null Sun 23 Dec 22:22:43 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 2ozg-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ozg-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ozg-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ozg-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/2ozg-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ozg-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 22:22:53 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/2ozg-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ozg-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 283 and 0 Target number of residues in the AU: 283 Target solvent content: 0.6388 Checking the provided sequence file Detected sequence length: 396 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 396 Adjusted target solvent content: 0.49 Input MTZ file: 2ozg-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: 155 Cell parameters: 175.031 175.031 71.923 90.000 90.000 120.000 Input sequence file: 2ozg-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 3168 target number of atoms Had to go as low as 0.75 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 Loops will be built when appropriate and at the last cycle Resolution range: 87.516 3.600 Wilson plot Bfac: 71.28 4978 reflections ( 99.72 % complete ) and 0 restraints for refining 3516 atoms. Observations/parameters ratio is 0.35 ------------------------------------------------------ Starting model: R = 0.3279 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2376 (Rfree = 0.000) for 3516 atoms. Found 19 (22 requested) and removed 23 (11 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.42 3.47 Search for helices and strands: 0 residues in 0 chains, 3592 seeds are put forward Round 1: 185 peptides, 37 chains. Longest chain 11 peptides. Score 0.324 Round 2: 221 peptides, 34 chains. Longest chain 16 peptides. Score 0.502 Round 3: 238 peptides, 34 chains. Longest chain 18 peptides. Score 0.555 Round 4: 239 peptides, 32 chains. Longest chain 20 peptides. Score 0.584 Round 5: 230 peptides, 33 chains. Longest chain 21 peptides. Score 0.544 Taking the results from Round 4 Chains 32, Residues 207, Estimated correctness of the model 8.3 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 4978 reflections ( 99.72 % complete ) and 6407 restraints for refining 2869 atoms. 5576 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2566 (Rfree = 0.000) for 2869 atoms. Found 9 (18 requested) and removed 12 (9 requested) atoms. Cycle 2: After refmac, R = 0.2379 (Rfree = 0.000) for 2844 atoms. Found 4 (18 requested) and removed 13 (9 requested) atoms. Cycle 3: After refmac, R = 0.2315 (Rfree = 0.000) for 2829 atoms. Found 5 (18 requested) and removed 11 (9 requested) atoms. Cycle 4: After refmac, R = 0.2222 (Rfree = 0.000) for 2822 atoms. Found 3 (18 requested) and removed 10 (9 requested) atoms. Cycle 5: After refmac, R = 0.2153 (Rfree = 0.000) for 2813 atoms. Found 3 (18 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.43 3.48 Search for helices and strands: 0 residues in 0 chains, 2906 seeds are put forward Round 1: 242 peptides, 43 chains. Longest chain 18 peptides. Score 0.442 Round 2: 244 peptides, 38 chains. Longest chain 13 peptides. Score 0.520 Round 3: 250 peptides, 36 chains. Longest chain 17 peptides. Score 0.565 Round 4: 239 peptides, 31 chains. Longest chain 16 peptides. Score 0.597 Round 5: 255 peptides, 34 chains. Longest chain 14 peptides. Score 0.604 Taking the results from Round 5 Chains 34, Residues 221, Estimated correctness of the model 16.2 % 5 chains (28 residues) have been docked in sequence ------------------------------------------------------ 4978 reflections ( 99.72 % complete ) and 6298 restraints for refining 2870 atoms. 5373 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2531 (Rfree = 0.000) for 2870 atoms. Found 18 (18 requested) and removed 14 (9 requested) atoms. Cycle 7: After refmac, R = 0.2212 (Rfree = 0.000) for 2861 atoms. Found 5 (18 requested) and removed 10 (9 requested) atoms. Cycle 8: After refmac, R = 0.2132 (Rfree = 0.000) for 2846 atoms. Found 1 (18 requested) and removed 9 (9 requested) atoms. Cycle 9: After refmac, R = 0.2088 (Rfree = 0.000) for 2831 atoms. Found 2 (18 requested) and removed 9 (9 requested) atoms. Cycle 10: After refmac, R = 0.2059 (Rfree = 0.000) for 2822 atoms. Found 2 (18 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.43 3.48 Search for helices and strands: 0 residues in 0 chains, 2919 seeds are put forward Round 1: 215 peptides, 39 chains. Longest chain 12 peptides. Score 0.406 Round 2: 236 peptides, 37 chains. Longest chain 12 peptides. Score 0.508 Round 3: 248 peptides, 34 chains. Longest chain 17 peptides. Score 0.585 Round 4: 252 peptides, 34 chains. Longest chain 19 peptides. Score 0.596 Round 5: 239 peptides, 33 chains. Longest chain 22 peptides. Score 0.572 Taking the results from Round 4 Chains 34, Residues 218, Estimated correctness of the model 13.1 % 1 chains (18 residues) have been docked in sequence ------------------------------------------------------ 4978 reflections ( 99.72 % complete ) and 6370 restraints for refining 2871 atoms. 5474 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2466 (Rfree = 0.000) for 2871 atoms. Found 13 (18 requested) and removed 16 (9 requested) atoms. Cycle 12: After refmac, R = 0.2174 (Rfree = 0.000) for 2862 atoms. Found 5 (18 requested) and removed 12 (9 requested) atoms. Cycle 13: After refmac, R = 0.2107 (Rfree = 0.000) for 2850 atoms. Found 8 (18 requested) and removed 10 (9 requested) atoms. Cycle 14: After refmac, R = 0.2010 (Rfree = 0.000) for 2845 atoms. Found 3 (18 requested) and removed 10 (9 requested) atoms. Cycle 15: After refmac, R = 0.1931 (Rfree = 0.000) for 2836 atoms. Found 3 (18 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.42 3.47 Search for helices and strands: 0 residues in 0 chains, 2933 seeds are put forward Round 1: 218 peptides, 36 chains. Longest chain 11 peptides. Score 0.462 Round 2: 235 peptides, 31 chains. Longest chain 19 peptides. Score 0.586 Round 3: 239 peptides, 33 chains. Longest chain 16 peptides. Score 0.572 Round 4: 242 peptides, 31 chains. Longest chain 27 peptides. Score 0.605 Round 5: 234 peptides, 31 chains. Longest chain 29 peptides. Score 0.583 Taking the results from Round 4 Chains 31, Residues 211, Estimated correctness of the model 16.6 % 3 chains (22 residues) have been docked in sequence ------------------------------------------------------ 4978 reflections ( 99.72 % complete ) and 6347 restraints for refining 2871 atoms. 5466 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2361 (Rfree = 0.000) for 2871 atoms. Found 16 (18 requested) and removed 11 (9 requested) atoms. Cycle 17: After refmac, R = 0.2195 (Rfree = 0.000) for 2867 atoms. Found 7 (18 requested) and removed 13 (9 requested) atoms. Cycle 18: After refmac, R = 0.2114 (Rfree = 0.000) for 2856 atoms. Found 1 (18 requested) and removed 9 (9 requested) atoms. Cycle 19: After refmac, R = 0.2025 (Rfree = 0.000) for 2845 atoms. Found 2 (18 requested) and removed 9 (9 requested) atoms. Cycle 20: After refmac, R = 0.1945 (Rfree = 0.000) for 2836 atoms. Found 3 (18 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.43 3.48 Search for helices and strands: 0 residues in 0 chains, 2926 seeds are put forward Round 1: 215 peptides, 39 chains. Longest chain 16 peptides. Score 0.406 Round 2: 200 peptides, 26 chains. Longest chain 26 peptides. Score 0.548 Round 3: 221 peptides, 28 chains. Longest chain 26 peptides. Score 0.584 Round 4: 225 peptides, 25 chains. Longest chain 31 peptides. Score 0.633 Round 5: 229 peptides, 25 chains. Longest chain 34 peptides. Score 0.644 Taking the results from Round 5 Chains 26, Residues 204, Estimated correctness of the model 31.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4978 reflections ( 99.72 % complete ) and 6550 restraints for refining 2871 atoms. 5738 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2216 (Rfree = 0.000) for 2871 atoms. Found 17 (18 requested) and removed 11 (9 requested) atoms. Cycle 22: After refmac, R = 0.2005 (Rfree = 0.000) for 2863 atoms. Found 4 (18 requested) and removed 10 (9 requested) atoms. Cycle 23: After refmac, R = 0.1907 (Rfree = 0.000) for 2854 atoms. Found 3 (18 requested) and removed 9 (9 requested) atoms. Cycle 24: After refmac, R = 0.1866 (Rfree = 0.000) for 2845 atoms. Found 4 (18 requested) and removed 9 (9 requested) atoms. Cycle 25: After refmac, R = 0.1833 (Rfree = 0.000) for 2840 atoms. Found 4 (18 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.50 3.55 Search for helices and strands: 0 residues in 0 chains, 2931 seeds are put forward Round 1: 191 peptides, 36 chains. Longest chain 14 peptides. Score 0.364 Round 2: 216 peptides, 31 chains. Longest chain 24 peptides. Score 0.528 Round 3: 215 peptides, 30 chains. Longest chain 18 peptides. Score 0.539 Round 4: 223 peptides, 29 chains. Longest chain 23 peptides. Score 0.577 Round 5: 221 peptides, 25 chains. Longest chain 19 peptides. Score 0.623 Taking the results from Round 5 Chains 27, Residues 196, Estimated correctness of the model 23.4 % 2 chains (28 residues) have been docked in sequence ------------------------------------------------------ 4978 reflections ( 99.72 % complete ) and 6348 restraints for refining 2871 atoms. 5483 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2178 (Rfree = 0.000) for 2871 atoms. Found 9 (18 requested) and removed 14 (9 requested) atoms. Cycle 27: After refmac, R = 0.2015 (Rfree = 0.000) for 2850 atoms. Found 4 (18 requested) and removed 9 (9 requested) atoms. Cycle 28: After refmac, R = 0.1959 (Rfree = 0.000) for 2837 atoms. Found 4 (18 requested) and removed 9 (9 requested) atoms. Cycle 29: After refmac, R = 0.1908 (Rfree = 0.000) for 2826 atoms. Found 1 (18 requested) and removed 9 (9 requested) atoms. Cycle 30: After refmac, R = 0.1879 (Rfree = 0.000) for 2817 atoms. Found 1 (18 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.54 3.59 Search for helices and strands: 0 residues in 0 chains, 2920 seeds are put forward Round 1: 181 peptides, 36 chains. Longest chain 10 peptides. Score 0.324 Round 2: 209 peptides, 31 chains. Longest chain 16 peptides. Score 0.506 Round 3: 206 peptides, 30 chains. Longest chain 15 peptides. Score 0.510 Round 4: 204 peptides, 32 chains. Longest chain 15 peptides. Score 0.474 Round 5: 204 peptides, 31 chains. Longest chain 15 peptides. Score 0.489 Taking the results from Round 3 Chains 30, Residues 176, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4978 reflections ( 99.72 % complete ) and 6771 restraints for refining 2871 atoms. 6097 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2138 (Rfree = 0.000) for 2871 atoms. Found 13 (18 requested) and removed 10 (9 requested) atoms. Cycle 32: After refmac, R = 0.2036 (Rfree = 0.000) for 2872 atoms. Found 9 (18 requested) and removed 10 (9 requested) atoms. Cycle 33: After refmac, R = 0.1943 (Rfree = 0.000) for 2868 atoms. Found 3 (18 requested) and removed 10 (9 requested) atoms. Cycle 34: After refmac, R = 0.1910 (Rfree = 0.000) for 2858 atoms. Found 2 (18 requested) and removed 9 (9 requested) atoms. Cycle 35: After refmac, R = 0.1867 (Rfree = 0.000) for 2848 atoms. Found 1 (18 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.52 3.57 Search for helices and strands: 0 residues in 0 chains, 2941 seeds are put forward Round 1: 169 peptides, 33 chains. Longest chain 12 peptides. Score 0.327 Round 2: 184 peptides, 28 chains. Longest chain 15 peptides. Score 0.465 Round 3: 187 peptides, 31 chains. Longest chain 13 peptides. Score 0.429 Round 4: 191 peptides, 27 chains. Longest chain 16 peptides. Score 0.504 Round 5: 203 peptides, 31 chains. Longest chain 17 peptides. Score 0.485 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 ------------------------------------------------------ 4978 reflections ( 99.72 % complete ) and 6799 restraints for refining 2871 atoms. 6170 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2145 (Rfree = 0.000) for 2871 atoms. Found 15 (18 requested) and removed 10 (9 requested) atoms. Cycle 37: After refmac, R = 0.1944 (Rfree = 0.000) for 2871 atoms. Found 6 (18 requested) and removed 9 (9 requested) atoms. Cycle 38: After refmac, R = 0.1917 (Rfree = 0.000) for 2866 atoms. Found 5 (18 requested) and removed 9 (9 requested) atoms. Cycle 39: After refmac, R = 0.1863 (Rfree = 0.000) for 2862 atoms. Found 2 (18 requested) and removed 9 (9 requested) atoms. Cycle 40: After refmac, R = 0.1828 (Rfree = 0.000) for 2855 atoms. Found 1 (18 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.47 3.52 Search for helices and strands: 0 residues in 0 chains, 2932 seeds are put forward Round 1: 167 peptides, 33 chains. Longest chain 12 peptides. Score 0.319 Round 2: 191 peptides, 30 chains. Longest chain 15 peptides. Score 0.459 Round 3: 202 peptides, 34 chains. Longest chain 15 peptides. Score 0.436 Round 4: 196 peptides, 27 chains. Longest chain 20 peptides. Score 0.521 Round 5: 198 peptides, 28 chains. Longest chain 16 peptides. Score 0.513 Taking the results from Round 4 Chains 27, Residues 169, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4978 reflections ( 99.72 % complete ) and 6741 restraints for refining 2871 atoms. 6092 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2153 (Rfree = 0.000) for 2871 atoms. Found 13 (18 requested) and removed 9 (9 requested) atoms. Cycle 42: After refmac, R = 0.1947 (Rfree = 0.000) for 2871 atoms. Found 4 (18 requested) and removed 9 (9 requested) atoms. Cycle 43: After refmac, R = 0.1899 (Rfree = 0.000) for 2862 atoms. Found 6 (18 requested) and removed 9 (9 requested) atoms. Cycle 44: After refmac, R = 0.1859 (Rfree = 0.000) for 2858 atoms. Found 1 (18 requested) and removed 9 (9 requested) atoms. Cycle 45: After refmac, R = 0.1850 (Rfree = 0.000) for 2848 atoms. Found 4 (18 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.52 3.57 Search for helices and strands: 0 residues in 0 chains, 2940 seeds are put forward Round 1: 163 peptides, 31 chains. Longest chain 11 peptides. Score 0.337 Round 2: 187 peptides, 29 chains. Longest chain 17 peptides. Score 0.460 Round 3: 182 peptides, 28 chains. Longest chain 18 peptides. Score 0.458 Round 4: 196 peptides, 29 chains. Longest chain 16 peptides. Score 0.491 Round 5: 175 peptides, 26 chains. Longest chain 21 peptides. Score 0.465 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 29, Residues 167, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence Sequence coverage is 4 % Consider running further cycles of model building using 2ozg-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4978 reflections ( 99.72 % complete ) and 6619 restraints for refining 2871 atoms. 5966 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2036 (Rfree = 0.000) for 2871 atoms. Found 0 (18 requested) and removed 6 (9 requested) atoms. Cycle 47: After refmac, R = 0.1968 (Rfree = 0.000) for 2861 atoms. Found 0 (18 requested) and removed 3 (9 requested) atoms. Cycle 48: After refmac, R = 0.1920 (Rfree = 0.000) for 2855 atoms. Found 0 (18 requested) and removed 4 (9 requested) atoms. Cycle 49: After refmac, R = 0.1864 (Rfree = 0.000) for 2849 atoms. Found 0 (18 requested) and removed 4 (9 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:19:01 GMT 2018 Job finished. TimeTaking 56.31 Used memory is bytes: 2771832