Sun 23 Dec 22:22:46 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2i5i-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2i5i-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2i5i-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2i5i-3.2-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/2i5i-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2i5i-3.2-parrot-hancs ############### 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 ============================================================ Sun 23 Dec 22:22:56 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/hancs/ArpWArp/wArpResults/WorkingDir/2i5i-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2i5i-3.2-parrot-hancs/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-hancs.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-hancs.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 4689 atoms. Observations/parameters ratio is 0.48 ------------------------------------------------------ Starting model: R = 0.3367 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2425 (Rfree = 0.000) for 4689 atoms. Found 20 (42 requested) and removed 48 (21 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.24 3.28 Search for helices and strands: 0 residues in 0 chains, 4724 seeds are put forward NCS extension: 0 residues added, 4724 seeds are put forward Round 1: 181 peptides, 40 chains. Longest chain 8 peptides. Score 0.239 Round 2: 267 peptides, 50 chains. Longest chain 12 peptides. Score 0.376 Round 3: 275 peptides, 50 chains. Longest chain 13 peptides. Score 0.398 Round 4: 287 peptides, 47 chains. Longest chain 20 peptides. Score 0.465 Round 5: 291 peptides, 50 chains. Longest chain 16 peptides. Score 0.442 Taking the results from Round 4 Chains 47, Residues 240, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8937 reflections ( 99.43 % complete ) and 8704 restraints for refining 3840 atoms. 7791 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2382 (Rfree = 0.000) for 3840 atoms. Found 30 (34 requested) and removed 29 (17 requested) atoms. Cycle 2: After refmac, R = 0.2246 (Rfree = 0.000) for 3820 atoms. Found 15 (34 requested) and removed 25 (17 requested) atoms. Cycle 3: After refmac, R = 0.2187 (Rfree = 0.000) for 3797 atoms. Found 14 (34 requested) and removed 18 (17 requested) atoms. Cycle 4: After refmac, R = 0.2232 (Rfree = 0.000) for 3784 atoms. Found 11 (34 requested) and removed 17 (17 requested) atoms. Cycle 5: After refmac, R = 0.2172 (Rfree = 0.000) for 3772 atoms. Found 11 (33 requested) and removed 16 (16 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.23 3.27 Search for helices and strands: 0 residues in 0 chains, 3892 seeds are put forward NCS extension: 28 residues added (1 deleted due to clashes), 3920 seeds are put forward Round 1: 235 peptides, 44 chains. Longest chain 12 peptides. Score 0.356 Round 2: 255 peptides, 42 chains. Longest chain 14 peptides. Score 0.437 Round 3: 250 peptides, 38 chains. Longest chain 16 peptides. Score 0.471 Round 4: 255 peptides, 37 chains. Longest chain 21 peptides. Score 0.495 Round 5: 258 peptides, 35 chains. Longest chain 23 peptides. Score 0.525 Taking the results from Round 5 Chains 36, Residues 223, Estimated correctness of the model 19.3 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 8937 reflections ( 99.43 % complete ) and 8610 restraints for refining 3841 atoms. 7706 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2349 (Rfree = 0.000) for 3841 atoms. Found 34 (34 requested) and removed 24 (17 requested) atoms. Cycle 7: After refmac, R = 0.2201 (Rfree = 0.000) for 3842 atoms. Found 13 (34 requested) and removed 21 (17 requested) atoms. Cycle 8: After refmac, R = 0.2173 (Rfree = 0.000) for 3829 atoms. Found 6 (34 requested) and removed 17 (17 requested) atoms. Cycle 9: After refmac, R = 0.2102 (Rfree = 0.000) for 3811 atoms. Found 8 (34 requested) and removed 17 (17 requested) atoms. Cycle 10: After refmac, R = 0.2046 (Rfree = 0.000) for 3798 atoms. Found 8 (34 requested) and removed 17 (17 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.23 3.27 Search for helices and strands: 0 residues in 0 chains, 3886 seeds are put forward NCS extension: 39 residues added (2 deleted due to clashes), 3925 seeds are put forward Round 1: 221 peptides, 41 chains. Longest chain 12 peptides. Score 0.353 Round 2: 269 peptides, 39 chains. Longest chain 18 peptides. Score 0.508 Round 3: 274 peptides, 43 chains. Longest chain 15 peptides. Score 0.476 Round 4: 275 peptides, 42 chains. Longest chain 16 peptides. Score 0.490 Round 5: 271 peptides, 42 chains. Longest chain 21 peptides. Score 0.480 Taking the results from Round 2 Chains 39, Residues 230, Estimated correctness of the model 13.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8937 reflections ( 99.43 % complete ) and 8595 restraints for refining 3837 atoms. 7714 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2155 (Rfree = 0.000) for 3837 atoms. Found 18 (34 requested) and removed 22 (17 requested) atoms. Cycle 12: After refmac, R = 0.2107 (Rfree = 0.000) for 3829 atoms. Found 6 (34 requested) and removed 18 (17 requested) atoms. Cycle 13: After refmac, R = 0.2051 (Rfree = 0.000) for 3813 atoms. Found 11 (34 requested) and removed 17 (17 requested) atoms. Cycle 14: After refmac, R = 0.2009 (Rfree = 0.000) for 3803 atoms. Found 2 (34 requested) and removed 17 (17 requested) atoms. Cycle 15: After refmac, R = 0.1872 (Rfree = 0.000) for 3783 atoms. Found 5 (33 requested) and removed 16 (16 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.25 3.29 Search for helices and strands: 0 residues in 0 chains, 3886 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 3904 seeds are put forward Round 1: 212 peptides, 42 chains. Longest chain 9 peptides. Score 0.312 Round 2: 250 peptides, 41 chains. Longest chain 14 peptides. Score 0.436 Round 3: 273 peptides, 44 chains. Longest chain 18 peptides. Score 0.462 Round 4: 264 peptides, 40 chains. Longest chain 19 peptides. Score 0.484 Round 5: 265 peptides, 41 chains. Longest chain 25 peptides. Score 0.476 Taking the results from Round 4 Chains 42, Residues 224, Estimated correctness of the model 6.1 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 8937 reflections ( 99.43 % complete ) and 8494 restraints for refining 3840 atoms. 7577 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2070 (Rfree = 0.000) for 3840 atoms. Found 22 (34 requested) and removed 23 (17 requested) atoms. Cycle 17: After refmac, R = 0.1967 (Rfree = 0.000) for 3834 atoms. Found 6 (34 requested) and removed 17 (17 requested) atoms. Cycle 18: After refmac, R = 0.1885 (Rfree = 0.000) for 3815 atoms. Found 10 (34 requested) and removed 19 (17 requested) atoms. Cycle 19: After refmac, R = 0.1884 (Rfree = 0.000) for 3800 atoms. Found 7 (34 requested) and removed 17 (17 requested) atoms. Cycle 20: After refmac, R = 0.1865 (Rfree = 0.000) for 3787 atoms. Found 6 (34 requested) and removed 17 (17 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.22 3.26 Search for helices and strands: 0 residues in 0 chains, 3875 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 3898 seeds are put forward Round 1: 242 peptides, 47 chains. Longest chain 14 peptides. Score 0.340 Round 2: 259 peptides, 44 chains. Longest chain 15 peptides. Score 0.425 Round 3: 256 peptides, 41 chains. Longest chain 15 peptides. Score 0.452 Round 4: 268 peptides, 42 chains. Longest chain 18 peptides. Score 0.472 Round 5: 270 peptides, 39 chains. Longest chain 25 peptides. Score 0.511 Taking the results from Round 5 Chains 41, Residues 231, Estimated correctness of the model 14.9 % 2 chains (19 residues) have been docked in sequence ------------------------------------------------------ 8937 reflections ( 99.43 % complete ) and 8333 restraints for refining 3841 atoms. 7392 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2009 (Rfree = 0.000) for 3841 atoms. Found 25 (34 requested) and removed 22 (17 requested) atoms. Cycle 22: After refmac, R = 0.1897 (Rfree = 0.000) for 3830 atoms. Found 15 (34 requested) and removed 18 (17 requested) atoms. Cycle 23: After refmac, R = 0.1837 (Rfree = 0.000) for 3823 atoms. Found 8 (34 requested) and removed 17 (17 requested) atoms. Cycle 24: After refmac, R = 0.1795 (Rfree = 0.000) for 3811 atoms. Found 8 (34 requested) and removed 18 (17 requested) atoms. Cycle 25: After refmac, R = 0.1731 (Rfree = 0.000) for 3795 atoms. Found 5 (34 requested) and removed 17 (17 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.21 3.25 Search for helices and strands: 0 residues in 0 chains, 3891 seeds are put forward NCS extension: 35 residues added (2 deleted due to clashes), 3926 seeds are put forward Round 1: 206 peptides, 41 chains. Longest chain 16 peptides. Score 0.307 Round 2: 239 peptides, 40 chains. Longest chain 24 peptides. Score 0.417 Round 3: 228 peptides, 35 chains. Longest chain 18 peptides. Score 0.447 Round 4: 242 peptides, 39 chains. Longest chain 19 peptides. Score 0.438 Round 5: 251 peptides, 37 chains. Longest chain 19 peptides. Score 0.485 Taking the results from Round 5 Chains 37, Residues 214, Estimated correctness of the model 6.4 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 8937 reflections ( 99.43 % complete ) and 8587 restraints for refining 3842 atoms. 7750 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1920 (Rfree = 0.000) for 3842 atoms. Found 23 (34 requested) and removed 17 (17 requested) atoms. Cycle 27: After refmac, R = 0.1799 (Rfree = 0.000) for 3843 atoms. Found 9 (34 requested) and removed 17 (17 requested) atoms. Cycle 28: After refmac, R = 0.1754 (Rfree = 0.000) for 3833 atoms. Found 8 (34 requested) and removed 17 (17 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.1679 (Rfree = 0.000) for 3823 atoms. Found 5 (34 requested) and removed 18 (17 requested) atoms. Cycle 30: After refmac, R = 0.1648 (Rfree = 0.000) for 3807 atoms. Found 6 (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, 3880 seeds are put forward NCS extension: 24 residues added (3 deleted due to clashes), 3904 seeds are put forward Round 1: 205 peptides, 38 chains. Longest chain 12 peptides. Score 0.343 Round 2: 256 peptides, 41 chains. Longest chain 17 peptides. Score 0.452 Round 3: 258 peptides, 40 chains. Longest chain 17 peptides. Score 0.469 Round 4: 262 peptides, 37 chains. Longest chain 17 peptides. Score 0.513 Round 5: 252 peptides, 40 chains. Longest chain 15 peptides. Score 0.453 Taking the results from Round 4 Chains 38, Residues 225, Estimated correctness of the model 15.5 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ 8937 reflections ( 99.43 % complete ) and 8422 restraints for refining 3842 atoms. 7500 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1872 (Rfree = 0.000) for 3842 atoms. Found 27 (34 requested) and removed 22 (17 requested) atoms. Cycle 32: After refmac, R = 0.1756 (Rfree = 0.000) for 3838 atoms. Found 9 (34 requested) and removed 17 (17 requested) atoms. Cycle 33: After refmac, R = 0.1700 (Rfree = 0.000) for 3825 atoms. Found 13 (34 requested) and removed 17 (17 requested) atoms. Cycle 34: After refmac, R = 0.1666 (Rfree = 0.000) for 3821 atoms. Found 5 (34 requested) and removed 17 (17 requested) atoms. Cycle 35: After refmac, R = 0.1660 (Rfree = 0.000) for 3807 atoms. Found 7 (34 requested) and removed 17 (17 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.25 3.29 Search for helices and strands: 0 residues in 0 chains, 3887 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 3906 seeds are put forward Round 1: 217 peptides, 39 chains. Longest chain 11 peptides. Score 0.366 Round 2: 232 peptides, 39 chains. Longest chain 12 peptides. Score 0.410 Round 3: 240 peptides, 36 chains. Longest chain 18 peptides. Score 0.468 Round 4: 228 peptides, 36 chains. Longest chain 15 peptides. Score 0.435 Round 5: 229 peptides, 37 chains. Longest chain 15 peptides. Score 0.426 Taking the results from Round 3 Chains 36, Residues 204, Estimated correctness of the model 0.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8937 reflections ( 99.43 % complete ) and 8517 restraints for refining 3842 atoms. 7737 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1819 (Rfree = 0.000) for 3842 atoms. Found 28 (34 requested) and removed 18 (17 requested) atoms. Cycle 37: After refmac, R = 0.1699 (Rfree = 0.000) for 3849 atoms. Found 5 (34 requested) and removed 17 (17 requested) atoms. Cycle 38: After refmac, R = 0.1668 (Rfree = 0.000) for 3836 atoms. Found 4 (34 requested) and removed 17 (17 requested) atoms. Cycle 39: After refmac, R = 0.1656 (Rfree = 0.000) for 3823 atoms. Found 5 (34 requested) and removed 17 (17 requested) atoms. Cycle 40: After refmac, R = 0.1648 (Rfree = 0.000) for 3811 atoms. Found 3 (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, 3858 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 3874 seeds are put forward Round 1: 190 peptides, 39 chains. Longest chain 9 peptides. Score 0.283 Round 2: 233 peptides, 37 chains. Longest chain 12 peptides. Score 0.437 Round 3: 227 peptides, 41 chains. Longest chain 10 peptides. Score 0.371 Round 4: 223 peptides, 38 chains. Longest chain 11 peptides. Score 0.396 Round 5: 203 peptides, 34 chains. Longest chain 13 peptides. Score 0.389 Taking the results from Round 2 Chains 37, Residues 196, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 8937 reflections ( 99.43 % complete ) and 8474 restraints for refining 3842 atoms. 7694 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1782 (Rfree = 0.000) for 3842 atoms. Found 19 (34 requested) and removed 21 (17 requested) atoms. Cycle 42: After refmac, R = 0.1693 (Rfree = 0.000) for 3839 atoms. Found 10 (34 requested) and removed 17 (17 requested) atoms. Cycle 43: After refmac, R = 0.1676 (Rfree = 0.000) for 3832 atoms. Found 4 (34 requested) and removed 17 (17 requested) atoms. Cycle 44: After refmac, R = 0.1662 (Rfree = 0.000) for 3818 atoms. Found 7 (34 requested) and removed 17 (17 requested) atoms. Cycle 45: After refmac, R = 0.1630 (Rfree = 0.000) for 3808 atoms. Found 3 (34 requested) and removed 17 (17 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.25 3.29 Search for helices and strands: 0 residues in 0 chains, 3862 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 3874 seeds are put forward Round 1: 191 peptides, 38 chains. Longest chain 11 peptides. Score 0.299 Round 2: 217 peptides, 35 chains. Longest chain 13 peptides. Score 0.417 Round 3: 215 peptides, 36 chains. Longest chain 13 peptides. Score 0.398 Round 4: 221 peptides, 35 chains. Longest chain 13 peptides. Score 0.428 Round 5: 204 peptides, 36 chains. Longest chain 11 peptides. Score 0.366 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 35, Residues 186, 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 8807 restraints for refining 3842 atoms. 8098 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1817 (Rfree = 0.000) for 3842 atoms. Found 0 (34 requested) and removed 10 (17 requested) atoms. Cycle 47: After refmac, R = 0.1744 (Rfree = 0.000) for 3830 atoms. Found 0 (34 requested) and removed 3 (17 requested) atoms. Cycle 48: After refmac, R = 0.1741 (Rfree = 0.000) for 3825 atoms. Found 0 (34 requested) and removed 2 (17 requested) atoms. Cycle 49: After refmac, R = 0.1685 (Rfree = 0.000) for 3821 atoms. Found 0 (34 requested) and removed 2 (17 requested) atoms. Writing output files ... TimeTaking 62.63