Mon 24 Dec 07:52:31 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-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2ogi-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2ogi-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ogi-3.4-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-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ogi-3.4-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 07:52:36 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-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ogi-3.4-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 289 and 0 Target number of residues in the AU: 289 Target solvent content: 0.6459 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-3.4-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-3.4-parrot-noncs.fasta_lf Building free atoms model in initial map for 3136 target number of atoms Had to go as low as 0.90 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 3.400 Wilson plot Bfac: 75.24 6172 reflections ( 99.82 % complete ) and 0 restraints for refining 3488 atoms. Observations/parameters ratio is 0.44 ------------------------------------------------------ Starting model: R = 0.3489 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3176 (Rfree = 0.000) for 3488 atoms. Found 26 (26 requested) and removed 22 (13 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.42 3.33 Search for helices and strands: 0 residues in 0 chains, 3594 seeds are put forward NCS extension: 0 residues added, 3594 seeds are put forward Round 1: 179 peptides, 34 chains. Longest chain 14 peptides. Score 0.344 Round 2: 217 peptides, 37 chains. Longest chain 14 peptides. Score 0.435 Round 3: 222 peptides, 36 chains. Longest chain 17 peptides. Score 0.467 Round 4: 240 peptides, 37 chains. Longest chain 18 peptides. Score 0.511 Round 5: 232 peptides, 33 chains. Longest chain 20 peptides. Score 0.539 Taking the results from Round 5 Chains 35, Residues 199, Estimated correctness of the model 7.5 % 3 chains (24 residues) have been docked in sequence ------------------------------------------------------ 6172 reflections ( 99.82 % complete ) and 6224 restraints for refining 2852 atoms. 5382 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2816 (Rfree = 0.000) for 2852 atoms. Found 18 (21 requested) and removed 37 (10 requested) atoms. Cycle 2: After refmac, R = 0.2648 (Rfree = 0.000) for 2809 atoms. Found 11 (21 requested) and removed 16 (10 requested) atoms. Cycle 3: After refmac, R = 0.2184 (Rfree = 0.000) for 2783 atoms. Found 10 (21 requested) and removed 14 (10 requested) atoms. Cycle 4: After refmac, R = 0.2288 (Rfree = 0.000) for 2769 atoms. Found 4 (20 requested) and removed 14 (10 requested) atoms. Cycle 5: After refmac, R = 0.2332 (Rfree = 0.000) for 2758 atoms. Found 10 (20 requested) and removed 15 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.41 3.32 Search for helices and strands: 0 residues in 0 chains, 2894 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 2920 seeds are put forward Round 1: 214 peptides, 35 chains. Longest chain 17 peptides. Score 0.455 Round 2: 235 peptides, 33 chains. Longest chain 18 peptides. Score 0.548 Round 3: 234 peptides, 33 chains. Longest chain 19 peptides. Score 0.545 Round 4: 234 peptides, 34 chains. Longest chain 20 peptides. Score 0.532 Round 5: 231 peptides, 35 chains. Longest chain 20 peptides. Score 0.510 Taking the results from Round 2 Chains 34, Residues 202, Estimated correctness of the model 10.8 % 3 chains (24 residues) have been docked in sequence ------------------------------------------------------ 6172 reflections ( 99.82 % complete ) and 6144 restraints for refining 2852 atoms. 5293 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2568 (Rfree = 0.000) for 2852 atoms. Found 10 (21 requested) and removed 28 (10 requested) atoms. Cycle 7: After refmac, R = 0.2538 (Rfree = 0.000) for 2819 atoms. Found 21 (21 requested) and removed 20 (10 requested) atoms. Cycle 8: After refmac, R = 0.2666 (Rfree = 0.000) for 2811 atoms. Found 21 (21 requested) and removed 24 (10 requested) atoms. Cycle 9: After refmac, R = 0.2721 (Rfree = 0.000) for 2797 atoms. Found 20 (21 requested) and removed 19 (10 requested) atoms. Cycle 10: After refmac, R = 0.2707 (Rfree = 0.000) for 2785 atoms. Found 21 (21 requested) and removed 20 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.44 3.35 Search for helices and strands: 0 residues in 0 chains, 2949 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 2964 seeds are put forward Round 1: 176 peptides, 32 chains. Longest chain 17 peptides. Score 0.365 Round 2: 213 peptides, 36 chains. Longest chain 16 peptides. Score 0.436 Round 3: 225 peptides, 36 chains. Longest chain 18 peptides. Score 0.477 Round 4: 211 peptides, 31 chains. Longest chain 26 peptides. Score 0.502 Round 5: 215 peptides, 33 chains. Longest chain 12 peptides. Score 0.487 Taking the results from Round 4 Chains 31, Residues 180, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6172 reflections ( 99.82 % complete ) and 6320 restraints for refining 2852 atoms. 5631 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2932 (Rfree = 0.000) for 2852 atoms. Found 21 (21 requested) and removed 34 (10 requested) atoms. Cycle 12: After refmac, R = 0.2849 (Rfree = 0.000) for 2807 atoms. Found 21 (21 requested) and removed 19 (10 requested) atoms. Cycle 13: After refmac, R = 0.2633 (Rfree = 0.000) for 2794 atoms. Found 16 (21 requested) and removed 19 (10 requested) atoms. Cycle 14: After refmac, R = 0.2470 (Rfree = 0.000) for 2781 atoms. Found 21 (21 requested) and removed 20 (10 requested) atoms. Cycle 15: After refmac, R = 0.2289 (Rfree = 0.000) for 2779 atoms. Found 21 (21 requested) and removed 18 (10 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.42 3.33 Search for helices and strands: 0 residues in 0 chains, 2950 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 2973 seeds are put forward Round 1: 165 peptides, 31 chains. Longest chain 11 peptides. Score 0.339 Round 2: 199 peptides, 32 chains. Longest chain 24 peptides. Score 0.448 Round 3: 197 peptides, 32 chains. Longest chain 14 peptides. Score 0.441 Round 4: 202 peptides, 31 chains. Longest chain 15 peptides. Score 0.473 Round 5: 196 peptides, 30 chains. Longest chain 21 peptides. Score 0.467 Taking the results from Round 4 Chains 31, Residues 171, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6172 reflections ( 99.82 % complete ) and 6348 restraints for refining 2850 atoms. 5695 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2565 (Rfree = 0.000) for 2850 atoms. Found 18 (21 requested) and removed 17 (10 requested) atoms. Cycle 17: After refmac, R = 0.2393 (Rfree = 0.000) for 2829 atoms. Found 21 (21 requested) and removed 17 (10 requested) atoms. Cycle 18: After refmac, R = 0.2286 (Rfree = 0.000) for 2823 atoms. Found 21 (21 requested) and removed 14 (10 requested) atoms. Cycle 19: After refmac, R = 0.2150 (Rfree = 0.000) for 2824 atoms. Found 19 (21 requested) and removed 17 (10 requested) atoms. Cycle 20: After refmac, R = 0.1830 (Rfree = 0.000) for 2824 atoms. Found 7 (21 requested) and removed 13 (10 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.40 3.31 Search for helices and strands: 0 residues in 0 chains, 2978 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 2998 seeds are put forward Round 1: 149 peptides, 29 chains. Longest chain 8 peptides. Score 0.310 Round 2: 185 peptides, 31 chains. Longest chain 13 peptides. Score 0.414 Round 3: 181 peptides, 30 chains. Longest chain 12 peptides. Score 0.415 Round 4: 186 peptides, 30 chains. Longest chain 11 peptides. Score 0.433 Round 5: 182 peptides, 30 chains. Longest chain 17 peptides. Score 0.419 Taking the results from Round 4 Chains 30, Residues 156, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 6172 reflections ( 99.82 % complete ) and 6351 restraints for refining 2851 atoms. 5736 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2335 (Rfree = 0.000) for 2851 atoms. Found 21 (21 requested) and removed 14 (10 requested) atoms. Cycle 22: After refmac, R = 0.2231 (Rfree = 0.000) for 2845 atoms. Found 14 (21 requested) and removed 12 (10 requested) atoms. Cycle 23: After refmac, R = 0.2143 (Rfree = 0.000) for 2843 atoms. Found 7 (21 requested) and removed 15 (10 requested) atoms. Cycle 24: After refmac, R = 0.2145 (Rfree = 0.000) for 2833 atoms. Found 17 (21 requested) and removed 15 (10 requested) atoms. Cycle 25: After refmac, R = 0.2084 (Rfree = 0.000) for 2833 atoms. Found 7 (21 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.41 3.32 Search for helices and strands: 0 residues in 0 chains, 2985 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 2999 seeds are put forward Round 1: 160 peptides, 34 chains. Longest chain 8 peptides. Score 0.269 Round 2: 181 peptides, 32 chains. Longest chain 13 peptides. Score 0.384 Round 3: 182 peptides, 31 chains. Longest chain 11 peptides. Score 0.403 Round 4: 177 peptides, 29 chains. Longest chain 14 peptides. Score 0.416 Round 5: 178 peptides, 29 chains. Longest chain 14 peptides. Score 0.420 Taking the results from Round 5 Chains 29, Residues 149, Estimated correctness of the model 0.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 6172 reflections ( 99.82 % complete ) and 6413 restraints for refining 2851 atoms. 5810 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2280 (Rfree = 0.000) for 2851 atoms. Found 15 (21 requested) and removed 18 (10 requested) atoms. Cycle 27: After refmac, R = 0.2102 (Rfree = 0.000) for 2837 atoms. Found 13 (21 requested) and removed 12 (10 requested) atoms. Cycle 28: After refmac, R = 0.2040 (Rfree = 0.000) for 2830 atoms. Found 12 (21 requested) and removed 12 (10 requested) atoms. Cycle 29: After refmac, R = 0.1941 (Rfree = 0.000) for 2826 atoms. Found 14 (21 requested) and removed 12 (10 requested) atoms. Cycle 30: After refmac, R = 0.1898 (Rfree = 0.000) for 2824 atoms. Found 12 (21 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.39 3.30 Search for helices and strands: 0 residues in 0 chains, 2973 seeds are put forward NCS extension: 26 residues added (0 deleted due to clashes), 2999 seeds are put forward Round 1: 152 peptides, 30 chains. Longest chain 8 peptides. Score 0.305 Round 2: 192 peptides, 34 chains. Longest chain 13 peptides. Score 0.393 Round 3: 176 peptides, 27 chains. Longest chain 14 peptides. Score 0.444 Round 4: 188 peptides, 30 chains. Longest chain 12 peptides. Score 0.440 Round 5: 176 peptides, 28 chains. Longest chain 15 peptides. Score 0.428 Taking the results from Round 3 Chains 27, Residues 149, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6172 reflections ( 99.82 % complete ) and 6587 restraints for refining 2852 atoms. 6018 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2045 (Rfree = 0.000) for 2852 atoms. Found 14 (21 requested) and removed 12 (10 requested) atoms. Cycle 32: After refmac, R = 0.1936 (Rfree = 0.000) for 2848 atoms. Found 6 (21 requested) and removed 13 (10 requested) atoms. Cycle 33: After refmac, R = 0.1821 (Rfree = 0.000) for 2840 atoms. Found 8 (21 requested) and removed 11 (10 requested) atoms. Cycle 34: After refmac, R = 0.1761 (Rfree = 0.000) for 2832 atoms. Found 6 (21 requested) and removed 11 (10 requested) atoms. Cycle 35: After refmac, R = 0.1642 (Rfree = 0.000) for 2826 atoms. Found 2 (21 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.39 3.30 Search for helices and strands: 0 residues in 0 chains, 2940 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 2959 seeds are put forward Round 1: 163 peptides, 34 chains. Longest chain 8 peptides. Score 0.281 Round 2: 189 peptides, 35 chains. Longest chain 11 peptides. Score 0.366 Round 3: 192 peptides, 34 chains. Longest chain 12 peptides. Score 0.393 Round 4: 183 peptides, 32 chains. Longest chain 15 peptides. Score 0.391 Round 5: 194 peptides, 31 chains. Longest chain 19 peptides. Score 0.445 Taking the results from Round 5 Chains 31, Residues 163, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6172 reflections ( 99.82 % complete ) and 6450 restraints for refining 2851 atoms. 5829 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2103 (Rfree = 0.000) for 2851 atoms. Found 18 (21 requested) and removed 12 (10 requested) atoms. Cycle 37: After refmac, R = 0.1907 (Rfree = 0.000) for 2849 atoms. Found 7 (21 requested) and removed 10 (10 requested) atoms. Cycle 38: After refmac, R = 0.1828 (Rfree = 0.000) for 2842 atoms. Found 4 (21 requested) and removed 10 (10 requested) atoms. Cycle 39: After refmac, R = 0.1862 (Rfree = 0.000) for 2830 atoms. Found 10 (21 requested) and removed 10 (10 requested) atoms. Cycle 40: After refmac, R = 0.1694 (Rfree = 0.000) for 2828 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.41 3.32 Search for helices and strands: 0 residues in 0 chains, 2954 seeds are put forward NCS extension: 28 residues added (0 deleted due to clashes), 2982 seeds are put forward Round 1: 159 peptides, 33 chains. Longest chain 8 peptides. Score 0.282 Round 2: 171 peptides, 31 chains. Longest chain 12 peptides. Score 0.362 Round 3: 160 peptides, 27 chains. Longest chain 12 peptides. Score 0.386 Round 4: 173 peptides, 28 chains. Longest chain 12 peptides. Score 0.418 Round 5: 176 peptides, 31 chains. Longest chain 12 peptides. Score 0.381 Taking the results from Round 4 Chains 28, Residues 145, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6172 reflections ( 99.82 % complete ) and 6610 restraints for refining 2851 atoms. 6058 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1936 (Rfree = 0.000) for 2851 atoms. Found 12 (21 requested) and removed 12 (10 requested) atoms. Cycle 42: After refmac, R = 0.1796 (Rfree = 0.000) for 2847 atoms. Found 7 (21 requested) and removed 11 (10 requested) atoms. Cycle 43: After refmac, R = 0.1760 (Rfree = 0.000) for 2839 atoms. Found 12 (21 requested) and removed 13 (10 requested) atoms. Cycle 44: After refmac, R = 0.1760 (Rfree = 0.000) for 2837 atoms. Found 7 (21 requested) and removed 10 (10 requested) atoms. Cycle 45: After refmac, R = 0.1778 (Rfree = 0.000) for 2834 atoms. Found 9 (21 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.42 3.33 Search for helices and strands: 0 residues in 0 chains, 2972 seeds are put forward NCS extension: 9 residues added (1 deleted due to clashes), 2981 seeds are put forward Round 1: 130 peptides, 28 chains. Longest chain 8 peptides. Score 0.248 Round 2: 143 peptides, 24 chains. Longest chain 12 peptides. Score 0.371 Round 3: 146 peptides, 26 chains. Longest chain 9 peptides. Score 0.349 Round 4: 141 peptides, 23 chains. Longest chain 16 peptides. Score 0.381 Round 5: 157 peptides, 28 chains. Longest chain 9 peptides. Score 0.358 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 23, Residues 118, 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. 6172 reflections ( 99.82 % complete ) and 6674 restraints for refining 2852 atoms. 6225 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1973 (Rfree = 0.000) for 2852 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 47: After refmac, R = 0.1870 (Rfree = 0.000) for 2840 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 48: After refmac, R = 0.1864 (Rfree = 0.000) for 2829 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 49: After refmac, R = 0.1904 (Rfree = 0.000) for 2817 atoms. TimeTaking 36.38