Sun 23 Dec 22:22:49 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-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ogi-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ogi-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ogi-3.4-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-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ogi-3.4-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 22:22:59 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-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ogi-3.4-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 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-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-3.4-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 3.400 Wilson plot Bfac: 75.24 6172 reflections ( 99.82 % complete ) and 0 restraints for refining 3501 atoms. Observations/parameters ratio is 0.44 ------------------------------------------------------ Starting model: R = 0.3381 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2951 (Rfree = 0.000) for 3501 atoms. Found 23 (26 requested) and removed 22 (13 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.41 3.32 Search for helices and strands: 0 residues in 0 chains, 3569 seeds are put forward NCS extension: 0 residues added, 3569 seeds are put forward Round 1: 184 peptides, 36 chains. Longest chain 10 peptides. Score 0.331 Round 2: 220 peptides, 38 chains. Longest chain 16 peptides. Score 0.431 Round 3: 213 peptides, 34 chains. Longest chain 16 peptides. Score 0.466 Round 4: 211 peptides, 34 chains. Longest chain 17 peptides. Score 0.459 Round 5: 222 peptides, 31 chains. Longest chain 23 peptides. Score 0.536 Taking the results from Round 5 Chains 32, Residues 191, Estimated correctness of the model 6.4 % 3 chains (30 residues) have been docked in sequence ------------------------------------------------------ 6172 reflections ( 99.82 % complete ) and 6167 restraints for refining 2851 atoms. 5340 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2434 (Rfree = 0.000) for 2851 atoms. Found 18 (21 requested) and removed 23 (10 requested) atoms. Cycle 2: After refmac, R = 0.2327 (Rfree = 0.000) for 2792 atoms. Found 14 (21 requested) and removed 21 (10 requested) atoms. Cycle 3: After refmac, R = 0.2314 (Rfree = 0.000) for 2769 atoms. Found 19 (21 requested) and removed 15 (10 requested) atoms. Cycle 4: After refmac, R = 0.1864 (Rfree = 0.000) for 2767 atoms. Found 4 (20 requested) and removed 14 (10 requested) atoms. Cycle 5: After refmac, R = 0.1831 (Rfree = 0.000) for 2749 atoms. Found 7 (20 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.38 3.29 Search for helices and strands: 0 residues in 0 chains, 2881 seeds are put forward NCS extension: 27 residues added (1 deleted due to clashes), 2908 seeds are put forward Round 1: 181 peptides, 33 chains. Longest chain 10 peptides. Score 0.368 Round 2: 229 peptides, 36 chains. Longest chain 16 peptides. Score 0.490 Round 3: 243 peptides, 35 chains. Longest chain 17 peptides. Score 0.546 Round 4: 250 peptides, 34 chains. Longest chain 17 peptides. Score 0.579 Round 5: 239 peptides, 33 chains. Longest chain 16 peptides. Score 0.560 Taking the results from Round 4 Chains 35, Residues 216, Estimated correctness of the model 21.7 % 2 chains (25 residues) have been docked in sequence ------------------------------------------------------ 6172 reflections ( 99.82 % complete ) and 6066 restraints for refining 2852 atoms. 5138 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2269 (Rfree = 0.000) for 2852 atoms. Found 18 (21 requested) and removed 21 (10 requested) atoms. Cycle 7: After refmac, R = 0.2232 (Rfree = 0.000) for 2831 atoms. Found 10 (21 requested) and removed 23 (10 requested) atoms. Cycle 8: After refmac, R = 0.2214 (Rfree = 0.000) for 2807 atoms. Found 15 (21 requested) and removed 25 (10 requested) atoms. Cycle 9: After refmac, R = 0.2130 (Rfree = 0.000) for 2792 atoms. Found 12 (21 requested) and removed 16 (10 requested) atoms. Cycle 10: After refmac, R = 0.2109 (Rfree = 0.000) for 2783 atoms. Found 8 (21 requested) and removed 14 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.37 3.28 Search for helices and strands: 0 residues in 0 chains, 2888 seeds are put forward NCS extension: 26 residues added (0 deleted due to clashes), 2914 seeds are put forward Round 1: 200 peptides, 31 chains. Longest chain 12 peptides. Score 0.466 Round 2: 232 peptides, 31 chains. Longest chain 23 peptides. Score 0.566 Round 3: 238 peptides, 32 chains. Longest chain 24 peptides. Score 0.570 Round 4: 230 peptides, 29 chains. Longest chain 17 peptides. Score 0.585 Round 5: 229 peptides, 34 chains. Longest chain 24 peptides. Score 0.517 Taking the results from Round 4 Chains 29, Residues 201, Estimated correctness of the model 23.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6172 reflections ( 99.82 % complete ) and 6375 restraints for refining 2852 atoms. 5600 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2207 (Rfree = 0.000) for 2852 atoms. Found 20 (21 requested) and removed 17 (10 requested) atoms. Failed to save intermediate PDB Cycle 12: After refmac, R = 0.2079 (Rfree = 0.000) for 2843 atoms. Found 11 (21 requested) and removed 15 (10 requested) atoms. Cycle 13: After refmac, R = 0.1826 (Rfree = 0.000) for 2831 atoms. Found 1 (21 requested) and removed 10 (10 requested) atoms. Cycle 14: After refmac, R = 0.1777 (Rfree = 0.000) for 2818 atoms. Found 5 (21 requested) and removed 12 (10 requested) atoms. Cycle 15: After refmac, R = 0.1985 (Rfree = 0.000) for 2810 atoms. Found 15 (21 requested) and removed 15 (10 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.37 3.28 Search for helices and strands: 0 residues in 0 chains, 2944 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 2963 seeds are put forward Round 1: 197 peptides, 32 chains. Longest chain 16 peptides. Score 0.441 Round 2: 235 peptides, 34 chains. Longest chain 16 peptides. Score 0.535 Round 3: 229 peptides, 35 chains. Longest chain 13 peptides. Score 0.503 Round 4: 229 peptides, 33 chains. Longest chain 16 peptides. Score 0.530 Round 5: 222 peptides, 35 chains. Longest chain 14 peptides. Score 0.481 Taking the results from Round 2 Chains 34, Residues 201, Estimated correctness of the model 6.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6172 reflections ( 99.82 % complete ) and 6341 restraints for refining 2852 atoms. 5571 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2012 (Rfree = 0.000) for 2852 atoms. Found 19 (21 requested) and removed 14 (10 requested) atoms. Cycle 17: After refmac, R = 0.1891 (Rfree = 0.000) for 2847 atoms. Found 12 (21 requested) and removed 14 (10 requested) atoms. Cycle 18: After refmac, R = 0.1867 (Rfree = 0.000) for 2841 atoms. Found 6 (21 requested) and removed 12 (10 requested) atoms. Cycle 19: After refmac, R = 0.1836 (Rfree = 0.000) for 2833 atoms. Found 3 (21 requested) and removed 11 (10 requested) atoms. Cycle 20: After refmac, R = 0.1791 (Rfree = 0.000) for 2823 atoms. Found 4 (21 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.39 3.30 Search for helices and strands: 0 residues in 0 chains, 2945 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 2966 seeds are put forward Round 1: 190 peptides, 34 chains. Longest chain 15 peptides. Score 0.385 Round 2: 198 peptides, 31 chains. Longest chain 18 peptides. Score 0.459 Round 3: 195 peptides, 30 chains. Longest chain 14 peptides. Score 0.464 Round 4: 206 peptides, 30 chains. Longest chain 16 peptides. Score 0.500 Round 5: 204 peptides, 32 chains. Longest chain 13 peptides. Score 0.465 Taking the results from Round 4 Chains 31, Residues 176, Estimated correctness of the model 0.0 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 6172 reflections ( 99.82 % complete ) and 6258 restraints for refining 2851 atoms. 5520 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2147 (Rfree = 0.000) for 2851 atoms. Found 19 (21 requested) and removed 14 (10 requested) atoms. Cycle 22: After refmac, R = 0.1960 (Rfree = 0.000) for 2838 atoms. Found 8 (21 requested) and removed 14 (10 requested) atoms. Cycle 23: After refmac, R = 0.2116 (Rfree = 0.000) for 2830 atoms. Found 20 (21 requested) and removed 15 (10 requested) atoms. Cycle 24: After refmac, R = 0.2104 (Rfree = 0.000) for 2832 atoms. Found 21 (21 requested) and removed 12 (10 requested) atoms. Cycle 25: After refmac, R = 0.1985 (Rfree = 0.000) for 2836 atoms. Found 14 (21 requested) and removed 15 (10 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.41 3.32 Search for helices and strands: 0 residues in 0 chains, 2965 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 2989 seeds are put forward Round 1: 169 peptides, 34 chains. Longest chain 11 peptides. Score 0.305 Round 2: 195 peptides, 33 chains. Longest chain 14 peptides. Score 0.419 Round 3: 201 peptides, 32 chains. Longest chain 15 peptides. Score 0.455 Round 4: 199 peptides, 32 chains. Longest chain 11 peptides. Score 0.448 Round 5: 203 peptides, 33 chains. Longest chain 23 peptides. Score 0.447 Taking the results from Round 3 Chains 32, Residues 169, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6172 reflections ( 99.82 % complete ) and 6584 restraints for refining 2852 atoms. 5940 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2232 (Rfree = 0.000) for 2852 atoms. Found 16 (21 requested) and removed 12 (10 requested) atoms. Cycle 27: After refmac, R = 0.2144 (Rfree = 0.000) for 2844 atoms. Found 21 (21 requested) and removed 11 (10 requested) atoms. Cycle 28: After refmac, R = 0.1715 (Rfree = 0.000) for 2847 atoms. Found 5 (21 requested) and removed 11 (10 requested) atoms. Cycle 29: After refmac, R = 0.2066 (Rfree = 0.000) for 2834 atoms. Found 17 (21 requested) and removed 14 (10 requested) atoms. Cycle 30: After refmac, R = 0.1956 (Rfree = 0.000) for 2835 atoms. Found 21 (21 requested) and removed 12 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.40 3.31 Search for helices and strands: 0 residues in 0 chains, 2965 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 2987 seeds are put forward Round 1: 152 peptides, 30 chains. Longest chain 9 peptides. Score 0.305 Round 2: 190 peptides, 31 chains. Longest chain 14 peptides. Score 0.432 Round 3: 189 peptides, 34 chains. Longest chain 11 peptides. Score 0.382 Round 4: 194 peptides, 32 chains. Longest chain 11 peptides. Score 0.430 Round 5: 189 peptides, 31 chains. Longest chain 11 peptides. Score 0.428 Taking the results from Round 2 Chains 31, Residues 159, Estimated correctness of the model 0.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 6172 reflections ( 99.82 % complete ) and 6395 restraints for refining 2852 atoms. 5741 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2000 (Rfree = 0.000) for 2852 atoms. Found 17 (21 requested) and removed 16 (10 requested) atoms. Cycle 32: After refmac, R = 0.1941 (Rfree = 0.000) for 2839 atoms. Found 18 (21 requested) and removed 14 (10 requested) atoms. Cycle 33: After refmac, R = 0.1808 (Rfree = 0.000) for 2831 atoms. Found 8 (21 requested) and removed 12 (10 requested) atoms. Cycle 34: After refmac, R = 0.2584 (Rfree = 0.000) for 2821 atoms. Found 21 (21 requested) and removed 15 (10 requested) atoms. Cycle 35: After refmac, R = 0.2017 (Rfree = 0.000) for 2816 atoms. Found 20 (21 requested) and removed 16 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.44 3.35 Search for helices and strands: 0 residues in 0 chains, 2940 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 2952 seeds are put forward Round 1: 156 peptides, 29 chains. Longest chain 8 peptides. Score 0.338 Round 2: 159 peptides, 28 chains. Longest chain 9 peptides. Score 0.366 Round 3: 160 peptides, 29 chains. Longest chain 8 peptides. Score 0.353 Round 4: 157 peptides, 26 chains. Longest chain 12 peptides. Score 0.391 Round 5: 172 peptides, 29 chains. Longest chain 11 peptides. Score 0.398 Taking the results from Round 5 Chains 29, Residues 143, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6172 reflections ( 99.82 % complete ) and 6499 restraints for refining 2852 atoms. 5956 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2460 (Rfree = 0.000) for 2852 atoms. Found 21 (21 requested) and removed 14 (10 requested) atoms. Cycle 37: After refmac, R = 0.2234 (Rfree = 0.000) for 2848 atoms. Found 21 (21 requested) and removed 19 (10 requested) atoms. Cycle 38: After refmac, R = 0.2754 (Rfree = 0.000) for 2844 atoms. Found 21 (21 requested) and removed 18 (10 requested) atoms. Cycle 39: After refmac, R = 0.2034 (Rfree = 0.000) for 2837 atoms. Found 21 (21 requested) and removed 12 (10 requested) atoms. Cycle 40: After refmac, R = 0.2592 (Rfree = 0.000) for 2840 atoms. Found 21 (21 requested) and removed 12 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.40 3.31 Search for helices and strands: 0 residues in 0 chains, 2967 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 2979 seeds are put forward Round 1: 128 peptides, 26 chains. Longest chain 9 peptides. Score 0.275 Round 2: 150 peptides, 25 chains. Longest chain 10 peptides. Score 0.381 Round 3: 145 peptides, 25 chains. Longest chain 12 peptides. Score 0.362 Round 4: 151 peptides, 27 chains. Longest chain 12 peptides. Score 0.352 Round 5: 161 peptides, 28 chains. Longest chain 10 peptides. Score 0.373 Taking the results from Round 2 Chains 25, Residues 125, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6172 reflections ( 99.82 % complete ) and 6412 restraints for refining 2825 atoms. 5937 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1929 (Rfree = 0.000) for 2825 atoms. Found 21 (21 requested) and removed 15 (10 requested) atoms. Cycle 42: After refmac, R = 0.2000 (Rfree = 0.000) for 2827 atoms. Found 21 (21 requested) and removed 14 (10 requested) atoms. Cycle 43: After refmac, R = 0.1898 (Rfree = 0.000) for 2828 atoms. Found 21 (21 requested) and removed 14 (10 requested) atoms. Cycle 44: After refmac, R = 0.1751 (Rfree = 0.000) for 2827 atoms. Found 14 (21 requested) and removed 13 (10 requested) atoms. Cycle 45: After refmac, R = 0.1715 (Rfree = 0.000) for 2825 atoms. Found 12 (21 requested) and removed 14 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.37 3.28 Search for helices and strands: 0 residues in 0 chains, 2923 seeds are put forward NCS extension: 0 residues added, 2923 seeds are put forward Round 1: 107 peptides, 24 chains. Longest chain 6 peptides. Score 0.219 Round 2: 130 peptides, 23 chains. Longest chain 10 peptides. Score 0.337 Round 3: 139 peptides, 27 chains. Longest chain 10 peptides. Score 0.304 Round 4: 125 peptides, 22 chains. Longest chain 12 peptides. Score 0.335 Round 5: 125 peptides, 22 chains. Longest chain 11 peptides. Score 0.335 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 23, Residues 107, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence Sequence coverage is 5 % 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 6236 restraints for refining 2772 atoms. 5810 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1825 (Rfree = 0.000) for 2772 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 47: After refmac, R = 0.2416 (Rfree = 0.000) for 2756 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 48: After refmac, R = 0.2663 (Rfree = 0.000) for 2740 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 49: After refmac, R = 0.2073 (Rfree = 0.000) for 2722 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Writing output files ... TimeTaking 50.8