null Mon 24 Dec 01:12:08 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-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2oyo-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2oyo-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2oyo-3.6-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-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2oyo-3.6-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 01:12:12 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-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2oyo-3.6-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 270 and 0 Target number of residues in the AU: 270 Target solvent content: 0.6507 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-3.6-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-3.6-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: 83.295 3.600 Wilson plot Bfac: 78.05 4986 reflections ( 99.82 % complete ) and 0 restraints for refining 3484 atoms. Observations/parameters ratio is 0.36 ------------------------------------------------------ Starting model: R = 0.3219 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2748 (Rfree = 0.000) for 3484 atoms. Found 22 (22 requested) and removed 19 (11 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.50 3.55 Search for helices and strands: 0 residues in 0 chains, 3579 seeds are put forward NCS extension: 0 residues added, 3579 seeds are put forward Round 1: 167 peptides, 34 chains. Longest chain 10 peptides. Score 0.303 Round 2: 206 peptides, 32 chains. Longest chain 14 peptides. Score 0.484 Round 3: 205 peptides, 32 chains. Longest chain 15 peptides. Score 0.480 Round 4: 206 peptides, 30 chains. Longest chain 16 peptides. Score 0.513 Round 5: 207 peptides, 29 chains. Longest chain 15 peptides. Score 0.531 Taking the results from Round 5 Chains 31, Residues 178, Estimated correctness of the model 0.0 % 4 chains (39 residues) have been docked in sequence ------------------------------------------------------ 4986 reflections ( 99.82 % complete ) and 6202 restraints for refining 2839 atoms. 5390 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2333 (Rfree = 0.000) for 2839 atoms. Found 10 (18 requested) and removed 22 (9 requested) atoms. Cycle 2: After refmac, R = 0.2131 (Rfree = 0.000) for 2793 atoms. Found 8 (18 requested) and removed 13 (9 requested) atoms. Cycle 3: After refmac, R = 0.2043 (Rfree = 0.000) for 2777 atoms. Found 3 (17 requested) and removed 12 (8 requested) atoms. Cycle 4: After refmac, R = 0.1958 (Rfree = 0.000) for 2763 atoms. Found 5 (17 requested) and removed 10 (8 requested) atoms. Cycle 5: After refmac, R = 0.1921 (Rfree = 0.000) for 2756 atoms. Found 2 (17 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.51 3.56 Search for helices and strands: 0 residues in 0 chains, 2897 seeds are put forward NCS extension: 15 residues added (6 deleted due to clashes), 2912 seeds are put forward Round 1: 201 peptides, 35 chains. Longest chain 18 peptides. Score 0.420 Round 2: 191 peptides, 29 chains. Longest chain 15 peptides. Score 0.477 Round 3: 217 peptides, 26 chains. Longest chain 19 peptides. Score 0.602 Round 4: 202 peptides, 26 chains. Longest chain 18 peptides. Score 0.558 Round 5: 208 peptides, 28 chains. Longest chain 18 peptides. Score 0.548 Taking the results from Round 3 Chains 28, Residues 191, Estimated correctness of the model 15.4 % 2 chains (26 residues) have been docked in sequence ------------------------------------------------------ 4986 reflections ( 99.82 % complete ) and 6208 restraints for refining 2843 atoms. 5372 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2176 (Rfree = 0.000) for 2843 atoms. Found 8 (18 requested) and removed 20 (9 requested) atoms. Cycle 7: After refmac, R = 0.2129 (Rfree = 0.000) for 2818 atoms. Found 2 (18 requested) and removed 19 (9 requested) atoms. Cycle 8: After refmac, R = 0.2067 (Rfree = 0.000) for 2792 atoms. Found 3 (17 requested) and removed 16 (8 requested) atoms. Cycle 9: After refmac, R = 0.2043 (Rfree = 0.000) for 2772 atoms. Found 4 (17 requested) and removed 14 (8 requested) atoms. Cycle 10: After refmac, R = 0.1973 (Rfree = 0.000) for 2760 atoms. Found 1 (17 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.47 3.52 Search for helices and strands: 0 residues in 0 chains, 2886 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 2908 seeds are put forward Round 1: 191 peptides, 28 chains. Longest chain 12 peptides. Score 0.492 Round 2: 208 peptides, 27 chains. Longest chain 14 peptides. Score 0.562 Round 3: 194 peptides, 24 chains. Longest chain 18 peptides. Score 0.561 Round 4: 196 peptides, 25 chains. Longest chain 16 peptides. Score 0.553 Round 5: 183 peptides, 27 chains. Longest chain 15 peptides. Score 0.480 Taking the results from Round 2 Chains 27, Residues 181, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 4986 reflections ( 99.82 % complete ) and 6445 restraints for refining 2842 atoms. 5721 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2037 (Rfree = 0.000) for 2842 atoms. Found 12 (18 requested) and removed 19 (9 requested) atoms. Cycle 12: After refmac, R = 0.1948 (Rfree = 0.000) for 2829 atoms. Found 6 (18 requested) and removed 10 (9 requested) atoms. Cycle 13: After refmac, R = 0.1935 (Rfree = 0.000) for 2823 atoms. Found 4 (18 requested) and removed 11 (9 requested) atoms. Cycle 14: After refmac, R = 0.1887 (Rfree = 0.000) for 2816 atoms. Found 4 (18 requested) and removed 11 (9 requested) atoms. Cycle 15: After refmac, R = 0.1881 (Rfree = 0.000) for 2809 atoms. Found 8 (18 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.46 3.51 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: 172 peptides, 28 chains. Longest chain 16 peptides. Score 0.424 Round 2: 194 peptides, 29 chains. Longest chain 21 peptides. Score 0.488 Round 3: 192 peptides, 27 chains. Longest chain 14 peptides. Score 0.511 Round 4: 201 peptides, 29 chains. Longest chain 21 peptides. Score 0.511 Round 5: 213 peptides, 31 chains. Longest chain 14 peptides. Score 0.522 Taking the results from Round 5 Chains 31, Residues 182, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 4986 reflections ( 99.82 % complete ) and 6529 restraints for refining 2843 atoms. 5817 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1981 (Rfree = 0.000) for 2843 atoms. Found 16 (18 requested) and removed 13 (9 requested) atoms. Cycle 17: After refmac, R = 0.1813 (Rfree = 0.000) for 2836 atoms. Found 8 (18 requested) and removed 15 (9 requested) atoms. Cycle 18: After refmac, R = 0.1806 (Rfree = 0.000) for 2827 atoms. Found 8 (18 requested) and removed 14 (9 requested) atoms. Cycle 19: After refmac, R = 0.1746 (Rfree = 0.000) for 2818 atoms. Found 3 (18 requested) and removed 9 (9 requested) atoms. Cycle 20: After refmac, R = 0.1689 (Rfree = 0.000) for 2807 atoms. Found 8 (18 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.50 3.55 Search for helices and strands: 0 residues in 0 chains, 2952 seeds are put forward NCS extension: 12 residues added (5 deleted due to clashes), 2964 seeds are put forward Round 1: 156 peptides, 30 chains. Longest chain 11 peptides. Score 0.327 Round 2: 186 peptides, 27 chains. Longest chain 24 peptides. Score 0.490 Round 3: 209 peptides, 31 chains. Longest chain 19 peptides. Score 0.509 Round 4: 212 peptides, 30 chains. Longest chain 23 peptides. Score 0.533 Round 5: 203 peptides, 29 chains. Longest chain 23 peptides. Score 0.518 Taking the results from Round 4 Chains 32, Residues 182, Estimated correctness of the model 0.0 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 4986 reflections ( 99.82 % complete ) and 6418 restraints for refining 2843 atoms. 5669 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2058 (Rfree = 0.000) for 2843 atoms. Found 17 (18 requested) and removed 10 (9 requested) atoms. Cycle 22: After refmac, R = 0.1889 (Rfree = 0.000) for 2844 atoms. Found 6 (18 requested) and removed 15 (9 requested) atoms. Cycle 23: After refmac, R = 0.1951 (Rfree = 0.000) for 2827 atoms. Found 12 (18 requested) and removed 14 (9 requested) atoms. Cycle 24: After refmac, R = 0.1864 (Rfree = 0.000) for 2821 atoms. Found 3 (18 requested) and removed 14 (9 requested) atoms. Cycle 25: After refmac, R = 0.2452 (Rfree = 0.000) for 2808 atoms. Found 18 (18 requested) and removed 20 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.47 3.52 Search for helices and strands: 0 residues in 0 chains, 2916 seeds are put forward NCS extension: 17 residues added (3 deleted due to clashes), 2933 seeds are put forward Round 1: 164 peptides, 32 chains. Longest chain 9 peptides. Score 0.325 Round 2: 183 peptides, 30 chains. Longest chain 13 peptides. Score 0.433 Round 3: 192 peptides, 30 chains. Longest chain 16 peptides. Score 0.465 Round 4: 191 peptides, 27 chains. Longest chain 14 peptides. Score 0.507 Round 5: 198 peptides, 32 chains. Longest chain 15 peptides. Score 0.456 Taking the results from Round 4 Chains 27, Residues 164, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4986 reflections ( 99.82 % complete ) and 6563 restraints for refining 2842 atoms. 5934 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2004 (Rfree = 0.000) for 2842 atoms. Found 12 (18 requested) and removed 14 (9 requested) atoms. Cycle 27: After refmac, R = 0.1915 (Rfree = 0.000) for 2829 atoms. Found 6 (18 requested) and removed 10 (9 requested) atoms. Cycle 28: After refmac, R = 0.1840 (Rfree = 0.000) for 2824 atoms. Found 4 (18 requested) and removed 10 (9 requested) atoms. Cycle 29: After refmac, R = 0.1835 (Rfree = 0.000) for 2815 atoms. Found 3 (18 requested) and removed 10 (9 requested) atoms. Cycle 30: After refmac, R = 0.1612 (Rfree = 0.000) for 2806 atoms. Found 2 (18 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.49 3.54 Search for helices and strands: 0 residues in 0 chains, 2960 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 2981 seeds are put forward Round 1: 121 peptides, 25 chains. Longest chain 9 peptides. Score 0.267 Round 2: 152 peptides, 25 chains. Longest chain 13 peptides. Score 0.398 Round 3: 158 peptides, 25 chains. Longest chain 11 peptides. Score 0.421 Round 4: 155 peptides, 25 chains. Longest chain 14 peptides. Score 0.409 Round 5: 163 peptides, 27 chains. Longest chain 11 peptides. Score 0.407 Taking the results from Round 3 Chains 25, Residues 133, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4986 reflections ( 99.82 % complete ) and 6855 restraints for refining 2843 atoms. 6348 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1819 (Rfree = 0.000) for 2843 atoms. Found 7 (18 requested) and removed 19 (9 requested) atoms. Cycle 32: After refmac, R = 0.1893 (Rfree = 0.000) for 2829 atoms. Found 5 (18 requested) and removed 12 (9 requested) atoms. Cycle 33: After refmac, R = 0.1907 (Rfree = 0.000) for 2821 atoms. Found 8 (18 requested) and removed 10 (9 requested) atoms. Cycle 34: After refmac, R = 0.1849 (Rfree = 0.000) for 2816 atoms. Found 12 (18 requested) and removed 10 (9 requested) atoms. Cycle 35: After refmac, R = 0.1550 (Rfree = 0.000) for 2816 atoms. Found 3 (18 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.48 3.53 Search for helices and strands: 0 residues in 0 chains, 2949 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 2960 seeds are put forward Round 1: 136 peptides, 27 chains. Longest chain 9 peptides. Score 0.296 Round 2: 149 peptides, 26 chains. Longest chain 14 peptides. Score 0.369 Round 3: 148 peptides, 25 chains. Longest chain 19 peptides. Score 0.382 Round 4: 149 peptides, 25 chains. Longest chain 14 peptides. Score 0.386 Round 5: 148 peptides, 25 chains. Longest chain 17 peptides. Score 0.382 Taking the results from Round 4 Chains 25, Residues 124, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 4986 reflections ( 99.82 % complete ) and 6770 restraints for refining 2843 atoms. 6282 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1977 (Rfree = 0.000) for 2843 atoms. Found 17 (18 requested) and removed 14 (9 requested) atoms. Cycle 37: After refmac, R = 0.1885 (Rfree = 0.000) for 2837 atoms. Found 9 (18 requested) and removed 12 (9 requested) atoms. Cycle 38: After refmac, R = 0.1921 (Rfree = 0.000) for 2831 atoms. Found 5 (18 requested) and removed 12 (9 requested) atoms. Cycle 39: After refmac, R = 0.1948 (Rfree = 0.000) for 2820 atoms. Found 7 (18 requested) and removed 12 (9 requested) atoms. Cycle 40: After refmac, R = 0.1628 (Rfree = 0.000) for 2813 atoms. Found 3 (18 requested) and removed 13 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.46 3.51 Search for helices and strands: 0 residues in 0 chains, 2951 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 2969 seeds are put forward Round 1: 129 peptides, 27 chains. Longest chain 8 peptides. Score 0.266 Round 2: 161 peptides, 32 chains. Longest chain 9 peptides. Score 0.313 Round 3: 164 peptides, 29 chains. Longest chain 13 peptides. Score 0.377 Round 4: 169 peptides, 30 chains. Longest chain 13 peptides. Score 0.379 Round 5: 174 peptides, 30 chains. Longest chain 13 peptides. Score 0.399 Taking the results from Round 5 Chains 30, Residues 144, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4986 reflections ( 99.82 % complete ) and 6688 restraints for refining 2842 atoms. 6142 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1915 (Rfree = 0.000) for 2842 atoms. Found 13 (18 requested) and removed 17 (9 requested) atoms. Cycle 42: After refmac, R = 0.1818 (Rfree = 0.000) for 2834 atoms. Found 10 (18 requested) and removed 11 (9 requested) atoms. Cycle 43: After refmac, R = 0.1842 (Rfree = 0.000) for 2830 atoms. Found 8 (18 requested) and removed 15 (9 requested) atoms. Cycle 44: After refmac, R = 0.1778 (Rfree = 0.000) for 2819 atoms. Found 10 (18 requested) and removed 11 (9 requested) atoms. Cycle 45: After refmac, R = 0.1794 (Rfree = 0.000) for 2814 atoms. Found 6 (18 requested) and removed 13 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.49 3.54 Search for helices and strands: 0 residues in 0 chains, 2954 seeds are put forward NCS extension: 11 residues added (0 deleted due to clashes), 2965 seeds are put forward Round 1: 143 peptides, 32 chains. Longest chain 8 peptides. Score 0.235 Round 2: 147 peptides, 28 chains. Longest chain 12 peptides. Score 0.325 Round 3: 158 peptides, 29 chains. Longest chain 16 peptides. Score 0.353 Round 4: 149 peptides, 26 chains. Longest chain 17 peptides. Score 0.369 Round 5: 160 peptides, 30 chains. Longest chain 11 peptides. Score 0.344 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 26, Residues 123, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence Sequence coverage is 7 % Consider running further cycles of model building using 2oyo-3_warpNtrace.pdb as input Building loops using Loopy2018 26 chains (123 residues) following loop building 2 chains (9 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4986 reflections ( 99.82 % complete ) and 6694 restraints for refining 2842 atoms. 6203 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1954 (Rfree = 0.000) for 2842 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.1907 (Rfree = 0.000) for 2829 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.1579 (Rfree = 0.000) for 2816 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.1529 (Rfree = 0.000) for 2806 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:46:37 GMT 2018 Job finished. TimeTaking 34.49 Used memory is bytes: 7375016