null Mon 24 Dec 00:30:42 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 2oyo-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2oyo-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2oyo-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2oyo-3.4-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/2oyo-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2oyo-3.4-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 00:30:46 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/2oyo-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2oyo-3.4-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 279 and 0 Target number of residues in the AU: 279 Target solvent content: 0.6391 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-3.4-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: 155 Cell parameters: 135.664 135.664 118.109 90.000 90.000 120.000 Input sequence file: 2oyo-3.4-parrot-mrncs.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 3.400 Wilson plot Bfac: 70.81 5885 reflections ( 99.85 % complete ) and 0 restraints for refining 3502 atoms. Observations/parameters ratio is 0.42 ------------------------------------------------------ Starting model: R = 0.3149 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2862 (Rfree = 0.000) for 3502 atoms. Found 26 (26 requested) and removed 21 (13 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.33 3.37 Search for helices and strands: 0 residues in 0 chains, 3599 seeds are put forward NCS extension: 0 residues added, 3599 seeds are put forward Round 1: 158 peptides, 33 chains. Longest chain 12 peptides. Score 0.283 Round 2: 188 peptides, 32 chains. Longest chain 11 peptides. Score 0.419 Round 3: 211 peptides, 33 chains. Longest chain 18 peptides. Score 0.486 Round 4: 220 peptides, 31 chains. Longest chain 18 peptides. Score 0.544 Round 5: 225 peptides, 32 chains. Longest chain 20 peptides. Score 0.546 Taking the results from Round 5 Chains 33, Residues 193, Estimated correctness of the model 10.1 % 3 chains (37 residues) have been docked in sequence ------------------------------------------------------ 5885 reflections ( 99.85 % complete ) and 6063 restraints for refining 2852 atoms. 5192 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2448 (Rfree = 0.000) for 2852 atoms. Found 14 (21 requested) and removed 31 (10 requested) atoms. Cycle 2: After refmac, R = 0.2314 (Rfree = 0.000) for 2808 atoms. Found 13 (21 requested) and removed 19 (10 requested) atoms. Cycle 3: After refmac, R = 0.2180 (Rfree = 0.000) for 2790 atoms. Found 9 (21 requested) and removed 13 (10 requested) atoms. Cycle 4: After refmac, R = 0.2106 (Rfree = 0.000) for 2776 atoms. Found 6 (21 requested) and removed 12 (10 requested) atoms. Cycle 5: After refmac, R = 0.2040 (Rfree = 0.000) for 2760 atoms. Found 7 (20 requested) and removed 13 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.27 3.31 Search for helices and strands: 0 residues in 0 chains, 2897 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 2922 seeds are put forward Round 1: 200 peptides, 36 chains. Longest chain 24 peptides. Score 0.400 Round 2: 232 peptides, 30 chains. Longest chain 26 peptides. Score 0.594 Round 3: 225 peptides, 32 chains. Longest chain 27 peptides. Score 0.546 Round 4: 223 peptides, 27 chains. Longest chain 27 peptides. Score 0.606 Round 5: 232 peptides, 29 chains. Longest chain 27 peptides. Score 0.606 Taking the results from Round 5 Chains 32, Residues 203, Estimated correctness of the model 30.6 % 5 chains (38 residues) have been docked in sequence ------------------------------------------------------ 5885 reflections ( 99.85 % complete ) and 5982 restraints for refining 2852 atoms. 5082 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2175 (Rfree = 0.000) for 2852 atoms. Found 16 (21 requested) and removed 24 (10 requested) atoms. Cycle 7: After refmac, R = 0.2010 (Rfree = 0.000) for 2822 atoms. Found 6 (21 requested) and removed 15 (10 requested) atoms. Cycle 8: After refmac, R = 0.2025 (Rfree = 0.000) for 2805 atoms. Found 4 (21 requested) and removed 11 (10 requested) atoms. Cycle 9: After refmac, R = 0.1944 (Rfree = 0.000) for 2795 atoms. Found 5 (21 requested) and removed 14 (10 requested) atoms. Cycle 10: After refmac, R = 0.1872 (Rfree = 0.000) for 2781 atoms. Found 3 (21 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.27 3.31 Search for helices and strands: 0 residues in 0 chains, 2930 seeds are put forward NCS extension: 45 residues added (6 deleted due to clashes), 2975 seeds are put forward Round 1: 199 peptides, 35 chains. Longest chain 15 peptides. Score 0.412 Round 2: 225 peptides, 32 chains. Longest chain 27 peptides. Score 0.546 Round 3: 227 peptides, 32 chains. Longest chain 17 peptides. Score 0.552 Round 4: 224 peptides, 28 chains. Longest chain 25 peptides. Score 0.596 Round 5: 224 peptides, 29 chains. Longest chain 26 peptides. Score 0.583 Taking the results from Round 4 Chains 30, Residues 196, Estimated correctness of the model 27.4 % 2 chains (19 residues) have been docked in sequence ------------------------------------------------------ 5885 reflections ( 99.85 % complete ) and 6200 restraints for refining 2851 atoms. 5385 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2102 (Rfree = 0.000) for 2851 atoms. Found 8 (21 requested) and removed 13 (10 requested) atoms. Cycle 12: After refmac, R = 0.1917 (Rfree = 0.000) for 2838 atoms. Found 5 (21 requested) and removed 12 (10 requested) atoms. Cycle 13: After refmac, R = 0.2005 (Rfree = 0.000) for 2829 atoms. Found 6 (21 requested) and removed 12 (10 requested) atoms. Cycle 14: After refmac, R = 0.2045 (Rfree = 0.000) for 2816 atoms. Found 7 (21 requested) and removed 14 (10 requested) atoms. Cycle 15: After refmac, R = 0.2237 (Rfree = 0.000) for 2805 atoms. Found 12 (21 requested) and removed 12 (10 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.24 3.28 Search for helices and strands: 0 residues in 0 chains, 2961 seeds are put forward NCS extension: 23 residues added (10 deleted due to clashes), 2984 seeds are put forward Round 1: 192 peptides, 33 chains. Longest chain 14 peptides. Score 0.418 Round 2: 212 peptides, 33 chains. Longest chain 15 peptides. Score 0.489 Round 3: 204 peptides, 31 chains. Longest chain 14 peptides. Score 0.492 Round 4: 203 peptides, 28 chains. Longest chain 24 peptides. Score 0.532 Round 5: 217 peptides, 29 chains. Longest chain 15 peptides. Score 0.562 Taking the results from Round 5 Chains 30, Residues 188, Estimated correctness of the model 15.8 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 5885 reflections ( 99.85 % complete ) and 6369 restraints for refining 2852 atoms. 5611 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2241 (Rfree = 0.000) for 2852 atoms. Found 14 (21 requested) and removed 16 (10 requested) atoms. Cycle 17: After refmac, R = 0.2135 (Rfree = 0.000) for 2847 atoms. Found 5 (21 requested) and removed 12 (10 requested) atoms. Cycle 18: After refmac, R = 0.2134 (Rfree = 0.000) for 2835 atoms. Found 4 (21 requested) and removed 12 (10 requested) atoms. Cycle 19: After refmac, R = 0.2197 (Rfree = 0.000) for 2824 atoms. Found 8 (21 requested) and removed 10 (10 requested) atoms. Cycle 20: After refmac, R = 0.2354 (Rfree = 0.000) for 2819 atoms. Found 15 (21 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.27 3.31 Search for helices and strands: 0 residues in 0 chains, 2973 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 2988 seeds are put forward Round 1: 193 peptides, 33 chains. Longest chain 16 peptides. Score 0.422 Round 2: 224 peptides, 35 chains. Longest chain 18 peptides. Score 0.500 Round 3: 210 peptides, 31 chains. Longest chain 18 peptides. Score 0.512 Round 4: 216 peptides, 31 chains. Longest chain 14 peptides. Score 0.531 Round 5: 221 peptides, 31 chains. Longest chain 16 peptides. Score 0.547 Taking the results from Round 5 Chains 33, Residues 190, Estimated correctness of the model 10.4 % 2 chains (25 residues) have been docked in sequence ------------------------------------------------------ 5885 reflections ( 99.85 % complete ) and 6290 restraints for refining 2852 atoms. 5468 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2542 (Rfree = 0.000) for 2852 atoms. Found 21 (21 requested) and removed 14 (10 requested) atoms. Cycle 22: After refmac, R = 0.2494 (Rfree = 0.000) for 2851 atoms. Found 21 (21 requested) and removed 17 (10 requested) atoms. Cycle 23: After refmac, R = 0.2186 (Rfree = 0.000) for 2848 atoms. Found 7 (21 requested) and removed 11 (10 requested) atoms. Cycle 24: After refmac, R = 0.1958 (Rfree = 0.000) for 2838 atoms. Found 5 (21 requested) and removed 11 (10 requested) atoms. Cycle 25: After refmac, R = 0.2024 (Rfree = 0.000) for 2829 atoms. Found 2 (21 requested) and removed 12 (10 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.27 3.31 Search for helices and strands: 0 residues in 0 chains, 2958 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 2973 seeds are put forward Round 1: 150 peptides, 30 chains. Longest chain 10 peptides. Score 0.302 Round 2: 174 peptides, 29 chains. Longest chain 17 peptides. Score 0.415 Round 3: 181 peptides, 25 chains. Longest chain 18 peptides. Score 0.504 Round 4: 177 peptides, 26 chains. Longest chain 18 peptides. Score 0.474 Round 5: 192 peptides, 30 chains. Longest chain 12 peptides. Score 0.465 Taking the results from Round 3 Chains 25, Residues 156, Estimated correctness of the model 0.0 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 5885 reflections ( 99.85 % complete ) and 6529 restraints for refining 2852 atoms. 5870 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2381 (Rfree = 0.000) for 2852 atoms. Found 13 (21 requested) and removed 14 (10 requested) atoms. Cycle 27: After refmac, R = 0.2303 (Rfree = 0.000) for 2845 atoms. Found 18 (21 requested) and removed 13 (10 requested) atoms. Cycle 28: After refmac, R = 0.2275 (Rfree = 0.000) for 2846 atoms. Found 6 (21 requested) and removed 12 (10 requested) atoms. Cycle 29: After refmac, R = 0.2347 (Rfree = 0.000) for 2837 atoms. Found 21 (21 requested) and removed 11 (10 requested) atoms. Cycle 30: After refmac, R = 0.2211 (Rfree = 0.000) for 2844 atoms. Found 8 (21 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.29 3.33 Search for helices and strands: 0 residues in 0 chains, 2961 seeds are put forward NCS extension: 33 residues added (1 deleted due to clashes), 2994 seeds are put forward Round 1: 132 peptides, 26 chains. Longest chain 8 peptides. Score 0.297 Round 2: 147 peptides, 25 chains. Longest chain 12 peptides. Score 0.378 Round 3: 155 peptides, 26 chains. Longest chain 13 peptides. Score 0.392 Round 4: 161 peptides, 26 chains. Longest chain 11 peptides. Score 0.416 Round 5: 166 peptides, 27 chains. Longest chain 10 peptides. Score 0.418 Taking the results from Round 5 Chains 27, Residues 139, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 5885 reflections ( 99.85 % complete ) and 6694 restraints for refining 2852 atoms. 6136 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2388 (Rfree = 0.000) for 2852 atoms. Found 11 (21 requested) and removed 18 (10 requested) atoms. Cycle 32: After refmac, R = 0.2367 (Rfree = 0.000) for 2843 atoms. Found 14 (21 requested) and removed 15 (10 requested) atoms. Cycle 33: After refmac, R = 0.2294 (Rfree = 0.000) for 2841 atoms. Found 12 (21 requested) and removed 12 (10 requested) atoms. Cycle 34: After refmac, R = 0.2236 (Rfree = 0.000) for 2837 atoms. Found 2 (21 requested) and removed 10 (10 requested) atoms. Cycle 35: After refmac, R = 0.2127 (Rfree = 0.000) for 2828 atoms. Found 1 (21 requested) and removed 13 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.25 3.29 Search for helices and strands: 0 residues in 0 chains, 2952 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 2964 seeds are put forward Round 1: 148 peptides, 31 chains. Longest chain 12 peptides. Score 0.276 Round 2: 168 peptides, 29 chains. Longest chain 12 peptides. Score 0.392 Round 3: 159 peptides, 30 chains. Longest chain 10 peptides. Score 0.339 Round 4: 166 peptides, 30 chains. Longest chain 11 peptides. Score 0.368 Round 5: 172 peptides, 33 chains. Longest chain 11 peptides. Score 0.341 Taking the results from Round 2 Chains 29, Residues 139, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5885 reflections ( 99.85 % complete ) and 6618 restraints for refining 2851 atoms. 6091 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2351 (Rfree = 0.000) for 2851 atoms. Found 11 (21 requested) and removed 11 (10 requested) atoms. Cycle 37: After refmac, R = 0.2314 (Rfree = 0.000) for 2847 atoms. Found 13 (21 requested) and removed 11 (10 requested) atoms. Cycle 38: After refmac, R = 0.2401 (Rfree = 0.000) for 2844 atoms. Found 19 (21 requested) and removed 11 (10 requested) atoms. Cycle 39: After refmac, R = 0.2023 (Rfree = 0.000) for 2848 atoms. Found 3 (21 requested) and removed 12 (10 requested) atoms. Cycle 40: After refmac, R = 0.2338 (Rfree = 0.000) for 2834 atoms. Found 15 (21 requested) and removed 15 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.31 3.35 Search for helices and strands: 0 residues in 0 chains, 2957 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 2973 seeds are put forward Round 1: 117 peptides, 26 chains. Longest chain 8 peptides. Score 0.230 Round 2: 146 peptides, 30 chains. Longest chain 8 peptides. Score 0.285 Round 3: 150 peptides, 27 chains. Longest chain 11 peptides. Score 0.355 Round 4: 150 peptides, 30 chains. Longest chain 10 peptides. Score 0.302 Round 5: 147 peptides, 25 chains. Longest chain 11 peptides. Score 0.378 Taking the results from Round 5 Chains 25, Residues 122, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 5885 reflections ( 99.85 % complete ) and 6485 restraints for refining 2833 atoms. 5986 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2729 (Rfree = 0.000) for 2833 atoms. Found 21 (21 requested) and removed 27 (10 requested) atoms. Cycle 42: After refmac, R = 0.2526 (Rfree = 0.000) for 2817 atoms. Found 21 (21 requested) and removed 19 (10 requested) atoms. Cycle 43: After refmac, R = 0.2511 (Rfree = 0.000) for 2811 atoms. Found 21 (21 requested) and removed 23 (10 requested) atoms. Cycle 44: After refmac, R = 0.2482 (Rfree = 0.000) for 2803 atoms. Found 21 (21 requested) and removed 17 (10 requested) atoms. Cycle 45: After refmac, R = 0.1979 (Rfree = 0.000) for 2801 atoms. Found 8 (21 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.26 3.30 Search for helices and strands: 0 residues in 0 chains, 2922 seeds are put forward NCS extension: 10 residues added (0 deleted due to clashes), 2932 seeds are put forward Round 1: 120 peptides, 27 chains. Longest chain 9 peptides. Score 0.224 Round 2: 149 peptides, 30 chains. Longest chain 10 peptides. Score 0.298 Round 3: 143 peptides, 28 chains. Longest chain 10 peptides. Score 0.308 Round 4: 140 peptides, 27 chains. Longest chain 8 peptides. Score 0.313 Round 5: 137 peptides, 28 chains. Longest chain 8 peptides. Score 0.282 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 27, Residues 113, 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 2oyo-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5885 reflections ( 99.85 % complete ) and 6548 restraints for refining 2801 atoms. 6123 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2418 (Rfree = 0.000) for 2801 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 47: After refmac, R = 0.2557 (Rfree = 0.000) for 2787 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 48: After refmac, R = 0.2005 (Rfree = 0.000) for 2768 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 49: After refmac, R = 0.1927 (Rfree = 0.000) for 2755 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:08:35 GMT 2018 Job finished. TimeTaking 37.89 Used memory is bytes: 17959568