null Mon 24 Dec 00:34:45 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2iiu-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2iiu-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2iiu-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2iiu-3.6-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2iiu-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2iiu-3.6-parrot-mrncs ############### 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 00:34:49 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/mrncs/ArpWArp/wArpResults/WorkingDir/2iiu-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2iiu-3.6-parrot-mrncs/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 527 and 0 Target number of residues in the AU: 527 Target solvent content: 0.6262 Checking the provided sequence file Detected sequence length: 227 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 3 Adjusted target number of residues: 681 Adjusted target solvent content: 0.52 Input MTZ file: 2iiu-3.6-parrot-mrncs.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: 155 Cell parameters: 99.900 99.900 397.311 90.000 90.000 120.000 Input sequence file: 2iiu-3.6-parrot-mrncs.fasta_lf Building free atoms model in initial map for 5448 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: 132.437 3.600 Wilson plot Bfac: 64.45 9174 reflections ( 98.96 % complete ) and 0 restraints for refining 6008 atoms. Observations/parameters ratio is 0.38 ------------------------------------------------------ Starting model: R = 0.3543 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3399 (Rfree = 0.000) for 6008 atoms. Found 35 (38 requested) and removed 49 (19 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.34 3.25 Search for helices and strands: 0 residues in 0 chains, 6112 seeds are put forward NCS extension: 0 residues added, 6112 seeds are put forward Round 1: 151 peptides, 33 chains. Longest chain 8 peptides. Score 0.223 Round 2: 228 peptides, 44 chains. Longest chain 12 peptides. Score 0.302 Round 3: 243 peptides, 48 chains. Longest chain 12 peptides. Score 0.297 Round 4: 279 peptides, 52 chains. Longest chain 15 peptides. Score 0.341 Round 5: 293 peptides, 54 chains. Longest chain 13 peptides. Score 0.353 Taking the results from Round 5 Chains 54, Residues 239, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9174 reflections ( 98.96 % complete ) and 11696 restraints for refining 4936 atoms. 10794 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3146 (Rfree = 0.000) for 4936 atoms. Found 31 (31 requested) and removed 47 (15 requested) atoms. Cycle 2: After refmac, R = 0.3030 (Rfree = 0.000) for 4827 atoms. Found 31 (31 requested) and removed 41 (15 requested) atoms. Cycle 3: After refmac, R = 0.2807 (Rfree = 0.000) for 4765 atoms. Found 28 (30 requested) and removed 36 (15 requested) atoms. Cycle 4: After refmac, R = 0.2735 (Rfree = 0.000) for 4730 atoms. Found 30 (30 requested) and removed 30 (15 requested) atoms. Cycle 5: After refmac, R = 0.2857 (Rfree = 0.000) for 4708 atoms. Found 30 (30 requested) and removed 28 (15 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.36 3.27 Search for helices and strands: 0 residues in 0 chains, 4933 seeds are put forward NCS extension: 14 residues added (3 deleted due to clashes), 4947 seeds are put forward Round 1: 245 peptides, 49 chains. Longest chain 9 peptides. Score 0.291 Round 2: 268 peptides, 46 chains. Longest chain 14 peptides. Score 0.374 Round 3: 303 peptides, 50 chains. Longest chain 13 peptides. Score 0.412 Round 4: 291 peptides, 47 chains. Longest chain 14 peptides. Score 0.414 Round 5: 316 peptides, 55 chains. Longest chain 12 peptides. Score 0.393 Taking the results from Round 4 Chains 47, Residues 244, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 9174 reflections ( 98.96 % complete ) and 10876 restraints for refining 4712 atoms. 9934 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2811 (Rfree = 0.000) for 4712 atoms. Found 30 (30 requested) and removed 48 (15 requested) atoms. Cycle 7: After refmac, R = 0.2525 (Rfree = 0.000) for 4643 atoms. Found 30 (30 requested) and removed 35 (15 requested) atoms. Cycle 8: After refmac, R = 0.2497 (Rfree = 0.000) for 4614 atoms. Found 29 (29 requested) and removed 30 (14 requested) atoms. Cycle 9: After refmac, R = 0.2429 (Rfree = 0.000) for 4596 atoms. Found 29 (29 requested) and removed 31 (14 requested) atoms. Cycle 10: After refmac, R = 0.2330 (Rfree = 0.000) for 4582 atoms. Found 22 (29 requested) and removed 28 (14 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.26 3.17 Search for helices and strands: 0 residues in 0 chains, 4841 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 4852 seeds are put forward Round 1: 258 peptides, 54 chains. Longest chain 9 peptides. Score 0.272 Round 2: 297 peptides, 53 chains. Longest chain 15 peptides. Score 0.371 Round 3: 292 peptides, 50 chains. Longest chain 11 peptides. Score 0.388 Round 4: 302 peptides, 49 chains. Longest chain 12 peptides. Score 0.419 Round 5: 314 peptides, 52 chains. Longest chain 15 peptides. Score 0.416 Taking the results from Round 4 Chains 49, Residues 253, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 9174 reflections ( 98.96 % complete ) and 11215 restraints for refining 4902 atoms. 10231 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2612 (Rfree = 0.000) for 4902 atoms. Found 31 (31 requested) and removed 34 (15 requested) atoms. Cycle 12: After refmac, R = 0.2463 (Rfree = 0.000) for 4854 atoms. Found 28 (31 requested) and removed 36 (15 requested) atoms. Cycle 13: After refmac, R = 0.2097 (Rfree = 0.000) for 4823 atoms. Found 10 (31 requested) and removed 28 (15 requested) atoms. Cycle 14: After refmac, R = 0.1993 (Rfree = 0.000) for 4783 atoms. Found 7 (30 requested) and removed 18 (15 requested) atoms. Cycle 15: After refmac, R = 0.2003 (Rfree = 0.000) for 4768 atoms. Found 10 (30 requested) and removed 16 (15 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.29 3.20 Search for helices and strands: 0 residues in 0 chains, 4926 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 4937 seeds are put forward Round 1: 283 peptides, 57 chains. Longest chain 9 peptides. Score 0.302 Round 2: 295 peptides, 49 chains. Longest chain 18 peptides. Score 0.404 Round 3: 299 peptides, 51 chains. Longest chain 12 peptides. Score 0.394 Round 4: 312 peptides, 51 chains. Longest chain 12 peptides. Score 0.421 Round 5: 316 peptides, 51 chains. Longest chain 18 peptides. Score 0.429 Taking the results from Round 5 Chains 51, Residues 265, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9174 reflections ( 98.96 % complete ) and 11312 restraints for refining 4939 atoms. 10303 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2667 (Rfree = 0.000) for 4939 atoms. Found 31 (31 requested) and removed 37 (15 requested) atoms. Cycle 17: After refmac, R = 0.2661 (Rfree = 0.000) for 4897 atoms. Found 31 (31 requested) and removed 36 (15 requested) atoms. Cycle 18: After refmac, R = 0.2564 (Rfree = 0.000) for 4874 atoms. Found 31 (31 requested) and removed 31 (15 requested) atoms. Cycle 19: After refmac, R = 0.2565 (Rfree = 0.000) for 4854 atoms. Found 31 (31 requested) and removed 27 (15 requested) atoms. Cycle 20: After refmac, R = 0.2572 (Rfree = 0.000) for 4831 atoms. Found 29 (31 requested) and removed 25 (15 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.28 3.19 Search for helices and strands: 0 residues in 0 chains, 5050 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 5063 seeds are put forward Round 1: 250 peptides, 55 chains. Longest chain 8 peptides. Score 0.243 Round 2: 281 peptides, 53 chains. Longest chain 10 peptides. Score 0.336 Round 3: 301 peptides, 53 chains. Longest chain 12 peptides. Score 0.380 Round 4: 309 peptides, 51 chains. Longest chain 17 peptides. Score 0.415 Round 5: 298 peptides, 47 chains. Longest chain 18 peptides. Score 0.428 Taking the results from Round 5 Chains 47, Residues 251, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 9174 reflections ( 98.96 % complete ) and 11290 restraints for refining 4937 atoms. 10306 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2731 (Rfree = 0.000) for 4937 atoms. Found 31 (31 requested) and removed 36 (15 requested) atoms. Cycle 22: After refmac, R = 0.2542 (Rfree = 0.000) for 4904 atoms. Found 31 (31 requested) and removed 29 (15 requested) atoms. Cycle 23: After refmac, R = 0.2398 (Rfree = 0.000) for 4885 atoms. Found 31 (31 requested) and removed 32 (15 requested) atoms. Cycle 24: After refmac, R = 0.2000 (Rfree = 0.000) for 4866 atoms. Found 9 (31 requested) and removed 23 (15 requested) atoms. Cycle 25: After refmac, R = 0.1896 (Rfree = 0.000) for 4843 atoms. Found 6 (31 requested) and removed 25 (15 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.25 3.16 Search for helices and strands: 0 residues in 0 chains, 5002 seeds are put forward NCS extension: 26 residues added (2 deleted due to clashes), 5028 seeds are put forward Round 1: 230 peptides, 48 chains. Longest chain 10 peptides. Score 0.265 Round 2: 275 peptides, 50 chains. Longest chain 12 peptides. Score 0.351 Round 3: 279 peptides, 49 chains. Longest chain 13 peptides. Score 0.369 Round 4: 277 peptides, 48 chains. Longest chain 13 peptides. Score 0.374 Round 5: 297 peptides, 52 chains. Longest chain 11 peptides. Score 0.380 Taking the results from Round 5 Chains 52, Residues 245, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9174 reflections ( 98.96 % complete ) and 11183 restraints for refining 4937 atoms. 10255 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2618 (Rfree = 0.000) for 4937 atoms. Found 31 (31 requested) and removed 41 (15 requested) atoms. Cycle 27: After refmac, R = 0.2520 (Rfree = 0.000) for 4900 atoms. Found 31 (31 requested) and removed 38 (15 requested) atoms. Cycle 28: After refmac, R = 0.2648 (Rfree = 0.000) for 4877 atoms. Found 31 (31 requested) and removed 28 (15 requested) atoms. Cycle 29: After refmac, R = 0.2476 (Rfree = 0.000) for 4865 atoms. Found 31 (31 requested) and removed 26 (15 requested) atoms. Cycle 30: After refmac, R = 0.2517 (Rfree = 0.000) for 4862 atoms. Found 31 (31 requested) and removed 25 (15 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.28 3.19 Search for helices and strands: 0 residues in 0 chains, 5069 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 5083 seeds are put forward Round 1: 212 peptides, 44 chains. Longest chain 9 peptides. Score 0.262 Round 2: 248 peptides, 45 chains. Longest chain 13 peptides. Score 0.339 Round 3: 267 peptides, 45 chains. Longest chain 10 peptides. Score 0.381 Round 4: 279 peptides, 45 chains. Longest chain 14 peptides. Score 0.407 Round 5: 269 peptides, 45 chains. Longest chain 13 peptides. Score 0.386 Taking the results from Round 4 Chains 45, Residues 234, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9174 reflections ( 98.96 % complete ) and 11241 restraints for refining 4938 atoms. 10350 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2567 (Rfree = 0.000) for 4938 atoms. Found 31 (31 requested) and removed 27 (15 requested) atoms. Cycle 32: After refmac, R = 0.2487 (Rfree = 0.000) for 4911 atoms. Found 31 (31 requested) and removed 22 (15 requested) atoms. Cycle 33: After refmac, R = 0.2332 (Rfree = 0.000) for 4897 atoms. Found 27 (31 requested) and removed 26 (15 requested) atoms. Cycle 34: After refmac, R = 0.2461 (Rfree = 0.000) for 4886 atoms. Found 31 (31 requested) and removed 22 (15 requested) atoms. Cycle 35: After refmac, R = 0.2295 (Rfree = 0.000) for 4890 atoms. Found 31 (31 requested) and removed 23 (15 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.33 3.24 Search for helices and strands: 0 residues in 0 chains, 5090 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 5109 seeds are put forward Round 1: 198 peptides, 44 chains. Longest chain 8 peptides. Score 0.226 Round 2: 247 peptides, 47 chains. Longest chain 11 peptides. Score 0.316 Round 3: 253 peptides, 45 chains. Longest chain 11 peptides. Score 0.350 Round 4: 255 peptides, 42 chains. Longest chain 14 peptides. Score 0.384 Round 5: 259 peptides, 42 chains. Longest chain 16 peptides. Score 0.393 Taking the results from Round 5 Chains 42, Residues 217, Estimated correctness of the model 0.0 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 9174 reflections ( 98.96 % complete ) and 11171 restraints for refining 4939 atoms. 10281 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2586 (Rfree = 0.000) for 4939 atoms. Found 31 (31 requested) and removed 27 (15 requested) atoms. Cycle 37: After refmac, R = 0.2430 (Rfree = 0.000) for 4921 atoms. Found 31 (31 requested) and removed 23 (15 requested) atoms. Cycle 38: After refmac, R = 0.2474 (Rfree = 0.000) for 4915 atoms. Found 31 (31 requested) and removed 22 (15 requested) atoms. Cycle 39: After refmac, R = 0.2436 (Rfree = 0.000) for 4909 atoms. Found 31 (31 requested) and removed 26 (15 requested) atoms. Cycle 40: After refmac, R = 0.2027 (Rfree = 0.000) for 4901 atoms. Found 23 (31 requested) and removed 19 (15 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.28 3.19 Search for helices and strands: 0 residues in 0 chains, 5094 seeds are put forward NCS extension: 15 residues added (3 deleted due to clashes), 5109 seeds are put forward Round 1: 217 peptides, 46 chains. Longest chain 10 peptides. Score 0.254 Round 2: 256 peptides, 49 chains. Longest chain 13 peptides. Score 0.317 Round 3: 256 peptides, 47 chains. Longest chain 14 peptides. Score 0.337 Round 4: 245 peptides, 42 chains. Longest chain 14 peptides. Score 0.361 Round 5: 265 peptides, 46 chains. Longest chain 15 peptides. Score 0.367 Taking the results from Round 5 Chains 46, Residues 219, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9174 reflections ( 98.96 % complete ) and 11320 restraints for refining 4939 atoms. 10490 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2481 (Rfree = 0.000) for 4939 atoms. Found 31 (31 requested) and removed 31 (15 requested) atoms. Cycle 42: After refmac, R = 0.2310 (Rfree = 0.000) for 4918 atoms. Found 31 (31 requested) and removed 27 (15 requested) atoms. Cycle 43: After refmac, R = 0.2370 (Rfree = 0.000) for 4912 atoms. Found 31 (31 requested) and removed 29 (15 requested) atoms. Cycle 44: After refmac, R = 0.2313 (Rfree = 0.000) for 4896 atoms. Found 31 (31 requested) and removed 26 (15 requested) atoms. Cycle 45: After refmac, R = 0.2244 (Rfree = 0.000) for 4896 atoms. Found 31 (31 requested) and removed 24 (15 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.29 3.20 Search for helices and strands: 0 residues in 0 chains, 5088 seeds are put forward NCS extension: 27 residues added (1 deleted due to clashes), 5115 seeds are put forward Round 1: 189 peptides, 41 chains. Longest chain 11 peptides. Score 0.236 Round 2: 196 peptides, 35 chains. Longest chain 13 peptides. Score 0.319 Round 3: 197 peptides, 36 chains. Longest chain 13 peptides. Score 0.310 Round 4: 194 peptides, 34 chains. Longest chain 15 peptides. Score 0.324 Round 5: 194 peptides, 36 chains. Longest chain 15 peptides. Score 0.303 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 34, Residues 160, 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 2iiu-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 9174 reflections ( 98.96 % complete ) and 11587 restraints for refining 4939 atoms. 10981 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2548 (Rfree = 0.000) for 4939 atoms. Found 0 (31 requested) and removed 15 (15 requested) atoms. Cycle 47: After refmac, R = 0.2550 (Rfree = 0.000) for 4901 atoms. Found 0 (31 requested) and removed 15 (15 requested) atoms. Cycle 48: After refmac, R = 0.2628 (Rfree = 0.000) for 4870 atoms. Found 0 (31 requested) and removed 15 (15 requested) atoms. Cycle 49: After refmac, R = 0.2531 (Rfree = 0.000) for 4849 atoms. Found 0 (31 requested) and removed 15 (15 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:36:50 GMT 2018 Job finished. TimeTaking 62.08 Used memory is bytes: 18775832