Mon 24 Dec 00:54:00 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-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2ogi-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2ogi-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ogi-3.2-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-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ogi-3.2-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 00:54:04 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-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ogi-3.2-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 297 and 0 Target number of residues in the AU: 297 Target solvent content: 0.6361 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-3.2-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-3.2-parrot-mrncs.fasta_lf Building free atoms model in initial map for 3136 target number of atoms Had to go as low as 0.85 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 3.200 Wilson plot Bfac: 69.78 7378 reflections ( 99.85 % complete ) and 0 restraints for refining 3473 atoms. Observations/parameters ratio is 0.53 ------------------------------------------------------ Starting model: R = 0.3289 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3280 (Rfree = 0.000) for 3473 atoms. Found 31 (31 requested) and removed 29 (15 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.43 3.34 Search for helices and strands: 0 residues in 0 chains, 3555 seeds are put forward NCS extension: 0 residues added, 3555 seeds are put forward Round 1: 180 peptides, 37 chains. Longest chain 9 peptides. Score 0.299 Round 2: 215 peptides, 36 chains. Longest chain 16 peptides. Score 0.443 Round 3: 225 peptides, 34 chains. Longest chain 11 peptides. Score 0.505 Round 4: 224 peptides, 33 chains. Longest chain 25 peptides. Score 0.515 Round 5: 222 peptides, 31 chains. Longest chain 19 peptides. Score 0.536 Taking the results from Round 5 Chains 31, Residues 191, Estimated correctness of the model 22.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7378 reflections ( 99.85 % complete ) and 6414 restraints for refining 2863 atoms. 5681 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2912 (Rfree = 0.000) for 2863 atoms. Found 23 (25 requested) and removed 28 (12 requested) atoms. Failed to save intermediate PDB Cycle 2: After refmac, R = 0.2703 (Rfree = 0.000) for 2833 atoms. Found 24 (25 requested) and removed 18 (12 requested) atoms. Cycle 3: After refmac, R = 0.2610 (Rfree = 0.000) for 2821 atoms. Found 17 (25 requested) and removed 17 (12 requested) atoms. Cycle 4: After refmac, R = 0.2424 (Rfree = 0.000) for 2807 atoms. Found 9 (25 requested) and removed 15 (12 requested) atoms. Cycle 5: After refmac, R = 0.2474 (Rfree = 0.000) for 2787 atoms. Found 17 (25 requested) and removed 15 (12 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.27 3.18 Search for helices and strands: 0 residues in 0 chains, 2926 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 2950 seeds are put forward Round 1: 192 peptides, 36 chains. Longest chain 9 peptides. Score 0.361 Round 2: 216 peptides, 32 chains. Longest chain 17 peptides. Score 0.504 Round 3: 219 peptides, 34 chains. Longest chain 17 peptides. Score 0.485 Round 4: 239 peptides, 34 chains. Longest chain 17 peptides. Score 0.547 Round 5: 233 peptides, 32 chains. Longest chain 17 peptides. Score 0.556 Taking the results from Round 5 Chains 32, Residues 201, Estimated correctness of the model 28.7 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 7378 reflections ( 99.85 % complete ) and 6340 restraints for refining 2841 atoms. 5557 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2570 (Rfree = 0.000) for 2841 atoms. Found 21 (25 requested) and removed 23 (12 requested) atoms. Cycle 7: After refmac, R = 0.2318 (Rfree = 0.000) for 2827 atoms. Found 12 (25 requested) and removed 14 (12 requested) atoms. Cycle 8: After refmac, R = 0.2296 (Rfree = 0.000) for 2806 atoms. Found 13 (25 requested) and removed 16 (12 requested) atoms. Cycle 9: After refmac, R = 0.2125 (Rfree = 0.000) for 2794 atoms. Found 9 (25 requested) and removed 13 (12 requested) atoms. Cycle 10: After refmac, R = 0.2123 (Rfree = 0.000) for 2786 atoms. Found 5 (25 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.24 3.15 Search for helices and strands: 0 residues in 0 chains, 2918 seeds are put forward NCS extension: 14 residues added (5 deleted due to clashes), 2932 seeds are put forward Round 1: 208 peptides, 33 chains. Longest chain 13 peptides. Score 0.463 Round 2: 226 peptides, 31 chains. Longest chain 16 peptides. Score 0.548 Round 3: 238 peptides, 32 chains. Longest chain 15 peptides. Score 0.570 Round 4: 240 peptides, 35 chains. Longest chain 15 peptides. Score 0.537 Round 5: 245 peptides, 32 chains. Longest chain 19 peptides. Score 0.590 Taking the results from Round 5 Chains 32, Residues 213, Estimated correctness of the model 38.3 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 7378 reflections ( 99.85 % complete ) and 6183 restraints for refining 2863 atoms. 5314 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2372 (Rfree = 0.000) for 2863 atoms. Found 16 (25 requested) and removed 17 (12 requested) atoms. Cycle 12: After refmac, R = 0.2232 (Rfree = 0.000) for 2851 atoms. Found 9 (25 requested) and removed 17 (12 requested) atoms. Cycle 13: After refmac, R = 0.2183 (Rfree = 0.000) for 2835 atoms. Found 9 (25 requested) and removed 13 (12 requested) atoms. Cycle 14: After refmac, R = 0.2190 (Rfree = 0.000) for 2824 atoms. Found 15 (25 requested) and removed 12 (12 requested) atoms. Cycle 15: After refmac, R = 0.1998 (Rfree = 0.000) for 2821 atoms. Found 5 (25 requested) and removed 14 (12 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.21 3.13 Search for helices and strands: 0 residues in 0 chains, 2955 seeds are put forward NCS extension: 20 residues added (4 deleted due to clashes), 2975 seeds are put forward Round 1: 213 peptides, 36 chains. Longest chain 14 peptides. Score 0.436 Round 2: 219 peptides, 25 chains. Longest chain 30 peptides. Score 0.605 Round 3: 221 peptides, 28 chains. Longest chain 19 peptides. Score 0.573 Round 4: 223 peptides, 31 chains. Longest chain 18 peptides. Score 0.539 Round 5: 229 peptides, 30 chains. Longest chain 17 peptides. Score 0.570 Taking the results from Round 2 Chains 25, Residues 194, Estimated correctness of the model 42.4 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 7378 reflections ( 99.85 % complete ) and 6214 restraints for refining 2833 atoms. 5436 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2277 (Rfree = 0.000) for 2833 atoms. Found 11 (25 requested) and removed 20 (12 requested) atoms. Cycle 17: After refmac, R = 0.2295 (Rfree = 0.000) for 2818 atoms. Found 18 (25 requested) and removed 17 (12 requested) atoms. Cycle 18: After refmac, R = 0.2052 (Rfree = 0.000) for 2814 atoms. Found 3 (25 requested) and removed 13 (12 requested) atoms. Cycle 19: After refmac, R = 0.2080 (Rfree = 0.000) for 2799 atoms. Found 6 (25 requested) and removed 12 (12 requested) atoms. Cycle 20: After refmac, R = 0.2049 (Rfree = 0.000) for 2791 atoms. Found 2 (25 requested) and removed 14 (12 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.22 3.14 Search for helices and strands: 0 residues in 0 chains, 2917 seeds are put forward NCS extension: 25 residues added (5 deleted due to clashes), 2942 seeds are put forward Round 1: 191 peptides, 36 chains. Longest chain 11 peptides. Score 0.358 Round 2: 242 peptides, 36 chains. Longest chain 18 peptides. Score 0.530 Round 3: 227 peptides, 30 chains. Longest chain 21 peptides. Score 0.564 Round 4: 230 peptides, 32 chains. Longest chain 17 peptides. Score 0.547 Round 5: 242 peptides, 35 chains. Longest chain 18 peptides. Score 0.543 Taking the results from Round 3 Chains 30, Residues 197, Estimated correctness of the model 31.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7378 reflections ( 99.85 % complete ) and 6248 restraints for refining 2863 atoms. 5490 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2223 (Rfree = 0.000) for 2863 atoms. Found 20 (25 requested) and removed 17 (12 requested) atoms. Cycle 22: After refmac, R = 0.2143 (Rfree = 0.000) for 2854 atoms. Found 13 (25 requested) and removed 16 (12 requested) atoms. Cycle 23: After refmac, R = 0.2038 (Rfree = 0.000) for 2847 atoms. Found 14 (25 requested) and removed 15 (12 requested) atoms. Cycle 24: After refmac, R = 0.1994 (Rfree = 0.000) for 2838 atoms. Found 16 (25 requested) and removed 14 (12 requested) atoms. Cycle 25: After refmac, R = 0.1875 (Rfree = 0.000) for 2838 atoms. Found 4 (25 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.22 3.14 Search for helices and strands: 0 residues in 0 chains, 2932 seeds are put forward NCS extension: 30 residues added (1 deleted due to clashes), 2962 seeds are put forward Round 1: 191 peptides, 36 chains. Longest chain 10 peptides. Score 0.358 Round 2: 212 peptides, 32 chains. Longest chain 16 peptides. Score 0.491 Round 3: 220 peptides, 35 chains. Longest chain 21 peptides. Score 0.474 Round 4: 215 peptides, 31 chains. Longest chain 17 peptides. Score 0.515 Round 5: 201 peptides, 32 chains. Longest chain 18 peptides. Score 0.455 Taking the results from Round 4 Chains 32, Residues 184, Estimated correctness of the model 16.1 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 7378 reflections ( 99.85 % complete ) and 6246 restraints for refining 2863 atoms. 5507 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2261 (Rfree = 0.000) for 2863 atoms. Found 18 (25 requested) and removed 19 (12 requested) atoms. Cycle 27: After refmac, R = 0.2115 (Rfree = 0.000) for 2854 atoms. Found 21 (25 requested) and removed 17 (12 requested) atoms. Cycle 28: After refmac, R = 0.1882 (Rfree = 0.000) for 2839 atoms. Found 9 (25 requested) and removed 15 (12 requested) atoms. Cycle 29: After refmac, R = 0.1898 (Rfree = 0.000) for 2830 atoms. Found 5 (25 requested) and removed 13 (12 requested) atoms. Cycle 30: After refmac, R = 0.2484 (Rfree = 0.000) for 2818 atoms. Found 25 (25 requested) and removed 14 (12 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.20 3.12 Search for helices and strands: 0 residues in 0 chains, 2944 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 2967 seeds are put forward Round 1: 172 peptides, 33 chains. Longest chain 10 peptides. Score 0.334 Round 2: 201 peptides, 30 chains. Longest chain 15 peptides. Score 0.484 Round 3: 190 peptides, 27 chains. Longest chain 15 peptides. Score 0.491 Round 4: 216 peptides, 29 chains. Longest chain 17 peptides. Score 0.545 Round 5: 219 peptides, 31 chains. Longest chain 16 peptides. Score 0.527 Taking the results from Round 4 Chains 31, Residues 187, Estimated correctness of the model 25.4 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 7378 reflections ( 99.85 % complete ) and 6180 restraints for refining 2863 atoms. 5423 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2173 (Rfree = 0.000) for 2863 atoms. Found 17 (25 requested) and removed 22 (12 requested) atoms. Cycle 32: After refmac, R = 0.2014 (Rfree = 0.000) for 2845 atoms. Found 11 (25 requested) and removed 13 (12 requested) atoms. Cycle 33: After refmac, R = 0.2013 (Rfree = 0.000) for 2835 atoms. Found 13 (25 requested) and removed 15 (12 requested) atoms. Cycle 34: After refmac, R = 0.1857 (Rfree = 0.000) for 2829 atoms. Found 4 (25 requested) and removed 12 (12 requested) atoms. Cycle 35: After refmac, R = 0.1987 (Rfree = 0.000) for 2818 atoms. Found 16 (25 requested) and removed 16 (12 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.20 3.12 Search for helices and strands: 0 residues in 0 chains, 2910 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 2930 seeds are put forward Round 1: 183 peptides, 34 chains. Longest chain 11 peptides. Score 0.359 Round 2: 202 peptides, 32 chains. Longest chain 18 peptides. Score 0.458 Round 3: 212 peptides, 34 chains. Longest chain 16 peptides. Score 0.462 Round 4: 205 peptides, 31 chains. Longest chain 15 peptides. Score 0.482 Round 5: 207 peptides, 31 chains. Longest chain 14 peptides. Score 0.489 Taking the results from Round 5 Chains 31, Residues 176, Estimated correctness of the model 7.7 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 7378 reflections ( 99.85 % complete ) and 6310 restraints for refining 2863 atoms. 5612 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2144 (Rfree = 0.000) for 2863 atoms. Found 16 (25 requested) and removed 13 (12 requested) atoms. Cycle 37: After refmac, R = 0.2046 (Rfree = 0.000) for 2853 atoms. Found 10 (25 requested) and removed 14 (12 requested) atoms. Cycle 38: After refmac, R = 0.1973 (Rfree = 0.000) for 2848 atoms. Found 9 (25 requested) and removed 14 (12 requested) atoms. Cycle 39: After refmac, R = 0.2165 (Rfree = 0.000) for 2838 atoms. Found 11 (25 requested) and removed 17 (12 requested) atoms. Cycle 40: After refmac, R = 0.1911 (Rfree = 0.000) for 2828 atoms. Found 9 (25 requested) and removed 16 (12 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.20 3.12 Search for helices and strands: 0 residues in 0 chains, 2929 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 2946 seeds are put forward Round 1: 154 peptides, 31 chains. Longest chain 11 peptides. Score 0.296 Round 2: 200 peptides, 34 chains. Longest chain 12 peptides. Score 0.421 Round 3: 186 peptides, 32 chains. Longest chain 12 peptides. Score 0.402 Round 4: 177 peptides, 31 chains. Longest chain 12 peptides. Score 0.385 Round 5: 183 peptides, 30 chains. Longest chain 15 peptides. Score 0.422 Taking the results from Round 5 Chains 30, Residues 153, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7378 reflections ( 99.85 % complete ) and 6457 restraints for refining 2861 atoms. 5875 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2121 (Rfree = 0.000) for 2861 atoms. Found 8 (25 requested) and removed 16 (12 requested) atoms. Cycle 42: After refmac, R = 0.2011 (Rfree = 0.000) for 2849 atoms. Found 20 (25 requested) and removed 13 (12 requested) atoms. Cycle 43: After refmac, R = 0.2001 (Rfree = 0.000) for 2855 atoms. Found 6 (25 requested) and removed 12 (12 requested) atoms. Cycle 44: After refmac, R = 0.1966 (Rfree = 0.000) for 2849 atoms. Found 11 (25 requested) and removed 13 (12 requested) atoms. Cycle 45: After refmac, R = 0.1902 (Rfree = 0.000) for 2845 atoms. Found 2 (25 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.22 3.14 Search for helices and strands: 0 residues in 0 chains, 2932 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 2946 seeds are put forward Round 1: 162 peptides, 28 chains. Longest chain 13 peptides. Score 0.377 Round 2: 174 peptides, 28 chains. Longest chain 12 peptides. Score 0.421 Round 3: 172 peptides, 28 chains. Longest chain 13 peptides. Score 0.414 Round 4: 173 peptides, 28 chains. Longest chain 13 peptides. Score 0.418 Round 5: 178 peptides, 27 chains. Longest chain 15 peptides. Score 0.451 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 27, Residues 151, 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. 7378 reflections ( 99.85 % complete ) and 6431 restraints for refining 2863 atoms. 5854 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1992 (Rfree = 0.000) for 2863 atoms. Found 0 (25 requested) and removed 12 (12 requested) atoms. Cycle 47: After refmac, R = 0.1891 (Rfree = 0.000) for 2846 atoms. Found 0 (25 requested) and removed 7 (12 requested) atoms. Cycle 48: After refmac, R = 0.1869 (Rfree = 0.000) for 2835 atoms. Found 0 (25 requested) and removed 9 (12 requested) atoms. Cycle 49: After refmac, R = 0.1833 (Rfree = 0.000) for 2825 atoms. TimeTaking 31.53