Tue 25 Dec 19:27:55 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 1vkh-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vkh-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vkh-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkh-3.8-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/1vkh-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkh-3.8-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 ============================================================ Tue 25 Dec 19:28:05 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/1vkh-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkh-3.8-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 358 and 0 Target number of residues in the AU: 358 Target solvent content: 0.6154 Checking the provided sequence file Detected sequence length: 273 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 546 Adjusted target solvent content: 0.41 Input MTZ file: 1vkh-3.8-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: 41.965 85.956 70.476 90.000 97.713 90.000 Input sequence file: 1vkh-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 4368 target number of atoms Had to go as low as 0.65 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: 19.289 3.800 Wilson plot Bfac: 59.30 4921 reflections ( 99.17 % complete ) and 0 restraints for refining 4807 atoms. Observations/parameters ratio is 0.26 ------------------------------------------------------ Starting model: R = 0.3323 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3176 (Rfree = 0.000) for 4807 atoms. Found 26 (26 requested) and removed 58 (13 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.35 3.78 Search for helices and strands: 0 residues in 0 chains, 4888 seeds are put forward NCS extension: 0 residues added, 4888 seeds are put forward Round 1: 183 peptides, 39 chains. Longest chain 11 peptides. Score 0.268 Round 2: 211 peptides, 40 chains. Longest chain 11 peptides. Score 0.350 Round 3: 234 peptides, 38 chains. Longest chain 15 peptides. Score 0.449 Round 4: 240 peptides, 40 chains. Longest chain 15 peptides. Score 0.441 Round 5: 257 peptides, 39 chains. Longest chain 16 peptides. Score 0.503 Taking the results from Round 5 Chains 39, Residues 218, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4921 reflections ( 99.17 % complete ) and 9414 restraints for refining 3951 atoms. 8581 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2575 (Rfree = 0.000) for 3951 atoms. Found 20 (21 requested) and removed 45 (10 requested) atoms. Cycle 2: After refmac, R = 0.2509 (Rfree = 0.000) for 3874 atoms. Found 21 (21 requested) and removed 27 (10 requested) atoms. Cycle 3: After refmac, R = 0.2379 (Rfree = 0.000) for 3835 atoms. Found 21 (21 requested) and removed 29 (10 requested) atoms. Cycle 4: After refmac, R = 0.1826 (Rfree = 0.000) for 3817 atoms. Found 8 (21 requested) and removed 20 (10 requested) atoms. Cycle 5: After refmac, R = 0.1641 (Rfree = 0.000) for 3799 atoms. Found 2 (20 requested) and removed 16 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.39 3.83 Search for helices and strands: 0 residues in 0 chains, 3942 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 3959 seeds are put forward Round 1: 184 peptides, 34 chains. Longest chain 11 peptides. Score 0.345 Round 2: 219 peptides, 37 chains. Longest chain 13 peptides. Score 0.417 Round 3: 223 peptides, 37 chains. Longest chain 16 peptides. Score 0.429 Round 4: 218 peptides, 35 chains. Longest chain 10 peptides. Score 0.440 Round 5: 222 peptides, 35 chains. Longest chain 12 peptides. Score 0.452 Taking the results from Round 5 Chains 35, Residues 187, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 4921 reflections ( 99.17 % complete ) and 9580 restraints for refining 3900 atoms. 8867 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2286 (Rfree = 0.000) for 3900 atoms. Found 21 (21 requested) and removed 36 (10 requested) atoms. Cycle 7: After refmac, R = 0.2150 (Rfree = 0.000) for 3861 atoms. Found 21 (21 requested) and removed 24 (10 requested) atoms. Cycle 8: After refmac, R = 0.1706 (Rfree = 0.000) for 3847 atoms. Found 6 (21 requested) and removed 16 (10 requested) atoms. Cycle 9: After refmac, R = 0.1682 (Rfree = 0.000) for 3831 atoms. Found 8 (21 requested) and removed 14 (10 requested) atoms. Cycle 10: After refmac, R = 0.1537 (Rfree = 0.000) for 3823 atoms. Found 3 (21 requested) and removed 13 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.38 3.82 Search for helices and strands: 0 residues in 0 chains, 3969 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 3982 seeds are put forward Round 1: 204 peptides, 40 chains. Longest chain 15 peptides. Score 0.326 Round 2: 212 peptides, 35 chains. Longest chain 13 peptides. Score 0.422 Round 3: 229 peptides, 34 chains. Longest chain 13 peptides. Score 0.486 Round 4: 232 peptides, 36 chains. Longest chain 15 peptides. Score 0.469 Round 5: 234 peptides, 37 chains. Longest chain 13 peptides. Score 0.462 Taking the results from Round 3 Chains 34, Residues 195, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4921 reflections ( 99.17 % complete ) and 9216 restraints for refining 3905 atoms. 8470 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2393 (Rfree = 0.000) for 3905 atoms. Found 21 (21 requested) and removed 34 (10 requested) atoms. Cycle 12: After refmac, R = 0.2179 (Rfree = 0.000) for 3870 atoms. Found 21 (21 requested) and removed 29 (10 requested) atoms. Failed to save intermediate PDB Cycle 13: After refmac, R = 0.1715 (Rfree = 0.000) for 3841 atoms. Found 15 (21 requested) and removed 16 (10 requested) atoms. Failed to save intermediate PDB Cycle 14: After refmac, R = 0.1640 (Rfree = 0.000) for 3827 atoms. Found 6 (21 requested) and removed 16 (10 requested) atoms. Cycle 15: After refmac, R = 0.1609 (Rfree = 0.000) for 3813 atoms. Found 6 (20 requested) and removed 12 (10 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.39 3.83 Search for helices and strands: 0 residues in 0 chains, 3945 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 3957 seeds are put forward Round 1: 192 peptides, 38 chains. Longest chain 11 peptides. Score 0.314 Round 2: 225 peptides, 36 chains. Longest chain 17 peptides. Score 0.448 Round 3: 228 peptides, 36 chains. Longest chain 14 peptides. Score 0.457 Round 4: 219 peptides, 36 chains. Longest chain 12 peptides. Score 0.430 Round 5: 218 peptides, 33 chains. Longest chain 16 peptides. Score 0.466 Taking the results from Round 5 Chains 33, Residues 185, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 4921 reflections ( 99.17 % complete ) and 9216 restraints for refining 3890 atoms. 8509 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2298 (Rfree = 0.000) for 3890 atoms. Found 21 (21 requested) and removed 36 (10 requested) atoms. Failed to save intermediate PDB Cycle 17: After refmac, R = 0.2213 (Rfree = 0.000) for 3862 atoms. Found 21 (21 requested) and removed 25 (10 requested) atoms. Cycle 18: After refmac, R = 0.2071 (Rfree = 0.000) for 3842 atoms. Found 21 (21 requested) and removed 29 (10 requested) atoms. Cycle 19: After refmac, R = 0.1533 (Rfree = 0.000) for 3818 atoms. Found 8 (21 requested) and removed 17 (10 requested) atoms. Cycle 20: After refmac, R = 0.1372 (Rfree = 0.000) for 3797 atoms. Found 5 (20 requested) and removed 13 (10 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.37 3.80 Search for helices and strands: 0 residues in 0 chains, 3918 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 3943 seeds are put forward Round 1: 199 peptides, 40 chains. Longest chain 14 peptides. Score 0.309 Round 2: 216 peptides, 38 chains. Longest chain 15 peptides. Score 0.394 Round 3: 216 peptides, 39 chains. Longest chain 12 peptides. Score 0.380 Round 4: 220 peptides, 36 chains. Longest chain 15 peptides. Score 0.433 Round 5: 233 peptides, 39 chains. Longest chain 15 peptides. Score 0.433 Taking the results from Round 5 Chains 39, Residues 194, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4921 reflections ( 99.17 % complete ) and 9467 restraints for refining 3922 atoms. 8730 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2147 (Rfree = 0.000) for 3922 atoms. Found 21 (21 requested) and removed 31 (10 requested) atoms. Cycle 22: After refmac, R = 0.2106 (Rfree = 0.000) for 3895 atoms. Found 21 (21 requested) and removed 35 (10 requested) atoms. Cycle 23: After refmac, R = 0.1865 (Rfree = 0.000) for 3875 atoms. Found 21 (21 requested) and removed 25 (10 requested) atoms. Cycle 24: After refmac, R = 0.1931 (Rfree = 0.000) for 3865 atoms. Found 21 (21 requested) and removed 23 (10 requested) atoms. Failed to save intermediate PDB Cycle 25: After refmac, R = 0.1932 (Rfree = 0.000) for 3859 atoms. Found 21 (21 requested) and removed 20 (10 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.34 3.77 Search for helices and strands: 0 residues in 0 chains, 3999 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 4022 seeds are put forward Round 1: 171 peptides, 36 chains. Longest chain 10 peptides. Score 0.269 Round 2: 203 peptides, 36 chains. Longest chain 13 peptides. Score 0.379 Round 3: 216 peptides, 37 chains. Longest chain 15 peptides. Score 0.407 Round 4: 215 peptides, 35 chains. Longest chain 13 peptides. Score 0.431 Round 5: 207 peptides, 33 chains. Longest chain 12 peptides. Score 0.433 Taking the results from Round 5 Chains 33, Residues 174, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4921 reflections ( 99.17 % complete ) and 9625 restraints for refining 3951 atoms. 8962 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2038 (Rfree = 0.000) for 3951 atoms. Found 21 (21 requested) and removed 29 (10 requested) atoms. Cycle 27: After refmac, R = 0.2107 (Rfree = 0.000) for 3928 atoms. Found 21 (21 requested) and removed 30 (10 requested) atoms. Cycle 28: After refmac, R = 0.1950 (Rfree = 0.000) for 3910 atoms. Found 21 (21 requested) and removed 24 (10 requested) atoms. Cycle 29: After refmac, R = 0.1880 (Rfree = 0.000) for 3895 atoms. Found 21 (21 requested) and removed 25 (10 requested) atoms. Cycle 30: After refmac, R = 0.1804 (Rfree = 0.000) for 3878 atoms. Found 21 (21 requested) and removed 20 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.34 3.77 Search for helices and strands: 0 residues in 0 chains, 4000 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 4014 seeds are put forward Round 1: 169 peptides, 33 chains. Longest chain 11 peptides. Score 0.308 Round 2: 172 peptides, 31 chains. Longest chain 9 peptides. Score 0.348 Round 3: 179 peptides, 35 chains. Longest chain 13 peptides. Score 0.313 Round 4: 184 peptides, 34 chains. Longest chain 10 peptides. Score 0.345 Round 5: 177 peptides, 29 chains. Longest chain 13 peptides. Score 0.394 Taking the results from Round 5 Chains 29, Residues 148, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4921 reflections ( 99.17 % complete ) and 9709 restraints for refining 3950 atoms. 9146 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2176 (Rfree = 0.000) for 3950 atoms. Found 21 (21 requested) and removed 28 (10 requested) atoms. Cycle 32: After refmac, R = 0.2044 (Rfree = 0.000) for 3931 atoms. Found 21 (21 requested) and removed 23 (10 requested) atoms. Cycle 33: After refmac, R = 0.2012 (Rfree = 0.000) for 3922 atoms. Found 21 (21 requested) and removed 24 (10 requested) atoms. Cycle 34: After refmac, R = 0.2061 (Rfree = 0.000) for 3912 atoms. Found 21 (21 requested) and removed 20 (10 requested) atoms. Cycle 35: After refmac, R = 0.1342 (Rfree = 0.000) for 3899 atoms. Found 12 (21 requested) and removed 12 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.34 3.77 Search for helices and strands: 0 residues in 0 chains, 4021 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 4040 seeds are put forward Round 1: 151 peptides, 32 chains. Longest chain 8 peptides. Score 0.257 Round 2: 165 peptides, 29 chains. Longest chain 13 peptides. Score 0.353 Round 3: 174 peptides, 31 chains. Longest chain 11 peptides. Score 0.355 Round 4: 174 peptides, 29 chains. Longest chain 10 peptides. Score 0.384 Round 5: 170 peptides, 29 chains. Longest chain 11 peptides. Score 0.370 Taking the results from Round 4 Chains 29, Residues 145, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4921 reflections ( 99.17 % complete ) and 9666 restraints for refining 3925 atoms. 9115 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1645 (Rfree = 0.000) for 3925 atoms. Found 21 (21 requested) and removed 29 (10 requested) atoms. Cycle 37: After refmac, R = 0.1758 (Rfree = 0.000) for 3906 atoms. Found 21 (21 requested) and removed 22 (10 requested) atoms. Failed to save intermediate PDB Cycle 38: After refmac, R = 0.1880 (Rfree = 0.000) for 3898 atoms. Found 21 (21 requested) and removed 15 (10 requested) atoms. Cycle 39: After refmac, R = 0.1827 (Rfree = 0.000) for 3895 atoms. Found 21 (21 requested) and removed 21 (10 requested) atoms. Cycle 40: After refmac, R = 0.1927 (Rfree = 0.000) for 3892 atoms. Found 21 (21 requested) and removed 20 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.31 3.74 Search for helices and strands: 0 residues in 0 chains, 3997 seeds are put forward NCS extension: 0 residues added, 3997 seeds are put forward Round 1: 127 peptides, 28 chains. Longest chain 8 peptides. Score 0.229 Round 2: 151 peptides, 30 chains. Longest chain 8 peptides. Score 0.288 Round 3: 144 peptides, 29 chains. Longest chain 8 peptides. Score 0.278 Round 4: 140 peptides, 26 chains. Longest chain 8 peptides. Score 0.311 Round 5: 144 peptides, 24 chains. Longest chain 11 peptides. Score 0.357 Taking the results from Round 5 Chains 24, Residues 120, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4921 reflections ( 99.17 % complete ) and 9751 restraints for refining 3950 atoms. 9295 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2090 (Rfree = 0.000) for 3950 atoms. Found 21 (21 requested) and removed 27 (10 requested) atoms. Cycle 42: After refmac, R = 0.1969 (Rfree = 0.000) for 3928 atoms. Found 21 (21 requested) and removed 21 (10 requested) atoms. Cycle 43: After refmac, R = 0.2006 (Rfree = 0.000) for 3920 atoms. Found 21 (21 requested) and removed 16 (10 requested) atoms. Cycle 44: After refmac, R = 0.1833 (Rfree = 0.000) for 3913 atoms. Found 21 (21 requested) and removed 17 (10 requested) atoms. Cycle 45: After refmac, R = 0.2101 (Rfree = 0.000) for 3911 atoms. Found 21 (21 requested) and removed 19 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.31 3.74 Search for helices and strands: 0 residues in 0 chains, 4014 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 4028 seeds are put forward Round 1: 94 peptides, 21 chains. Longest chain 7 peptides. Score 0.213 Round 2: 112 peptides, 22 chains. Longest chain 10 peptides. Score 0.270 Round 3: 115 peptides, 24 chains. Longest chain 10 peptides. Score 0.248 Round 4: 118 peptides, 22 chains. Longest chain 10 peptides. Score 0.294 Round 5: 111 peptides, 22 chains. Longest chain 8 peptides. Score 0.266 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 22, Residues 96, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 1vkh-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4921 reflections ( 99.17 % complete ) and 9613 restraints for refining 3871 atoms. 9226 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1974 (Rfree = 0.000) for 3871 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 47: After refmac, R = 0.1990 (Rfree = 0.000) for 3851 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 48: After refmac, R = 0.1997 (Rfree = 0.000) for 3833 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 49: After refmac, R = 0.1951 (Rfree = 0.000) for 3818 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Writing output files ... TimeTaking 60.64