null Mon 24 Dec 08:04:59 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 2ogi-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2ogi-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2ogi-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ogi-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/2ogi-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ogi-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 08:05:04 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/2ogi-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ogi-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 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-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: 4 Cell parameters: 65.860 52.534 70.037 90.000 114.298 90.000 Input sequence file: 2ogi-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 0.85 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 3492 atoms. Observations/parameters ratio is 0.53 ------------------------------------------------------ Starting model: R = 0.3367 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3327 (Rfree = 0.000) for 3492 atoms. Found 31 (31 requested) and removed 31 (15 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.46 3.37 Search for helices and strands: 0 residues in 0 chains, 3578 seeds are put forward NCS extension: 0 residues added, 3578 seeds are put forward Round 1: 180 peptides, 38 chains. Longest chain 9 peptides. Score 0.283 Round 2: 219 peptides, 37 chains. Longest chain 16 peptides. Score 0.442 Round 3: 212 peptides, 29 chains. Longest chain 21 peptides. Score 0.533 Round 4: 217 peptides, 34 chains. Longest chain 16 peptides. Score 0.479 Round 5: 235 peptides, 35 chains. Longest chain 21 peptides. Score 0.522 Taking the results from Round 3 Chains 30, Residues 183, Estimated correctness of the model 21.7 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 7378 reflections ( 99.85 % complete ) and 6272 restraints for refining 2862 atoms. 5544 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2722 (Rfree = 0.000) for 2862 atoms. Found 23 (25 requested) and removed 21 (12 requested) atoms. Cycle 2: After refmac, R = 0.2744 (Rfree = 0.000) for 2820 atoms. Found 25 (25 requested) and removed 17 (12 requested) atoms. Cycle 3: After refmac, R = 0.2681 (Rfree = 0.000) for 2813 atoms. Found 25 (25 requested) and removed 21 (12 requested) atoms. Cycle 4: After refmac, R = 0.2440 (Rfree = 0.000) for 2796 atoms. Found 22 (25 requested) and removed 15 (12 requested) atoms. Cycle 5: After refmac, R = 0.2212 (Rfree = 0.000) for 2789 atoms. Found 9 (25 requested) and removed 17 (12 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.23 3.15 Search for helices and strands: 0 residues in 0 chains, 2947 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 2970 seeds are put forward Round 1: 198 peptides, 37 chains. Longest chain 12 peptides. Score 0.368 Round 2: 234 peptides, 32 chains. Longest chain 17 peptides. Score 0.558 Round 3: 242 peptides, 33 chains. Longest chain 17 peptides. Score 0.569 Round 4: 231 peptides, 33 chains. Longest chain 17 peptides. Score 0.537 Round 5: 238 peptides, 32 chains. Longest chain 16 peptides. Score 0.570 Taking the results from Round 5 Chains 32, Residues 206, Estimated correctness of the model 32.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7378 reflections ( 99.85 % complete ) and 6303 restraints for refining 2826 atoms. 5511 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2531 (Rfree = 0.000) for 2826 atoms. Found 20 (25 requested) and removed 25 (12 requested) atoms. Cycle 7: After refmac, R = 0.2396 (Rfree = 0.000) for 2806 atoms. Found 16 (25 requested) and removed 19 (12 requested) atoms. Cycle 8: After refmac, R = 0.2030 (Rfree = 0.000) for 2798 atoms. Found 9 (25 requested) and removed 18 (12 requested) atoms. Cycle 9: After refmac, R = 0.2282 (Rfree = 0.000) for 2784 atoms. Found 14 (25 requested) and removed 15 (12 requested) atoms. Cycle 10: After refmac, R = 0.2116 (Rfree = 0.000) for 2779 atoms. Found 11 (24 requested) and removed 14 (12 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.23 3.15 Search for helices and strands: 0 residues in 0 chains, 2923 seeds are put forward NCS extension: 14 residues added (3 deleted due to clashes), 2937 seeds are put forward Round 1: 221 peptides, 37 chains. Longest chain 17 peptides. Score 0.449 Round 2: 224 peptides, 28 chains. Longest chain 16 peptides. Score 0.581 Round 3: 215 peptides, 26 chains. Longest chain 28 peptides. Score 0.581 Round 4: 221 peptides, 25 chains. Longest chain 33 peptides. Score 0.611 Round 5: 243 peptides, 34 chains. Longest chain 16 peptides. Score 0.559 Taking the results from Round 4 Chains 26, Residues 196, Estimated correctness of the model 44.0 % 3 chains (53 residues) have been docked in sequence ------------------------------------------------------ 7378 reflections ( 99.85 % complete ) and 5865 restraints for refining 2863 atoms. 4896 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2446 (Rfree = 0.000) for 2863 atoms. Found 17 (25 requested) and removed 25 (12 requested) atoms. Cycle 12: After refmac, R = 0.2256 (Rfree = 0.000) for 2835 atoms. Found 11 (25 requested) and removed 16 (12 requested) atoms. Cycle 13: After refmac, R = 0.2145 (Rfree = 0.000) for 2824 atoms. Found 11 (25 requested) and removed 13 (12 requested) atoms. Cycle 14: After refmac, R = 0.2036 (Rfree = 0.000) for 2814 atoms. Found 11 (25 requested) and removed 13 (12 requested) atoms. Cycle 15: After refmac, R = 0.1946 (Rfree = 0.000) for 2807 atoms. Found 9 (25 requested) and removed 17 (12 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.24 3.15 Search for helices and strands: 0 residues in 0 chains, 2911 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 2926 seeds are put forward Round 1: 209 peptides, 35 chains. Longest chain 14 peptides. Score 0.438 Round 2: 232 peptides, 29 chains. Longest chain 27 peptides. Score 0.591 Round 3: 232 peptides, 32 chains. Longest chain 30 peptides. Score 0.553 Round 4: 233 peptides, 30 chains. Longest chain 21 peptides. Score 0.581 Round 5: 239 peptides, 28 chains. Longest chain 24 peptides. Score 0.622 Taking the results from Round 5 Chains 30, Residues 211, Estimated correctness of the model 46.9 % 2 chains (26 residues) have been docked in sequence ------------------------------------------------------ 7378 reflections ( 99.85 % complete ) and 5959 restraints for refining 2863 atoms. 5041 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2272 (Rfree = 0.000) for 2863 atoms. Found 25 (25 requested) and removed 18 (12 requested) atoms. Cycle 17: After refmac, R = 0.2077 (Rfree = 0.000) for 2861 atoms. Found 12 (25 requested) and removed 14 (12 requested) atoms. Cycle 18: After refmac, R = 0.1976 (Rfree = 0.000) for 2856 atoms. Found 9 (25 requested) and removed 13 (12 requested) atoms. Cycle 19: After refmac, R = 0.1927 (Rfree = 0.000) for 2848 atoms. Found 7 (25 requested) and removed 14 (12 requested) atoms. Cycle 20: After refmac, R = 0.1873 (Rfree = 0.000) for 2837 atoms. Found 9 (25 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.25 3.16 Search for helices and strands: 0 residues in 0 chains, 2952 seeds are put forward NCS extension: 30 residues added (1 deleted due to clashes), 2982 seeds are put forward Round 1: 200 peptides, 31 chains. Longest chain 16 peptides. Score 0.466 Round 2: 233 peptides, 32 chains. Longest chain 16 peptides. Score 0.556 Round 3: 211 peptides, 29 chains. Longest chain 15 peptides. Score 0.530 Round 4: 235 peptides, 29 chains. Longest chain 20 peptides. Score 0.599 Round 5: 226 peptides, 33 chains. Longest chain 17 peptides. Score 0.521 Taking the results from Round 4 Chains 30, Residues 206, Estimated correctness of the model 40.8 % 2 chains (19 residues) have been docked in sequence ------------------------------------------------------ 7378 reflections ( 99.85 % complete ) and 6007 restraints for refining 2863 atoms. 5148 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2163 (Rfree = 0.000) for 2863 atoms. Found 20 (25 requested) and removed 13 (12 requested) atoms. Cycle 22: After refmac, R = 0.2013 (Rfree = 0.000) for 2863 atoms. Found 5 (25 requested) and removed 13 (12 requested) atoms. Cycle 23: After refmac, R = 0.1984 (Rfree = 0.000) for 2852 atoms. Found 4 (25 requested) and removed 14 (12 requested) atoms. Cycle 24: After refmac, R = 0.2004 (Rfree = 0.000) for 2839 atoms. Found 5 (25 requested) and removed 14 (12 requested) atoms. Cycle 25: After refmac, R = 0.1882 (Rfree = 0.000) for 2826 atoms. Found 5 (25 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.27 3.18 Search for helices and strands: 0 residues in 0 chains, 2943 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 2961 seeds are put forward Round 1: 211 peptides, 37 chains. Longest chain 15 peptides. Score 0.415 Round 2: 218 peptides, 28 chains. Longest chain 34 peptides. Score 0.564 Round 3: 230 peptides, 31 chains. Longest chain 28 peptides. Score 0.560 Round 4: 236 peptides, 31 chains. Longest chain 32 peptides. Score 0.577 Round 5: 237 peptides, 29 chains. Longest chain 20 peptides. Score 0.604 Taking the results from Round 5 Chains 29, Residues 208, Estimated correctness of the model 42.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7378 reflections ( 99.85 % complete ) and 6240 restraints for refining 2863 atoms. 5437 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2212 (Rfree = 0.000) for 2863 atoms. Found 23 (25 requested) and removed 14 (12 requested) atoms. Cycle 27: After refmac, R = 0.2075 (Rfree = 0.000) for 2866 atoms. Found 10 (25 requested) and removed 14 (12 requested) atoms. Cycle 28: After refmac, R = 0.1990 (Rfree = 0.000) for 2856 atoms. Found 7 (25 requested) and removed 12 (12 requested) atoms. Cycle 29: After refmac, R = 0.2013 (Rfree = 0.000) for 2847 atoms. Found 4 (25 requested) and removed 12 (12 requested) atoms. Cycle 30: After refmac, R = 0.1894 (Rfree = 0.000) for 2838 atoms. Found 2 (25 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.27 3.18 Search for helices and strands: 0 residues in 0 chains, 2945 seeds are put forward NCS extension: 24 residues added (4 deleted due to clashes), 2969 seeds are put forward Round 1: 190 peptides, 33 chains. Longest chain 12 peptides. Score 0.401 Round 2: 216 peptides, 32 chains. Longest chain 14 peptides. Score 0.504 Round 3: 216 peptides, 33 chains. Longest chain 15 peptides. Score 0.490 Round 4: 221 peptides, 32 chains. Longest chain 14 peptides. Score 0.519 Round 5: 216 peptides, 32 chains. Longest chain 18 peptides. Score 0.504 Taking the results from Round 4 Chains 32, Residues 189, Estimated correctness of the model 17.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7378 reflections ( 99.85 % complete ) and 6499 restraints for refining 2863 atoms. 5775 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2152 (Rfree = 0.000) for 2863 atoms. Found 14 (25 requested) and removed 12 (12 requested) atoms. Cycle 32: After refmac, R = 0.1975 (Rfree = 0.000) for 2857 atoms. Found 2 (25 requested) and removed 13 (12 requested) atoms. Cycle 33: After refmac, R = 0.2017 (Rfree = 0.000) for 2838 atoms. Found 9 (25 requested) and removed 14 (12 requested) atoms. Cycle 34: After refmac, R = 0.1879 (Rfree = 0.000) for 2833 atoms. Found 3 (25 requested) and removed 12 (12 requested) atoms. Cycle 35: After refmac, R = 0.1895 (Rfree = 0.000) for 2819 atoms. Found 6 (25 requested) and removed 14 (12 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.25 3.16 Search for helices and strands: 0 residues in 0 chains, 2930 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 2947 seeds are put forward Round 1: 158 peptides, 28 chains. Longest chain 12 peptides. Score 0.362 Round 2: 184 peptides, 28 chains. Longest chain 14 peptides. Score 0.456 Round 3: 176 peptides, 26 chains. Longest chain 18 peptides. Score 0.459 Round 4: 191 peptides, 28 chains. Longest chain 14 peptides. Score 0.480 Round 5: 196 peptides, 29 chains. Longest chain 18 peptides. Score 0.482 Taking the results from Round 5 Chains 29, Residues 167, Estimated correctness of the model 5.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7378 reflections ( 99.85 % complete ) and 6479 restraints for refining 2863 atoms. 5840 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2047 (Rfree = 0.000) for 2863 atoms. Found 19 (25 requested) and removed 13 (12 requested) atoms. Cycle 37: After refmac, R = 0.1965 (Rfree = 0.000) for 2864 atoms. Found 11 (25 requested) and removed 12 (12 requested) atoms. Cycle 38: After refmac, R = 0.1923 (Rfree = 0.000) for 2857 atoms. Found 8 (25 requested) and removed 14 (12 requested) atoms. Cycle 39: After refmac, R = 0.1981 (Rfree = 0.000) for 2849 atoms. Found 20 (25 requested) and removed 16 (12 requested) atoms. Cycle 40: After refmac, R = 0.1826 (Rfree = 0.000) for 2849 atoms. Found 11 (25 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.25 3.16 Search for helices and strands: 0 residues in 0 chains, 2963 seeds are put forward NCS extension: 31 residues added (3 deleted due to clashes), 2994 seeds are put forward Round 1: 150 peptides, 28 chains. Longest chain 16 peptides. Score 0.331 Round 2: 186 peptides, 28 chains. Longest chain 19 peptides. Score 0.463 Round 3: 193 peptides, 31 chains. Longest chain 19 peptides. Score 0.442 Round 4: 192 peptides, 32 chains. Longest chain 18 peptides. Score 0.423 Round 5: 189 peptides, 28 chains. Longest chain 20 peptides. Score 0.473 Taking the results from Round 5 Chains 28, Residues 161, Estimated correctness of the model 2.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7378 reflections ( 99.85 % complete ) and 6542 restraints for refining 2863 atoms. 5926 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2091 (Rfree = 0.000) for 2863 atoms. Found 25 (25 requested) and removed 12 (12 requested) atoms. Cycle 42: After refmac, R = 0.1889 (Rfree = 0.000) for 2867 atoms. Found 7 (25 requested) and removed 12 (12 requested) atoms. Cycle 43: After refmac, R = 0.1775 (Rfree = 0.000) for 2857 atoms. Found 8 (25 requested) and removed 12 (12 requested) atoms. Cycle 44: After refmac, R = 0.1773 (Rfree = 0.000) for 2849 atoms. Found 3 (25 requested) and removed 12 (12 requested) atoms. Cycle 45: After refmac, R = 0.1931 (Rfree = 0.000) for 2837 atoms. Found 13 (25 requested) and removed 14 (12 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.23 3.15 Search for helices and strands: 0 residues in 0 chains, 2985 seeds are put forward NCS extension: 35 residues added (2 deleted due to clashes), 3020 seeds are put forward Round 1: 164 peptides, 31 chains. Longest chain 24 peptides. Score 0.335 Round 2: 189 peptides, 30 chains. Longest chain 26 peptides. Score 0.443 Round 3: 187 peptides, 30 chains. Longest chain 21 peptides. Score 0.436 Round 4: 188 peptides, 28 chains. Longest chain 27 peptides. Score 0.470 Round 5: 193 peptides, 29 chains. Longest chain 17 peptides. Score 0.472 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 30, Residues 164, Estimated correctness of the model 2.0 % 3 chains (25 residues) have been docked in sequence Sequence coverage is 15 % Consider running further cycles of model building using 2ogi-3_warpNtrace.pdb as input Building loops using Loopy2018 30 chains (164 residues) following loop building 3 chains (25 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7378 reflections ( 99.85 % complete ) and 6319 restraints for refining 2863 atoms. 5607 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2047 (Rfree = 0.000) for 2863 atoms. Found 0 (25 requested) and removed 12 (12 requested) atoms. Cycle 47: After refmac, R = 0.1952 (Rfree = 0.000) for 2849 atoms. Found 0 (25 requested) and removed 4 (12 requested) atoms. Cycle 48: After refmac, R = 0.1932 (Rfree = 0.000) for 2843 atoms. Found 0 (25 requested) and removed 4 (12 requested) atoms. Cycle 49: After refmac, R = 0.1950 (Rfree = 0.000) for 2836 atoms. Found 0 (25 requested) and removed 0 (12 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:38:17 GMT 2018 Job finished. TimeTaking 33.3 Used memory is bytes: 4409960