null Mon 24 Dec 07:52:56 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 2op5-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2op5-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2op5-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2op5-3.4-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/2op5-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2op5-3.4-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 07:53:01 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/2op5-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2op5-3.4-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 506 and 0 Target number of residues in the AU: 506 Target solvent content: 0.6053 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: 2op5-3.4-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: 19 Cell parameters: 56.562 84.634 144.950 90.000 90.000 90.000 Input sequence file: 2op5-3.4-parrot-noncs.fasta_lf Building free atoms model in initial map for 5616 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: 73.087 3.400 Wilson plot Bfac: 54.52 10070 reflections ( 99.83 % complete ) and 0 restraints for refining 6201 atoms. Observations/parameters ratio is 0.41 ------------------------------------------------------ Starting model: R = 0.3374 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2994 (Rfree = 0.000) for 6201 atoms. Found 36 (46 requested) and removed 68 (23 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.15 3.37 Search for helices and strands: 0 residues in 0 chains, 6272 seeds are put forward NCS extension: 0 residues added, 6272 seeds are put forward Round 1: 257 peptides, 51 chains. Longest chain 10 peptides. Score 0.310 Round 2: 338 peptides, 60 chains. Longest chain 16 peptides. Score 0.412 Round 3: 353 peptides, 57 chains. Longest chain 14 peptides. Score 0.472 Round 4: 341 peptides, 54 chains. Longest chain 16 peptides. Score 0.474 Round 5: 357 peptides, 56 chains. Longest chain 14 peptides. Score 0.489 Taking the results from Round 5 Chains 56, Residues 301, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10070 reflections ( 99.83 % complete ) and 11860 restraints for refining 5104 atoms. 10712 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2595 (Rfree = 0.000) for 5104 atoms. Found 36 (38 requested) and removed 31 (19 requested) atoms. Cycle 2: After refmac, R = 0.2415 (Rfree = 0.000) for 5066 atoms. Found 15 (38 requested) and removed 28 (19 requested) atoms. Cycle 3: After refmac, R = 0.2491 (Rfree = 0.000) for 5031 atoms. Found 20 (38 requested) and removed 28 (19 requested) atoms. Cycle 4: After refmac, R = 0.2142 (Rfree = 0.000) for 5007 atoms. Found 6 (37 requested) and removed 18 (18 requested) atoms. Cycle 5: After refmac, R = 0.2186 (Rfree = 0.000) for 4989 atoms. Found 8 (37 requested) and removed 21 (18 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.13 3.35 Search for helices and strands: 0 residues in 0 chains, 5152 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 5169 seeds are put forward Round 1: 308 peptides, 57 chains. Longest chain 12 peptides. Score 0.372 Round 2: 336 peptides, 49 chains. Longest chain 18 peptides. Score 0.509 Round 3: 353 peptides, 52 chains. Longest chain 17 peptides. Score 0.516 Round 4: 359 peptides, 53 chains. Longest chain 24 peptides. Score 0.519 Round 5: 365 peptides, 53 chains. Longest chain 19 peptides. Score 0.531 Taking the results from Round 5 Chains 53, Residues 312, Estimated correctness of the model 4.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10070 reflections ( 99.83 % complete ) and 11746 restraints for refining 5105 atoms. 10551 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2526 (Rfree = 0.000) for 5105 atoms. Found 25 (38 requested) and removed 48 (19 requested) atoms. Cycle 7: After refmac, R = 0.2442 (Rfree = 0.000) for 5056 atoms. Found 34 (38 requested) and removed 44 (19 requested) atoms. Cycle 8: After refmac, R = 0.2106 (Rfree = 0.000) for 5027 atoms. Found 14 (38 requested) and removed 29 (19 requested) atoms. Cycle 9: After refmac, R = 0.2214 (Rfree = 0.000) for 4996 atoms. Found 23 (37 requested) and removed 22 (18 requested) atoms. Cycle 10: After refmac, R = 0.2067 (Rfree = 0.000) for 4989 atoms. Found 17 (37 requested) and removed 27 (18 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.09 3.30 Search for helices and strands: 0 residues in 0 chains, 5128 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 5149 seeds are put forward Round 1: 308 peptides, 61 chains. Longest chain 14 peptides. Score 0.332 Round 2: 315 peptides, 51 chains. Longest chain 15 peptides. Score 0.446 Round 3: 337 peptides, 53 chains. Longest chain 16 peptides. Score 0.475 Round 4: 319 peptides, 49 chains. Longest chain 13 peptides. Score 0.474 Round 5: 345 peptides, 52 chains. Longest chain 16 peptides. Score 0.500 Taking the results from Round 5 Chains 52, Residues 293, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10070 reflections ( 99.83 % complete ) and 11748 restraints for refining 5103 atoms. 10628 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2368 (Rfree = 0.000) for 5103 atoms. Found 20 (38 requested) and removed 33 (19 requested) atoms. Cycle 12: After refmac, R = 0.2222 (Rfree = 0.000) for 5080 atoms. Found 10 (38 requested) and removed 22 (19 requested) atoms. Cycle 13: After refmac, R = 0.2165 (Rfree = 0.000) for 5063 atoms. Found 5 (38 requested) and removed 22 (19 requested) atoms. Cycle 14: After refmac, R = 0.2120 (Rfree = 0.000) for 5045 atoms. Found 5 (38 requested) and removed 19 (19 requested) atoms. Cycle 15: After refmac, R = 0.2086 (Rfree = 0.000) for 5025 atoms. Found 6 (37 requested) and removed 19 (18 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.13 3.35 Search for helices and strands: 0 residues in 0 chains, 5157 seeds are put forward NCS extension: 14 residues added (5 deleted due to clashes), 5171 seeds are put forward Round 1: 302 peptides, 57 chains. Longest chain 12 peptides. Score 0.358 Round 2: 310 peptides, 50 chains. Longest chain 14 peptides. Score 0.445 Round 3: 339 peptides, 57 chains. Longest chain 16 peptides. Score 0.442 Round 4: 330 peptides, 54 chains. Longest chain 14 peptides. Score 0.451 Round 5: 330 peptides, 52 chains. Longest chain 14 peptides. Score 0.469 Taking the results from Round 5 Chains 52, Residues 278, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10070 reflections ( 99.83 % complete ) and 12015 restraints for refining 5104 atoms. 10955 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2388 (Rfree = 0.000) for 5104 atoms. Found 31 (38 requested) and removed 26 (19 requested) atoms. Cycle 17: After refmac, R = 0.2185 (Rfree = 0.000) for 5094 atoms. Found 14 (38 requested) and removed 25 (19 requested) atoms. Cycle 18: After refmac, R = 0.2122 (Rfree = 0.000) for 5074 atoms. Found 7 (38 requested) and removed 23 (19 requested) atoms. Cycle 19: After refmac, R = 0.2075 (Rfree = 0.000) for 5051 atoms. Found 5 (38 requested) and removed 20 (19 requested) atoms. Cycle 20: After refmac, R = 0.2067 (Rfree = 0.000) for 5031 atoms. Found 5 (38 requested) and removed 21 (19 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.12 3.34 Search for helices and strands: 0 residues in 0 chains, 5150 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 5168 seeds are put forward Round 1: 273 peptides, 52 chains. Longest chain 10 peptides. Score 0.339 Round 2: 313 peptides, 53 chains. Longest chain 13 peptides. Score 0.423 Round 3: 325 peptides, 51 chains. Longest chain 16 peptides. Score 0.468 Round 4: 321 peptides, 50 chains. Longest chain 13 peptides. Score 0.468 Round 5: 316 peptides, 49 chains. Longest chain 14 peptides. Score 0.467 Taking the results from Round 4 Chains 50, Residues 271, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 10070 reflections ( 99.83 % complete ) and 11829 restraints for refining 5104 atoms. 10780 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2295 (Rfree = 0.000) for 5104 atoms. Found 20 (38 requested) and removed 34 (19 requested) atoms. Cycle 22: After refmac, R = 0.2254 (Rfree = 0.000) for 5075 atoms. Found 17 (38 requested) and removed 25 (19 requested) atoms. Cycle 23: After refmac, R = 0.2289 (Rfree = 0.000) for 5059 atoms. Found 17 (38 requested) and removed 30 (19 requested) atoms. Cycle 24: After refmac, R = 0.2217 (Rfree = 0.000) for 5032 atoms. Found 19 (38 requested) and removed 25 (19 requested) atoms. Cycle 25: After refmac, R = 0.2120 (Rfree = 0.000) for 5016 atoms. Found 13 (37 requested) and removed 25 (18 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.14 3.36 Search for helices and strands: 0 residues in 0 chains, 5127 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 5141 seeds are put forward Round 1: 269 peptides, 55 chains. Longest chain 10 peptides. Score 0.298 Round 2: 289 peptides, 49 chains. Longest chain 11 peptides. Score 0.407 Round 3: 305 peptides, 51 chains. Longest chain 12 peptides. Score 0.424 Round 4: 311 peptides, 46 chains. Longest chain 18 peptides. Score 0.484 Round 5: 330 peptides, 51 chains. Longest chain 14 peptides. Score 0.478 Taking the results from Round 4 Chains 46, Residues 265, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10070 reflections ( 99.83 % complete ) and 11690 restraints for refining 5060 atoms. 10676 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2295 (Rfree = 0.000) for 5060 atoms. Found 27 (38 requested) and removed 31 (19 requested) atoms. Cycle 27: After refmac, R = 0.2289 (Rfree = 0.000) for 5049 atoms. Found 30 (38 requested) and removed 24 (19 requested) atoms. Cycle 28: After refmac, R = 0.2210 (Rfree = 0.000) for 5046 atoms. Found 29 (38 requested) and removed 31 (19 requested) atoms. Cycle 29: After refmac, R = 0.2149 (Rfree = 0.000) for 5037 atoms. Found 29 (38 requested) and removed 24 (19 requested) atoms. Cycle 30: After refmac, R = 0.1834 (Rfree = 0.000) for 5036 atoms. Found 9 (38 requested) and removed 22 (19 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.13 3.35 Search for helices and strands: 0 residues in 0 chains, 5149 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 5174 seeds are put forward Round 1: 254 peptides, 51 chains. Longest chain 8 peptides. Score 0.302 Round 2: 278 peptides, 48 chains. Longest chain 14 peptides. Score 0.392 Round 3: 284 peptides, 45 chains. Longest chain 14 peptides. Score 0.435 Round 4: 299 peptides, 48 chains. Longest chain 16 peptides. Score 0.440 Round 5: 292 peptides, 49 chains. Longest chain 16 peptides. Score 0.414 Taking the results from Round 4 Chains 48, Residues 251, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10070 reflections ( 99.83 % complete ) and 11918 restraints for refining 5106 atoms. 10962 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2128 (Rfree = 0.000) for 5106 atoms. Found 17 (38 requested) and removed 27 (19 requested) atoms. Cycle 32: After refmac, R = 0.2156 (Rfree = 0.000) for 5082 atoms. Found 22 (38 requested) and removed 23 (19 requested) atoms. Cycle 33: After refmac, R = 0.2199 (Rfree = 0.000) for 5075 atoms. Found 36 (38 requested) and removed 26 (19 requested) atoms. Cycle 34: After refmac, R = 0.1830 (Rfree = 0.000) for 5081 atoms. Found 9 (38 requested) and removed 19 (19 requested) atoms. Cycle 35: After refmac, R = 0.1878 (Rfree = 0.000) for 5069 atoms. Found 6 (38 requested) and removed 20 (19 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.11 3.32 Search for helices and strands: 0 residues in 0 chains, 5192 seeds are put forward NCS extension: 29 residues added (0 deleted due to clashes), 5221 seeds are put forward Round 1: 244 peptides, 47 chains. Longest chain 17 peptides. Score 0.320 Round 2: 278 peptides, 43 chains. Longest chain 21 peptides. Score 0.442 Round 3: 257 peptides, 47 chains. Longest chain 10 peptides. Score 0.352 Round 4: 271 peptides, 44 chains. Longest chain 12 peptides. Score 0.416 Round 5: 262 peptides, 49 chains. Longest chain 12 peptides. Score 0.343 Taking the results from Round 2 Chains 43, Residues 235, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10070 reflections ( 99.83 % complete ) and 11912 restraints for refining 5106 atoms. 11015 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2094 (Rfree = 0.000) for 5106 atoms. Found 31 (38 requested) and removed 26 (19 requested) atoms. Cycle 37: After refmac, R = 0.2067 (Rfree = 0.000) for 5103 atoms. Found 24 (38 requested) and removed 21 (19 requested) atoms. Cycle 38: After refmac, R = 0.2013 (Rfree = 0.000) for 5102 atoms. Found 14 (38 requested) and removed 23 (19 requested) atoms. Cycle 39: After refmac, R = 0.1930 (Rfree = 0.000) for 5087 atoms. Found 11 (38 requested) and removed 23 (19 requested) atoms. Cycle 40: After refmac, R = 0.1955 (Rfree = 0.000) for 5072 atoms. Found 8 (38 requested) and removed 22 (19 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.11 3.32 Search for helices and strands: 0 residues in 0 chains, 5215 seeds are put forward NCS extension: 28 residues added (4 deleted due to clashes), 5243 seeds are put forward Round 1: 218 peptides, 41 chains. Longest chain 12 peptides. Score 0.319 Round 2: 238 peptides, 45 chains. Longest chain 12 peptides. Score 0.326 Round 3: 242 peptides, 41 chains. Longest chain 16 peptides. Score 0.379 Round 4: 240 peptides, 42 chains. Longest chain 10 peptides. Score 0.363 Round 5: 229 peptides, 40 chains. Longest chain 11 peptides. Score 0.357 Taking the results from Round 3 Chains 41, Residues 201, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10070 reflections ( 99.83 % complete ) and 12105 restraints for refining 5106 atoms. 11342 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2048 (Rfree = 0.000) for 5106 atoms. Found 17 (38 requested) and removed 22 (19 requested) atoms. Cycle 42: After refmac, R = 0.2148 (Rfree = 0.000) for 5097 atoms. Found 21 (38 requested) and removed 20 (19 requested) atoms. Cycle 43: After refmac, R = 0.2179 (Rfree = 0.000) for 5093 atoms. Found 22 (38 requested) and removed 24 (19 requested) atoms. Cycle 44: After refmac, R = 0.2080 (Rfree = 0.000) for 5083 atoms. Found 21 (38 requested) and removed 22 (19 requested) atoms. Cycle 45: After refmac, R = 0.1782 (Rfree = 0.000) for 5074 atoms. Found 6 (38 requested) and removed 24 (19 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.12 3.34 Search for helices and strands: 0 residues in 0 chains, 5194 seeds are put forward NCS extension: 21 residues added (3 deleted due to clashes), 5215 seeds are put forward Round 1: 215 peptides, 42 chains. Longest chain 14 peptides. Score 0.300 Round 2: 240 peptides, 42 chains. Longest chain 15 peptides. Score 0.363 Round 3: 257 peptides, 43 chains. Longest chain 16 peptides. Score 0.394 Round 4: 251 peptides, 39 chains. Longest chain 16 peptides. Score 0.421 Round 5: 263 peptides, 47 chains. Longest chain 13 peptides. Score 0.367 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 39, Residues 212, 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. 10070 reflections ( 99.83 % complete ) and 11883 restraints for refining 5105 atoms. 11074 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2066 (Rfree = 0.000) for 5105 atoms. Found 0 (38 requested) and removed 19 (19 requested) atoms. Cycle 47: After refmac, R = 0.2109 (Rfree = 0.000) for 5080 atoms. Found 0 (38 requested) and removed 19 (19 requested) atoms. Cycle 48: After refmac, R = 0.2165 (Rfree = 0.000) for 5058 atoms. Found 0 (38 requested) and removed 19 (19 requested) atoms. Cycle 49: After refmac, R = 0.1812 (Rfree = 0.000) for 5033 atoms. Found 0 (38 requested) and removed 19 (19 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:45:11 GMT 2018 Job finished. TimeTaking 52.25 Used memory is bytes: 10402776