Sun 23 Dec 23:53:24 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 2ogi-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2ogi-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2ogi-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ogi-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/2ogi-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ogi-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 ============================================================ Sun 23 Dec 23:53:29 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/2ogi-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ogi-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 271 and 0 Target number of residues in the AU: 271 Target solvent content: 0.6680 Checking the provided sequence file Detected sequence length: 196 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 392 Adjusted target solvent content: 0.52 Input MTZ file: 2ogi-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: 4 Cell parameters: 65.860 52.534 70.037 90.000 114.298 90.000 Input sequence file: 2ogi-3.8-parrot-mrncs.fasta_lf Building free atoms model in initial map for 3136 target number of atoms Had to go as low as 0.90 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: 63.833 3.800 Wilson plot Bfac: 90.13 4427 reflections ( 99.77 % complete ) and 0 restraints for refining 3486 atoms. Observations/parameters ratio is 0.32 ------------------------------------------------------ Starting model: R = 0.3601 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2477 (Rfree = 0.000) for 3486 atoms. Found 17 (19 requested) and removed 127 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.62 3.52 Search for helices and strands: 0 residues in 0 chains, 3406 seeds are put forward NCS extension: 0 residues added, 3406 seeds are put forward Round 1: 112 peptides, 25 chains. Longest chain 7 peptides. Score 0.223 Round 2: 144 peptides, 27 chains. Longest chain 10 peptides. Score 0.324 Round 3: 167 peptides, 28 chains. Longest chain 10 peptides. Score 0.396 Round 4: 169 peptides, 27 chains. Longest chain 10 peptides. Score 0.419 Round 5: 168 peptides, 27 chains. Longest chain 11 peptides. Score 0.415 Taking the results from Round 4 Chains 27, Residues 142, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4427 reflections ( 99.77 % complete ) and 6668 restraints for refining 2836 atoms. 6127 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2405 (Rfree = 0.000) for 2836 atoms. Found 15 (15 requested) and removed 36 (7 requested) atoms. Cycle 2: After refmac, R = 0.2744 (Rfree = 0.000) for 2792 atoms. Found 15 (15 requested) and removed 22 (7 requested) atoms. Cycle 3: After refmac, R = 0.2201 (Rfree = 0.000) for 2769 atoms. Found 11 (15 requested) and removed 19 (7 requested) atoms. Cycle 4: After refmac, R = 0.2213 (Rfree = 0.000) for 2745 atoms. Found 9 (15 requested) and removed 14 (7 requested) atoms. Cycle 5: After refmac, R = 0.2263 (Rfree = 0.000) for 2729 atoms. Found 13 (15 requested) and removed 14 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.71 3.61 Search for helices and strands: 0 residues in 0 chains, 2870 seeds are put forward NCS extension: 10 residues added (2 deleted due to clashes), 2880 seeds are put forward Round 1: 182 peptides, 37 chains. Longest chain 11 peptides. Score 0.307 Round 2: 210 peptides, 32 chains. Longest chain 18 peptides. Score 0.484 Round 3: 208 peptides, 33 chains. Longest chain 17 peptides. Score 0.463 Round 4: 218 peptides, 33 chains. Longest chain 16 peptides. Score 0.496 Round 5: 229 peptides, 32 chains. Longest chain 20 peptides. Score 0.544 Taking the results from Round 5 Chains 34, Residues 197, Estimated correctness of the model 0.0 % 2 chains (19 residues) have been docked in sequence ------------------------------------------------------ 4427 reflections ( 99.77 % complete ) and 6131 restraints for refining 2821 atoms. 5318 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2313 (Rfree = 0.000) for 2821 atoms. Found 15 (15 requested) and removed 31 (7 requested) atoms. Cycle 7: After refmac, R = 0.2227 (Rfree = 0.000) for 2785 atoms. Found 15 (15 requested) and removed 24 (7 requested) atoms. Cycle 8: After refmac, R = 0.1995 (Rfree = 0.000) for 2757 atoms. Found 11 (15 requested) and removed 21 (7 requested) atoms. Cycle 9: After refmac, R = 0.2159 (Rfree = 0.000) for 2733 atoms. Found 15 (15 requested) and removed 15 (7 requested) atoms. Cycle 10: After refmac, R = 0.1951 (Rfree = 0.000) for 2724 atoms. Found 15 (15 requested) and removed 15 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.74 3.64 Search for helices and strands: 0 residues in 0 chains, 2897 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 2916 seeds are put forward Round 1: 174 peptides, 33 chains. Longest chain 9 peptides. Score 0.341 Round 2: 191 peptides, 30 chains. Longest chain 14 peptides. Score 0.450 Round 3: 198 peptides, 30 chains. Longest chain 16 peptides. Score 0.474 Round 4: 199 peptides, 31 chains. Longest chain 15 peptides. Score 0.463 Round 5: 200 peptides, 29 chains. Longest chain 16 peptides. Score 0.495 Taking the results from Round 5 Chains 30, Residues 171, Estimated correctness of the model 0.0 % 3 chains (22 residues) have been docked in sequence ------------------------------------------------------ 4427 reflections ( 99.77 % complete ) and 6279 restraints for refining 2836 atoms. 5559 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2317 (Rfree = 0.000) for 2836 atoms. Found 15 (15 requested) and removed 29 (7 requested) atoms. Cycle 12: After refmac, R = 0.2102 (Rfree = 0.000) for 2806 atoms. Found 9 (15 requested) and removed 23 (7 requested) atoms. Cycle 13: After refmac, R = 0.2028 (Rfree = 0.000) for 2784 atoms. Found 15 (15 requested) and removed 15 (7 requested) atoms. Cycle 14: After refmac, R = 0.1681 (Rfree = 0.000) for 2773 atoms. Found 6 (15 requested) and removed 14 (7 requested) atoms. Cycle 15: After refmac, R = 0.1941 (Rfree = 0.000) for 2762 atoms. Found 8 (15 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.72 3.62 Search for helices and strands: 0 residues in 0 chains, 2883 seeds are put forward NCS extension: 14 residues added (4 deleted due to clashes), 2897 seeds are put forward Round 1: 165 peptides, 32 chains. Longest chain 10 peptides. Score 0.323 Round 2: 187 peptides, 29 chains. Longest chain 15 peptides. Score 0.452 Round 3: 188 peptides, 30 chains. Longest chain 11 peptides. Score 0.440 Round 4: 188 peptides, 29 chains. Longest chain 13 peptides. Score 0.455 Round 5: 193 peptides, 31 chains. Longest chain 13 peptides. Score 0.442 Taking the results from Round 4 Chains 29, Residues 159, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 4427 reflections ( 99.77 % complete ) and 6472 restraints for refining 2836 atoms. 5853 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2107 (Rfree = 0.000) for 2836 atoms. Found 15 (15 requested) and removed 24 (7 requested) atoms. Cycle 17: After refmac, R = 0.2248 (Rfree = 0.000) for 2806 atoms. Found 15 (15 requested) and removed 20 (7 requested) atoms. Cycle 18: After refmac, R = 0.2236 (Rfree = 0.000) for 2788 atoms. Found 15 (15 requested) and removed 15 (7 requested) atoms. Cycle 19: After refmac, R = 0.2170 (Rfree = 0.000) for 2780 atoms. Found 15 (15 requested) and removed 12 (7 requested) atoms. Cycle 20: After refmac, R = 0.2002 (Rfree = 0.000) for 2774 atoms. Found 13 (15 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.79 3.69 Search for helices and strands: 0 residues in 0 chains, 2912 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 2928 seeds are put forward Round 1: 140 peptides, 29 chains. Longest chain 7 peptides. Score 0.273 Round 2: 163 peptides, 31 chains. Longest chain 8 peptides. Score 0.332 Round 3: 175 peptides, 31 chains. Longest chain 9 peptides. Score 0.377 Round 4: 187 peptides, 31 chains. Longest chain 10 peptides. Score 0.421 Round 5: 176 peptides, 30 chains. Longest chain 10 peptides. Score 0.397 Taking the results from Round 4 Chains 31, Residues 156, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 4427 reflections ( 99.77 % complete ) and 6352 restraints for refining 2784 atoms. 5747 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2045 (Rfree = 0.000) for 2784 atoms. Found 9 (15 requested) and removed 20 (7 requested) atoms. Cycle 22: After refmac, R = 0.2032 (Rfree = 0.000) for 2760 atoms. Found 8 (15 requested) and removed 18 (7 requested) atoms. Failed to save intermediate PDB Cycle 23: After refmac, R = 0.1655 (Rfree = 0.000) for 2745 atoms. Found 6 (15 requested) and removed 12 (7 requested) atoms. Cycle 24: After refmac, R = 0.1518 (Rfree = 0.000) for 2736 atoms. Found 4 (15 requested) and removed 13 (7 requested) atoms. Cycle 25: After refmac, R = 0.1473 (Rfree = 0.000) for 2727 atoms. Found 2 (14 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.77 3.67 Search for helices and strands: 0 residues in 0 chains, 2851 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 2862 seeds are put forward Round 1: 148 peptides, 31 chains. Longest chain 7 peptides. Score 0.271 Round 2: 185 peptides, 33 chains. Longest chain 14 peptides. Score 0.383 Round 3: 192 peptides, 33 chains. Longest chain 13 peptides. Score 0.408 Round 4: 203 peptides, 33 chains. Longest chain 12 peptides. Score 0.447 Round 5: 199 peptides, 32 chains. Longest chain 13 peptides. Score 0.448 Taking the results from Round 5 Chains 32, Residues 167, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4427 reflections ( 99.77 % complete ) and 6541 restraints for refining 2834 atoms. 5905 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2275 (Rfree = 0.000) for 2834 atoms. Found 15 (15 requested) and removed 24 (7 requested) atoms. Cycle 27: After refmac, R = 0.2291 (Rfree = 0.000) for 2813 atoms. Found 15 (15 requested) and removed 17 (7 requested) atoms. Cycle 28: After refmac, R = 0.2187 (Rfree = 0.000) for 2799 atoms. Found 15 (15 requested) and removed 16 (7 requested) atoms. Cycle 29: After refmac, R = 0.2031 (Rfree = 0.000) for 2790 atoms. Found 15 (15 requested) and removed 14 (7 requested) atoms. Cycle 30: After refmac, R = 0.2088 (Rfree = 0.000) for 2784 atoms. Found 14 (15 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.76 3.66 Search for helices and strands: 0 residues in 0 chains, 2926 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 2945 seeds are put forward Round 1: 154 peptides, 32 chains. Longest chain 7 peptides. Score 0.279 Round 2: 169 peptides, 30 chains. Longest chain 12 peptides. Score 0.371 Round 3: 179 peptides, 33 chains. Longest chain 8 peptides. Score 0.360 Round 4: 184 peptides, 32 chains. Longest chain 11 peptides. Score 0.395 Round 5: 196 peptides, 32 chains. Longest chain 12 peptides. Score 0.437 Taking the results from Round 5 Chains 32, Residues 164, Estimated correctness of the model 0.0 % 2 chains (16 residues) have been docked in sequence ------------------------------------------------------ 4427 reflections ( 99.77 % complete ) and 6321 restraints for refining 2836 atoms. 5653 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2337 (Rfree = 0.000) for 2836 atoms. Found 15 (15 requested) and removed 23 (7 requested) atoms. Cycle 32: After refmac, R = 0.2122 (Rfree = 0.000) for 2820 atoms. Found 15 (15 requested) and removed 19 (7 requested) atoms. Cycle 33: After refmac, R = 0.2022 (Rfree = 0.000) for 2813 atoms. Found 15 (15 requested) and removed 12 (7 requested) atoms. Cycle 34: After refmac, R = 0.1649 (Rfree = 0.000) for 2814 atoms. Found 6 (15 requested) and removed 9 (7 requested) atoms. Cycle 35: After refmac, R = 0.1530 (Rfree = 0.000) for 2808 atoms. Found 3 (15 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.75 3.65 Search for helices and strands: 0 residues in 0 chains, 2934 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 2949 seeds are put forward Round 1: 146 peptides, 28 chains. Longest chain 9 peptides. Score 0.315 Round 2: 160 peptides, 29 chains. Longest chain 11 peptides. Score 0.353 Round 3: 160 peptides, 29 chains. Longest chain 11 peptides. Score 0.353 Round 4: 160 peptides, 30 chains. Longest chain 13 peptides. Score 0.336 Round 5: 160 peptides, 27 chains. Longest chain 13 peptides. Score 0.386 Taking the results from Round 5 Chains 27, Residues 133, Estimated correctness of the model 0.0 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 4427 reflections ( 99.77 % complete ) and 6489 restraints for refining 2835 atoms. 5933 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2105 (Rfree = 0.000) for 2835 atoms. Found 15 (15 requested) and removed 15 (7 requested) atoms. Cycle 37: After refmac, R = 0.2069 (Rfree = 0.000) for 2815 atoms. Found 13 (15 requested) and removed 9 (7 requested) atoms. Cycle 38: After refmac, R = 0.1969 (Rfree = 0.000) for 2810 atoms. Found 15 (15 requested) and removed 8 (7 requested) atoms. Cycle 39: After refmac, R = 0.1997 (Rfree = 0.000) for 2803 atoms. Found 15 (15 requested) and removed 11 (7 requested) atoms. Cycle 40: After refmac, R = 0.2161 (Rfree = 0.000) for 2802 atoms. Found 15 (15 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.76 3.66 Search for helices and strands: 0 residues in 0 chains, 2940 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 2952 seeds are put forward Round 1: 138 peptides, 31 chains. Longest chain 7 peptides. Score 0.229 Round 2: 155 peptides, 29 chains. Longest chain 9 peptides. Score 0.334 Round 3: 158 peptides, 26 chains. Longest chain 11 peptides. Score 0.395 Round 4: 159 peptides, 27 chains. Longest chain 11 peptides. Score 0.382 Round 5: 156 peptides, 26 chains. Longest chain 13 peptides. Score 0.387 Taking the results from Round 3 Chains 26, Residues 132, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4427 reflections ( 99.77 % complete ) and 6620 restraints for refining 2794 atoms. 6118 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2058 (Rfree = 0.000) for 2794 atoms. Found 15 (15 requested) and removed 13 (7 requested) atoms. Cycle 42: After refmac, R = 0.2006 (Rfree = 0.000) for 2779 atoms. Found 15 (15 requested) and removed 14 (7 requested) atoms. Cycle 43: After refmac, R = 0.1616 (Rfree = 0.000) for 2767 atoms. Found 7 (15 requested) and removed 10 (7 requested) atoms. Cycle 44: After refmac, R = 0.1630 (Rfree = 0.000) for 2761 atoms. Found 8 (15 requested) and removed 8 (7 requested) atoms. Cycle 45: After refmac, R = 0.1472 (Rfree = 0.000) for 2757 atoms. Found 3 (15 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.75 3.65 Search for helices and strands: 0 residues in 0 chains, 2846 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 2858 seeds are put forward Round 1: 123 peptides, 25 chains. Longest chain 7 peptides. Score 0.272 Round 2: 127 peptides, 23 chains. Longest chain 8 peptides. Score 0.325 Round 3: 146 peptides, 26 chains. Longest chain 11 peptides. Score 0.349 Round 4: 145 peptides, 25 chains. Longest chain 16 peptides. Score 0.362 Round 5: 139 peptides, 25 chains. Longest chain 9 peptides. Score 0.338 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 25, Residues 120, 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 2ogi-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4427 reflections ( 99.77 % complete ) and 6795 restraints for refining 2821 atoms. 6340 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2033 (Rfree = 0.000) for 2821 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Failed to save intermediate PDB Cycle 47: After refmac, R = 0.2080 (Rfree = 0.000) for 2802 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.2017 (Rfree = 0.000) for 2790 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.1635 (Rfree = 0.000) for 2773 atoms. TimeTaking 38.05