null Mon 24 Dec 00:32:30 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 2i5i-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2i5i-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2i5i-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2i5i-3.2-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/2i5i-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2i5i-3.2-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 00:32:35 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/2i5i-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2i5i-3.2-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 382 and 0 Target number of residues in the AU: 382 Target solvent content: 0.6324 Checking the provided sequence file Detected sequence length: 263 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 526 Adjusted target solvent content: 0.49 Input MTZ file: 2i5i-3.2-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: 146 Cell parameters: 130.530 130.530 85.760 90.000 90.000 120.000 Input sequence file: 2i5i-3.2-parrot-mrncs.fasta_lf Building free atoms model in initial map for 4208 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: 29.446 3.200 Wilson plot Bfac: 67.70 8937 reflections ( 99.43 % complete ) and 0 restraints for refining 4665 atoms. Observations/parameters ratio is 0.48 ------------------------------------------------------ Starting model: R = 0.3373 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2537 (Rfree = 0.000) for 4665 atoms. Found 12 (41 requested) and removed 53 (20 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.24 3.28 Search for helices and strands: 0 residues in 0 chains, 4693 seeds are put forward NCS extension: 0 residues added, 4693 seeds are put forward Round 1: 181 peptides, 42 chains. Longest chain 6 peptides. Score 0.212 Round 2: 223 peptides, 45 chains. Longest chain 7 peptides. Score 0.307 Round 3: 237 peptides, 42 chains. Longest chain 14 peptides. Score 0.387 Round 4: 250 peptides, 43 chains. Longest chain 18 peptides. Score 0.412 Round 5: 257 peptides, 44 chains. Longest chain 14 peptides. Score 0.419 Taking the results from Round 5 Chains 44, Residues 213, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 8937 reflections ( 99.43 % complete ) and 8640 restraints for refining 3842 atoms. 7801 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2451 (Rfree = 0.000) for 3842 atoms. Found 33 (34 requested) and removed 30 (17 requested) atoms. Cycle 2: After refmac, R = 0.2298 (Rfree = 0.000) for 3816 atoms. Found 15 (34 requested) and removed 22 (17 requested) atoms. Cycle 3: After refmac, R = 0.2219 (Rfree = 0.000) for 3799 atoms. Found 5 (34 requested) and removed 18 (17 requested) atoms. Cycle 4: After refmac, R = 0.2177 (Rfree = 0.000) for 3782 atoms. Found 1 (33 requested) and removed 18 (16 requested) atoms. Cycle 5: After refmac, R = 0.2167 (Rfree = 0.000) for 3760 atoms. Found 6 (33 requested) and removed 16 (16 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.22 3.26 Search for helices and strands: 0 residues in 0 chains, 3844 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 3857 seeds are put forward Round 1: 222 peptides, 45 chains. Longest chain 11 peptides. Score 0.304 Round 2: 252 peptides, 44 chains. Longest chain 18 peptides. Score 0.405 Round 3: 260 peptides, 42 chains. Longest chain 20 peptides. Score 0.451 Round 4: 254 peptides, 44 chains. Longest chain 10 peptides. Score 0.411 Round 5: 258 peptides, 42 chains. Longest chain 13 peptides. Score 0.446 Taking the results from Round 3 Chains 43, Residues 218, Estimated correctness of the model 0.0 % 1 chains (17 residues) have been docked in sequence ------------------------------------------------------ 8937 reflections ( 99.43 % complete ) and 8482 restraints for refining 3783 atoms. 7589 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2373 (Rfree = 0.000) for 3783 atoms. Found 25 (33 requested) and removed 24 (16 requested) atoms. Cycle 7: After refmac, R = 0.2414 (Rfree = 0.000) for 3767 atoms. Found 22 (33 requested) and removed 19 (16 requested) atoms. Cycle 8: After refmac, R = 0.2055 (Rfree = 0.000) for 3753 atoms. Found 8 (33 requested) and removed 18 (16 requested) atoms. Cycle 9: After refmac, R = 0.2141 (Rfree = 0.000) for 3723 atoms. Found 18 (33 requested) and removed 18 (16 requested) atoms. Cycle 10: After refmac, R = 0.2113 (Rfree = 0.000) for 3713 atoms. Found 16 (33 requested) and removed 24 (16 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.19 3.23 Search for helices and strands: 0 residues in 0 chains, 3814 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 3831 seeds are put forward Round 1: 217 peptides, 41 chains. Longest chain 10 peptides. Score 0.341 Round 2: 242 peptides, 38 chains. Longest chain 16 peptides. Score 0.449 Round 3: 243 peptides, 38 chains. Longest chain 18 peptides. Score 0.452 Round 4: 248 peptides, 38 chains. Longest chain 23 peptides. Score 0.466 Round 5: 231 peptides, 37 chains. Longest chain 12 peptides. Score 0.431 Taking the results from Round 4 Chains 38, Residues 210, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8937 reflections ( 99.43 % complete ) and 8830 restraints for refining 3828 atoms. 8028 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2127 (Rfree = 0.000) for 3828 atoms. Found 21 (34 requested) and removed 27 (17 requested) atoms. Cycle 12: After refmac, R = 0.2430 (Rfree = 0.000) for 3811 atoms. Found 32 (34 requested) and removed 28 (17 requested) atoms. Cycle 13: After refmac, R = 0.1801 (Rfree = 0.000) for 3809 atoms. Found 11 (34 requested) and removed 25 (17 requested) atoms. Cycle 14: After refmac, R = 0.1815 (Rfree = 0.000) for 3785 atoms. Found 13 (34 requested) and removed 23 (17 requested) atoms. Cycle 15: After refmac, R = 0.1672 (Rfree = 0.000) for 3771 atoms. Found 6 (33 requested) and removed 18 (16 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.23 3.27 Search for helices and strands: 0 residues in 0 chains, 3878 seeds are put forward NCS extension: 33 residues added (1 deleted due to clashes), 3911 seeds are put forward Round 1: 212 peptides, 43 chains. Longest chain 9 peptides. Score 0.299 Round 2: 246 peptides, 44 chains. Longest chain 12 peptides. Score 0.388 Round 3: 238 peptides, 41 chains. Longest chain 10 peptides. Score 0.402 Round 4: 262 peptides, 41 chains. Longest chain 12 peptides. Score 0.468 Round 5: 268 peptides, 44 chains. Longest chain 14 peptides. Score 0.449 Taking the results from Round 4 Chains 41, Residues 221, Estimated correctness of the model 0.7 % 2 chains (11 residues) have been docked in sequence ------------------------------------------------------ 8937 reflections ( 99.43 % complete ) and 8547 restraints for refining 3842 atoms. 7669 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1991 (Rfree = 0.000) for 3842 atoms. Found 34 (34 requested) and removed 20 (17 requested) atoms. Cycle 17: After refmac, R = 0.1836 (Rfree = 0.000) for 3846 atoms. Found 15 (34 requested) and removed 22 (17 requested) atoms. Cycle 18: After refmac, R = 0.1746 (Rfree = 0.000) for 3833 atoms. Found 6 (34 requested) and removed 17 (17 requested) atoms. Cycle 19: After refmac, R = 0.1699 (Rfree = 0.000) for 3818 atoms. Found 7 (34 requested) and removed 17 (17 requested) atoms. Cycle 20: After refmac, R = 0.1642 (Rfree = 0.000) for 3807 atoms. Found 5 (34 requested) and removed 17 (17 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.24 3.28 Search for helices and strands: 0 residues in 0 chains, 3875 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 3889 seeds are put forward Round 1: 245 peptides, 48 chains. Longest chain 14 peptides. Score 0.336 Round 2: 262 peptides, 41 chains. Longest chain 16 peptides. Score 0.468 Round 3: 260 peptides, 40 chains. Longest chain 14 peptides. Score 0.474 Round 4: 271 peptides, 41 chains. Longest chain 19 peptides. Score 0.491 Round 5: 273 peptides, 42 chains. Longest chain 17 peptides. Score 0.485 Taking the results from Round 4 Chains 41, Residues 230, Estimated correctness of the model 8.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8937 reflections ( 99.43 % complete ) and 8522 restraints for refining 3842 atoms. 7643 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1887 (Rfree = 0.000) for 3842 atoms. Found 17 (34 requested) and removed 20 (17 requested) atoms. Cycle 22: After refmac, R = 0.1800 (Rfree = 0.000) for 3834 atoms. Found 8 (34 requested) and removed 19 (17 requested) atoms. Cycle 23: After refmac, R = 0.1751 (Rfree = 0.000) for 3819 atoms. Found 8 (34 requested) and removed 18 (17 requested) atoms. Cycle 24: After refmac, R = 0.1698 (Rfree = 0.000) for 3807 atoms. Found 6 (34 requested) and removed 17 (17 requested) atoms. Cycle 25: After refmac, R = 0.1667 (Rfree = 0.000) for 3794 atoms. Found 11 (34 requested) and removed 17 (17 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.22 3.26 Search for helices and strands: 0 residues in 0 chains, 3858 seeds are put forward NCS extension: 0 residues added, 3858 seeds are put forward Round 1: 223 peptides, 43 chains. Longest chain 9 peptides. Score 0.333 Round 2: 268 peptides, 43 chains. Longest chain 17 peptides. Score 0.461 Round 3: 253 peptides, 42 chains. Longest chain 13 peptides. Score 0.432 Round 4: 271 peptides, 45 chains. Longest chain 14 peptides. Score 0.446 Round 5: 279 peptides, 47 chains. Longest chain 13 peptides. Score 0.444 Taking the results from Round 2 Chains 43, Residues 225, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8937 reflections ( 99.43 % complete ) and 8646 restraints for refining 3842 atoms. 7789 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1891 (Rfree = 0.000) for 3842 atoms. Found 30 (34 requested) and removed 18 (17 requested) atoms. Cycle 27: After refmac, R = 0.1785 (Rfree = 0.000) for 3852 atoms. Found 9 (34 requested) and removed 18 (17 requested) atoms. Cycle 28: After refmac, R = 0.1747 (Rfree = 0.000) for 3840 atoms. Found 9 (34 requested) and removed 17 (17 requested) atoms. Cycle 29: After refmac, R = 0.1697 (Rfree = 0.000) for 3829 atoms. Found 7 (34 requested) and removed 17 (17 requested) atoms. Cycle 30: After refmac, R = 0.1654 (Rfree = 0.000) for 3817 atoms. Found 7 (34 requested) and removed 17 (17 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.23 3.27 Search for helices and strands: 0 residues in 0 chains, 3873 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 3898 seeds are put forward Round 1: 204 peptides, 41 chains. Longest chain 8 peptides. Score 0.301 Round 2: 239 peptides, 40 chains. Longest chain 14 peptides. Score 0.417 Round 3: 244 peptides, 40 chains. Longest chain 14 peptides. Score 0.431 Round 4: 250 peptides, 40 chains. Longest chain 14 peptides. Score 0.447 Round 5: 251 peptides, 39 chains. Longest chain 18 peptides. Score 0.462 Taking the results from Round 5 Chains 39, Residues 212, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8937 reflections ( 99.43 % complete ) and 8644 restraints for refining 3842 atoms. 7835 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1883 (Rfree = 0.000) for 3842 atoms. Found 32 (34 requested) and removed 18 (17 requested) atoms. Cycle 32: After refmac, R = 0.1786 (Rfree = 0.000) for 3852 atoms. Found 6 (34 requested) and removed 17 (17 requested) atoms. Cycle 33: After refmac, R = 0.1771 (Rfree = 0.000) for 3838 atoms. Found 12 (34 requested) and removed 17 (17 requested) atoms. Cycle 34: After refmac, R = 0.1715 (Rfree = 0.000) for 3832 atoms. Found 6 (34 requested) and removed 17 (17 requested) atoms. Cycle 35: After refmac, R = 0.1672 (Rfree = 0.000) for 3819 atoms. Found 4 (34 requested) and removed 17 (17 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.23 3.27 Search for helices and strands: 0 residues in 0 chains, 3883 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 3901 seeds are put forward Round 1: 209 peptides, 42 chains. Longest chain 10 peptides. Score 0.303 Round 2: 231 peptides, 40 chains. Longest chain 15 peptides. Score 0.395 Round 3: 240 peptides, 37 chains. Longest chain 14 peptides. Score 0.456 Round 4: 235 peptides, 36 chains. Longest chain 17 peptides. Score 0.454 Round 5: 226 peptides, 37 chains. Longest chain 15 peptides. Score 0.417 Taking the results from Round 3 Chains 37, Residues 203, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8937 reflections ( 99.43 % complete ) and 8627 restraints for refining 3842 atoms. 7852 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1860 (Rfree = 0.000) for 3842 atoms. Found 29 (34 requested) and removed 18 (17 requested) atoms. Cycle 37: After refmac, R = 0.1769 (Rfree = 0.000) for 3846 atoms. Found 17 (34 requested) and removed 17 (17 requested) atoms. Cycle 38: After refmac, R = 0.1745 (Rfree = 0.000) for 3843 atoms. Found 6 (34 requested) and removed 17 (17 requested) atoms. Cycle 39: After refmac, R = 0.1688 (Rfree = 0.000) for 3830 atoms. Found 5 (34 requested) and removed 17 (17 requested) atoms. Cycle 40: After refmac, R = 0.1673 (Rfree = 0.000) for 3814 atoms. Found 7 (34 requested) and removed 17 (17 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.25 3.29 Search for helices and strands: 0 residues in 0 chains, 3860 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 3872 seeds are put forward Round 1: 216 peptides, 42 chains. Longest chain 12 peptides. Score 0.325 Round 2: 233 peptides, 40 chains. Longest chain 15 peptides. Score 0.400 Round 3: 239 peptides, 40 chains. Longest chain 16 peptides. Score 0.417 Round 4: 223 peptides, 36 chains. Longest chain 17 peptides. Score 0.421 Round 5: 235 peptides, 38 chains. Longest chain 18 peptides. Score 0.430 Taking the results from Round 5 Chains 38, Residues 197, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8937 reflections ( 99.43 % complete ) and 8743 restraints for refining 3842 atoms. 7993 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1856 (Rfree = 0.000) for 3842 atoms. Found 33 (34 requested) and removed 18 (17 requested) atoms. Cycle 42: After refmac, R = 0.1755 (Rfree = 0.000) for 3854 atoms. Found 12 (34 requested) and removed 20 (17 requested) atoms. Cycle 43: After refmac, R = 0.1708 (Rfree = 0.000) for 3842 atoms. Found 8 (34 requested) and removed 17 (17 requested) atoms. Cycle 44: After refmac, R = 0.1666 (Rfree = 0.000) for 3829 atoms. Found 5 (34 requested) and removed 18 (17 requested) atoms. Cycle 45: After refmac, R = 0.1626 (Rfree = 0.000) for 3815 atoms. Found 7 (34 requested) and removed 18 (17 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.26 3.30 Search for helices and strands: 0 residues in 0 chains, 3877 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 3891 seeds are put forward Round 1: 197 peptides, 39 chains. Longest chain 8 peptides. Score 0.305 Round 2: 216 peptides, 41 chains. Longest chain 9 peptides. Score 0.338 Round 3: 202 peptides, 34 chains. Longest chain 11 peptides. Score 0.386 Round 4: 218 peptides, 37 chains. Longest chain 11 peptides. Score 0.395 Round 5: 207 peptides, 34 chains. Longest chain 11 peptides. Score 0.401 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 34, Residues 173, 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 2i5i-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8937 reflections ( 99.43 % complete ) and 8934 restraints for refining 3842 atoms. 8276 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1747 (Rfree = 0.000) for 3842 atoms. Found 0 (34 requested) and removed 17 (17 requested) atoms. Cycle 47: After refmac, R = 0.1725 (Rfree = 0.000) for 3821 atoms. Found 0 (34 requested) and removed 13 (17 requested) atoms. Cycle 48: After refmac, R = 0.1670 (Rfree = 0.000) for 3804 atoms. Found 0 (34 requested) and removed 6 (17 requested) atoms. Cycle 49: After refmac, R = 0.1650 (Rfree = 0.000) for 3796 atoms. Found 0 (34 requested) and removed 14 (17 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:17:47 GMT 2018 Job finished. TimeTaking 45.29 Used memory is bytes: 7005704