17 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.30 3.78 Search for helices and strands: 0 residues in 0 chains, 4840 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 4857 seeds are put forward Round 1: 267 peptides, 50 chains. Longest chain 13 peptides. Score 0.363 Round 2: 303 peptides, 48 chains. Longest chain 18 peptides. Score 0.477 Round 3: 307 peptides, 48 chains. Longest chain 15 peptides. Score 0.486 Round 4: 313 peptides, 46 chains. Longest chain 16 peptides. Score 0.520 Round 5: 305 peptides, 46 chains. Longest chain 17 peptides. Score 0.502 Taking the results from Round 4 Chains 46, Residues 267, Estimated correctness of the model 0.4 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 8387 reflections ( 99.63 % complete ) and 11098 restraints for refining 4795 atoms. 10057 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1872 (Rfree = 0.000) for 4795 atoms. Found 20 (36 requested) and removed 32 (18 requested) atoms. Cycle 22: After refmac, R = 0.1783 (Rfree = 0.000) for 4772 atoms. Found 12 (36 requested) and removed 26 (18 requested) atoms. Cycle 23: After refmac, R = 0.1794 (Rfree = 0.000) for 4750 atoms. Found 29 (35 requested) and removed 26 (17 requested) atoms. Cycle 24: After refmac, R = 0.1751 (Rfree = 0.000) for 4752 atoms. Found 22 (35 requested) and removed 22 (17 requested) atoms. Cycle 25: After refmac, R = 0.1744 (Rfree = 0.000) for 4746 atoms. Found 18 (35 requested) and removed 21 (17 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.31 3.79 Search for helices and strands: 0 residues in 0 chains, 4942 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 4958 seeds are put forward Round 1: 251 peptides, 46 chains. Longest chain 12 peptides. Score 0.366 Round 2: 281 peptides, 47 chains. Longest chain 15 peptides. Score 0.433 Round 3: 290 peptides, 43 chains. Longest chain 19 peptides. Score 0.497 Round 4: 301 peptides, 46 chains. Longest chain 21 peptides. Score 0.492 Round 5: 288 peptides, 41 chains. Longest chain 18 peptides. Score 0.513 Taking the results from Round 5 Chains 41, Residues 247, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8387 reflections ( 99.63 % complete ) and 11276 restraints for refining 4822 atoms. 10329 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1999 (Rfree = 0.000) for 4822 atoms. Found 31 (36 requested) and removed 28 (18 requested) atoms. Cycle 27: After refmac, R = 0.1900 (Rfree = 0.000) for 4812 atoms. Found 20 (36 requested) and removed 32 (18 requested) atoms. Cycle 28: After refmac, R = 0.1903 (Rfree = 0.000) for 4795 atoms. Found 25 (36 requested) and removed 30 (18 requested) atoms. Cycle 29: After refmac, R = 0.1783 (Rfree = 0.000) for 4784 atoms. Found 21 (36 requested) and removed 21 (18 requested) atoms. Cycle 30: After refmac, R = 0.1589 (Rfree = 0.000) for 4781 atoms. Found 5 (36 requested) and removed 23 (18 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.31 3.79 Search for helices and strands: 0 residues in 0 chains, 4963 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 4986 seeds are put forward Round 1: 243 peptides, 48 chains. Longest chain 10 peptides. Score 0.321 Round 2: 265 peptides, 44 chains. Longest chain 14 peptides. Score 0.426 Round 3: 271 peptides, 44 chains. Longest chain 16 peptides. Score 0.441 Round 4: 261 peptides, 43 chains. Longest chain 14 peptides. Score 0.427 Round 5: 278 peptides, 49 chains. Longest chain 12 peptides. Score 0.404 Taking the results from Round 3 Chains 47, Residues 227, Estimated correctness of the model 0.0 % 3 chains (24 residues) have been docked in sequence ------------------------------------------------------ 8387 reflections ( 99.63 % complete ) and 11268 restraints for refining 4874 atoms. 10326 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1900 (Rfree = 0.000) for 4874 atoms. Found 32 (36 requested) and removed 34 (18 requested) atoms. Cycle 32: After refmac, R = 0.1950 (Rfree = 0.000) for 4857 atoms. Found 32 (36 requested) and removed 31 (18 requested) atoms. Cycle 33: After refmac, R = 0.1878 (Rfree = 0.000) for 4848 atoms. Found 29 (36 requested) and removed 23 (18 requested) atoms. Cycle 34: After refmac, R = 0.1881 (Rfree = 0.000) for 4850 atoms. Found 21 (36 requested) and removed 24 (18 requested) atoms. Cycle 35: After refmac, R = 0.1886 (Rfree = 0.000) for 4843 atoms. Found 27 (36 requested) and removed 20 (18 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.32 3.80 Search for helices and strands: 0 residues in 0 chains, 5053 seeds are put forward NCS extension: 27 residues added (3 deleted due to clashes), 5080 seeds are put forward Round 1: 205 peptides, 43 chains. Longest chain 12 peptides. Score 0.271 Round 2: 207 peptides, 37 chains. Longest chain 16 peptides. Score 0.351 Round 3: 219 peptides, 41 chains. Longest chain 12 peptides. Score 0.336 Round 4: 237 peptides, 37 chains. Longest chain 26 peptides. Score 0.432 Round 5: 232 peptides, 41 chains. Longest chain 13 peptides. Score 0.373 Taking the results from Round 4 Chains 38, Residues 200, Estimated correctness of the model 0.0 % 4 chains (36 residues) have been docked in sequence ------------------------------------------------------ 8387 reflections ( 99.63 % complete ) and 11454 restraints for refining 4874 atoms. 10569 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2112 (Rfree = 0.000) for 4874 atoms. Found 35 (36 requested) and removed 39 (18 requested) atoms. Cycle 37: After refmac, R = 0.2045 (Rfree = 0.000) for 4859 atoms. Found 36 (36 requested) and removed 26 (18 requested) atoms. Cycle 38: After refmac, R = 0.2003 (Rfree = 0.000) for 4858 atoms. Found 28 (36 requested) and removed 28 (18 requested) atoms. Cycle 39: After refmac, R = 0.1992 (Rfree = 0.000) for 4851 atoms. Found 36 (36 requested) and removed 25 (18 requested) atoms. Cycle 40: After refmac, R = 0.2005 (Rfree = 0.000) for 4857 atoms. Found 33 (36 requested) and removed 24 (18 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.33 3.81 Search for helices and strands: 0 residues in 0 chains, 5061 seeds are put forward NCS extension: 37 residues added (1 deleted due to clashes), 5098 seeds are put forward Round 1: 189 peptides, 42 chains. Longest chain 10 peptides. Score 0.235 Round 2: 206 peptides, 39 chains. Longest chain 16 peptides. Score 0.324 Round 3: 195 peptides, 37 chains. Longest chain 9 peptides. Score 0.317 Round 4: 191 peptides, 33 chains. Longest chain 16 peptides. Score 0.355 Round 5: 188 peptides, 34 chains. Longest chain 11 peptides. Score 0.334 Taking the results from Round 4 Chains 34, Residues 158, Estimated correctness of the model 0.0 % 4 chains (22 residues) have been docked in sequence ------------------------------------------------------ 8387 reflections ( 99.63 % complete ) and 11678 restraints for refining 4874 atoms. 11016 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1956 (Rfree = 0.000) for 4874 atoms. Found 23 (36 requested) and removed 30 (18 requested) atoms. Failed to save intermediate PDB Cycle 42: After refmac, R = 0.1900 (Rfree = 0.000) for 4859 atoms. Found 27 (36 requested) and removed 27 (18 requested) atoms. Cycle 43: After refmac, R = 0.1951 (Rfree = 0.000) for 4848 atoms. Found 30 (36 requested) and removed 27 (18 requested) atoms. Cycle 44: After refmac, R = 0.1854 (Rfree = 0.000) for 4842 atoms. Found 20 (36 requested) and removed 22 (18 requested) atoms. Cycle 45: After refmac, R = 0.1928 (Rfree = 0.000) for 4834 atoms. Found 35 (36 requested) and removed 23 (18 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.31 3.79 Search for helices and strands: 0 residues in 0 chains, 5051 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 5072 seeds are put forward Round 1: 163 peptides, 37 chains. Longest chain 7 peptides. Score 0.217 Round 2: 175 peptides, 34 chains. Longest chain 9 peptides. Score 0.295 Round 3: 170 peptides, 28 chains. Longest chain 17 peptides. Score 0.358 Round 4: 184 peptides, 35 chains. Longest chain 9 peptides. Score 0.309 Round 5: 191 peptides, 34 chains. Longest chain 11 peptides. Score 0.343 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 29, Residues 142, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence Sequence coverage is 9 % Consider running further cycles of model building using 1z82-3_warpNtrace.pdb as input Building loops using Loopy2018 29 chains (142 residues) following loop building 2 chains (13 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8387 reflections ( 99.63 % complete ) and 12013 restraints for refining 4874 atoms. 11428 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1866 (Rfree = 0.000) for 4874 atoms. Found 0 (36 requested) and removed 18 (18 requested) atoms. Cycle 47: After refmac, R = 0.1869 (Rfree = 0.000) for 4846 atoms. Found 0 (36 requested) and removed 18 (18 requested) atoms. Cycle 48: After refmac, R = 0.1805 (Rfree = 0.000) for 4824 atoms. Found 0 (36 requested) and removed 18 (18 requested) atoms. Cycle 49: After refmac, R = 0.1787 (Rfree = 0.000) for 4803 atoms. Found 0 (36 requested) and removed 18 (18 requested) atoms. TimeTaking 47.82