Tue 25 Dec 19:27:55 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 2owp-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2owp-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2owp-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2owp-3.6-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/2owp-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2owp-3.6-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 ============================================================ Tue 25 Dec 19:28:05 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/2owp-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2owp-3.6-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 299 and 0 Target number of residues in the AU: 299 Target solvent content: 0.6281 Checking the provided sequence file Detected sequence length: 129 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 258 Adjusted target solvent content: 0.68 Input MTZ file: 2owp-3.6-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: 152 Cell parameters: 80.518 80.518 116.256 90.000 90.000 120.000 Input sequence file: 2owp-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 2064 target number of atoms Had to go as low as 1.15 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: 29.899 3.600 Wilson plot Bfac: 64.92 5332 reflections ( 99.20 % complete ) and 0 restraints for refining 2289 atoms. Observations/parameters ratio is 0.58 ------------------------------------------------------ Starting model: R = 0.3582 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3556 (Rfree = 0.000) for 2289 atoms. Found 14 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.40 2.65 Search for helices and strands: 0 residues in 0 chains, 2336 seeds are put forward NCS extension: 0 residues added, 2336 seeds are put forward Round 1: 124 peptides, 21 chains. Longest chain 12 peptides. Score 0.350 Round 2: 172 peptides, 26 chains. Longest chain 17 peptides. Score 0.448 Round 3: 184 peptides, 22 chains. Longest chain 22 peptides. Score 0.548 Round 4: 187 peptides, 22 chains. Longest chain 33 peptides. Score 0.557 Round 5: 185 peptides, 21 chains. Longest chain 17 peptides. Score 0.565 Taking the results from Round 5 Chains 21, Residues 164, Estimated correctness of the model 0.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5332 reflections ( 99.20 % complete ) and 3886 restraints for refining 1869 atoms. 3251 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3278 (Rfree = 0.000) for 1869 atoms. Found 12 (12 requested) and removed 7 (6 requested) atoms. Cycle 2: After refmac, R = 0.3080 (Rfree = 0.000) for 1848 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 3: After refmac, R = 0.2976 (Rfree = 0.000) for 1834 atoms. Found 7 (11 requested) and removed 7 (5 requested) atoms. Cycle 4: After refmac, R = 0.2895 (Rfree = 0.000) for 1821 atoms. Found 4 (11 requested) and removed 8 (5 requested) atoms. Cycle 5: After refmac, R = 0.2835 (Rfree = 0.000) for 1806 atoms. Found 8 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.30 2.57 Search for helices and strands: 0 residues in 0 chains, 1886 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 1903 seeds are put forward Round 1: 176 peptides, 28 chains. Longest chain 22 peptides. Score 0.431 Round 2: 187 peptides, 22 chains. Longest chain 28 peptides. Score 0.557 Round 3: 186 peptides, 22 chains. Longest chain 22 peptides. Score 0.554 Round 4: 184 peptides, 20 chains. Longest chain 23 peptides. Score 0.576 Round 5: 190 peptides, 18 chains. Longest chain 37 peptides. Score 0.620 Taking the results from Round 5 Chains 22, Residues 172, Estimated correctness of the model 22.3 % 2 chains (23 residues) have been docked in sequence ------------------------------------------------------ 5332 reflections ( 99.20 % complete ) and 3634 restraints for refining 1870 atoms. 2872 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3613 (Rfree = 0.000) for 1870 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 7: After refmac, R = 0.3580 (Rfree = 0.000) for 1834 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 8: After refmac, R = 0.3555 (Rfree = 0.000) for 1808 atoms. Found 11 (11 requested) and removed 15 (5 requested) atoms. Cycle 9: After refmac, R = 0.3523 (Rfree = 0.000) for 1781 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 10: After refmac, R = 0.3476 (Rfree = 0.000) for 1767 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.69 2.87 Search for helices and strands: 0 residues in 0 chains, 1824 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 1844 seeds are put forward Round 1: 153 peptides, 24 chains. Longest chain 13 peptides. Score 0.412 Round 2: 165 peptides, 24 chains. Longest chain 16 peptides. Score 0.455 Round 3: 165 peptides, 23 chains. Longest chain 15 peptides. Score 0.471 Round 4: 181 peptides, 24 chains. Longest chain 20 peptides. Score 0.509 Round 5: 168 peptides, 23 chains. Longest chain 19 peptides. Score 0.481 Taking the results from Round 4 Chains 24, Residues 157, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5332 reflections ( 99.20 % complete ) and 4114 restraints for refining 1871 atoms. 3510 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3564 (Rfree = 0.000) for 1871 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Failed to save intermediate PDB Cycle 12: After refmac, R = 0.3204 (Rfree = 0.000) for 1853 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 13: After refmac, R = 0.3204 (Rfree = 0.000) for 1828 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 14: After refmac, R = 0.3028 (Rfree = 0.000) for 1819 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 15: After refmac, R = 0.3121 (Rfree = 0.000) for 1813 atoms. Found 7 (11 requested) and removed 13 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.13 2.44 Search for helices and strands: 0 residues in 0 chains, 1876 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 1898 seeds are put forward Round 1: 160 peptides, 25 chains. Longest chain 18 peptides. Score 0.421 Round 2: 163 peptides, 23 chains. Longest chain 16 peptides. Score 0.464 Round 3: 179 peptides, 26 chains. Longest chain 22 peptides. Score 0.473 Round 4: 175 peptides, 25 chains. Longest chain 18 peptides. Score 0.474 Round 5: 170 peptides, 22 chains. Longest chain 19 peptides. Score 0.503 Taking the results from Round 5 Chains 24, Residues 148, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 5332 reflections ( 99.20 % complete ) and 3920 restraints for refining 1871 atoms. 3314 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3509 (Rfree = 0.000) for 1871 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 17: After refmac, R = 0.3408 (Rfree = 0.000) for 1858 atoms. Found 12 (12 requested) and removed 16 (6 requested) atoms. Cycle 18: After refmac, R = 0.3384 (Rfree = 0.000) for 1835 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.3279 (Rfree = 0.000) for 1817 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 20: After refmac, R = 0.3339 (Rfree = 0.000) for 1810 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.10 2.41 Search for helices and strands: 0 residues in 0 chains, 1884 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 1901 seeds are put forward Round 1: 143 peptides, 27 chains. Longest chain 13 peptides. Score 0.322 Round 2: 165 peptides, 26 chains. Longest chain 14 peptides. Score 0.423 Round 3: 151 peptides, 23 chains. Longest chain 12 peptides. Score 0.421 Round 4: 164 peptides, 25 chains. Longest chain 14 peptides. Score 0.436 Round 5: 159 peptides, 20 chains. Longest chain 27 peptides. Score 0.497 Taking the results from Round 5 Chains 22, Residues 139, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 5332 reflections ( 99.20 % complete ) and 3881 restraints for refining 1871 atoms. 3282 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3467 (Rfree = 0.000) for 1871 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 22: After refmac, R = 0.3291 (Rfree = 0.000) for 1854 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 23: After refmac, R = 0.3469 (Rfree = 0.000) for 1844 atoms. Found 11 (11 requested) and removed 7 (5 requested) atoms. Failed to save intermediate PDB Cycle 24: After refmac, R = 0.3496 (Rfree = 0.000) for 1832 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 25: After refmac, R = 0.3538 (Rfree = 0.000) for 1821 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.28 2.55 Search for helices and strands: 0 residues in 0 chains, 1897 seeds are put forward NCS extension: 0 residues added, 1897 seeds are put forward Round 1: 142 peptides, 27 chains. Longest chain 10 peptides. Score 0.317 Round 2: 160 peptides, 25 chains. Longest chain 17 peptides. Score 0.421 Round 3: 155 peptides, 23 chains. Longest chain 16 peptides. Score 0.435 Round 4: 153 peptides, 22 chains. Longest chain 17 peptides. Score 0.444 Round 5: 146 peptides, 20 chains. Longest chain 13 peptides. Score 0.452 Taking the results from Round 5 Chains 20, Residues 126, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5332 reflections ( 99.20 % complete ) and 4139 restraints for refining 1871 atoms. 3655 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3695 (Rfree = 0.000) for 1871 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Failed to save intermediate PDB Cycle 27: After refmac, R = 0.3522 (Rfree = 0.000) for 1857 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 28: After refmac, R = 0.3511 (Rfree = 0.000) for 1849 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. Cycle 29: After refmac, R = 0.3383 (Rfree = 0.000) for 1839 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 30: After refmac, R = 0.3378 (Rfree = 0.000) for 1829 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.19 2.48 Search for helices and strands: 0 residues in 0 chains, 1895 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 1909 seeds are put forward Round 1: 128 peptides, 24 chains. Longest chain 13 peptides. Score 0.313 Round 2: 147 peptides, 23 chains. Longest chain 16 peptides. Score 0.406 Round 3: 157 peptides, 26 chains. Longest chain 13 peptides. Score 0.394 Round 4: 139 peptides, 21 chains. Longest chain 18 peptides. Score 0.409 Round 5: 156 peptides, 23 chains. Longest chain 18 peptides. Score 0.439 Taking the results from Round 5 Chains 25, Residues 133, Estimated correctness of the model 0.0 % 2 chains (14 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 5332 reflections ( 99.20 % complete ) and 3953 restraints for refining 1871 atoms. 3386 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3397 (Rfree = 0.000) for 1871 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 32: After refmac, R = 0.3503 (Rfree = 0.000) for 1848 atoms. Found 12 (12 requested) and removed 7 (6 requested) atoms. Cycle 33: After refmac, R = 0.3189 (Rfree = 0.000) for 1836 atoms. Found 11 (11 requested) and removed 7 (5 requested) atoms. Cycle 34: After refmac, R = 0.3438 (Rfree = 0.000) for 1836 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 35: After refmac, R = 0.3143 (Rfree = 0.000) for 1824 atoms. Found 10 (11 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.24 2.52 Search for helices and strands: 0 residues in 0 chains, 1891 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 1910 seeds are put forward Round 1: 127 peptides, 25 chains. Longest chain 13 peptides. Score 0.290 Round 2: 153 peptides, 27 chains. Longest chain 10 peptides. Score 0.361 Round 3: 144 peptides, 26 chains. Longest chain 15 peptides. Score 0.343 Round 4: 157 peptides, 26 chains. Longest chain 16 peptides. Score 0.394 Round 5: 152 peptides, 26 chains. Longest chain 15 peptides. Score 0.374 Taking the results from Round 4 Chains 26, Residues 131, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5332 reflections ( 99.20 % complete ) and 3965 restraints for refining 1870 atoms. 3467 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3679 (Rfree = 0.000) for 1870 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 37: After refmac, R = 0.3422 (Rfree = 0.000) for 1859 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 38: After refmac, R = 0.3268 (Rfree = 0.000) for 1849 atoms. Found 11 (11 requested) and removed 7 (5 requested) atoms. Cycle 39: After refmac, R = 0.3362 (Rfree = 0.000) for 1842 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 40: After refmac, R = 0.3277 (Rfree = 0.000) for 1833 atoms. Found 11 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.25 2.53 Search for helices and strands: 0 residues in 0 chains, 1905 seeds are put forward NCS extension: 32 residues added (0 deleted due to clashes), 1937 seeds are put forward Round 1: 117 peptides, 24 chains. Longest chain 8 peptides. Score 0.265 Round 2: 141 peptides, 23 chains. Longest chain 11 peptides. Score 0.383 Round 3: 125 peptides, 21 chains. Longest chain 12 peptides. Score 0.354 Round 4: 132 peptides, 24 chains. Longest chain 12 peptides. Score 0.329 Round 5: 136 peptides, 22 chains. Longest chain 12 peptides. Score 0.381 Taking the results from Round 2 Chains 23, Residues 118, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 5332 reflections ( 99.20 % complete ) and 3974 restraints for refining 1865 atoms. 3486 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3509 (Rfree = 0.000) for 1865 atoms. Found 11 (11 requested) and removed 18 (5 requested) atoms. Cycle 42: After refmac, R = 0.3494 (Rfree = 0.000) for 1847 atoms. Found 11 (11 requested) and removed 16 (5 requested) atoms. Cycle 43: After refmac, R = 0.3444 (Rfree = 0.000) for 1829 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 44: After refmac, R = 0.3459 (Rfree = 0.000) for 1818 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 45: After refmac, R = 0.3546 (Rfree = 0.000) for 1811 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.17 2.47 Search for helices and strands: 0 residues in 0 chains, 1878 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 1892 seeds are put forward Round 1: 102 peptides, 22 chains. Longest chain 6 peptides. Score 0.236 Round 2: 124 peptides, 22 chains. Longest chain 15 peptides. Score 0.332 Round 3: 125 peptides, 21 chains. Longest chain 17 peptides. Score 0.354 Round 4: 139 peptides, 24 chains. Longest chain 12 peptides. Score 0.358 Round 5: 147 peptides, 24 chains. Longest chain 18 peptides. Score 0.389 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 24, Residues 123, 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 2owp-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5332 reflections ( 99.20 % complete ) and 4062 restraints for refining 1871 atoms. 3594 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3608 (Rfree = 0.000) for 1871 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.3481 (Rfree = 0.000) for 1854 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Failed to save intermediate PDB Cycle 48: After refmac, R = 0.3464 (Rfree = 0.000) for 1843 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.3617 (Rfree = 0.000) for 1836 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Writing output files ... Failed to save intermediate PDB TimeTaking 43.83