null Sun 23 Dec 22:22:59 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 2hi0-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2hi0-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2hi0-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hi0-4.0-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/2hi0-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hi0-4.0-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 22:23:08 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/2hi0-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hi0-4.0-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 289 and 0 Target number of residues in the AU: 289 Target solvent content: 0.6639 Checking the provided sequence file Detected sequence length: 240 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 480 Adjusted target solvent content: 0.44 Input MTZ file: 2hi0-4.0-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: 4 Cell parameters: 58.636 38.695 103.583 90.000 98.094 90.000 Input sequence file: 2hi0-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 3840 target number of atoms Had to go as low as 0.70 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: 102.551 4.000 Wilson plot Bfac: 87.44 4096 reflections ( 99.71 % complete ) and 0 restraints for refining 4236 atoms. Observations/parameters ratio is 0.24 ------------------------------------------------------ Starting model: R = 0.3275 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3006 (Rfree = 0.000) for 4236 atoms. Found 18 (20 requested) and removed 32 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.84 4.16 Search for helices and strands: 0 residues in 0 chains, 4315 seeds are put forward NCS extension: 0 residues added, 4315 seeds are put forward Round 1: 136 peptides, 31 chains. Longest chain 7 peptides. Score 0.218 Round 2: 175 peptides, 34 chains. Longest chain 9 peptides. Score 0.323 Round 3: 204 peptides, 40 chains. Longest chain 9 peptides. Score 0.336 Round 4: 217 peptides, 37 chains. Longest chain 11 peptides. Score 0.425 Round 5: 218 peptides, 37 chains. Longest chain 14 peptides. Score 0.429 Taking the results from Round 5 Chains 39, Residues 181, Estimated correctness of the model 0.0 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 4096 reflections ( 99.71 % complete ) and 8177 restraints for refining 3465 atoms. 7438 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2300 (Rfree = 0.000) for 3465 atoms. Found 10 (16 requested) and removed 27 (8 requested) atoms. Cycle 2: After refmac, R = 0.2323 (Rfree = 0.000) for 3374 atoms. Found 15 (16 requested) and removed 21 (8 requested) atoms. Cycle 3: After refmac, R = 0.2202 (Rfree = 0.000) for 3342 atoms. Found 14 (16 requested) and removed 17 (8 requested) atoms. Cycle 4: After refmac, R = 0.1648 (Rfree = 0.000) for 3315 atoms. Found 4 (15 requested) and removed 13 (7 requested) atoms. Cycle 5: After refmac, R = 0.1651 (Rfree = 0.000) for 3289 atoms. Found 5 (15 requested) and removed 14 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.77 4.09 Search for helices and strands: 0 residues in 0 chains, 3417 seeds are put forward NCS extension: 0 residues added, 3417 seeds are put forward Round 1: 163 peptides, 33 chains. Longest chain 11 peptides. Score 0.293 Round 2: 195 peptides, 35 chains. Longest chain 9 peptides. Score 0.379 Round 3: 203 peptides, 32 chains. Longest chain 12 peptides. Score 0.450 Round 4: 205 peptides, 33 chains. Longest chain 14 peptides. Score 0.443 Round 5: 219 peptides, 34 chains. Longest chain 15 peptides. Score 0.474 Taking the results from Round 5 Chains 34, Residues 185, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 4096 reflections ( 99.71 % complete ) and 7843 restraints for refining 3331 atoms. 7119 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2010 (Rfree = 0.000) for 3331 atoms. Found 14 (15 requested) and removed 20 (7 requested) atoms. Cycle 7: After refmac, R = 0.2110 (Rfree = 0.000) for 3302 atoms. Found 15 (15 requested) and removed 18 (7 requested) atoms. Cycle 8: After refmac, R = 0.1688 (Rfree = 0.000) for 3281 atoms. Found 15 (15 requested) and removed 13 (7 requested) atoms. Cycle 9: After refmac, R = 0.1753 (Rfree = 0.000) for 3274 atoms. Found 15 (15 requested) and removed 17 (7 requested) atoms. Cycle 10: After refmac, R = 0.1670 (Rfree = 0.000) for 3265 atoms. Found 15 (15 requested) and removed 13 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.74 4.05 Search for helices and strands: 0 residues in 0 chains, 3427 seeds are put forward NCS extension: 20 residues added (3 deleted due to clashes), 3447 seeds are put forward Round 1: 188 peptides, 40 chains. Longest chain 12 peptides. Score 0.277 Round 2: 205 peptides, 35 chains. Longest chain 18 peptides. Score 0.414 Round 3: 217 peptides, 35 chains. Longest chain 19 peptides. Score 0.453 Round 4: 202 peptides, 33 chains. Longest chain 10 peptides. Score 0.433 Round 5: 223 peptides, 35 chains. Longest chain 16 peptides. Score 0.472 Taking the results from Round 5 Chains 35, Residues 188, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4096 reflections ( 99.71 % complete ) and 8008 restraints for refining 3409 atoms. 7291 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1870 (Rfree = 0.000) for 3409 atoms. Found 16 (16 requested) and removed 28 (8 requested) atoms. Cycle 12: After refmac, R = 0.1868 (Rfree = 0.000) for 3371 atoms. Found 16 (16 requested) and removed 25 (8 requested) atoms. Cycle 13: After refmac, R = 0.1804 (Rfree = 0.000) for 3352 atoms. Found 15 (15 requested) and removed 16 (7 requested) atoms. Cycle 14: After refmac, R = 0.1715 (Rfree = 0.000) for 3344 atoms. Found 15 (15 requested) and removed 20 (7 requested) atoms. Cycle 15: After refmac, R = 0.1231 (Rfree = 0.000) for 3330 atoms. Found 5 (15 requested) and removed 14 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.76 4.07 Search for helices and strands: 0 residues in 0 chains, 3439 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 3453 seeds are put forward Round 1: 165 peptides, 35 chains. Longest chain 10 peptides. Score 0.269 Round 2: 206 peptides, 39 chains. Longest chain 13 peptides. Score 0.358 Round 3: 208 peptides, 36 chains. Longest chain 10 peptides. Score 0.409 Round 4: 208 peptides, 35 chains. Longest chain 16 peptides. Score 0.424 Round 5: 205 peptides, 34 chains. Longest chain 12 peptides. Score 0.428 Taking the results from Round 5 Chains 34, Residues 171, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4096 reflections ( 99.71 % complete ) and 8245 restraints for refining 3444 atoms. 7595 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1676 (Rfree = 0.000) for 3444 atoms. Found 16 (16 requested) and removed 30 (8 requested) atoms. Cycle 17: After refmac, R = 0.1765 (Rfree = 0.000) for 3410 atoms. Found 16 (16 requested) and removed 20 (8 requested) atoms. Cycle 18: After refmac, R = 0.1787 (Rfree = 0.000) for 3398 atoms. Found 16 (16 requested) and removed 17 (8 requested) atoms. Cycle 19: After refmac, R = 0.1650 (Rfree = 0.000) for 3390 atoms. Found 16 (16 requested) and removed 13 (8 requested) atoms. Cycle 20: After refmac, R = 0.1550 (Rfree = 0.000) for 3385 atoms. Found 16 (16 requested) and removed 15 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.71 4.02 Search for helices and strands: 0 residues in 0 chains, 3536 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 3547 seeds are put forward Round 1: 135 peptides, 30 chains. Longest chain 8 peptides. Score 0.231 Round 2: 172 peptides, 31 chains. Longest chain 11 peptides. Score 0.359 Round 3: 175 peptides, 32 chains. Longest chain 10 peptides. Score 0.354 Round 4: 173 peptides, 30 chains. Longest chain 11 peptides. Score 0.378 Round 5: 180 peptides, 32 chains. Longest chain 10 peptides. Score 0.372 Taking the results from Round 4 Chains 30, Residues 143, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4096 reflections ( 99.71 % complete ) and 8238 restraints for refining 3466 atoms. 7696 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1948 (Rfree = 0.000) for 3466 atoms. Found 16 (16 requested) and removed 30 (8 requested) atoms. Cycle 22: After refmac, R = 0.1803 (Rfree = 0.000) for 3427 atoms. Found 16 (16 requested) and removed 17 (8 requested) atoms. Cycle 23: After refmac, R = 0.1168 (Rfree = 0.000) for 3415 atoms. Found 9 (16 requested) and removed 15 (8 requested) atoms. Cycle 24: After refmac, R = 0.1019 (Rfree = 0.000) for 3404 atoms. Found 2 (16 requested) and removed 9 (8 requested) atoms. Cycle 25: After refmac, R = 0.0980 (Rfree = 0.000) for 3391 atoms. Found 4 (16 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.76 4.07 Search for helices and strands: 0 residues in 0 chains, 3497 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 3510 seeds are put forward Round 1: 127 peptides, 28 chains. Longest chain 7 peptides. Score 0.233 Round 2: 148 peptides, 30 chains. Longest chain 9 peptides. Score 0.284 Round 3: 158 peptides, 27 chains. Longest chain 14 peptides. Score 0.371 Round 4: 160 peptides, 30 chains. Longest chain 10 peptides. Score 0.330 Round 5: 171 peptides, 30 chains. Longest chain 11 peptides. Score 0.371 Taking the results from Round 5 Chains 30, Residues 141, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4096 reflections ( 99.71 % complete ) and 8202 restraints for refining 3464 atoms. 7668 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1928 (Rfree = 0.000) for 3464 atoms. Found 16 (16 requested) and removed 46 (8 requested) atoms. Cycle 27: After refmac, R = 0.1814 (Rfree = 0.000) for 3417 atoms. Found 16 (16 requested) and removed 31 (8 requested) atoms. Cycle 28: After refmac, R = 0.1786 (Rfree = 0.000) for 3393 atoms. Found 16 (16 requested) and removed 34 (8 requested) atoms. Cycle 29: After refmac, R = 0.1790 (Rfree = 0.000) for 3368 atoms. Found 16 (16 requested) and removed 35 (8 requested) atoms. Cycle 30: After refmac, R = 0.1769 (Rfree = 0.000) for 3345 atoms. Found 15 (15 requested) and removed 27 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.70 4.01 Search for helices and strands: 0 residues in 0 chains, 3463 seeds are put forward NCS extension: 0 residues added, 3463 seeds are put forward Round 1: 164 peptides, 34 chains. Longest chain 9 peptides. Score 0.281 Round 2: 173 peptides, 33 chains. Longest chain 10 peptides. Score 0.331 Round 3: 179 peptides, 33 chains. Longest chain 15 peptides. Score 0.353 Round 4: 172 peptides, 31 chains. Longest chain 11 peptides. Score 0.359 Round 5: 164 peptides, 27 chains. Longest chain 14 peptides. Score 0.392 Taking the results from Round 5 Chains 27, Residues 137, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4096 reflections ( 99.71 % complete ) and 8103 restraints for refining 3422 atoms. 7582 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1899 (Rfree = 0.000) for 3422 atoms. Found 16 (16 requested) and removed 25 (8 requested) atoms. Cycle 32: After refmac, R = 0.1985 (Rfree = 0.000) for 3401 atoms. Found 16 (16 requested) and removed 38 (8 requested) atoms. Cycle 33: After refmac, R = 0.1755 (Rfree = 0.000) for 3371 atoms. Found 16 (16 requested) and removed 19 (8 requested) atoms. Cycle 34: After refmac, R = 0.1751 (Rfree = 0.000) for 3360 atoms. Found 16 (16 requested) and removed 25 (8 requested) atoms. Cycle 35: After refmac, R = 0.1813 (Rfree = 0.000) for 3349 atoms. Found 15 (15 requested) and removed 21 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.75 4.06 Search for helices and strands: 0 residues in 0 chains, 3437 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 3454 seeds are put forward Round 1: 104 peptides, 24 chains. Longest chain 6 peptides. Score 0.204 Round 2: 146 peptides, 30 chains. Longest chain 9 peptides. Score 0.276 Round 3: 157 peptides, 29 chains. Longest chain 12 peptides. Score 0.335 Round 4: 157 peptides, 28 chains. Longest chain 11 peptides. Score 0.351 Round 5: 163 peptides, 29 chains. Longest chain 10 peptides. Score 0.357 Taking the results from Round 5 Chains 29, Residues 134, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 4096 reflections ( 99.71 % complete ) and 8167 restraints for refining 3462 atoms. 7639 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1856 (Rfree = 0.000) for 3462 atoms. Found 16 (16 requested) and removed 22 (8 requested) atoms. Cycle 37: After refmac, R = 0.1930 (Rfree = 0.000) for 3435 atoms. Found 16 (16 requested) and removed 14 (8 requested) atoms. Cycle 38: After refmac, R = 0.1775 (Rfree = 0.000) for 3425 atoms. Found 16 (16 requested) and removed 16 (8 requested) atoms. Cycle 39: After refmac, R = 0.1650 (Rfree = 0.000) for 3419 atoms. Found 16 (16 requested) and removed 15 (8 requested) atoms. Cycle 40: After refmac, R = 0.1708 (Rfree = 0.000) for 3415 atoms. Found 16 (16 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.67 3.98 Search for helices and strands: 0 residues in 0 chains, 3511 seeds are put forward NCS extension: 2 residues added (1 deleted due to clashes), 3513 seeds are put forward Round 1: 114 peptides, 25 chains. Longest chain 8 peptides. Score 0.230 Round 2: 131 peptides, 27 chains. Longest chain 7 peptides. Score 0.266 Round 3: 135 peptides, 26 chains. Longest chain 8 peptides. Score 0.300 Round 4: 132 peptides, 25 chains. Longest chain 9 peptides. Score 0.305 Round 5: 137 peptides, 25 chains. Longest chain 9 peptides. Score 0.325 Taking the results from Round 5 Chains 25, Residues 112, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 4096 reflections ( 99.71 % complete ) and 8319 restraints for refining 3452 atoms. 7878 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2074 (Rfree = 0.000) for 3452 atoms. Found 16 (16 requested) and removed 24 (8 requested) atoms. Cycle 42: After refmac, R = 0.1847 (Rfree = 0.000) for 3431 atoms. Found 16 (16 requested) and removed 17 (8 requested) atoms. Cycle 43: After refmac, R = 0.1914 (Rfree = 0.000) for 3415 atoms. Found 16 (16 requested) and removed 18 (8 requested) atoms. Cycle 44: After refmac, R = 0.1762 (Rfree = 0.000) for 3404 atoms. Found 16 (16 requested) and removed 18 (8 requested) atoms. Cycle 45: After refmac, R = 0.1343 (Rfree = 0.000) for 3395 atoms. Found 13 (16 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.68 3.99 Search for helices and strands: 0 residues in 0 chains, 3497 seeds are put forward NCS extension: 0 residues added, 3497 seeds are put forward Round 1: 114 peptides, 25 chains. Longest chain 8 peptides. Score 0.230 Round 2: 124 peptides, 25 chains. Longest chain 9 peptides. Score 0.273 Round 3: 137 peptides, 25 chains. Longest chain 12 peptides. Score 0.325 Round 4: 133 peptides, 25 chains. Longest chain 9 peptides. Score 0.309 Round 5: 137 peptides, 24 chains. Longest chain 15 peptides. Score 0.341 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 24, Residues 113, Estimated correctness of the model 0.0 % 1 chains (14 residues) have been docked in sequence Sequence coverage is 12 % Consider running further cycles of model building using 2hi0-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4096 reflections ( 99.71 % complete ) and 7806 restraints for refining 3365 atoms. 7322 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1779 (Rfree = 0.000) for 3365 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.1912 (Rfree = 0.000) for 3334 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.1798 (Rfree = 0.000) for 3315 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.1822 (Rfree = 0.000) for 3295 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:16:04 GMT 2018 Job finished. TimeTaking 53.1 Used memory is bytes: 8531816