Mon 24 Dec 07:58:00 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2oyo-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2oyo-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2oyo-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2oyo-3.2-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2oyo-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2oyo-3.2-parrot-noncs ############### 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 07:58:04 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/noncs/ArpWArp/wArpResults/WorkingDir/2oyo-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2oyo-3.2-parrot-noncs/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 288 and 0 Target number of residues in the AU: 288 Target solvent content: 0.6274 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: 0.49 Input MTZ file: 2oyo-3.2-parrot-noncs.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: 155 Cell parameters: 135.664 135.664 118.109 90.000 90.000 120.000 Input sequence file: 2oyo-3.2-parrot-noncs.fasta_lf Building free atoms model in initial map for 3136 target number of atoms Had to go as low as 0.80 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: 83.295 3.200 Wilson plot Bfac: 64.87 7050 reflections ( 99.87 % complete ) and 0 restraints for refining 3514 atoms. Observations/parameters ratio is 0.50 ------------------------------------------------------ Starting model: R = 0.3181 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2507 (Rfree = 0.000) for 3514 atoms. Found 20 (31 requested) and removed 25 (15 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.18 3.22 Search for helices and strands: 0 residues in 0 chains, 3604 seeds are put forward NCS extension: 0 residues added, 3604 seeds are put forward Round 1: 208 peptides, 40 chains. Longest chain 8 peptides. Score 0.366 Round 2: 247 peptides, 35 chains. Longest chain 15 peptides. Score 0.573 Round 3: 250 peptides, 33 chains. Longest chain 16 peptides. Score 0.607 Round 4: 268 peptides, 32 chains. Longest chain 19 peptides. Score 0.665 Round 5: 258 peptides, 31 chains. Longest chain 28 peptides. Score 0.651 Taking the results from Round 4 Chains 35, Residues 236, Estimated correctness of the model 57.4 % 4 chains (41 residues) have been docked in sequence ------------------------------------------------------ 7050 reflections ( 99.87 % complete ) and 5683 restraints for refining 2862 atoms. 4626 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2531 (Rfree = 0.000) for 2862 atoms. Found 15 (25 requested) and removed 26 (12 requested) atoms. Cycle 2: After refmac, R = 0.2354 (Rfree = 0.000) for 2819 atoms. Found 6 (25 requested) and removed 14 (12 requested) atoms. Cycle 3: After refmac, R = 0.2277 (Rfree = 0.000) for 2797 atoms. Found 4 (25 requested) and removed 12 (12 requested) atoms. Cycle 4: After refmac, R = 0.2221 (Rfree = 0.000) for 2784 atoms. Found 7 (25 requested) and removed 12 (12 requested) atoms. Cycle 5: After refmac, R = 0.2165 (Rfree = 0.000) for 2774 atoms. Found 1 (24 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.19 3.23 Search for helices and strands: 0 residues in 0 chains, 2888 seeds are put forward NCS extension: 18 residues added (6 deleted due to clashes), 2906 seeds are put forward Round 1: 231 peptides, 32 chains. Longest chain 18 peptides. Score 0.564 Round 2: 254 peptides, 30 chains. Longest chain 24 peptides. Score 0.653 Round 3: 257 peptides, 29 chains. Longest chain 24 peptides. Score 0.671 Round 4: 258 peptides, 31 chains. Longest chain 26 peptides. Score 0.651 Round 5: 253 peptides, 31 chains. Longest chain 21 peptides. Score 0.639 Taking the results from Round 3 Chains 29, Residues 228, Estimated correctness of the model 58.8 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 7050 reflections ( 99.87 % complete ) and 5989 restraints for refining 2807 atoms. 5076 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2381 (Rfree = 0.000) for 2807 atoms. Found 8 (25 requested) and removed 17 (12 requested) atoms. Cycle 7: After refmac, R = 0.2238 (Rfree = 0.000) for 2793 atoms. Found 4 (25 requested) and removed 16 (12 requested) atoms. Cycle 8: After refmac, R = 0.2158 (Rfree = 0.000) for 2777 atoms. Found 2 (24 requested) and removed 12 (12 requested) atoms. Cycle 9: After refmac, R = 0.2120 (Rfree = 0.000) for 2763 atoms. Found 5 (24 requested) and removed 12 (12 requested) atoms. Cycle 10: After refmac, R = 0.2162 (Rfree = 0.000) for 2754 atoms. Found 2 (24 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.17 3.21 Search for helices and strands: 0 residues in 0 chains, 2880 seeds are put forward NCS extension: 28 residues added (1 deleted due to clashes), 2908 seeds are put forward Round 1: 226 peptides, 33 chains. Longest chain 20 peptides. Score 0.535 Round 2: 259 peptides, 35 chains. Longest chain 19 peptides. Score 0.607 Round 3: 259 peptides, 30 chains. Longest chain 18 peptides. Score 0.665 Round 4: 251 peptides, 29 chains. Longest chain 26 peptides. Score 0.657 Round 5: 243 peptides, 31 chains. Longest chain 23 peptides. Score 0.612 Taking the results from Round 3 Chains 34, Residues 229, Estimated correctness of the model 57.4 % 4 chains (39 residues) have been docked in sequence ------------------------------------------------------ 7050 reflections ( 99.87 % complete ) and 5884 restraints for refining 2860 atoms. 4836 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2391 (Rfree = 0.000) for 2860 atoms. Found 16 (25 requested) and removed 18 (12 requested) atoms. Cycle 12: After refmac, R = 0.2208 (Rfree = 0.000) for 2857 atoms. Found 5 (25 requested) and removed 18 (12 requested) atoms. Cycle 13: After refmac, R = 0.2115 (Rfree = 0.000) for 2838 atoms. Found 3 (25 requested) and removed 12 (12 requested) atoms. Cycle 14: After refmac, R = 0.2055 (Rfree = 0.000) for 2826 atoms. Found 2 (25 requested) and removed 12 (12 requested) atoms. Cycle 15: After refmac, R = 0.2029 (Rfree = 0.000) for 2816 atoms. Found 1 (25 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.21 3.25 Search for helices and strands: 0 residues in 0 chains, 2915 seeds are put forward NCS extension: 0 residues added, 2915 seeds are put forward Round 1: 229 peptides, 35 chains. Longest chain 21 peptides. Score 0.517 Round 2: 252 peptides, 29 chains. Longest chain 22 peptides. Score 0.659 Round 3: 257 peptides, 29 chains. Longest chain 25 peptides. Score 0.671 Round 4: 249 peptides, 32 chains. Longest chain 21 peptides. Score 0.616 Round 5: 253 peptides, 30 chains. Longest chain 21 peptides. Score 0.650 Taking the results from Round 3 Chains 33, Residues 228, Estimated correctness of the model 58.8 % 6 chains (60 residues) have been docked in sequence ------------------------------------------------------ 7050 reflections ( 99.87 % complete ) and 5643 restraints for refining 2862 atoms. 4550 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2382 (Rfree = 0.000) for 2862 atoms. Found 8 (25 requested) and removed 23 (12 requested) atoms. Cycle 17: After refmac, R = 0.2234 (Rfree = 0.000) for 2836 atoms. Found 8 (25 requested) and removed 15 (12 requested) atoms. Cycle 18: After refmac, R = 0.2192 (Rfree = 0.000) for 2822 atoms. Found 4 (25 requested) and removed 13 (12 requested) atoms. Cycle 19: After refmac, R = 0.2185 (Rfree = 0.000) for 2808 atoms. Found 4 (25 requested) and removed 12 (12 requested) atoms. Cycle 20: After refmac, R = 0.2146 (Rfree = 0.000) for 2797 atoms. Found 6 (25 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.19 3.23 Search for helices and strands: 0 residues in 0 chains, 2919 seeds are put forward NCS extension: 21 residues added (5 deleted due to clashes), 2940 seeds are put forward Round 1: 216 peptides, 32 chains. Longest chain 21 peptides. Score 0.517 Round 2: 245 peptides, 30 chains. Longest chain 21 peptides. Score 0.630 Round 3: 253 peptides, 34 chains. Longest chain 26 peptides. Score 0.602 Round 4: 250 peptides, 32 chains. Longest chain 21 peptides. Score 0.619 Round 5: 245 peptides, 30 chains. Longest chain 20 peptides. Score 0.630 Taking the results from Round 5 Chains 34, Residues 215, Estimated correctness of the model 48.9 % 4 chains (40 residues) have been docked in sequence ------------------------------------------------------ 7050 reflections ( 99.87 % complete ) and 6003 restraints for refining 2863 atoms. 5039 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2494 (Rfree = 0.000) for 2863 atoms. Found 18 (25 requested) and removed 21 (12 requested) atoms. Cycle 22: After refmac, R = 0.2303 (Rfree = 0.000) for 2858 atoms. Found 2 (25 requested) and removed 15 (12 requested) atoms. Cycle 23: After refmac, R = 0.2222 (Rfree = 0.000) for 2840 atoms. Found 8 (25 requested) and removed 12 (12 requested) atoms. Cycle 24: After refmac, R = 0.2117 (Rfree = 0.000) for 2835 atoms. Found 2 (25 requested) and removed 12 (12 requested) atoms. Cycle 25: After refmac, R = 0.2017 (Rfree = 0.000) for 2817 atoms. Found 4 (25 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.21 3.25 Search for helices and strands: 0 residues in 0 chains, 2939 seeds are put forward NCS extension: 13 residues added (3 deleted due to clashes), 2952 seeds are put forward Round 1: 196 peptides, 28 chains. Longest chain 32 peptides. Score 0.509 Round 2: 216 peptides, 29 chains. Longest chain 23 peptides. Score 0.559 Round 3: 228 peptides, 32 chains. Longest chain 23 peptides. Score 0.555 Round 4: 229 peptides, 30 chains. Longest chain 17 peptides. Score 0.585 Round 5: 226 peptides, 31 chains. Longest chain 23 peptides. Score 0.563 Taking the results from Round 4 Chains 30, Residues 199, Estimated correctness of the model 37.0 % 2 chains (24 residues) have been docked in sequence ------------------------------------------------------ 7050 reflections ( 99.87 % complete ) and 6210 restraints for refining 2863 atoms. 5351 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2370 (Rfree = 0.000) for 2863 atoms. Found 21 (25 requested) and removed 12 (12 requested) atoms. Cycle 27: After refmac, R = 0.2168 (Rfree = 0.000) for 2865 atoms. Found 2 (25 requested) and removed 16 (12 requested) atoms. Cycle 28: After refmac, R = 0.2073 (Rfree = 0.000) for 2844 atoms. Found 4 (25 requested) and removed 12 (12 requested) atoms. Cycle 29: After refmac, R = 0.2021 (Rfree = 0.000) for 2831 atoms. Found 2 (25 requested) and removed 12 (12 requested) atoms. Cycle 30: After refmac, R = 0.1983 (Rfree = 0.000) for 2820 atoms. Found 2 (25 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.18 3.22 Search for helices and strands: 0 residues in 0 chains, 2920 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 2939 seeds are put forward Round 1: 181 peptides, 25 chains. Longest chain 22 peptides. Score 0.504 Round 2: 213 peptides, 27 chains. Longest chain 23 peptides. Score 0.577 Round 3: 217 peptides, 25 chains. Longest chain 26 peptides. Score 0.615 Round 4: 220 peptides, 30 chains. Longest chain 24 peptides. Score 0.558 Round 5: 220 peptides, 28 chains. Longest chain 27 peptides. Score 0.585 Taking the results from Round 3 Chains 28, Residues 192, Estimated correctness of the model 45.0 % 4 chains (61 residues) have been docked in sequence ------------------------------------------------------ 7050 reflections ( 99.87 % complete ) and 5832 restraints for refining 2862 atoms. 4859 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2318 (Rfree = 0.000) for 2862 atoms. Found 24 (25 requested) and removed 22 (12 requested) atoms. Cycle 32: After refmac, R = 0.2137 (Rfree = 0.000) for 2862 atoms. Found 5 (25 requested) and removed 13 (12 requested) atoms. Cycle 33: After refmac, R = 0.2059 (Rfree = 0.000) for 2853 atoms. Found 7 (25 requested) and removed 12 (12 requested) atoms. Cycle 34: After refmac, R = 0.1963 (Rfree = 0.000) for 2847 atoms. Found 1 (25 requested) and removed 12 (12 requested) atoms. Cycle 35: After refmac, R = 0.1935 (Rfree = 0.000) for 2834 atoms. Found 3 (25 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.17 3.21 Search for helices and strands: 0 residues in 0 chains, 2911 seeds are put forward NCS extension: 25 residues added (3 deleted due to clashes), 2936 seeds are put forward Round 1: 167 peptides, 28 chains. Longest chain 17 peptides. Score 0.405 Round 2: 182 peptides, 27 chains. Longest chain 14 peptides. Score 0.476 Round 3: 194 peptides, 28 chains. Longest chain 24 peptides. Score 0.503 Round 4: 185 peptides, 24 chains. Longest chain 15 peptides. Score 0.532 Round 5: 190 peptides, 26 chains. Longest chain 24 peptides. Score 0.519 Taking the results from Round 4 Chains 26, Residues 161, Estimated correctness of the model 21.4 % 4 chains (27 residues) have been docked in sequence ------------------------------------------------------ 7050 reflections ( 99.87 % complete ) and 6459 restraints for refining 2863 atoms. 5752 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2088 (Rfree = 0.000) for 2863 atoms. Found 19 (25 requested) and removed 14 (12 requested) atoms. Cycle 37: After refmac, R = 0.1973 (Rfree = 0.000) for 2866 atoms. Found 7 (25 requested) and removed 12 (12 requested) atoms. Cycle 38: After refmac, R = 0.1912 (Rfree = 0.000) for 2856 atoms. Found 3 (25 requested) and removed 12 (12 requested) atoms. Cycle 39: After refmac, R = 0.1916 (Rfree = 0.000) for 2843 atoms. Found 3 (25 requested) and removed 12 (12 requested) atoms. Cycle 40: After refmac, R = 0.1871 (Rfree = 0.000) for 2830 atoms. Found 3 (25 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.14 3.18 Search for helices and strands: 0 residues in 0 chains, 2948 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 2967 seeds are put forward Round 1: 173 peptides, 30 chains. Longest chain 14 peptides. Score 0.395 Round 2: 189 peptides, 28 chains. Longest chain 19 peptides. Score 0.486 Round 3: 189 peptides, 25 chains. Longest chain 23 peptides. Score 0.531 Round 4: 179 peptides, 26 chains. Longest chain 17 peptides. Score 0.482 Round 5: 178 peptides, 25 chains. Longest chain 21 peptides. Score 0.494 Taking the results from Round 3 Chains 27, Residues 164, Estimated correctness of the model 21.1 % 3 chains (28 residues) have been docked in sequence ------------------------------------------------------ 7050 reflections ( 99.87 % complete ) and 6279 restraints for refining 2861 atoms. 5553 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2008 (Rfree = 0.000) for 2861 atoms. Found 18 (25 requested) and removed 14 (12 requested) atoms. Cycle 42: After refmac, R = 0.2151 (Rfree = 0.000) for 2860 atoms. Found 19 (25 requested) and removed 13 (12 requested) atoms. Cycle 43: After refmac, R = 0.1777 (Rfree = 0.000) for 2855 atoms. Found 5 (25 requested) and removed 13 (12 requested) atoms. Cycle 44: After refmac, R = 0.2211 (Rfree = 0.000) for 2842 atoms. Found 25 (25 requested) and removed 16 (12 requested) atoms. Cycle 45: After refmac, R = 0.1788 (Rfree = 0.000) for 2849 atoms. Found 10 (25 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.15 3.19 Search for helices and strands: 0 residues in 0 chains, 2975 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 2990 seeds are put forward Round 1: 154 peptides, 26 chains. Longest chain 17 peptides. Score 0.389 Round 2: 164 peptides, 28 chains. Longest chain 16 peptides. Score 0.394 Round 3: 170 peptides, 26 chains. Longest chain 21 peptides. Score 0.449 Round 4: 170 peptides, 26 chains. Longest chain 16 peptides. Score 0.449 Round 5: 172 peptides, 26 chains. Longest chain 21 peptides. Score 0.457 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 26, Residues 146, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence Sequence coverage is 5 % Consider running further cycles of model building using 2oyo-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7050 reflections ( 99.87 % complete ) and 6576 restraints for refining 2862 atoms. 5991 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1947 (Rfree = 0.000) for 2862 atoms. Found 0 (25 requested) and removed 12 (12 requested) atoms. Cycle 47: After refmac, R = 0.1878 (Rfree = 0.000) for 2841 atoms. Found 0 (25 requested) and removed 12 (12 requested) atoms. Cycle 48: After refmac, R = 0.1897 (Rfree = 0.000) for 2829 atoms. Found 0 (25 requested) and removed 11 (12 requested) atoms. Cycle 49: After refmac, R = 0.1758 (Rfree = 0.000) for 2815 atoms. TimeTaking 38.05