null Mon 24 Dec 07:59:12 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 2oh1-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2oh1-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2oh1-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2oh1-3.8-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/2oh1-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2oh1-3.8-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 07:59:17 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/2oh1-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2oh1-3.8-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 501 and 0 Target number of residues in the AU: 501 Target solvent content: 0.6635 Checking the provided sequence file Detected sequence length: 179 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 716 Adjusted target solvent content: 0.52 Input MTZ file: 2oh1-3.8-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: 65.646 99.855 122.905 90.000 90.000 90.000 Input sequence file: 2oh1-3.8-parrot-noncs.fasta_lf Building free atoms model in initial map for 5728 target number of atoms Had to go as low as 0.80 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: 77.501 3.800 Wilson plot Bfac: 87.48 8322 reflections ( 99.07 % complete ) and 0 restraints for refining 6322 atoms. Observations/parameters ratio is 0.33 ------------------------------------------------------ Starting model: R = 0.3330 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3153 (Rfree = 0.000) for 6322 atoms. Found 34 (34 requested) and removed 61 (17 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.71 3.61 Search for helices and strands: 0 residues in 0 chains, 6423 seeds are put forward NCS extension: 0 residues added, 6423 seeds are put forward Round 1: 301 peptides, 56 chains. Longest chain 12 peptides. Score 0.345 Round 2: 386 peptides, 57 chains. Longest chain 17 peptides. Score 0.501 Round 3: 415 peptides, 54 chains. Longest chain 24 peptides. Score 0.571 Round 4: 419 peptides, 55 chains. Longest chain 26 peptides. Score 0.570 Round 5: 423 peptides, 50 chains. Longest chain 27 peptides. Score 0.610 Taking the results from Round 5 Chains 53, Residues 373, Estimated correctness of the model 3.5 % 4 chains (42 residues) have been docked in sequence ------------------------------------------------------ 8322 reflections ( 99.07 % complete ) and 11146 restraints for refining 5179 atoms. 9547 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2440 (Rfree = 0.000) for 5179 atoms. Found 7 (28 requested) and removed 30 (14 requested) atoms. Cycle 2: After refmac, R = 0.2299 (Rfree = 0.000) for 5094 atoms. Found 7 (28 requested) and removed 20 (14 requested) atoms. Cycle 3: After refmac, R = 0.2251 (Rfree = 0.000) for 5053 atoms. Found 6 (27 requested) and removed 15 (13 requested) atoms. Cycle 4: After refmac, R = 0.2211 (Rfree = 0.000) for 5038 atoms. Found 1 (27 requested) and removed 16 (13 requested) atoms. Cycle 5: After refmac, R = 0.2205 (Rfree = 0.000) for 5021 atoms. Found 1 (27 requested) and removed 16 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.70 3.60 Search for helices and strands: 0 residues in 0 chains, 5164 seeds are put forward NCS extension: 37 residues added (4 deleted due to clashes), 5201 seeds are put forward Round 1: 364 peptides, 61 chains. Longest chain 13 peptides. Score 0.428 Round 2: 390 peptides, 53 chains. Longest chain 24 peptides. Score 0.538 Round 3: 408 peptides, 51 chains. Longest chain 21 peptides. Score 0.581 Round 4: 410 peptides, 49 chains. Longest chain 26 peptides. Score 0.598 Round 5: 416 peptides, 47 chains. Longest chain 18 peptides. Score 0.620 Taking the results from Round 5 Chains 47, Residues 369, Estimated correctness of the model 8.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8322 reflections ( 99.07 % complete ) and 11715 restraints for refining 5180 atoms. 10286 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2352 (Rfree = 0.000) for 5180 atoms. Found 13 (28 requested) and removed 30 (14 requested) atoms. Cycle 7: After refmac, R = 0.2162 (Rfree = 0.000) for 5136 atoms. Found 3 (28 requested) and removed 31 (14 requested) atoms. Cycle 8: After refmac, R = 0.2136 (Rfree = 0.000) for 5101 atoms. Found 2 (28 requested) and removed 18 (14 requested) atoms. Cycle 9: After refmac, R = 0.2119 (Rfree = 0.000) for 5080 atoms. Found 0 (27 requested) and removed 16 (13 requested) atoms. Cycle 10: After refmac, R = 0.2112 (Rfree = 0.000) for 5062 atoms. Found 1 (27 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.71 3.61 Search for helices and strands: 0 residues in 0 chains, 5194 seeds are put forward NCS extension: 13 residues added (4 deleted due to clashes), 5207 seeds are put forward Round 1: 363 peptides, 61 chains. Longest chain 13 peptides. Score 0.426 Round 2: 401 peptides, 54 chains. Longest chain 23 peptides. Score 0.548 Round 3: 403 peptides, 50 chains. Longest chain 22 peptides. Score 0.580 Round 4: 432 peptides, 53 chains. Longest chain 30 peptides. Score 0.604 Round 5: 404 peptides, 47 chains. Longest chain 22 peptides. Score 0.603 Taking the results from Round 4 Chains 53, Residues 379, Estimated correctness of the model 0.7 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 8322 reflections ( 99.07 % complete ) and 11590 restraints for refining 5180 atoms. 10114 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2364 (Rfree = 0.000) for 5180 atoms. Found 9 (28 requested) and removed 31 (14 requested) atoms. Cycle 12: After refmac, R = 0.2225 (Rfree = 0.000) for 5133 atoms. Found 5 (28 requested) and removed 23 (14 requested) atoms. Cycle 13: After refmac, R = 0.2225 (Rfree = 0.000) for 5109 atoms. Found 5 (28 requested) and removed 19 (14 requested) atoms. Cycle 14: After refmac, R = 0.2194 (Rfree = 0.000) for 5093 atoms. Found 4 (28 requested) and removed 15 (14 requested) atoms. Cycle 15: After refmac, R = 0.2202 (Rfree = 0.000) for 5079 atoms. Found 2 (27 requested) and removed 15 (13 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.72 3.62 Search for helices and strands: 0 residues in 0 chains, 5238 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 5257 seeds are put forward Round 1: 339 peptides, 51 chains. Longest chain 19 peptides. Score 0.463 Round 2: 377 peptides, 49 chains. Longest chain 24 peptides. Score 0.546 Round 3: 371 peptides, 48 chains. Longest chain 18 peptides. Score 0.543 Round 4: 378 peptides, 50 chains. Longest chain 19 peptides. Score 0.540 Round 5: 407 peptides, 50 chains. Longest chain 18 peptides. Score 0.587 Taking the results from Round 5 Chains 50, Residues 357, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8322 reflections ( 99.07 % complete ) and 11724 restraints for refining 5180 atoms. 10346 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2433 (Rfree = 0.000) for 5180 atoms. Found 9 (28 requested) and removed 26 (14 requested) atoms. Cycle 17: After refmac, R = 0.2290 (Rfree = 0.000) for 5124 atoms. Found 10 (28 requested) and removed 19 (14 requested) atoms. Cycle 18: After refmac, R = 0.2108 (Rfree = 0.000) for 5096 atoms. Found 6 (28 requested) and removed 22 (14 requested) atoms. Cycle 19: After refmac, R = 0.2104 (Rfree = 0.000) for 5071 atoms. Found 4 (27 requested) and removed 15 (13 requested) atoms. Cycle 20: After refmac, R = 0.2202 (Rfree = 0.000) for 5058 atoms. Found 11 (27 requested) and removed 20 (13 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.67 3.57 Search for helices and strands: 0 residues in 0 chains, 5223 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 5249 seeds are put forward Round 1: 335 peptides, 58 chains. Longest chain 16 peptides. Score 0.397 Round 2: 391 peptides, 57 chains. Longest chain 15 peptides. Score 0.509 Round 3: 391 peptides, 55 chains. Longest chain 17 peptides. Score 0.524 Round 4: 375 peptides, 51 chains. Longest chain 16 peptides. Score 0.528 Round 5: 397 peptides, 52 chains. Longest chain 18 peptides. Score 0.557 Taking the results from Round 5 Chains 52, Residues 345, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8322 reflections ( 99.07 % complete ) and 11662 restraints for refining 5181 atoms. 10334 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2426 (Rfree = 0.000) for 5181 atoms. Found 7 (28 requested) and removed 29 (14 requested) atoms. Cycle 22: After refmac, R = 0.2384 (Rfree = 0.000) for 5142 atoms. Found 10 (28 requested) and removed 27 (14 requested) atoms. Cycle 23: After refmac, R = 0.2214 (Rfree = 0.000) for 5122 atoms. Found 4 (28 requested) and removed 21 (14 requested) atoms. Cycle 24: After refmac, R = 0.2207 (Rfree = 0.000) for 5097 atoms. Found 4 (28 requested) and removed 21 (14 requested) atoms. Cycle 25: After refmac, R = 0.2121 (Rfree = 0.000) for 5075 atoms. Found 0 (27 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.68 3.58 Search for helices and strands: 0 residues in 0 chains, 5217 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 5236 seeds are put forward Round 1: 317 peptides, 60 chains. Longest chain 13 peptides. Score 0.342 Round 2: 352 peptides, 57 chains. Longest chain 13 peptides. Score 0.438 Round 3: 360 peptides, 55 chains. Longest chain 18 peptides. Score 0.470 Round 4: 366 peptides, 56 chains. Longest chain 15 peptides. Score 0.473 Round 5: 361 peptides, 56 chains. Longest chain 14 peptides. Score 0.463 Taking the results from Round 4 Chains 56, Residues 310, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 8322 reflections ( 99.07 % complete ) and 11857 restraints for refining 5181 atoms. 10654 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2315 (Rfree = 0.000) for 5181 atoms. Found 13 (28 requested) and removed 17 (14 requested) atoms. Cycle 27: After refmac, R = 0.2298 (Rfree = 0.000) for 5151 atoms. Found 10 (28 requested) and removed 22 (14 requested) atoms. Cycle 28: After refmac, R = 0.2298 (Rfree = 0.000) for 5127 atoms. Found 25 (28 requested) and removed 23 (14 requested) atoms. Cycle 29: After refmac, R = 0.2292 (Rfree = 0.000) for 5113 atoms. Found 20 (28 requested) and removed 27 (14 requested) atoms. Cycle 30: After refmac, R = 0.1880 (Rfree = 0.000) for 5091 atoms. Found 4 (28 requested) and removed 19 (14 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.69 3.59 Search for helices and strands: 0 residues in 0 chains, 5214 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 5228 seeds are put forward Round 1: 286 peptides, 61 chains. Longest chain 9 peptides. Score 0.266 Round 2: 319 peptides, 51 chains. Longest chain 16 peptides. Score 0.425 Round 3: 328 peptides, 55 chains. Longest chain 12 peptides. Score 0.409 Round 4: 332 peptides, 54 chains. Longest chain 13 peptides. Score 0.425 Round 5: 338 peptides, 53 chains. Longest chain 19 peptides. Score 0.445 Taking the results from Round 5 Chains 53, Residues 285, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8322 reflections ( 99.07 % complete ) and 12095 restraints for refining 5181 atoms. 11008 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2240 (Rfree = 0.000) for 5181 atoms. Found 16 (28 requested) and removed 21 (14 requested) atoms. Cycle 32: After refmac, R = 0.2305 (Rfree = 0.000) for 5157 atoms. Found 17 (28 requested) and removed 25 (14 requested) atoms. Cycle 33: After refmac, R = 0.2172 (Rfree = 0.000) for 5141 atoms. Found 21 (28 requested) and removed 28 (14 requested) atoms. Cycle 34: After refmac, R = 0.2103 (Rfree = 0.000) for 5124 atoms. Found 22 (28 requested) and removed 25 (14 requested) atoms. Cycle 35: After refmac, R = 0.2046 (Rfree = 0.000) for 5116 atoms. Found 28 (28 requested) and removed 24 (14 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.70 3.60 Search for helices and strands: 0 residues in 0 chains, 5296 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 5312 seeds are put forward Round 1: 266 peptides, 55 chains. Longest chain 10 peptides. Score 0.277 Round 2: 291 peptides, 47 chains. Longest chain 17 peptides. Score 0.405 Round 3: 295 peptides, 49 chains. Longest chain 16 peptides. Score 0.395 Round 4: 305 peptides, 49 chains. Longest chain 15 peptides. Score 0.415 Round 5: 294 peptides, 47 chains. Longest chain 15 peptides. Score 0.411 Taking the results from Round 4 Chains 49, Residues 256, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8322 reflections ( 99.07 % complete ) and 12005 restraints for refining 5181 atoms. 11030 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2268 (Rfree = 0.000) for 5181 atoms. Found 11 (28 requested) and removed 20 (14 requested) atoms. Cycle 37: After refmac, R = 0.2139 (Rfree = 0.000) for 5162 atoms. Found 13 (28 requested) and removed 21 (14 requested) atoms. Cycle 38: After refmac, R = 0.2198 (Rfree = 0.000) for 5132 atoms. Found 26 (28 requested) and removed 26 (14 requested) atoms. Cycle 39: After refmac, R = 0.1798 (Rfree = 0.000) for 5125 atoms. Found 2 (28 requested) and removed 15 (14 requested) atoms. Cycle 40: After refmac, R = 0.1885 (Rfree = 0.000) for 5106 atoms. Found 6 (28 requested) and removed 16 (14 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.70 3.60 Search for helices and strands: 0 residues in 0 chains, 5247 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 5262 seeds are put forward Round 1: 239 peptides, 50 chains. Longest chain 9 peptides. Score 0.263 Round 2: 267 peptides, 45 chains. Longest chain 15 peptides. Score 0.373 Round 3: 288 peptides, 50 chains. Longest chain 11 peptides. Score 0.371 Round 4: 286 peptides, 51 chains. Longest chain 11 peptides. Score 0.358 Round 5: 307 peptides, 47 chains. Longest chain 15 peptides. Score 0.436 Taking the results from Round 5 Chains 47, Residues 260, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 8322 reflections ( 99.07 % complete ) and 12031 restraints for refining 5181 atoms. 11012 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2170 (Rfree = 0.000) for 5181 atoms. Found 5 (28 requested) and removed 24 (14 requested) atoms. Cycle 42: After refmac, R = 0.2041 (Rfree = 0.000) for 5141 atoms. Found 6 (28 requested) and removed 20 (14 requested) atoms. Cycle 43: After refmac, R = 0.1990 (Rfree = 0.000) for 5120 atoms. Found 3 (28 requested) and removed 20 (14 requested) atoms. Cycle 44: After refmac, R = 0.1969 (Rfree = 0.000) for 5099 atoms. Found 7 (28 requested) and removed 27 (14 requested) atoms. Cycle 45: After refmac, R = 0.1927 (Rfree = 0.000) for 5075 atoms. Found 2 (27 requested) and removed 18 (13 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.65 3.55 Search for helices and strands: 0 residues in 0 chains, 5184 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 5206 seeds are put forward Round 1: 245 peptides, 51 chains. Longest chain 10 peptides. Score 0.267 Round 2: 275 peptides, 49 chains. Longest chain 16 peptides. Score 0.353 Round 3: 282 peptides, 46 chains. Longest chain 17 peptides. Score 0.395 Round 4: 280 peptides, 44 chains. Longest chain 15 peptides. Score 0.409 Round 5: 273 peptides, 43 chains. Longest chain 23 peptides. Score 0.404 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 44, Residues 236, Estimated correctness of the model 0.0 % 2 chains (10 residues) have been docked in sequence Sequence coverage is 4 % Consider running further cycles of model building using 2oh1-3_warpNtrace.pdb as input Building loops using Loopy2018 44 chains (236 residues) following loop building 2 chains (10 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8322 reflections ( 99.07 % complete ) and 12026 restraints for refining 5181 atoms. 11100 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2047 (Rfree = 0.000) for 5181 atoms. Found 0 (28 requested) and removed 14 (14 requested) atoms. Cycle 47: After refmac, R = 0.2010 (Rfree = 0.000) for 5154 atoms. Found 0 (28 requested) and removed 14 (14 requested) atoms. Cycle 48: After refmac, R = 0.1958 (Rfree = 0.000) for 5134 atoms. Found 0 (28 requested) and removed 14 (14 requested) atoms. Cycle 49: After refmac, R = 0.1987 (Rfree = 0.000) for 5118 atoms. Found 0 (28 requested) and removed 14 (14 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:57:50 GMT 2018 Job finished. TimeTaking 58.63 Used memory is bytes: 12048080