Mon 24 Dec 00:56:07 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 2owp-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2owp-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2owp-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2owp-3.8-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/2owp-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2owp-3.8-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 00:56:11 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/2owp-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2owp-3.8-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 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-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: 152 Cell parameters: 80.518 80.518 116.256 90.000 90.000 120.000 Input sequence file: 2owp-3.8-parrot-mrncs.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 3.802 Wilson plot Bfac: 71.04 4543 reflections ( 99.15 % complete ) and 0 restraints for refining 2271 atoms. Observations/parameters ratio is 0.50 ------------------------------------------------------ Starting model: R = 0.3560 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3531 (Rfree = 0.000) for 2271 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.56 2.77 Search for helices and strands: 0 residues in 0 chains, 2310 seeds are put forward NCS extension: 0 residues added, 2310 seeds are put forward Round 1: 125 peptides, 23 chains. Longest chain 10 peptides. Score 0.318 Round 2: 170 peptides, 26 chains. Longest chain 15 peptides. Score 0.441 Round 3: 175 peptides, 24 chains. Longest chain 22 peptides. Score 0.490 Round 4: 173 peptides, 23 chains. Longest chain 13 peptides. Score 0.498 Round 5: 177 peptides, 22 chains. Longest chain 28 peptides. Score 0.526 Taking the results from Round 5 Chains 22, Residues 155, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4543 reflections ( 99.15 % complete ) and 3981 restraints for refining 1866 atoms. 3383 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3766 (Rfree = 0.000) for 1866 atoms. Found 10 (10 requested) and removed 16 (5 requested) atoms. Cycle 2: After refmac, R = 0.3388 (Rfree = 0.000) for 1816 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. Cycle 3: After refmac, R = 0.3519 (Rfree = 0.000) for 1780 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Cycle 4: After refmac, R = 0.3379 (Rfree = 0.000) for 1745 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. Cycle 5: After refmac, R = 0.3243 (Rfree = 0.000) for 1734 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.51 2.73 Search for helices and strands: 0 residues in 0 chains, 1807 seeds are put forward NCS extension: 28 residues added (0 deleted due to clashes), 1835 seeds are put forward Round 1: 143 peptides, 23 chains. Longest chain 10 peptides. Score 0.391 Round 2: 172 peptides, 24 chains. Longest chain 13 peptides. Score 0.479 Round 3: 179 peptides, 20 chains. Longest chain 28 peptides. Score 0.561 Round 4: 174 peptides, 23 chains. Longest chain 16 peptides. Score 0.501 Round 5: 176 peptides, 22 chains. Longest chain 15 peptides. Score 0.523 Taking the results from Round 3 Chains 21, Residues 159, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 4543 reflections ( 99.15 % complete ) and 3967 restraints for refining 1867 atoms. 3319 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3590 (Rfree = 0.000) for 1867 atoms. Found 10 (10 requested) and removed 18 (5 requested) atoms. Cycle 7: After refmac, R = 0.3591 (Rfree = 0.000) for 1835 atoms. Found 10 (10 requested) and removed 18 (5 requested) atoms. Cycle 8: After refmac, R = 0.3443 (Rfree = 0.000) for 1798 atoms. Found 9 (10 requested) and removed 18 (5 requested) atoms. Cycle 9: After refmac, R = 0.3493 (Rfree = 0.000) for 1774 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. Cycle 10: After refmac, R = 0.3567 (Rfree = 0.000) for 1757 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.40 2.65 Search for helices and strands: 0 residues in 0 chains, 1817 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 1838 seeds are put forward Round 1: 159 peptides, 28 chains. Longest chain 11 peptides. Score 0.368 Round 2: 176 peptides, 24 chains. Longest chain 23 peptides. Score 0.493 Round 3: 185 peptides, 28 chains. Longest chain 15 peptides. Score 0.463 Round 4: 177 peptides, 24 chains. Longest chain 16 peptides. Score 0.496 Round 5: 179 peptides, 28 chains. Longest chain 12 peptides. Score 0.442 Taking the results from Round 4 Chains 24, Residues 153, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4543 reflections ( 99.15 % complete ) and 4016 restraints for refining 1867 atoms. 3428 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3756 (Rfree = 0.000) for 1867 atoms. Found 10 (10 requested) and removed 16 (5 requested) atoms. Cycle 12: After refmac, R = 0.3593 (Rfree = 0.000) for 1837 atoms. Found 10 (10 requested) and removed 24 (5 requested) atoms. Cycle 13: After refmac, R = 0.3414 (Rfree = 0.000) for 1805 atoms. Found 10 (10 requested) and removed 16 (5 requested) atoms. Cycle 14: After refmac, R = 0.3491 (Rfree = 0.000) for 1787 atoms. Found 9 (9 requested) and removed 15 (4 requested) atoms. Cycle 15: After refmac, R = 0.3468 (Rfree = 0.000) for 1765 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.38 2.63 Search for helices and strands: 0 residues in 0 chains, 1838 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 1856 seeds are put forward Round 1: 163 peptides, 29 chains. Longest chain 10 peptides. Score 0.367 Round 2: 170 peptides, 26 chains. Longest chain 16 peptides. Score 0.441 Round 3: 178 peptides, 26 chains. Longest chain 17 peptides. Score 0.469 Round 4: 166 peptides, 22 chains. Longest chain 19 peptides. Score 0.490 Round 5: 170 peptides, 24 chains. Longest chain 16 peptides. Score 0.473 Taking the results from Round 4 Chains 22, Residues 144, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4543 reflections ( 99.15 % complete ) and 4030 restraints for refining 1867 atoms. 3476 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3841 (Rfree = 0.000) for 1867 atoms. Found 10 (10 requested) and removed 14 (5 requested) atoms. Cycle 17: After refmac, R = 0.3670 (Rfree = 0.000) for 1836 atoms. Found 10 (10 requested) and removed 13 (5 requested) atoms. Cycle 18: After refmac, R = 0.3736 (Rfree = 0.000) for 1816 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. Cycle 19: After refmac, R = 0.3608 (Rfree = 0.000) for 1797 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 20: After refmac, R = 0.3726 (Rfree = 0.000) for 1780 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.49 2.72 Search for helices and strands: 0 residues in 0 chains, 1838 seeds are put forward NCS extension: 31 residues added (1 deleted due to clashes), 1869 seeds are put forward Round 1: 143 peptides, 24 chains. Longest chain 12 peptides. Score 0.373 Round 2: 172 peptides, 26 chains. Longest chain 15 peptides. Score 0.448 Round 3: 163 peptides, 24 chains. Longest chain 20 peptides. Score 0.448 Round 4: 156 peptides, 21 chains. Longest chain 18 peptides. Score 0.471 Round 5: 170 peptides, 22 chains. Longest chain 20 peptides. Score 0.503 Taking the results from Round 5 Chains 24, Residues 148, Estimated correctness of the model 0.0 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 4543 reflections ( 99.15 % complete ) and 3831 restraints for refining 1867 atoms. 3177 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3828 (Rfree = 0.000) for 1867 atoms. Found 10 (10 requested) and removed 18 (5 requested) atoms. Cycle 22: After refmac, R = 0.3703 (Rfree = 0.000) for 1839 atoms. Found 10 (10 requested) and removed 20 (5 requested) atoms. Cycle 23: After refmac, R = 0.3687 (Rfree = 0.000) for 1811 atoms. Found 10 (10 requested) and removed 15 (5 requested) atoms. Cycle 24: After refmac, R = 0.3679 (Rfree = 0.000) for 1792 atoms. Found 9 (9 requested) and removed 14 (4 requested) atoms. Cycle 25: After refmac, R = 0.3723 (Rfree = 0.000) for 1769 atoms. Found 9 (9 requested) and removed 14 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.41 2.65 Search for helices and strands: 0 residues in 0 chains, 1821 seeds are put forward NCS extension: 23 residues added (3 deleted due to clashes), 1844 seeds are put forward Round 1: 162 peptides, 25 chains. Longest chain 15 peptides. Score 0.428 Round 2: 156 peptides, 22 chains. Longest chain 21 peptides. Score 0.455 Round 3: 154 peptides, 21 chains. Longest chain 17 peptides. Score 0.464 Round 4: 158 peptides, 24 chains. Longest chain 16 peptides. Score 0.430 Round 5: 159 peptides, 20 chains. Longest chain 19 peptides. Score 0.497 Taking the results from Round 5 Chains 22, Residues 139, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 4543 reflections ( 99.15 % complete ) and 4036 restraints for refining 1866 atoms. 3468 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3831 (Rfree = 0.000) for 1866 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. Cycle 27: After refmac, R = 0.3537 (Rfree = 0.000) for 1851 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. Cycle 28: After refmac, R = 0.3635 (Rfree = 0.000) for 1835 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. Cycle 29: After refmac, R = 0.3557 (Rfree = 0.000) for 1819 atoms. Found 10 (10 requested) and removed 16 (5 requested) atoms. Cycle 30: After refmac, R = 0.3638 (Rfree = 0.000) for 1797 atoms. Found 9 (9 requested) and removed 20 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.46 2.69 Search for helices and strands: 0 residues in 0 chains, 1857 seeds are put forward NCS extension: 28 residues added (5 deleted due to clashes), 1885 seeds are put forward Round 1: 143 peptides, 24 chains. Longest chain 12 peptides. Score 0.373 Round 2: 158 peptides, 23 chains. Longest chain 15 peptides. Score 0.446 Round 3: 154 peptides, 21 chains. Longest chain 16 peptides. Score 0.464 Round 4: 159 peptides, 21 chains. Longest chain 16 peptides. Score 0.481 Round 5: 165 peptides, 21 chains. Longest chain 14 peptides. Score 0.502 Taking the results from Round 5 Chains 21, Residues 144, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4543 reflections ( 99.15 % complete ) and 3873 restraints for refining 1866 atoms. 3276 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3790 (Rfree = 0.000) for 1866 atoms. Found 10 (10 requested) and removed 16 (5 requested) atoms. Cycle 32: After refmac, R = 0.3764 (Rfree = 0.000) for 1836 atoms. Found 10 (10 requested) and removed 20 (5 requested) atoms. Cycle 33: After refmac, R = 0.3711 (Rfree = 0.000) for 1803 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. Cycle 34: After refmac, R = 0.3713 (Rfree = 0.000) for 1781 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Cycle 35: After refmac, R = 0.3625 (Rfree = 0.000) for 1768 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.39 2.64 Search for helices and strands: 0 residues in 0 chains, 1822 seeds are put forward NCS extension: 0 residues added, 1822 seeds are put forward Round 1: 125 peptides, 24 chains. Longest chain 10 peptides. Score 0.300 Round 2: 144 peptides, 21 chains. Longest chain 17 peptides. Score 0.428 Round 3: 156 peptides, 24 chains. Longest chain 19 peptides. Score 0.423 Round 4: 147 peptides, 18 chains. Longest chain 17 peptides. Score 0.488 Round 5: 151 peptides, 19 chains. Longest chain 19 peptides. Score 0.486 Taking the results from Round 4 Chains 19, Residues 129, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4543 reflections ( 99.15 % complete ) and 3995 restraints for refining 1867 atoms. 3463 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 36: After refmac, R = 0.4060 (Rfree = 0.000) for 1867 atoms. Found 10 (10 requested) and removed 28 (5 requested) atoms. Cycle 37: After refmac, R = 0.3803 (Rfree = 0.000) for 1825 atoms. Found 10 (10 requested) and removed 31 (5 requested) atoms. Cycle 38: After refmac, R = 0.3582 (Rfree = 0.000) for 1796 atoms. Found 9 (9 requested) and removed 14 (4 requested) atoms. Cycle 39: After refmac, R = 0.3457 (Rfree = 0.000) for 1783 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. Cycle 40: After refmac, R = 0.3355 (Rfree = 0.000) for 1779 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.97 3.09 Search for helices and strands: 0 residues in 0 chains, 1816 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 1834 seeds are put forward Round 1: 126 peptides, 25 chains. Longest chain 9 peptides. Score 0.286 Round 2: 140 peptides, 21 chains. Longest chain 12 peptides. Score 0.413 Round 3: 150 peptides, 25 chains. Longest chain 14 peptides. Score 0.384 Round 4: 139 peptides, 22 chains. Longest chain 12 peptides. Score 0.392 Round 5: 149 peptides, 19 chains. Longest chain 16 peptides. Score 0.479 Taking the results from Round 5 Chains 20, Residues 130, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4543 reflections ( 99.15 % complete ) and 4010 restraints for refining 1867 atoms. 3466 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3638 (Rfree = 0.000) for 1867 atoms. Found 10 (10 requested) and removed 13 (5 requested) atoms. Cycle 42: After refmac, R = 0.3521 (Rfree = 0.000) for 1851 atoms. Found 10 (10 requested) and removed 18 (5 requested) atoms. Cycle 43: After refmac, R = 0.3376 (Rfree = 0.000) for 1831 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. Cycle 44: After refmac, R = 0.3436 (Rfree = 0.000) for 1823 atoms. Found 10 (10 requested) and removed 13 (5 requested) atoms. Cycle 45: After refmac, R = 0.3480 (Rfree = 0.000) for 1811 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.27 2.54 Search for helices and strands: 0 residues in 0 chains, 1854 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 1873 seeds are put forward Round 1: 114 peptides, 23 chains. Longest chain 10 peptides. Score 0.271 Round 2: 132 peptides, 20 chains. Longest chain 16 peptides. Score 0.400 Round 3: 135 peptides, 20 chains. Longest chain 13 peptides. Score 0.411 Round 4: 142 peptides, 24 chains. Longest chain 15 peptides. Score 0.370 Round 5: 146 peptides, 24 chains. Longest chain 13 peptides. Score 0.385 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 21, Residues 115, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence Sequence coverage is 10 % Consider running further cycles of model building using 2owp-3_warpNtrace.pdb as input Building loops using Loopy2018 21 chains (115 residues) following loop building 2 chains (12 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4543 reflections ( 99.15 % complete ) and 3942 restraints for refining 1867 atoms. 3452 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3833 (Rfree = 0.000) for 1867 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.3695 (Rfree = 0.000) for 1838 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.3480 (Rfree = 0.000) for 1824 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.3675 (Rfree = 0.000) for 1810 atoms. TimeTaking 27.32