Sun 23 Dec 22:22:46 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 2op5-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2op5-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2op5-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2op5-3.8-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/2op5-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2op5-3.8-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 22:22:56 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/2op5-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2op5-3.8-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 467 and 0 Target number of residues in the AU: 467 Target solvent content: 0.6358 Checking the provided sequence file Detected sequence length: 117 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 6 Adjusted target number of residues: 702 Adjusted target solvent content: 0.45 Input MTZ file: 2op5-3.8-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: 19 Cell parameters: 56.562 84.634 144.950 90.000 90.000 90.000 Input sequence file: 2op5-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 5616 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: 73.087 3.800 Wilson plot Bfac: 69.37 Failed to save intermediate PDB 7266 reflections ( 99.77 % complete ) and 0 restraints for refining 6249 atoms. Observations/parameters ratio is 0.29 ------------------------------------------------------ Starting model: R = 0.3372 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3120 (Rfree = 0.000) for 6249 atoms. Found 19 (34 requested) and removed 43 (17 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.49 3.73 Search for helices and strands: 0 residues in 0 chains, 6359 seeds are put forward NCS extension: 0 residues added, 6359 seeds are put forward Round 1: 231 peptides, 46 chains. Longest chain 10 peptides. Score 0.297 Round 2: 299 peptides, 51 chains. Longest chain 13 peptides. Score 0.411 Round 3: 305 peptides, 46 chains. Longest chain 15 peptides. Score 0.472 Round 4: 306 peptides, 46 chains. Longest chain 15 peptides. Score 0.474 Round 5: 329 peptides, 46 chains. Longest chain 15 peptides. Score 0.521 Taking the results from Round 5 Chains 46, Residues 283, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7266 reflections ( 99.77 % complete ) and 11996 restraints for refining 5079 atoms. 10910 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2607 (Rfree = 0.000) for 5079 atoms. Found 16 (27 requested) and removed 47 (13 requested) atoms. Cycle 2: After refmac, R = 0.2488 (Rfree = 0.000) for 4954 atoms. Found 21 (27 requested) and removed 38 (13 requested) atoms. Cycle 3: After refmac, R = 0.2136 (Rfree = 0.000) for 4893 atoms. Found 13 (27 requested) and removed 33 (13 requested) atoms. Cycle 4: After refmac, R = 0.2203 (Rfree = 0.000) for 4855 atoms. Found 20 (26 requested) and removed 25 (13 requested) atoms. Cycle 5: After refmac, R = 0.2029 (Rfree = 0.000) for 4829 atoms. Found 16 (26 requested) and removed 21 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.36 3.59 Search for helices and strands: 0 residues in 0 chains, 5025 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 5043 seeds are put forward Round 1: 234 peptides, 46 chains. Longest chain 10 peptides. Score 0.305 Round 2: 300 peptides, 51 chains. Longest chain 15 peptides. Score 0.413 Round 3: 300 peptides, 48 chains. Longest chain 14 peptides. Score 0.442 Round 4: 288 peptides, 47 chains. Longest chain 16 peptides. Score 0.425 Round 5: 305 peptides, 49 chains. Longest chain 16 peptides. Score 0.443 Taking the results from Round 5 Chains 49, Residues 256, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7266 reflections ( 99.77 % complete ) and 11579 restraints for refining 4954 atoms. 10604 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2359 (Rfree = 0.000) for 4954 atoms. Found 21 (27 requested) and removed 46 (13 requested) atoms. Cycle 7: After refmac, R = 0.2129 (Rfree = 0.000) for 4875 atoms. Found 18 (27 requested) and removed 33 (13 requested) atoms. Cycle 8: After refmac, R = 0.1915 (Rfree = 0.000) for 4829 atoms. Found 11 (26 requested) and removed 26 (13 requested) atoms. Cycle 9: After refmac, R = 0.1536 (Rfree = 0.000) for 4796 atoms. Found 4 (26 requested) and removed 22 (13 requested) atoms. Cycle 10: After refmac, R = 0.1737 (Rfree = 0.000) for 4768 atoms. Found 9 (26 requested) and removed 21 (13 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.43 3.67 Search for helices and strands: 0 residues in 0 chains, 4930 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 4949 seeds are put forward Round 1: 257 peptides, 54 chains. Longest chain 9 peptides. Score 0.278 Round 2: 315 peptides, 58 chains. Longest chain 12 peptides. Score 0.378 Round 3: 327 peptides, 53 chains. Longest chain 16 peptides. Score 0.453 Round 4: 327 peptides, 54 chains. Longest chain 15 peptides. Score 0.444 Round 5: 311 peptides, 46 chains. Longest chain 21 peptides. Score 0.484 Taking the results from Round 5 Chains 46, Residues 265, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7266 reflections ( 99.77 % complete ) and 11965 restraints for refining 5071 atoms. 10951 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2323 (Rfree = 0.000) for 5071 atoms. Found 18 (27 requested) and removed 55 (13 requested) atoms. Cycle 12: After refmac, R = 0.1945 (Rfree = 0.000) for 5004 atoms. Found 12 (27 requested) and removed 31 (13 requested) atoms. Cycle 13: After refmac, R = 0.1957 (Rfree = 0.000) for 4960 atoms. Found 10 (27 requested) and removed 33 (13 requested) atoms. Cycle 14: After refmac, R = 0.1911 (Rfree = 0.000) for 4921 atoms. Found 7 (27 requested) and removed 21 (13 requested) atoms. Cycle 15: After refmac, R = 0.1934 (Rfree = 0.000) for 4894 atoms. Found 13 (26 requested) and removed 27 (13 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.44 3.68 Search for helices and strands: 0 residues in 0 chains, 5036 seeds are put forward NCS extension: 30 residues added (2 deleted due to clashes), 5066 seeds are put forward Round 1: 248 peptides, 51 chains. Longest chain 10 peptides. Score 0.287 Round 2: 279 peptides, 48 chains. Longest chain 13 peptides. Score 0.394 Round 3: 285 peptides, 50 chains. Longest chain 12 peptides. Score 0.388 Round 4: 302 peptides, 52 chains. Longest chain 14 peptides. Score 0.408 Round 5: 317 peptides, 52 chains. Longest chain 16 peptides. Score 0.441 Taking the results from Round 5 Chains 52, Residues 265, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7266 reflections ( 99.77 % complete ) and 11592 restraints for refining 5080 atoms. 10584 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2112 (Rfree = 0.000) for 5080 atoms. Found 13 (27 requested) and removed 38 (13 requested) atoms. Cycle 17: After refmac, R = 0.1936 (Rfree = 0.000) for 5029 atoms. Found 13 (27 requested) and removed 26 (13 requested) atoms. Cycle 18: After refmac, R = 0.1970 (Rfree = 0.000) for 4991 atoms. Found 21 (27 requested) and removed 35 (13 requested) atoms. Cycle 19: After refmac, R = 0.1502 (Rfree = 0.000) for 4960 atoms. Found 8 (27 requested) and removed 16 (13 requested) atoms. Cycle 20: After refmac, R = 0.1649 (Rfree = 0.000) for 4936 atoms. Found 8 (27 requested) and removed 18 (13 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.46 3.70 Search for helices and strands: 0 residues in 0 chains, 5131 seeds are put forward NCS extension: 27 residues added (1 deleted due to clashes), 5158 seeds are put forward Round 1: 243 peptides, 48 chains. Longest chain 14 peptides. Score 0.306 Round 2: 270 peptides, 47 chains. Longest chain 21 peptides. Score 0.383 Round 3: 256 peptides, 45 chains. Longest chain 18 peptides. Score 0.370 Round 4: 282 peptides, 45 chains. Longest chain 16 peptides. Score 0.431 Round 5: 279 peptides, 45 chains. Longest chain 15 peptides. Score 0.424 Taking the results from Round 4 Chains 45, Residues 237, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7266 reflections ( 99.77 % complete ) and 11852 restraints for refining 5078 atoms. 10949 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2134 (Rfree = 0.000) for 5078 atoms. Found 18 (27 requested) and removed 34 (13 requested) atoms. Cycle 22: After refmac, R = 0.2029 (Rfree = 0.000) for 5039 atoms. Found 23 (27 requested) and removed 32 (13 requested) atoms. Cycle 23: After refmac, R = 0.1946 (Rfree = 0.000) for 5020 atoms. Found 18 (27 requested) and removed 21 (13 requested) atoms. Cycle 24: After refmac, R = 0.1962 (Rfree = 0.000) for 5010 atoms. Found 27 (27 requested) and removed 29 (13 requested) atoms. Cycle 25: After refmac, R = 0.1466 (Rfree = 0.000) for 4994 atoms. Found 6 (27 requested) and removed 16 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.48 3.72 Search for helices and strands: 0 residues in 0 chains, 5140 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 5156 seeds are put forward Round 1: 268 peptides, 56 chains. Longest chain 11 peptides. Score 0.284 Round 2: 327 peptides, 56 chains. Longest chain 18 peptides. Score 0.425 Round 3: 309 peptides, 57 chains. Longest chain 20 peptides. Score 0.374 Round 4: 326 peptides, 60 chains. Longest chain 15 peptides. Score 0.384 Round 5: 325 peptides, 56 chains. Longest chain 15 peptides. Score 0.421 Taking the results from Round 2 Chains 56, Residues 271, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7266 reflections ( 99.77 % complete ) and 11640 restraints for refining 5080 atoms. 10612 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1847 (Rfree = 0.000) for 5080 atoms. Found 16 (27 requested) and removed 28 (13 requested) atoms. Cycle 27: After refmac, R = 0.1830 (Rfree = 0.000) for 5052 atoms. Found 12 (27 requested) and removed 27 (13 requested) atoms. Cycle 28: After refmac, R = 0.1769 (Rfree = 0.000) for 5029 atoms. Found 8 (27 requested) and removed 28 (13 requested) atoms. Cycle 29: After refmac, R = 0.1661 (Rfree = 0.000) for 5001 atoms. Found 8 (27 requested) and removed 21 (13 requested) atoms. Cycle 30: After refmac, R = 0.1638 (Rfree = 0.000) for 4981 atoms. Found 7 (27 requested) and removed 20 (13 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.42 3.66 Search for helices and strands: 0 residues in 0 chains, 5127 seeds are put forward NCS extension: 27 residues added (3 deleted due to clashes), 5154 seeds are put forward Round 1: 232 peptides, 50 chains. Longest chain 10 peptides. Score 0.256 Round 2: 268 peptides, 49 chains. Longest chain 15 peptides. Score 0.358 Round 3: 281 peptides, 45 chains. Longest chain 18 peptides. Score 0.429 Round 4: 272 peptides, 42 chains. Longest chain 16 peptides. Score 0.438 Round 5: 269 peptides, 44 chains. Longest chain 13 peptides. Score 0.411 Taking the results from Round 4 Chains 42, Residues 230, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7266 reflections ( 99.77 % complete ) and 12011 restraints for refining 5079 atoms. 11133 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2037 (Rfree = 0.000) for 5079 atoms. Found 17 (27 requested) and removed 21 (13 requested) atoms. Cycle 32: After refmac, R = 0.1905 (Rfree = 0.000) for 5052 atoms. Found 24 (27 requested) and removed 24 (13 requested) atoms. Cycle 33: After refmac, R = 0.1822 (Rfree = 0.000) for 5046 atoms. Found 7 (27 requested) and removed 27 (13 requested) atoms. Cycle 34: After refmac, R = 0.1656 (Rfree = 0.000) for 5021 atoms. Found 7 (27 requested) and removed 23 (13 requested) atoms. Cycle 35: After refmac, R = 0.1723 (Rfree = 0.000) for 5000 atoms. Found 15 (27 requested) and removed 20 (13 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.43 3.67 Search for helices and strands: 0 residues in 0 chains, 5132 seeds are put forward NCS extension: 18 residues added (3 deleted due to clashes), 5150 seeds are put forward Round 1: 213 peptides, 45 chains. Longest chain 9 peptides. Score 0.261 Round 2: 238 peptides, 44 chains. Longest chain 12 peptides. Score 0.337 Round 3: 249 peptides, 45 chains. Longest chain 12 peptides. Score 0.353 Round 4: 261 peptides, 40 chains. Longest chain 25 peptides. Score 0.433 Round 5: 247 peptides, 43 chains. Longest chain 13 peptides. Score 0.370 Taking the results from Round 4 Chains 40, Residues 221, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7266 reflections ( 99.77 % complete ) and 11968 restraints for refining 5080 atoms. 11124 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1911 (Rfree = 0.000) for 5080 atoms. Found 15 (27 requested) and removed 24 (13 requested) atoms. Cycle 37: After refmac, R = 0.1839 (Rfree = 0.000) for 5056 atoms. Found 23 (27 requested) and removed 23 (13 requested) atoms. Cycle 38: After refmac, R = 0.1750 (Rfree = 0.000) for 5038 atoms. Found 15 (27 requested) and removed 19 (13 requested) atoms. Cycle 39: After refmac, R = 0.1875 (Rfree = 0.000) for 5026 atoms. Found 25 (27 requested) and removed 22 (13 requested) atoms. Cycle 40: After refmac, R = 0.1699 (Rfree = 0.000) for 5022 atoms. Found 19 (27 requested) and removed 15 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.48 3.72 Search for helices and strands: 0 residues in 0 chains, 5183 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 5206 seeds are put forward Round 1: 210 peptides, 47 chains. Longest chain 7 peptides. Score 0.230 Round 2: 250 peptides, 44 chains. Longest chain 17 peptides. Score 0.366 Round 3: 242 peptides, 44 chains. Longest chain 12 peptides. Score 0.347 Round 4: 255 peptides, 42 chains. Longest chain 15 peptides. Score 0.399 Round 5: 266 peptides, 47 chains. Longest chain 11 peptides. Score 0.374 Taking the results from Round 4 Chains 43, Residues 213, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 7266 reflections ( 99.77 % complete ) and 11971 restraints for refining 5080 atoms. 11137 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1956 (Rfree = 0.000) for 5080 atoms. Found 18 (27 requested) and removed 26 (13 requested) atoms. Cycle 42: After refmac, R = 0.1802 (Rfree = 0.000) for 5055 atoms. Found 19 (27 requested) and removed 28 (13 requested) atoms. Cycle 43: After refmac, R = 0.1847 (Rfree = 0.000) for 5037 atoms. Found 22 (27 requested) and removed 20 (13 requested) atoms. Cycle 44: After refmac, R = 0.1726 (Rfree = 0.000) for 5030 atoms. Found 14 (27 requested) and removed 23 (13 requested) atoms. Cycle 45: After refmac, R = 0.1370 (Rfree = 0.000) for 5015 atoms. Found 2 (27 requested) and removed 15 (13 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.45 3.69 Search for helices and strands: 0 residues in 0 chains, 5129 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 5147 seeds are put forward Round 1: 179 peptides, 39 chains. Longest chain 8 peptides. Score 0.236 Round 2: 212 peptides, 44 chains. Longest chain 10 peptides. Score 0.269 Round 3: 228 peptides, 44 chains. Longest chain 10 peptides. Score 0.311 Round 4: 216 peptides, 38 chains. Longest chain 11 peptides. Score 0.347 Round 5: 225 peptides, 40 chains. Longest chain 11 peptides. Score 0.347 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 40, Residues 185, 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 2op5-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7266 reflections ( 99.77 % complete ) and 12139 restraints for refining 5080 atoms. 11439 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1821 (Rfree = 0.000) for 5080 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Cycle 47: After refmac, R = 0.1946 (Rfree = 0.000) for 5052 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Cycle 48: After refmac, R = 0.2000 (Rfree = 0.000) for 5030 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Cycle 49: After refmac, R = 0.1755 (Rfree = 0.000) for 5005 atoms. TimeTaking 69.13