null Sun 23 Dec 23:45:27 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vkh-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vkh-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vkh-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkh-3.8-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/1vkh-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkh-3.8-parrot-mrncs ############### 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 23:45:32 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/mrncs/ArpWArp/wArpResults/WorkingDir/1vkh-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkh-3.8-parrot-mrncs/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-mrncs.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-mrncs.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 4835 atoms. Observations/parameters ratio is 0.25 ------------------------------------------------------ Starting model: R = 0.3297 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3254 (Rfree = 0.000) for 4835 atoms. Found 26 (26 requested) and removed 81 (13 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.28 3.70 Search for helices and strands: 0 residues in 0 chains, 4898 seeds are put forward NCS extension: 0 residues added, 4898 seeds are put forward Round 1: 169 peptides, 37 chains. Longest chain 7 peptides. Score 0.247 Round 2: 198 peptides, 38 chains. Longest chain 8 peptides. Score 0.335 Round 3: 222 peptides, 41 chains. Longest chain 10 peptides. Score 0.372 Round 4: 232 peptides, 41 chains. Longest chain 9 peptides. Score 0.404 Round 5: 238 peptides, 38 chains. Longest chain 11 peptides. Score 0.461 Taking the results from Round 5 Chains 38, Residues 200, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4921 reflections ( 99.17 % complete ) and 9342 restraints for refining 3949 atoms. 8580 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2698 (Rfree = 0.000) for 3949 atoms. Found 21 (21 requested) and removed 39 (10 requested) atoms. Cycle 2: After refmac, R = 0.2395 (Rfree = 0.000) for 3873 atoms. Found 21 (21 requested) and removed 33 (10 requested) atoms. Cycle 3: After refmac, R = 0.2320 (Rfree = 0.000) for 3834 atoms. Found 21 (21 requested) and removed 30 (10 requested) atoms. Cycle 4: After refmac, R = 0.1817 (Rfree = 0.000) for 3801 atoms. Found 7 (21 requested) and removed 17 (10 requested) atoms. Cycle 5: After refmac, R = 0.1699 (Rfree = 0.000) for 3785 atoms. Found 7 (20 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.39 3.83 Search for helices and strands: 0 residues in 0 chains, 3926 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 3937 seeds are put forward Round 1: 208 peptides, 44 chains. Longest chain 8 peptides. Score 0.283 Round 2: 215 peptides, 38 chains. Longest chain 11 peptides. Score 0.390 Round 3: 244 peptides, 36 chains. Longest chain 14 peptides. Score 0.503 Round 4: 242 peptides, 38 chains. Longest chain 13 peptides. Score 0.473 Round 5: 235 peptides, 36 chains. Longest chain 15 peptides. Score 0.478 Taking the results from Round 3 Chains 37, Residues 208, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4921 reflections ( 99.17 % complete ) and 8999 restraints for refining 3885 atoms. 8170 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2204 (Rfree = 0.000) for 3885 atoms. Found 20 (21 requested) and removed 37 (10 requested) atoms. Cycle 7: After refmac, R = 0.2106 (Rfree = 0.000) for 3848 atoms. Found 21 (21 requested) and removed 28 (10 requested) atoms. Cycle 8: After refmac, R = 0.2265 (Rfree = 0.000) for 3828 atoms. Found 21 (21 requested) and removed 37 (10 requested) atoms. Cycle 9: After refmac, R = 0.1684 (Rfree = 0.000) for 3801 atoms. Found 6 (20 requested) and removed 19 (10 requested) atoms. Cycle 10: After refmac, R = 0.1596 (Rfree = 0.000) for 3781 atoms. Found 7 (20 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.37 3.80 Search for helices and strands: 0 residues in 0 chains, 3925 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 3940 seeds are put forward Round 1: 201 peptides, 40 chains. Longest chain 9 peptides. Score 0.316 Round 2: 250 peptides, 44 chains. Longest chain 15 peptides. Score 0.420 Round 3: 243 peptides, 43 chains. Longest chain 10 peptides. Score 0.411 Round 4: 252 peptides, 40 chains. Longest chain 15 peptides. Score 0.476 Round 5: 256 peptides, 42 chains. Longest chain 14 peptides. Score 0.463 Taking the results from Round 4 Chains 40, Residues 212, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4921 reflections ( 99.17 % complete ) and 9227 restraints for refining 3904 atoms. 8419 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2145 (Rfree = 0.000) for 3904 atoms. Found 21 (21 requested) and removed 56 (10 requested) atoms. Cycle 12: After refmac, R = 0.2092 (Rfree = 0.000) for 3850 atoms. Found 21 (21 requested) and removed 30 (10 requested) atoms. Cycle 13: After refmac, R = 0.1692 (Rfree = 0.000) for 3827 atoms. Found 9 (21 requested) and removed 16 (10 requested) atoms. Cycle 14: After refmac, R = 0.1768 (Rfree = 0.000) for 3806 atoms. Found 14 (21 requested) and removed 15 (10 requested) atoms. Cycle 15: After refmac, R = 0.2114 (Rfree = 0.000) for 3795 atoms. Found 20 (20 requested) and removed 22 (10 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.38 3.82 Search for helices and strands: 0 residues in 0 chains, 3945 seeds are put forward NCS extension: 17 residues added (3 deleted due to clashes), 3962 seeds are put forward Round 1: 176 peptides, 37 chains. Longest chain 8 peptides. Score 0.272 Round 2: 189 peptides, 37 chains. Longest chain 10 peptides. Score 0.318 Round 3: 206 peptides, 36 chains. Longest chain 13 peptides. Score 0.389 Round 4: 212 peptides, 37 chains. Longest chain 11 peptides. Score 0.395 Round 5: 228 peptides, 41 chains. Longest chain 13 peptides. Score 0.391 Taking the results from Round 4 Chains 37, Residues 175, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 4921 reflections ( 99.17 % complete ) and 9260 restraints for refining 3905 atoms. 8562 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2473 (Rfree = 0.000) for 3905 atoms. Found 21 (21 requested) and removed 38 (10 requested) atoms. Cycle 17: After refmac, R = 0.2375 (Rfree = 0.000) for 3862 atoms. Found 21 (21 requested) and removed 38 (10 requested) atoms. Cycle 18: After refmac, R = 0.1882 (Rfree = 0.000) for 3831 atoms. Found 9 (21 requested) and removed 20 (10 requested) atoms. Cycle 19: After refmac, R = 0.2024 (Rfree = 0.000) for 3810 atoms. Found 21 (21 requested) and removed 35 (10 requested) atoms. Cycle 20: After refmac, R = 0.1808 (Rfree = 0.000) for 3792 atoms. Found 9 (20 requested) and removed 17 (10 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.39 3.83 Search for helices and strands: 0 residues in 0 chains, 3927 seeds are put forward NCS extension: 11 residues added (2 deleted due to clashes), 3938 seeds are put forward Round 1: 186 peptides, 40 chains. Longest chain 9 peptides. Score 0.264 Round 2: 207 peptides, 38 chains. Longest chain 9 peptides. Score 0.365 Round 3: 210 peptides, 36 chains. Longest chain 12 peptides. Score 0.402 Round 4: 193 peptides, 32 chains. Longest chain 9 peptides. Score 0.403 Round 5: 204 peptides, 33 chains. Longest chain 10 peptides. Score 0.424 Taking the results from Round 5 Chains 33, Residues 171, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4921 reflections ( 99.17 % complete ) and 9447 restraints for refining 3919 atoms. 8796 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2267 (Rfree = 0.000) for 3919 atoms. Found 21 (21 requested) and removed 94 (10 requested) atoms. Cycle 22: After refmac, R = 0.2221 (Rfree = 0.000) for 3835 atoms. Found 21 (21 requested) and removed 38 (10 requested) atoms. Cycle 23: After refmac, R = 0.1689 (Rfree = 0.000) for 3803 atoms. Found 12 (20 requested) and removed 20 (10 requested) atoms. Cycle 24: After refmac, R = 0.1700 (Rfree = 0.000) for 3792 atoms. Found 6 (20 requested) and removed 17 (10 requested) atoms. Cycle 25: After refmac, R = 0.1624 (Rfree = 0.000) for 3776 atoms. Found 2 (20 requested) and removed 18 (10 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.39 3.83 Search for helices and strands: 0 residues in 0 chains, 3908 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 3920 seeds are put forward Round 1: 187 peptides, 39 chains. Longest chain 9 peptides. Score 0.282 Round 2: 213 peptides, 42 chains. Longest chain 10 peptides. Score 0.328 Round 3: 220 peptides, 38 chains. Longest chain 11 peptides. Score 0.406 Round 4: 218 peptides, 36 chains. Longest chain 12 peptides. Score 0.427 Round 5: 211 peptides, 37 chains. Longest chain 13 peptides. Score 0.391 Taking the results from Round 4 Chains 36, Residues 182, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4921 reflections ( 99.17 % complete ) and 9368 restraints for refining 3920 atoms. 8676 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2011 (Rfree = 0.000) for 3920 atoms. Found 21 (21 requested) and removed 88 (10 requested) atoms. Cycle 27: After refmac, R = 0.2166 (Rfree = 0.000) for 3844 atoms. Found 21 (21 requested) and removed 30 (10 requested) atoms. Cycle 28: After refmac, R = 0.2094 (Rfree = 0.000) for 3832 atoms. Found 21 (21 requested) and removed 27 (10 requested) atoms. Cycle 29: After refmac, R = 0.1509 (Rfree = 0.000) for 3819 atoms. Found 7 (21 requested) and removed 16 (10 requested) atoms. Cycle 30: After refmac, R = 0.1456 (Rfree = 0.000) for 3808 atoms. Found 7 (20 requested) and removed 14 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.37 3.80 Search for helices and strands: 0 residues in 0 chains, 3917 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 3933 seeds are put forward Round 1: 171 peptides, 38 chains. Longest chain 6 peptides. Score 0.239 Round 2: 189 peptides, 37 chains. Longest chain 9 peptides. Score 0.318 Round 3: 182 peptides, 34 chains. Longest chain 11 peptides. Score 0.338 Round 4: 181 peptides, 35 chains. Longest chain 8 peptides. Score 0.320 Round 5: 182 peptides, 33 chains. Longest chain 9 peptides. Score 0.352 Taking the results from Round 5 Chains 33, Residues 149, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4921 reflections ( 99.17 % complete ) and 9586 restraints for refining 3940 atoms. 9023 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2271 (Rfree = 0.000) for 3940 atoms. Found 21 (21 requested) and removed 138 (10 requested) atoms. Cycle 32: After refmac, R = 0.2378 (Rfree = 0.000) for 3810 atoms. Found 21 (21 requested) and removed 32 (10 requested) atoms. Cycle 33: After refmac, R = 0.1820 (Rfree = 0.000) for 3789 atoms. Found 16 (20 requested) and removed 31 (10 requested) atoms. Cycle 34: After refmac, R = 0.1827 (Rfree = 0.000) for 3765 atoms. Found 8 (20 requested) and removed 39 (10 requested) atoms. Cycle 35: After refmac, R = 0.2053 (Rfree = 0.000) for 3731 atoms. Found 8 (20 requested) and removed 16 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.33 3.76 Search for helices and strands: 0 residues in 0 chains, 3843 seeds are put forward NCS extension: 0 residues added, 3843 seeds are put forward Round 1: 147 peptides, 31 chains. Longest chain 10 peptides. Score 0.258 Round 2: 160 peptides, 32 chains. Longest chain 9 peptides. Score 0.290 Round 3: 165 peptides, 32 chains. Longest chain 9 peptides. Score 0.308 Round 4: 164 peptides, 30 chains. Longest chain 12 peptides. Score 0.335 Round 5: 159 peptides, 29 chains. Longest chain 14 peptides. Score 0.333 Taking the results from Round 4 Chains 30, Residues 134, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4921 reflections ( 99.17 % complete ) and 9328 restraints for refining 3815 atoms. 8822 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2296 (Rfree = 0.000) for 3815 atoms. Found 20 (20 requested) and removed 30 (10 requested) atoms. Cycle 37: After refmac, R = 0.2385 (Rfree = 0.000) for 3793 atoms. Found 20 (20 requested) and removed 38 (10 requested) atoms. Cycle 38: After refmac, R = 0.1865 (Rfree = 0.000) for 3772 atoms. Found 20 (20 requested) and removed 53 (10 requested) atoms. Cycle 39: After refmac, R = 0.1724 (Rfree = 0.000) for 3736 atoms. Found 8 (20 requested) and removed 20 (10 requested) atoms. Cycle 40: After refmac, R = 0.1614 (Rfree = 0.000) for 3721 atoms. Found 5 (20 requested) and removed 14 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.30 3.73 Search for helices and strands: 0 residues in 0 chains, 3826 seeds are put forward NCS extension: 3 residues added (0 deleted due to clashes), 3829 seeds are put forward Round 1: 141 peptides, 32 chains. Longest chain 8 peptides. Score 0.219 Round 2: 172 peptides, 34 chains. Longest chain 10 peptides. Score 0.303 Round 3: 175 peptides, 31 chains. Longest chain 12 peptides. Score 0.358 Round 4: 162 peptides, 30 chains. Longest chain 9 peptides. Score 0.328 Round 5: 184 peptides, 33 chains. Longest chain 9 peptides. Score 0.359 Taking the results from Round 5 Chains 33, Residues 151, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4921 reflections ( 99.17 % complete ) and 9091 restraints for refining 3820 atoms. 8520 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2072 (Rfree = 0.000) for 3820 atoms. Found 21 (21 requested) and removed 34 (10 requested) atoms. Cycle 42: After refmac, R = 0.1619 (Rfree = 0.000) for 3791 atoms. Found 8 (20 requested) and removed 23 (10 requested) atoms. Cycle 43: After refmac, R = 0.1573 (Rfree = 0.000) for 3770 atoms. Found 9 (20 requested) and removed 15 (10 requested) atoms. Cycle 44: After refmac, R = 0.1475 (Rfree = 0.000) for 3763 atoms. Found 5 (20 requested) and removed 17 (10 requested) atoms. Cycle 45: After refmac, R = 0.1555 (Rfree = 0.000) for 3749 atoms. Found 12 (20 requested) and removed 16 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.27 3.69 Search for helices and strands: 0 residues in 0 chains, 3885 seeds are put forward NCS extension: 0 residues added, 3885 seeds are put forward Round 1: 139 peptides, 33 chains. Longest chain 6 peptides. Score 0.195 Round 2: 149 peptides, 29 chains. Longest chain 14 peptides. Score 0.297 Round 3: 146 peptides, 30 chains. Longest chain 9 peptides. Score 0.270 Round 4: 153 peptides, 27 chains. Longest chain 11 peptides. Score 0.342 Round 5: 159 peptides, 30 chains. Longest chain 9 peptides. Score 0.317 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 27, Residues 126, 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 1vkh-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4921 reflections ( 99.17 % complete ) and 9362 restraints for refining 3849 atoms. 8885 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1934 (Rfree = 0.000) for 3849 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 47: After refmac, R = 0.2094 (Rfree = 0.000) for 3830 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 48: After refmac, R = 0.1905 (Rfree = 0.000) for 3817 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 49: After refmac, R = 0.1402 (Rfree = 0.000) for 3802 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 00:27:01 GMT 2018 Job finished. TimeTaking 41.56 Used memory is bytes: 4463232