null Mon 24 Dec 00:22:26 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-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2iiu-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2iiu-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2iiu-4.0-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-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2iiu-4.0-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 00:22:31 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-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2iiu-4.0-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 487 and 0 Target number of residues in the AU: 487 Target solvent content: 0.6546 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-4.0-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-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 5448 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: 132.437 4.000 Wilson plot Bfac: 80.80 6724 reflections ( 98.74 % complete ) and 0 restraints for refining 6031 atoms. Observations/parameters ratio is 0.28 ------------------------------------------------------ Starting model: R = 0.3739 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2929 (Rfree = 0.000) for 6031 atoms. Found 14 (28 requested) and removed 64 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.72 3.62 Search for helices and strands: 0 residues in 0 chains, 6098 seeds are put forward NCS extension: 0 residues added, 6098 seeds are put forward Round 1: 162 peptides, 35 chains. Longest chain 10 peptides. Score 0.231 Round 2: 196 peptides, 39 chains. Longest chain 10 peptides. Score 0.275 Round 3: 200 peptides, 37 chains. Longest chain 10 peptides. Score 0.307 Round 4: 204 peptides, 33 chains. Longest chain 13 peptides. Score 0.359 Round 5: 191 peptides, 34 chains. Longest chain 12 peptides. Score 0.317 Taking the results from Round 4 Chains 35, Residues 171, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 6724 reflections ( 98.74 % complete ) and 12322 restraints for refining 4919 atoms. 11633 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2984 (Rfree = 0.000) for 4919 atoms. Found 23 (23 requested) and removed 13 (11 requested) atoms. Cycle 2: After refmac, R = 0.2793 (Rfree = 0.000) for 4906 atoms. Found 10 (23 requested) and removed 16 (11 requested) atoms. Cycle 3: After refmac, R = 0.2702 (Rfree = 0.000) for 4886 atoms. Found 10 (23 requested) and removed 14 (11 requested) atoms. Cycle 4: After refmac, R = 0.2883 (Rfree = 0.000) for 4872 atoms. Found 11 (23 requested) and removed 12 (11 requested) atoms. Cycle 5: After refmac, R = 0.2696 (Rfree = 0.000) for 4852 atoms. Found 10 (23 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.66 3.56 Search for helices and strands: 0 residues in 0 chains, 5015 seeds are put forward NCS extension: 11 residues added (2 deleted due to clashes), 5026 seeds are put forward Round 1: 189 peptides, 40 chains. Longest chain 8 peptides. Score 0.247 Round 2: 220 peptides, 40 chains. Longest chain 11 peptides. Score 0.324 Round 3: 247 peptides, 41 chains. Longest chain 16 peptides. Score 0.376 Round 4: 246 peptides, 42 chains. Longest chain 12 peptides. Score 0.364 Round 5: 241 peptides, 41 chains. Longest chain 11 peptides. Score 0.362 Taking the results from Round 3 Chains 41, Residues 206, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6724 reflections ( 98.74 % complete ) and 11306 restraints for refining 4735 atoms. 10523 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2784 (Rfree = 0.000) for 4735 atoms. Found 22 (22 requested) and removed 22 (11 requested) atoms. Cycle 7: After refmac, R = 0.2613 (Rfree = 0.000) for 4716 atoms. Found 15 (22 requested) and removed 17 (11 requested) atoms. Cycle 8: After refmac, R = 0.2764 (Rfree = 0.000) for 4703 atoms. Found 9 (22 requested) and removed 15 (11 requested) atoms. Cycle 9: After refmac, R = 0.2683 (Rfree = 0.000) for 4677 atoms. Found 4 (22 requested) and removed 14 (11 requested) atoms. Cycle 10: After refmac, R = 0.2632 (Rfree = 0.000) for 4665 atoms. Found 0 (22 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.67 3.57 Search for helices and strands: 0 residues in 0 chains, 4839 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 4860 seeds are put forward Round 1: 205 peptides, 42 chains. Longest chain 11 peptides. Score 0.266 Round 2: 252 peptides, 47 chains. Longest chain 10 peptides. Score 0.328 Round 3: 256 peptides, 43 chains. Longest chain 11 peptides. Score 0.376 Round 4: 261 peptides, 44 chains. Longest chain 13 peptides. Score 0.378 Round 5: 235 peptides, 39 chains. Longest chain 12 peptides. Score 0.369 Taking the results from Round 4 Chains 44, Residues 217, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6724 reflections ( 98.74 % complete ) and 11510 restraints for refining 4779 atoms. 10686 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2801 (Rfree = 0.000) for 4779 atoms. Found 16 (22 requested) and removed 37 (11 requested) atoms. Cycle 12: After refmac, R = 0.2656 (Rfree = 0.000) for 4742 atoms. Found 7 (22 requested) and removed 14 (11 requested) atoms. Cycle 13: After refmac, R = 0.2647 (Rfree = 0.000) for 4727 atoms. Found 4 (22 requested) and removed 15 (11 requested) atoms. Cycle 14: After refmac, R = 0.2583 (Rfree = 0.000) for 4714 atoms. Found 4 (22 requested) and removed 12 (11 requested) atoms. Cycle 15: After refmac, R = 0.2555 (Rfree = 0.000) for 4704 atoms. Found 4 (22 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.69 3.59 Search for helices and strands: 0 residues in 0 chains, 4873 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 4885 seeds are put forward Round 1: 209 peptides, 42 chains. Longest chain 9 peptides. Score 0.276 Round 2: 247 peptides, 44 chains. Longest chain 13 peptides. Score 0.346 Round 3: 244 peptides, 41 chains. Longest chain 10 peptides. Score 0.369 Round 4: 246 peptides, 44 chains. Longest chain 14 peptides. Score 0.344 Round 5: 248 peptides, 40 chains. Longest chain 12 peptides. Score 0.388 Taking the results from Round 5 Chains 40, Residues 208, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6724 reflections ( 98.74 % complete ) and 12157 restraints for refining 4917 atoms. 11365 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2612 (Rfree = 0.000) for 4917 atoms. Found 13 (23 requested) and removed 33 (11 requested) atoms. Cycle 17: After refmac, R = 0.2456 (Rfree = 0.000) for 4872 atoms. Found 5 (23 requested) and removed 18 (11 requested) atoms. Cycle 18: After refmac, R = 0.2529 (Rfree = 0.000) for 4855 atoms. Found 10 (23 requested) and removed 17 (11 requested) atoms. Cycle 19: After refmac, R = 0.2393 (Rfree = 0.000) for 4839 atoms. Found 4 (23 requested) and removed 12 (11 requested) atoms. Cycle 20: After refmac, R = 0.2363 (Rfree = 0.000) for 4829 atoms. Found 1 (22 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.67 3.57 Search for helices and strands: 0 residues in 0 chains, 4994 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 5007 seeds are put forward Round 1: 174 peptides, 37 chains. Longest chain 7 peptides. Score 0.240 Round 2: 212 peptides, 38 chains. Longest chain 14 peptides. Score 0.325 Round 3: 215 peptides, 35 chains. Longest chain 15 peptides. Score 0.364 Round 4: 232 peptides, 35 chains. Longest chain 15 peptides. Score 0.402 Round 5: 253 peptides, 41 chains. Longest chain 15 peptides. Score 0.389 Taking the results from Round 4 Chains 35, Residues 197, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6724 reflections ( 98.74 % complete ) and 11959 restraints for refining 4920 atoms. 11206 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2741 (Rfree = 0.000) for 4920 atoms. Found 18 (23 requested) and removed 22 (11 requested) atoms. Cycle 22: After refmac, R = 0.2586 (Rfree = 0.000) for 4911 atoms. Found 3 (23 requested) and removed 12 (11 requested) atoms. Cycle 23: After refmac, R = 0.2530 (Rfree = 0.000) for 4900 atoms. Found 2 (23 requested) and removed 11 (11 requested) atoms. Cycle 24: After refmac, R = 0.2502 (Rfree = 0.000) for 4889 atoms. Found 1 (23 requested) and removed 11 (11 requested) atoms. Cycle 25: After refmac, R = 0.2470 (Rfree = 0.000) for 4878 atoms. Found 2 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.70 3.60 Search for helices and strands: 0 residues in 0 chains, 5046 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 5061 seeds are put forward Round 1: 199 peptides, 39 chains. Longest chain 16 peptides. Score 0.283 Round 2: 216 peptides, 37 chains. Longest chain 13 peptides. Score 0.345 Round 3: 236 peptides, 41 chains. Longest chain 15 peptides. Score 0.351 Round 4: 239 peptides, 39 chains. Longest chain 17 peptides. Score 0.378 Round 5: 231 peptides, 39 chains. Longest chain 15 peptides. Score 0.360 Taking the results from Round 4 Chains 39, Residues 200, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6724 reflections ( 98.74 % complete ) and 12025 restraints for refining 4919 atoms. 11264 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2834 (Rfree = 0.000) for 4919 atoms. Found 23 (23 requested) and removed 17 (11 requested) atoms. Cycle 27: After refmac, R = 0.2640 (Rfree = 0.000) for 4920 atoms. Found 10 (23 requested) and removed 12 (11 requested) atoms. Cycle 28: After refmac, R = 0.2588 (Rfree = 0.000) for 4918 atoms. Found 3 (23 requested) and removed 11 (11 requested) atoms. Cycle 29: After refmac, R = 0.2546 (Rfree = 0.000) for 4909 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 30: After refmac, R = 0.2528 (Rfree = 0.000) for 4898 atoms. Found 3 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.69 3.59 Search for helices and strands: 0 residues in 0 chains, 5044 seeds are put forward NCS extension: 29 residues added (0 deleted due to clashes), 5073 seeds are put forward Round 1: 194 peptides, 42 chains. Longest chain 8 peptides. Score 0.238 Round 2: 209 peptides, 36 chains. Longest chain 11 peptides. Score 0.339 Round 3: 197 peptides, 37 chains. Longest chain 11 peptides. Score 0.300 Round 4: 209 peptides, 35 chains. Longest chain 13 peptides. Score 0.350 Round 5: 195 peptides, 34 chains. Longest chain 14 peptides. Score 0.327 Taking the results from Round 4 Chains 35, Residues 174, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6724 reflections ( 98.74 % complete ) and 12280 restraints for refining 4919 atoms. 11619 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2767 (Rfree = 0.000) for 4919 atoms. Found 23 (23 requested) and removed 11 (11 requested) atoms. Cycle 32: After refmac, R = 0.2621 (Rfree = 0.000) for 4928 atoms. Found 5 (23 requested) and removed 11 (11 requested) atoms. Cycle 33: After refmac, R = 0.2600 (Rfree = 0.000) for 4920 atoms. Found 6 (23 requested) and removed 11 (11 requested) atoms. Cycle 34: After refmac, R = 0.2572 (Rfree = 0.000) for 4913 atoms. Found 2 (23 requested) and removed 11 (11 requested) atoms. Cycle 35: After refmac, R = 0.2546 (Rfree = 0.000) for 4904 atoms. Found 2 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.74 3.64 Search for helices and strands: 0 residues in 0 chains, 5049 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 5067 seeds are put forward Round 1: 179 peptides, 37 chains. Longest chain 8 peptides. Score 0.254 Round 2: 210 peptides, 40 chains. Longest chain 11 peptides. Score 0.300 Round 3: 212 peptides, 37 chains. Longest chain 13 peptides. Score 0.336 Round 4: 215 peptides, 40 chains. Longest chain 12 peptides. Score 0.312 Round 5: 219 peptides, 38 chains. Longest chain 14 peptides. Score 0.342 Taking the results from Round 5 Chains 38, Residues 181, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6724 reflections ( 98.74 % complete ) and 12193 restraints for refining 4917 atoms. 11507 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2807 (Rfree = 0.000) for 4917 atoms. Found 23 (23 requested) and removed 17 (11 requested) atoms. Cycle 37: After refmac, R = 0.2726 (Rfree = 0.000) for 4923 atoms. Found 6 (23 requested) and removed 11 (11 requested) atoms. Cycle 38: After refmac, R = 0.2699 (Rfree = 0.000) for 4916 atoms. Found 9 (23 requested) and removed 12 (11 requested) atoms. Cycle 39: After refmac, R = 0.2600 (Rfree = 0.000) for 4910 atoms. Found 2 (23 requested) and removed 11 (11 requested) atoms. Cycle 40: After refmac, R = 0.2586 (Rfree = 0.000) for 4898 atoms. Found 1 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.72 3.62 Search for helices and strands: 0 residues in 0 chains, 5049 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 5070 seeds are put forward Round 1: 157 peptides, 32 chains. Longest chain 9 peptides. Score 0.252 Round 2: 189 peptides, 32 chains. Longest chain 14 peptides. Score 0.334 Round 3: 195 peptides, 33 chains. Longest chain 12 peptides. Score 0.338 Round 4: 194 peptides, 31 chains. Longest chain 12 peptides. Score 0.357 Round 5: 196 peptides, 29 chains. Longest chain 14 peptides. Score 0.382 Taking the results from Round 5 Chains 29, Residues 167, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6724 reflections ( 98.74 % complete ) and 12116 restraints for refining 4919 atoms. 11477 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2866 (Rfree = 0.000) for 4919 atoms. Found 23 (23 requested) and removed 12 (11 requested) atoms. Cycle 42: After refmac, R = 0.2732 (Rfree = 0.000) for 4930 atoms. Found 7 (23 requested) and removed 11 (11 requested) atoms. Cycle 43: After refmac, R = 0.2651 (Rfree = 0.000) for 4926 atoms. Found 2 (23 requested) and removed 11 (11 requested) atoms. Cycle 44: After refmac, R = 0.2634 (Rfree = 0.000) for 4917 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 45: After refmac, R = 0.2601 (Rfree = 0.000) for 4906 atoms. Found 3 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.73 3.63 Search for helices and strands: 0 residues in 0 chains, 5070 seeds are put forward NCS extension: 12 residues added (3 deleted due to clashes), 5082 seeds are put forward Round 1: 166 peptides, 34 chains. Longest chain 11 peptides. Score 0.253 Round 2: 186 peptides, 38 chains. Longest chain 9 peptides. Score 0.261 Round 3: 194 peptides, 35 chains. Longest chain 12 peptides. Score 0.314 Round 4: 186 peptides, 34 chains. Longest chain 8 peptides. Score 0.305 Round 5: 188 peptides, 33 chains. Longest chain 14 peptides. Score 0.321 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 33, Residues 155, 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-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6724 reflections ( 98.74 % complete ) and 12351 restraints for refining 4920 atoms. 11764 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2899 (Rfree = 0.000) for 4920 atoms. Found 0 (23 requested) and removed 10 (11 requested) atoms. Cycle 47: After refmac, R = 0.2846 (Rfree = 0.000) for 4909 atoms. Found 0 (23 requested) and removed 3 (11 requested) atoms. Cycle 48: After refmac, R = 0.2794 (Rfree = 0.000) for 4906 atoms. Found 0 (23 requested) and removed 2 (11 requested) atoms. Cycle 49: After refmac, R = 0.2750 (Rfree = 0.000) for 4903 atoms. Found 0 (23 requested) and removed 1 (11 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:11:48 GMT 2018 Job finished. TimeTaking 49.36 Used memory is bytes: 22039656