null Sun 23 Dec 22:22:59 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-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ogi-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ogi-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ogi-3.2-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-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ogi-3.2-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 22:23:08 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-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ogi-3.2-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 297 and 0 Target number of residues in the AU: 297 Target solvent content: 0.6361 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-3.2-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-3.2-parrot-hancs.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: 63.833 3.200 Wilson plot Bfac: 69.78 7378 reflections ( 99.85 % complete ) and 0 restraints for refining 3474 atoms. Observations/parameters ratio is 0.53 ------------------------------------------------------ Starting model: R = 0.3316 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3088 (Rfree = 0.000) for 3474 atoms. Found 31 (31 requested) and removed 33 (15 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.32 3.23 Search for helices and strands: 0 residues in 0 chains, 3562 seeds are put forward NCS extension: 0 residues added, 3562 seeds are put forward Round 1: 166 peptides, 35 chains. Longest chain 11 peptides. Score 0.277 Round 2: 213 peptides, 34 chains. Longest chain 17 peptides. Score 0.466 Round 3: 240 peptides, 37 chains. Longest chain 15 peptides. Score 0.511 Round 4: 248 peptides, 34 chains. Longest chain 14 peptides. Score 0.573 Round 5: 252 peptides, 35 chains. Longest chain 15 peptides. Score 0.572 Taking the results from Round 4 Chains 34, Residues 214, Estimated correctness of the model 33.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7378 reflections ( 99.85 % complete ) and 6294 restraints for refining 2861 atoms. 5472 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2582 (Rfree = 0.000) for 2861 atoms. Found 15 (25 requested) and removed 19 (12 requested) atoms. Cycle 2: After refmac, R = 0.2526 (Rfree = 0.000) for 2823 atoms. Found 9 (25 requested) and removed 19 (12 requested) atoms. Cycle 3: After refmac, R = 0.2416 (Rfree = 0.000) for 2800 atoms. Found 9 (25 requested) and removed 17 (12 requested) atoms. Cycle 4: After refmac, R = 0.2366 (Rfree = 0.000) for 2789 atoms. Found 16 (25 requested) and removed 15 (12 requested) atoms. Cycle 5: After refmac, R = 0.2673 (Rfree = 0.000) for 2787 atoms. Found 25 (25 requested) and removed 30 (12 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.25 3.16 Search for helices and strands: 0 residues in 0 chains, 2972 seeds are put forward NCS extension: 15 residues added (3 deleted due to clashes), 2987 seeds are put forward Round 1: 225 peptides, 36 chains. Longest chain 13 peptides. Score 0.477 Round 2: 237 peptides, 32 chains. Longest chain 17 peptides. Score 0.567 Round 3: 266 peptides, 34 chains. Longest chain 24 peptides. Score 0.621 Round 4: 248 peptides, 32 chains. Longest chain 16 peptides. Score 0.598 Round 5: 246 peptides, 31 chains. Longest chain 18 peptides. Score 0.604 Taking the results from Round 3 Chains 35, Residues 232, Estimated correctness of the model 46.6 % 1 chains (19 residues) have been docked in sequence ------------------------------------------------------ 7378 reflections ( 99.85 % complete ) and 6043 restraints for refining 2863 atoms. 5077 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2536 (Rfree = 0.000) for 2863 atoms. Found 16 (25 requested) and removed 19 (12 requested) atoms. Cycle 7: After refmac, R = 0.2505 (Rfree = 0.000) for 2845 atoms. Found 6 (25 requested) and removed 17 (12 requested) atoms. Cycle 8: After refmac, R = 0.2377 (Rfree = 0.000) for 2829 atoms. Found 7 (25 requested) and removed 16 (12 requested) atoms. Cycle 9: After refmac, R = 0.2280 (Rfree = 0.000) for 2817 atoms. Found 4 (25 requested) and removed 18 (12 requested) atoms. Cycle 10: After refmac, R = 0.2169 (Rfree = 0.000) for 2798 atoms. Found 7 (25 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.21 3.13 Search for helices and strands: 0 residues in 0 chains, 2939 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 2953 seeds are put forward Round 1: 221 peptides, 38 chains. Longest chain 14 peptides. Score 0.435 Round 2: 245 peptides, 34 chains. Longest chain 18 peptides. Score 0.565 Round 3: 245 peptides, 31 chains. Longest chain 25 peptides. Score 0.602 Round 4: 240 peptides, 33 chains. Longest chain 17 peptides. Score 0.563 Round 5: 238 peptides, 33 chains. Longest chain 17 peptides. Score 0.557 Taking the results from Round 3 Chains 31, Residues 214, Estimated correctness of the model 41.6 % 2 chains (22 residues) have been docked in sequence ------------------------------------------------------ 7378 reflections ( 99.85 % complete ) and 6178 restraints for refining 2863 atoms. 5273 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2383 (Rfree = 0.000) for 2863 atoms. Found 19 (25 requested) and removed 19 (12 requested) atoms. Cycle 12: After refmac, R = 0.2237 (Rfree = 0.000) for 2852 atoms. Found 8 (25 requested) and removed 14 (12 requested) atoms. Cycle 13: After refmac, R = 0.2191 (Rfree = 0.000) for 2839 atoms. Found 5 (25 requested) and removed 19 (12 requested) atoms. Cycle 14: After refmac, R = 0.2219 (Rfree = 0.000) for 2818 atoms. Found 10 (25 requested) and removed 15 (12 requested) atoms. Cycle 15: After refmac, R = 0.2108 (Rfree = 0.000) for 2808 atoms. Found 9 (25 requested) and removed 14 (12 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.24 3.15 Search for helices and strands: 0 residues in 0 chains, 2942 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 2963 seeds are put forward Round 1: 234 peptides, 38 chains. Longest chain 23 peptides. Score 0.478 Round 2: 257 peptides, 37 chains. Longest chain 20 peptides. Score 0.561 Round 3: 252 peptides, 35 chains. Longest chain 16 peptides. Score 0.572 Round 4: 265 peptides, 36 chains. Longest chain 23 peptides. Score 0.595 Round 5: 253 peptides, 32 chains. Longest chain 20 peptides. Score 0.611 Taking the results from Round 5 Chains 34, Residues 221, Estimated correctness of the model 44.0 % 3 chains (34 residues) have been docked in sequence ------------------------------------------------------ 7378 reflections ( 99.85 % complete ) and 5782 restraints for refining 2862 atoms. 4803 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2558 (Rfree = 0.000) for 2862 atoms. Found 21 (25 requested) and removed 20 (12 requested) atoms. Cycle 17: After refmac, R = 0.2411 (Rfree = 0.000) for 2845 atoms. Found 6 (25 requested) and removed 14 (12 requested) atoms. Cycle 18: After refmac, R = 0.2314 (Rfree = 0.000) for 2832 atoms. Found 8 (25 requested) and removed 14 (12 requested) atoms. Cycle 19: After refmac, R = 0.2188 (Rfree = 0.000) for 2820 atoms. Found 7 (25 requested) and removed 17 (12 requested) atoms. Cycle 20: After refmac, R = 0.2222 (Rfree = 0.000) for 2804 atoms. Found 5 (25 requested) and removed 15 (12 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.22 3.14 Search for helices and strands: 0 residues in 0 chains, 2920 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 2938 seeds are put forward Round 1: 195 peptides, 31 chains. Longest chain 16 peptides. Score 0.449 Round 2: 214 peptides, 29 chains. Longest chain 17 peptides. Score 0.539 Round 3: 232 peptides, 32 chains. Longest chain 19 peptides. Score 0.553 Round 4: 236 peptides, 28 chains. Longest chain 20 peptides. Score 0.614 Round 5: 236 peptides, 30 chains. Longest chain 26 peptides. Score 0.589 Taking the results from Round 4 Chains 32, Residues 208, Estimated correctness of the model 44.8 % 3 chains (28 residues) have been docked in sequence ------------------------------------------------------ 7378 reflections ( 99.85 % complete ) and 6059 restraints for refining 2863 atoms. 5162 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2430 (Rfree = 0.000) for 2863 atoms. Found 12 (25 requested) and removed 18 (12 requested) atoms. Cycle 22: After refmac, R = 0.2236 (Rfree = 0.000) for 2843 atoms. Found 4 (25 requested) and removed 15 (12 requested) atoms. Cycle 23: After refmac, R = 0.2174 (Rfree = 0.000) for 2820 atoms. Found 6 (25 requested) and removed 13 (12 requested) atoms. Cycle 24: After refmac, R = 0.2153 (Rfree = 0.000) for 2807 atoms. Found 3 (25 requested) and removed 13 (12 requested) atoms. Cycle 25: After refmac, R = 0.2163 (Rfree = 0.000) for 2795 atoms. Found 3 (25 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.22 3.14 Search for helices and strands: 0 residues in 0 chains, 2912 seeds are put forward NCS extension: 19 residues added (3 deleted due to clashes), 2931 seeds are put forward Round 1: 189 peptides, 30 chains. Longest chain 17 peptides. Score 0.443 Round 2: 211 peptides, 31 chains. Longest chain 16 peptides. Score 0.502 Round 3: 205 peptides, 28 chains. Longest chain 23 peptides. Score 0.525 Round 4: 212 peptides, 30 chains. Longest chain 18 peptides. Score 0.519 Round 5: 213 peptides, 30 chains. Longest chain 22 peptides. Score 0.522 Taking the results from Round 3 Chains 30, Residues 177, Estimated correctness of the model 19.3 % 4 chains (30 residues) have been docked in sequence ------------------------------------------------------ 7378 reflections ( 99.85 % complete ) and 6238 restraints for refining 2863 atoms. 5455 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2324 (Rfree = 0.000) for 2863 atoms. Found 10 (25 requested) and removed 16 (12 requested) atoms. Cycle 27: After refmac, R = 0.2335 (Rfree = 0.000) for 2842 atoms. Found 8 (25 requested) and removed 15 (12 requested) atoms. Cycle 28: After refmac, R = 0.2295 (Rfree = 0.000) for 2826 atoms. Found 13 (25 requested) and removed 14 (12 requested) atoms. Cycle 29: After refmac, R = 0.2201 (Rfree = 0.000) for 2820 atoms. Found 3 (25 requested) and removed 19 (12 requested) atoms. Cycle 30: After refmac, R = 0.2125 (Rfree = 0.000) for 2800 atoms. Found 10 (25 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.21 3.13 Search for helices and strands: 0 residues in 0 chains, 2922 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 2941 seeds are put forward Round 1: 184 peptides, 28 chains. Longest chain 23 peptides. Score 0.456 Round 2: 189 peptides, 26 chains. Longest chain 25 peptides. Score 0.503 Round 3: 195 peptides, 26 chains. Longest chain 23 peptides. Score 0.522 Round 4: 197 peptides, 26 chains. Longest chain 25 peptides. Score 0.528 Round 5: 197 peptides, 25 chains. Longest chain 25 peptides. Score 0.542 Taking the results from Round 5 Chains 27, Residues 172, Estimated correctness of the model 24.5 % 2 chains (30 residues) have been docked in sequence ------------------------------------------------------ 7378 reflections ( 99.85 % complete ) and 6120 restraints for refining 2863 atoms. 5320 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2329 (Rfree = 0.000) for 2863 atoms. Found 22 (25 requested) and removed 22 (12 requested) atoms. Cycle 32: After refmac, R = 0.2165 (Rfree = 0.000) for 2855 atoms. Found 7 (25 requested) and removed 15 (12 requested) atoms. Cycle 33: After refmac, R = 0.2263 (Rfree = 0.000) for 2844 atoms. Found 25 (25 requested) and removed 16 (12 requested) atoms. Cycle 34: After refmac, R = 0.2065 (Rfree = 0.000) for 2849 atoms. Found 11 (25 requested) and removed 16 (12 requested) atoms. Cycle 35: After refmac, R = 0.1968 (Rfree = 0.000) for 2843 atoms. Found 9 (25 requested) and removed 15 (12 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.21 3.13 Search for helices and strands: 0 residues in 0 chains, 2952 seeds are put forward NCS extension: 15 residues added (5 deleted due to clashes), 2967 seeds are put forward Round 1: 173 peptides, 31 chains. Longest chain 16 peptides. Score 0.370 Round 2: 201 peptides, 30 chains. Longest chain 17 peptides. Score 0.484 Round 3: 206 peptides, 33 chains. Longest chain 18 peptides. Score 0.457 Round 4: 192 peptides, 29 chains. Longest chain 18 peptides. Score 0.468 Round 5: 203 peptides, 34 chains. Longest chain 14 peptides. Score 0.432 Taking the results from Round 2 Chains 31, Residues 171, Estimated correctness of the model 6.1 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ 7378 reflections ( 99.85 % complete ) and 6221 restraints for refining 2863 atoms. 5505 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2121 (Rfree = 0.000) for 2863 atoms. Found 19 (25 requested) and removed 16 (12 requested) atoms. Cycle 37: After refmac, R = 0.2067 (Rfree = 0.000) for 2860 atoms. Found 8 (25 requested) and removed 19 (12 requested) atoms. Cycle 38: After refmac, R = 0.1983 (Rfree = 0.000) for 2841 atoms. Found 9 (25 requested) and removed 14 (12 requested) atoms. Cycle 39: After refmac, R = 0.1895 (Rfree = 0.000) for 2832 atoms. Found 2 (25 requested) and removed 12 (12 requested) atoms. Cycle 40: After refmac, R = 0.1870 (Rfree = 0.000) for 2817 atoms. Found 5 (25 requested) and removed 14 (12 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.22 3.14 Search for helices and strands: 0 residues in 0 chains, 2948 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 2968 seeds are put forward Round 1: 168 peptides, 29 chains. Longest chain 13 peptides. Score 0.383 Round 2: 185 peptides, 28 chains. Longest chain 21 peptides. Score 0.460 Round 3: 184 peptides, 28 chains. Longest chain 16 peptides. Score 0.456 Round 4: 191 peptides, 27 chains. Longest chain 21 peptides. Score 0.495 Round 5: 181 peptides, 25 chains. Longest chain 21 peptides. Score 0.491 Taking the results from Round 4 Chains 29, Residues 164, Estimated correctness of the model 9.7 % 2 chains (21 residues) have been docked in sequence ------------------------------------------------------ 7378 reflections ( 99.85 % complete ) and 6125 restraints for refining 2863 atoms. 5422 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2085 (Rfree = 0.000) for 2863 atoms. Found 18 (25 requested) and removed 15 (12 requested) atoms. Cycle 42: After refmac, R = 0.2061 (Rfree = 0.000) for 2861 atoms. Found 12 (25 requested) and removed 14 (12 requested) atoms. Cycle 43: After refmac, R = 0.2186 (Rfree = 0.000) for 2849 atoms. Found 23 (25 requested) and removed 16 (12 requested) atoms. Cycle 44: After refmac, R = 0.2212 (Rfree = 0.000) for 2848 atoms. Found 25 (25 requested) and removed 16 (12 requested) atoms. Cycle 45: After refmac, R = 0.1747 (Rfree = 0.000) for 2849 atoms. Found 4 (25 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.21 3.13 Search for helices and strands: 0 residues in 0 chains, 2962 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 2977 seeds are put forward Round 1: 144 peptides, 26 chains. Longest chain 14 peptides. Score 0.341 Round 2: 171 peptides, 28 chains. Longest chain 14 peptides. Score 0.411 Round 3: 178 peptides, 27 chains. Longest chain 12 peptides. Score 0.451 Round 4: 187 peptides, 29 chains. Longest chain 17 peptides. Score 0.452 Round 5: 187 peptides, 29 chains. Longest chain 10 peptides. Score 0.452 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 29, Residues 158, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence Sequence coverage is 3 % Consider running further cycles of model building using 2ogi-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7378 reflections ( 99.85 % complete ) and 6353 restraints for refining 2863 atoms. 5738 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2053 (Rfree = 0.000) for 2863 atoms. Found 0 (25 requested) and removed 12 (12 requested) atoms. Cycle 47: After refmac, R = 0.1974 (Rfree = 0.000) for 2845 atoms. Found 0 (25 requested) and removed 12 (12 requested) atoms. Cycle 48: After refmac, R = 0.1897 (Rfree = 0.000) for 2827 atoms. Found 0 (25 requested) and removed 12 (12 requested) atoms. Cycle 49: After refmac, R = 0.1847 (Rfree = 0.000) for 2813 atoms. Found 0 (25 requested) and removed 12 (12 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:13:36 GMT 2018 Job finished. TimeTaking 50.63 Used memory is bytes: 8083704