null Sun 23 Dec 22:23:02 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2ogi-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ogi-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ogi-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ogi-3.6-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/2ogi-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ogi-3.6-parrot-hancs ############### 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 ============================================================ Sun 23 Dec 22:23:12 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/hancs/ArpWArp/wArpResults/WorkingDir/2ogi-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ogi-3.6-parrot-hancs/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 281 and 0 Target number of residues in the AU: 281 Target solvent content: 0.6557 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-3.6-parrot-hancs.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-3.6-parrot-hancs.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 3.600 Wilson plot Bfac: 81.58 5214 reflections ( 99.79 % complete ) and 0 restraints for refining 3465 atoms. Observations/parameters ratio is 0.38 ------------------------------------------------------ Starting model: R = 0.3496 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3152 (Rfree = 0.000) for 3465 atoms. Found 14 (22 requested) and removed 23 (11 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.56 3.47 Search for helices and strands: 0 residues in 0 chains, 3546 seeds are put forward NCS extension: 0 residues added, 3546 seeds are put forward Round 1: 160 peptides, 30 chains. Longest chain 13 peptides. Score 0.336 Round 2: 202 peptides, 32 chains. Longest chain 16 peptides. Score 0.458 Round 3: 196 peptides, 27 chains. Longest chain 14 peptides. Score 0.511 Round 4: 210 peptides, 30 chains. Longest chain 16 peptides. Score 0.513 Round 5: 221 peptides, 28 chains. Longest chain 19 peptides. Score 0.573 Taking the results from Round 5 Chains 30, Residues 193, Estimated correctness of the model 3.8 % 4 chains (33 residues) have been docked in sequence ------------------------------------------------------ 5214 reflections ( 99.79 % complete ) and 6135 restraints for refining 2842 atoms. 5288 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2603 (Rfree = 0.000) for 2842 atoms. Found 10 (18 requested) and removed 22 (9 requested) atoms. Cycle 2: After refmac, R = 0.2494 (Rfree = 0.000) for 2772 atoms. Found 6 (18 requested) and removed 18 (9 requested) atoms. Cycle 3: After refmac, R = 0.2344 (Rfree = 0.000) for 2738 atoms. Found 14 (17 requested) and removed 17 (8 requested) atoms. Cycle 4: After refmac, R = 0.2204 (Rfree = 0.000) for 2720 atoms. Found 8 (17 requested) and removed 13 (8 requested) atoms. Cycle 5: After refmac, R = 0.2067 (Rfree = 0.000) for 2706 atoms. Found 5 (17 requested) and removed 17 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.46 3.37 Search for helices and strands: 0 residues in 0 chains, 2829 seeds are put forward NCS extension: 16 residues added (5 deleted due to clashes), 2845 seeds are put forward Round 1: 195 peptides, 32 chains. Longest chain 17 peptides. Score 0.434 Round 2: 227 peptides, 31 chains. Longest chain 18 peptides. Score 0.551 Round 3: 227 peptides, 31 chains. Longest chain 18 peptides. Score 0.551 Round 4: 226 peptides, 31 chains. Longest chain 18 peptides. Score 0.548 Round 5: 220 peptides, 31 chains. Longest chain 15 peptides. Score 0.530 Taking the results from Round 3 Chains 31, Residues 196, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 5214 reflections ( 99.79 % complete ) and 6166 restraints for refining 2810 atoms. 5382 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2368 (Rfree = 0.000) for 2810 atoms. Found 13 (18 requested) and removed 21 (9 requested) atoms. Cycle 7: After refmac, R = 0.2164 (Rfree = 0.000) for 2782 atoms. Found 17 (17 requested) and removed 17 (8 requested) atoms. Cycle 8: After refmac, R = 0.2140 (Rfree = 0.000) for 2774 atoms. Found 11 (17 requested) and removed 14 (8 requested) atoms. Cycle 9: After refmac, R = 0.2047 (Rfree = 0.000) for 2762 atoms. Found 16 (17 requested) and removed 11 (8 requested) atoms. Cycle 10: After refmac, R = 0.1865 (Rfree = 0.000) for 2759 atoms. Found 13 (17 requested) and removed 16 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.51 3.42 Search for helices and strands: 0 residues in 0 chains, 2895 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 2917 seeds are put forward Round 1: 193 peptides, 35 chains. Longest chain 10 peptides. Score 0.381 Round 2: 212 peptides, 32 chains. Longest chain 14 peptides. Score 0.491 Round 3: 224 peptides, 28 chains. Longest chain 17 peptides. Score 0.581 Round 4: 224 peptides, 29 chains. Longest chain 17 peptides. Score 0.568 Round 5: 230 peptides, 26 chains. Longest chain 21 peptides. Score 0.622 Taking the results from Round 5 Chains 27, Residues 204, Estimated correctness of the model 23.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 5214 reflections ( 99.79 % complete ) and 6114 restraints for refining 2843 atoms. 5278 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2124 (Rfree = 0.000) for 2843 atoms. Found 10 (18 requested) and removed 15 (9 requested) atoms. Cycle 12: After refmac, R = 0.1933 (Rfree = 0.000) for 2817 atoms. Found 13 (18 requested) and removed 13 (9 requested) atoms. Cycle 13: After refmac, R = 0.1850 (Rfree = 0.000) for 2809 atoms. Found 7 (18 requested) and removed 11 (9 requested) atoms. Cycle 14: After refmac, R = 0.1842 (Rfree = 0.000) for 2799 atoms. Found 5 (17 requested) and removed 11 (8 requested) atoms. Cycle 15: After refmac, R = 0.1804 (Rfree = 0.000) for 2787 atoms. Found 6 (17 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.48 3.39 Search for helices and strands: 0 residues in 0 chains, 2903 seeds are put forward NCS extension: 32 residues added (0 deleted due to clashes), 2935 seeds are put forward Round 1: 185 peptides, 32 chains. Longest chain 19 peptides. Score 0.398 Round 2: 199 peptides, 31 chains. Longest chain 19 peptides. Score 0.463 Round 3: 207 peptides, 30 chains. Longest chain 22 peptides. Score 0.503 Round 4: 208 peptides, 29 chains. Longest chain 18 peptides. Score 0.520 Round 5: 221 peptides, 30 chains. Longest chain 26 peptides. Score 0.546 Taking the results from Round 5 Chains 32, Residues 191, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 5214 reflections ( 99.79 % complete ) and 6270 restraints for refining 2843 atoms. 5505 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2049 (Rfree = 0.000) for 2843 atoms. Found 11 (18 requested) and removed 29 (9 requested) atoms. Cycle 17: After refmac, R = 0.2471 (Rfree = 0.000) for 2818 atoms. Found 18 (18 requested) and removed 16 (9 requested) atoms. Cycle 18: After refmac, R = 0.1870 (Rfree = 0.000) for 2814 atoms. Found 10 (18 requested) and removed 14 (9 requested) atoms. Cycle 19: After refmac, R = 0.1867 (Rfree = 0.000) for 2807 atoms. Found 6 (18 requested) and removed 16 (9 requested) atoms. Cycle 20: After refmac, R = 0.1839 (Rfree = 0.000) for 2793 atoms. Found 8 (17 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.52 3.43 Search for helices and strands: 0 residues in 0 chains, 2950 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 2965 seeds are put forward Round 1: 168 peptides, 32 chains. Longest chain 16 peptides. Score 0.334 Round 2: 198 peptides, 30 chains. Longest chain 17 peptides. Score 0.474 Round 3: 194 peptides, 31 chains. Longest chain 16 peptides. Score 0.445 Round 4: 197 peptides, 30 chains. Longest chain 14 peptides. Score 0.471 Round 5: 186 peptides, 28 chains. Longest chain 16 peptides. Score 0.463 Taking the results from Round 2 Chains 30, Residues 168, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 5214 reflections ( 99.79 % complete ) and 6207 restraints for refining 2843 atoms. 5527 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1993 (Rfree = 0.000) for 2843 atoms. Found 10 (18 requested) and removed 29 (9 requested) atoms. Cycle 22: After refmac, R = 0.2665 (Rfree = 0.000) for 2803 atoms. Found 18 (18 requested) and removed 22 (9 requested) atoms. Cycle 23: After refmac, R = 0.2454 (Rfree = 0.000) for 2784 atoms. Found 17 (17 requested) and removed 18 (8 requested) atoms. Cycle 24: After refmac, R = 0.1823 (Rfree = 0.000) for 2772 atoms. Found 10 (17 requested) and removed 11 (8 requested) atoms. Cycle 25: After refmac, R = 0.1876 (Rfree = 0.000) for 2764 atoms. Found 17 (17 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.47 3.38 Search for helices and strands: 0 residues in 0 chains, 2899 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 2918 seeds are put forward Round 1: 170 peptides, 36 chains. Longest chain 9 peptides. Score 0.276 Round 2: 201 peptides, 38 chains. Longest chain 12 peptides. Score 0.363 Round 3: 212 peptides, 35 chains. Longest chain 19 peptides. Score 0.448 Round 4: 206 peptides, 32 chains. Longest chain 16 peptides. Score 0.471 Round 5: 200 peptides, 32 chains. Longest chain 15 peptides. Score 0.451 Taking the results from Round 4 Chains 32, Residues 174, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5214 reflections ( 99.79 % complete ) and 6158 restraints for refining 2810 atoms. 5494 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2061 (Rfree = 0.000) for 2810 atoms. Found 18 (18 requested) and removed 22 (9 requested) atoms. Cycle 27: After refmac, R = 0.1898 (Rfree = 0.000) for 2799 atoms. Found 10 (18 requested) and removed 15 (9 requested) atoms. Cycle 28: After refmac, R = 0.1600 (Rfree = 0.000) for 2789 atoms. Found 2 (17 requested) and removed 12 (8 requested) atoms. Cycle 29: After refmac, R = 0.1556 (Rfree = 0.000) for 2777 atoms. Found 4 (17 requested) and removed 11 (8 requested) atoms. Cycle 30: After refmac, R = 0.1511 (Rfree = 0.000) for 2768 atoms. Found 3 (17 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.48 3.39 Search for helices and strands: 0 residues in 0 chains, 2888 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 2905 seeds are put forward Round 1: 179 peptides, 35 chains. Longest chain 8 peptides. Score 0.328 Round 2: 198 peptides, 33 chains. Longest chain 13 peptides. Score 0.429 Round 3: 201 peptides, 33 chains. Longest chain 13 peptides. Score 0.440 Round 4: 199 peptides, 33 chains. Longest chain 11 peptides. Score 0.433 Round 5: 197 peptides, 32 chains. Longest chain 13 peptides. Score 0.441 Taking the results from Round 5 Chains 33, Residues 165, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 5214 reflections ( 99.79 % complete ) and 6410 restraints for refining 2843 atoms. 5745 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2000 (Rfree = 0.000) for 2843 atoms. Found 18 (18 requested) and removed 15 (9 requested) atoms. Cycle 32: After refmac, R = 0.1837 (Rfree = 0.000) for 2834 atoms. Found 11 (18 requested) and removed 11 (9 requested) atoms. Cycle 33: After refmac, R = 0.1821 (Rfree = 0.000) for 2832 atoms. Found 14 (18 requested) and removed 10 (9 requested) atoms. Cycle 34: After refmac, R = 0.1813 (Rfree = 0.000) for 2831 atoms. Found 12 (18 requested) and removed 12 (9 requested) atoms. Cycle 35: After refmac, R = 0.1970 (Rfree = 0.000) for 2821 atoms. Found 18 (18 requested) and removed 15 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.48 3.39 Search for helices and strands: 0 residues in 0 chains, 2944 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 2961 seeds are put forward Round 1: 137 peptides, 26 chains. Longest chain 14 peptides. Score 0.313 Round 2: 177 peptides, 28 chains. Longest chain 16 peptides. Score 0.432 Round 3: 183 peptides, 31 chains. Longest chain 15 peptides. Score 0.407 Round 4: 181 peptides, 28 chains. Longest chain 15 peptides. Score 0.446 Round 5: 182 peptides, 26 chains. Longest chain 15 peptides. Score 0.480 Taking the results from Round 5 Chains 26, Residues 156, Estimated correctness of the model 0.0 % 2 chains (22 residues) have been docked in sequence ------------------------------------------------------ 5214 reflections ( 99.79 % complete ) and 6062 restraints for refining 2843 atoms. 5384 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1901 (Rfree = 0.000) for 2843 atoms. Found 18 (18 requested) and removed 20 (9 requested) atoms. Cycle 37: After refmac, R = 0.1958 (Rfree = 0.000) for 2824 atoms. Found 18 (18 requested) and removed 11 (9 requested) atoms. Cycle 38: After refmac, R = 0.1934 (Rfree = 0.000) for 2827 atoms. Found 16 (18 requested) and removed 15 (9 requested) atoms. Cycle 39: After refmac, R = 0.1986 (Rfree = 0.000) for 2820 atoms. Found 17 (18 requested) and removed 11 (9 requested) atoms. Cycle 40: After refmac, R = 0.1892 (Rfree = 0.000) for 2817 atoms. Found 14 (18 requested) and removed 16 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.54 3.45 Search for helices and strands: 0 residues in 0 chains, 2892 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 2914 seeds are put forward Round 1: 152 peptides, 30 chains. Longest chain 14 peptides. Score 0.305 Round 2: 159 peptides, 27 chains. Longest chain 13 peptides. Score 0.382 Round 3: 162 peptides, 27 chains. Longest chain 13 peptides. Score 0.393 Round 4: 159 peptides, 26 chains. Longest chain 14 peptides. Score 0.399 Round 5: 160 peptides, 27 chains. Longest chain 11 peptides. Score 0.386 Taking the results from Round 4 Chains 26, Residues 133, Estimated correctness of the model 0.0 % 3 chains (25 residues) have been docked in sequence ------------------------------------------------------ 5214 reflections ( 99.79 % complete ) and 5998 restraints for refining 2829 atoms. 5398 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1832 (Rfree = 0.000) for 2829 atoms. Found 15 (18 requested) and removed 20 (9 requested) atoms. Cycle 42: After refmac, R = 0.1696 (Rfree = 0.000) for 2814 atoms. Found 12 (18 requested) and removed 12 (9 requested) atoms. Cycle 43: After refmac, R = 0.1754 (Rfree = 0.000) for 2809 atoms. Found 15 (18 requested) and removed 12 (9 requested) atoms. Cycle 44: After refmac, R = 0.1696 (Rfree = 0.000) for 2810 atoms. Found 16 (18 requested) and removed 17 (9 requested) atoms. Cycle 45: After refmac, R = 0.1602 (Rfree = 0.000) for 2803 atoms. Found 10 (18 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.51 3.42 Search for helices and strands: 0 residues in 0 chains, 2902 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 2918 seeds are put forward Round 1: 126 peptides, 27 chains. Longest chain 7 peptides. Score 0.249 Round 2: 147 peptides, 27 chains. Longest chain 13 peptides. Score 0.336 Round 3: 161 peptides, 27 chains. Longest chain 12 peptides. Score 0.390 Round 4: 156 peptides, 25 chains. Longest chain 15 peptides. Score 0.404 Round 5: 154 peptides, 28 chains. Longest chain 11 peptides. Score 0.347 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 25, Residues 131, 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. 5214 reflections ( 99.79 % complete ) and 6491 restraints for refining 2843 atoms. 5992 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1720 (Rfree = 0.000) for 2843 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.1752 (Rfree = 0.000) for 2830 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.1751 (Rfree = 0.000) for 2821 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.1363 (Rfree = 0.000) for 2809 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:12:46 GMT 2018 Job finished. TimeTaking 49.73 Used memory is bytes: 6889704