null 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-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2owp-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2owp-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2owp-3.8-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-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2owp-3.8-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-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2owp-3.8-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 290 and 0 Target number of residues in the AU: 290 Target solvent content: 0.6393 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-3.8-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-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 2064 target number of atoms Had to go as low as 1.20 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 3.802 Wilson plot Bfac: 71.04 4543 reflections ( 99.15 % complete ) and 0 restraints for refining 2304 atoms. Observations/parameters ratio is 0.49 ------------------------------------------------------ Starting model: R = 0.3623 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3675 (Rfree = 0.000) for 2304 atoms. Found 12 (12 requested) and removed 19 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.60 2.80 Search for helices and strands: 0 residues in 0 chains, 2347 seeds are put forward NCS extension: 0 residues added, 2347 seeds are put forward Round 1: 101 peptides, 20 chains. Longest chain 7 peptides. Score 0.270 Round 2: 130 peptides, 20 chains. Longest chain 12 peptides. Score 0.392 Round 3: 145 peptides, 21 chains. Longest chain 12 peptides. Score 0.432 Round 4: 152 peptides, 21 chains. Longest chain 14 peptides. Score 0.457 Round 5: 166 peptides, 23 chains. Longest chain 15 peptides. Score 0.474 Taking the results from Round 5 Chains 23, Residues 143, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 4543 reflections ( 99.15 % complete ) and 4037 restraints for refining 1867 atoms. 3456 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3642 (Rfree = 0.000) for 1867 atoms. Found 10 (10 requested) and removed 16 (5 requested) atoms. Cycle 2: After refmac, R = 0.3490 (Rfree = 0.000) for 1828 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 3: After refmac, R = 0.3470 (Rfree = 0.000) for 1805 atoms. Found 10 (10 requested) and removed 18 (5 requested) atoms. Cycle 4: After refmac, R = 0.3546 (Rfree = 0.000) for 1776 atoms. Found 9 (9 requested) and removed 14 (4 requested) atoms. Cycle 5: After refmac, R = 0.3494 (Rfree = 0.000) for 1753 atoms. Found 9 (9 requested) and removed 15 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.43 2.67 Search for helices and strands: 0 residues in 0 chains, 1808 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 1830 seeds are put forward Round 1: 158 peptides, 24 chains. Longest chain 20 peptides. Score 0.430 Round 2: 174 peptides, 24 chains. Longest chain 13 peptides. Score 0.486 Round 3: 174 peptides, 22 chains. Longest chain 19 peptides. Score 0.516 Round 4: 173 peptides, 23 chains. Longest chain 19 peptides. Score 0.498 Round 5: 175 peptides, 23 chains. Longest chain 19 peptides. Score 0.505 Taking the results from Round 3 Chains 22, Residues 152, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4543 reflections ( 99.15 % complete ) and 3965 restraints for refining 1867 atoms. 3347 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3627 (Rfree = 0.000) for 1867 atoms. Found 10 (10 requested) and removed 18 (5 requested) atoms. Cycle 7: After refmac, R = 0.3648 (Rfree = 0.000) for 1837 atoms. Found 10 (10 requested) and removed 30 (5 requested) atoms. Cycle 8: After refmac, R = 0.3535 (Rfree = 0.000) for 1803 atoms. Found 9 (9 requested) and removed 26 (4 requested) atoms. Cycle 9: After refmac, R = 0.3487 (Rfree = 0.000) for 1767 atoms. Found 9 (9 requested) and removed 18 (4 requested) atoms. Cycle 10: After refmac, R = 0.3516 (Rfree = 0.000) for 1747 atoms. Found 9 (9 requested) and removed 17 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.25 2.53 Search for helices and strands: 0 residues in 0 chains, 1808 seeds are put forward NCS extension: 15 residues added (3 deleted due to clashes), 1823 seeds are put forward Round 1: 137 peptides, 25 chains. Longest chain 8 peptides. Score 0.332 Round 2: 163 peptides, 23 chains. Longest chain 18 peptides. Score 0.464 Round 3: 167 peptides, 23 chains. Longest chain 22 peptides. Score 0.478 Round 4: 177 peptides, 25 chains. Longest chain 14 peptides. Score 0.481 Round 5: 183 peptides, 24 chains. Longest chain 19 peptides. Score 0.516 Taking the results from Round 5 Chains 25, Residues 159, Estimated correctness of the model 0.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 4543 reflections ( 99.15 % complete ) and 3864 restraints for refining 1867 atoms. 3206 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3575 (Rfree = 0.000) for 1867 atoms. Found 10 (10 requested) and removed 23 (5 requested) atoms. Cycle 12: After refmac, R = 0.3522 (Rfree = 0.000) for 1824 atoms. Found 10 (10 requested) and removed 18 (5 requested) atoms. Cycle 13: After refmac, R = 0.3585 (Rfree = 0.000) for 1791 atoms. Found 9 (9 requested) and removed 21 (4 requested) atoms. Cycle 14: After refmac, R = 0.3167 (Rfree = 0.000) for 1754 atoms. Found 9 (9 requested) and removed 16 (4 requested) atoms. Cycle 15: After refmac, R = 0.3279 (Rfree = 0.000) for 1740 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.28 2.55 Search for helices and strands: 0 residues in 0 chains, 1823 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 1839 seeds are put forward Round 1: 138 peptides, 25 chains. Longest chain 12 peptides. Score 0.336 Round 2: 175 peptides, 23 chains. Longest chain 24 peptides. Score 0.505 Round 3: 167 peptides, 23 chains. Longest chain 18 peptides. Score 0.478 Round 4: 168 peptides, 23 chains. Longest chain 26 peptides. Score 0.481 Round 5: 169 peptides, 23 chains. Longest chain 28 peptides. Score 0.485 Taking the results from Round 2 Chains 23, Residues 152, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4543 reflections ( 99.15 % complete ) and 3865 restraints for refining 1866 atoms. 3280 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3543 (Rfree = 0.000) for 1866 atoms. Found 10 (10 requested) and removed 18 (5 requested) atoms. Cycle 17: After refmac, R = 0.3585 (Rfree = 0.000) for 1831 atoms. Found 10 (10 requested) and removed 20 (5 requested) atoms. Cycle 18: After refmac, R = 0.3552 (Rfree = 0.000) for 1801 atoms. Found 9 (9 requested) and removed 22 (4 requested) atoms. Cycle 19: After refmac, R = 0.3471 (Rfree = 0.000) for 1771 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. Cycle 20: After refmac, R = 0.3453 (Rfree = 0.000) for 1752 atoms. Found 9 (9 requested) and removed 16 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.48 2.71 Search for helices and strands: 0 residues in 0 chains, 1827 seeds are put forward NCS extension: 32 residues added (1 deleted due to clashes), 1859 seeds are put forward Round 1: 158 peptides, 29 chains. Longest chain 10 peptides. Score 0.347 Round 2: 155 peptides, 22 chains. Longest chain 14 peptides. Score 0.452 Round 3: 158 peptides, 25 chains. Longest chain 11 peptides. Score 0.414 Round 4: 173 peptides, 22 chains. Longest chain 19 peptides. Score 0.513 Round 5: 165 peptides, 20 chains. Longest chain 17 peptides. Score 0.517 Taking the results from Round 5 Chains 20, Residues 145, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4543 reflections ( 99.15 % complete ) and 3922 restraints for refining 1867 atoms. 3362 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3673 (Rfree = 0.000) for 1867 atoms. Found 10 (10 requested) and removed 17 (5 requested) atoms. Cycle 22: After refmac, R = 0.3578 (Rfree = 0.000) for 1830 atoms. Found 10 (10 requested) and removed 22 (5 requested) atoms. Cycle 23: After refmac, R = 0.3555 (Rfree = 0.000) for 1796 atoms. Found 9 (9 requested) and removed 24 (4 requested) atoms. Cycle 24: After refmac, R = 0.3539 (Rfree = 0.000) for 1765 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 25: After refmac, R = 0.3556 (Rfree = 0.000) for 1755 atoms. Found 9 (9 requested) and removed 15 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.37 2.62 Search for helices and strands: 0 residues in 0 chains, 1817 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 1838 seeds are put forward Round 1: 140 peptides, 25 chains. Longest chain 14 peptides. Score 0.344 Round 2: 162 peptides, 25 chains. Longest chain 14 peptides. Score 0.428 Round 3: 156 peptides, 25 chains. Longest chain 14 peptides. Score 0.406 Round 4: 165 peptides, 24 chains. Longest chain 13 peptides. Score 0.455 Round 5: 169 peptides, 25 chains. Longest chain 14 peptides. Score 0.453 Taking the results from Round 4 Chains 24, Residues 141, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4543 reflections ( 99.15 % complete ) and 4024 restraints for refining 1865 atoms. 3484 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3686 (Rfree = 0.000) for 1865 atoms. Found 10 (10 requested) and removed 16 (5 requested) atoms. Cycle 27: After refmac, R = 0.3551 (Rfree = 0.000) for 1832 atoms. Found 10 (10 requested) and removed 16 (5 requested) atoms. Cycle 28: After refmac, R = 0.3431 (Rfree = 0.000) for 1809 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 29: After refmac, R = 0.3554 (Rfree = 0.000) for 1794 atoms. Found 9 (9 requested) and removed 5 (4 requested) atoms. Cycle 30: After refmac, R = 0.3486 (Rfree = 0.000) for 1779 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.33 2.59 Search for helices and strands: 0 residues in 0 chains, 1828 seeds are put forward NCS extension: 0 residues added, 1828 seeds are put forward Round 1: 138 peptides, 28 chains. Longest chain 9 peptides. Score 0.283 Round 2: 157 peptides, 26 chains. Longest chain 14 peptides. Score 0.394 Round 3: 158 peptides, 26 chains. Longest chain 11 peptides. Score 0.397 Round 4: 145 peptides, 24 chains. Longest chain 13 peptides. Score 0.381 Round 5: 147 peptides, 22 chains. Longest chain 19 peptides. Score 0.423 Taking the results from Round 5 Chains 22, Residues 125, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4543 reflections ( 99.15 % complete ) and 4087 restraints for refining 1867 atoms. 3609 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3790 (Rfree = 0.000) for 1867 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 32: After refmac, R = 0.3604 (Rfree = 0.000) for 1835 atoms. Found 10 (10 requested) and removed 13 (5 requested) atoms. Cycle 33: After refmac, R = 0.3636 (Rfree = 0.000) for 1823 atoms. Found 10 (10 requested) and removed 17 (5 requested) atoms. Cycle 34: After refmac, R = 0.3545 (Rfree = 0.000) for 1805 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 35: After refmac, R = 0.3130 (Rfree = 0.000) for 1797 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.37 2.62 Search for helices and strands: 0 residues in 0 chains, 1855 seeds are put forward NCS extension: 33 residues added (3 deleted due to clashes), 1888 seeds are put forward Round 1: 121 peptides, 27 chains. Longest chain 7 peptides. Score 0.227 Round 2: 129 peptides, 25 chains. Longest chain 11 peptides. Score 0.299 Round 3: 136 peptides, 24 chains. Longest chain 12 peptides. Score 0.346 Round 4: 132 peptides, 24 chains. Longest chain 13 peptides. Score 0.329 Round 5: 140 peptides, 25 chains. Longest chain 10 peptides. Score 0.344 Taking the results from Round 3 Chains 24, Residues 112, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4543 reflections ( 99.15 % complete ) and 4116 restraints for refining 1842 atoms. 3692 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3553 (Rfree = 0.000) for 1842 atoms. Found 10 (10 requested) and removed 17 (5 requested) atoms. Cycle 37: After refmac, R = 0.3565 (Rfree = 0.000) for 1815 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. Cycle 38: After refmac, R = 0.3439 (Rfree = 0.000) for 1797 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Cycle 39: After refmac, R = 0.3322 (Rfree = 0.000) for 1786 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 40: After refmac, R = 0.3437 (Rfree = 0.000) for 1779 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.23 2.51 Search for helices and strands: 0 residues in 0 chains, 1856 seeds are put forward NCS extension: 0 residues added, 1856 seeds are put forward Round 1: 120 peptides, 27 chains. Longest chain 7 peptides. Score 0.223 Round 2: 121 peptides, 21 chains. Longest chain 11 peptides. Score 0.338 Round 3: 118 peptides, 22 chains. Longest chain 10 peptides. Score 0.307 Round 4: 124 peptides, 21 chains. Longest chain 12 peptides. Score 0.350 Round 5: 135 peptides, 21 chains. Longest chain 12 peptides. Score 0.394 Taking the results from Round 5 Chains 21, Residues 114, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4543 reflections ( 99.15 % complete ) and 4070 restraints for refining 1867 atoms. 3635 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3526 (Rfree = 0.000) for 1867 atoms. Found 10 (10 requested) and removed 14 (5 requested) atoms. Cycle 42: After refmac, R = 0.3546 (Rfree = 0.000) for 1841 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 43: After refmac, R = 0.3524 (Rfree = 0.000) for 1817 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. Cycle 44: After refmac, R = 0.3567 (Rfree = 0.000) for 1808 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. Cycle 45: After refmac, R = 0.3561 (Rfree = 0.000) for 1797 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.18 2.47 Search for helices and strands: 0 residues in 0 chains, 1860 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 1877 seeds are put forward Round 1: 90 peptides, 20 chains. Longest chain 7 peptides. Score 0.218 Round 2: 116 peptides, 21 chains. Longest chain 12 peptides. Score 0.317 Round 3: 114 peptides, 20 chains. Longest chain 12 peptides. Score 0.327 Round 4: 123 peptides, 23 chains. Longest chain 9 peptides. Score 0.310 Round 5: 116 peptides, 22 chains. Longest chain 11 peptides. Score 0.298 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 20, Residues 94, 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. 4543 reflections ( 99.15 % complete ) and 3981 restraints for refining 1804 atoms. 3625 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3791 (Rfree = 0.000) for 1804 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.3738 (Rfree = 0.000) for 1784 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.3461 (Rfree = 0.000) for 1769 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.3240 (Rfree = 0.000) for 1756 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:11:18 GMT 2018 Job finished. TimeTaking 43.39 Used memory is bytes: 8327576