Mon 24 Dec 07:58:14 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vkh-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vkh-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vkh-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkh-3.8-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/1vkh-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkh-3.8-parrot-noncs ############### 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 ============================================================ Mon 24 Dec 07:58:18 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/noncs/ArpWArp/wArpResults/WorkingDir/1vkh-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkh-3.8-parrot-noncs/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-noncs.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-noncs.fasta_lf Building free atoms model in initial map for 4368 target number of atoms Had to go as low as 0.60 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 4820 atoms. Observations/parameters ratio is 0.26 ------------------------------------------------------ Starting model: R = 0.3401 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3136 (Rfree = 0.000) for 4820 atoms. Found 26 (26 requested) and removed 70 (13 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.32 3.75 Search for helices and strands: 0 residues in 0 chains, 4878 seeds are put forward NCS extension: 0 residues added, 4878 seeds are put forward Round 1: 143 peptides, 30 chains. Longest chain 8 peptides. Score 0.259 Round 2: 211 peptides, 37 chains. Longest chain 14 peptides. Score 0.391 Round 3: 220 peptides, 35 chains. Longest chain 14 peptides. Score 0.446 Round 4: 219 peptides, 38 chains. Longest chain 13 peptides. Score 0.403 Round 5: 245 peptides, 38 chains. Longest chain 14 peptides. Score 0.481 Taking the results from Round 5 Chains 39, Residues 207, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4921 reflections ( 99.17 % complete ) and 9141 restraints for refining 3949 atoms. 8322 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2648 (Rfree = 0.000) for 3949 atoms. Found 13 (21 requested) and removed 101 (10 requested) atoms. Cycle 2: After refmac, R = 0.2474 (Rfree = 0.000) for 3799 atoms. Found 21 (21 requested) and removed 32 (10 requested) atoms. Cycle 3: After refmac, R = 0.2242 (Rfree = 0.000) for 3758 atoms. Found 20 (20 requested) and removed 30 (10 requested) atoms. Cycle 4: After refmac, R = 0.2120 (Rfree = 0.000) for 3726 atoms. Found 20 (20 requested) and removed 24 (10 requested) atoms. Cycle 5: After refmac, R = 0.2100 (Rfree = 0.000) for 3712 atoms. Found 20 (20 requested) and removed 22 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.36 3.79 Search for helices and strands: 0 residues in 0 chains, 3856 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 3870 seeds are put forward Round 1: 184 peptides, 38 chains. Longest chain 8 peptides. Score 0.286 Round 2: 210 peptides, 37 chains. Longest chain 12 peptides. Score 0.388 Round 3: 222 peptides, 38 chains. Longest chain 11 peptides. Score 0.412 Round 4: 216 peptides, 34 chains. Longest chain 13 peptides. Score 0.447 Round 5: 222 peptides, 35 chains. Longest chain 13 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 ------------------------------------------------------ 4921 reflections ( 99.17 % complete ) and 9078 restraints for refining 3802 atoms. 8365 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2396 (Rfree = 0.000) for 3802 atoms. Found 20 (20 requested) and removed 36 (10 requested) atoms. Cycle 7: After refmac, R = 0.2203 (Rfree = 0.000) for 3772 atoms. Found 20 (20 requested) and removed 29 (10 requested) atoms. Cycle 8: After refmac, R = 0.1796 (Rfree = 0.000) for 3748 atoms. Found 4 (20 requested) and removed 19 (10 requested) atoms. Cycle 9: After refmac, R = 0.1805 (Rfree = 0.000) for 3722 atoms. Found 9 (20 requested) and removed 15 (10 requested) atoms. Cycle 10: After refmac, R = 0.1617 (Rfree = 0.000) for 3713 atoms. Found 0 (20 requested) and removed 16 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.37 3.80 Search for helices and strands: 0 residues in 0 chains, 3855 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 3872 seeds are put forward Round 1: 208 peptides, 41 chains. Longest chain 9 peptides. Score 0.326 Round 2: 246 peptides, 40 chains. Longest chain 17 peptides. Score 0.459 Round 3: 244 peptides, 42 chains. Longest chain 16 peptides. Score 0.427 Round 4: 252 peptides, 37 chains. Longest chain 18 peptides. Score 0.513 Round 5: 243 peptides, 36 chains. Longest chain 16 peptides. Score 0.500 Taking the results from Round 4 Chains 37, Residues 215, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4921 reflections ( 99.17 % complete ) and 9061 restraints for refining 3900 atoms. 8238 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2270 (Rfree = 0.000) for 3900 atoms. Found 21 (21 requested) and removed 56 (10 requested) atoms. Cycle 12: After refmac, R = 0.2296 (Rfree = 0.000) for 3853 atoms. Found 21 (21 requested) and removed 36 (10 requested) atoms. Cycle 13: After refmac, R = 0.2171 (Rfree = 0.000) for 3835 atoms. Found 21 (21 requested) and removed 27 (10 requested) atoms. Cycle 14: After refmac, R = 0.1638 (Rfree = 0.000) for 3821 atoms. Found 5 (21 requested) and removed 19 (10 requested) atoms. Cycle 15: After refmac, R = 0.1575 (Rfree = 0.000) for 3802 atoms. Found 4 (20 requested) and removed 13 (10 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.37 3.80 Search for helices and strands: 0 residues in 0 chains, 3935 seeds are put forward NCS extension: 26 residues added (5 deleted due to clashes), 3961 seeds are put forward Round 1: 202 peptides, 39 chains. Longest chain 11 peptides. Score 0.334 Round 2: 220 peptides, 37 chains. Longest chain 15 peptides. Score 0.420 Round 3: 216 peptides, 33 chains. Longest chain 23 peptides. Score 0.461 Round 4: 225 peptides, 33 chains. Longest chain 15 peptides. Score 0.487 Round 5: 215 peptides, 33 chains. Longest chain 19 peptides. Score 0.458 Taking the results from Round 4 Chains 33, Residues 192, 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 9406 restraints for refining 3950 atoms. 8671 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2303 (Rfree = 0.000) for 3950 atoms. Found 21 (21 requested) and removed 44 (10 requested) atoms. Cycle 17: After refmac, R = 0.2190 (Rfree = 0.000) for 3902 atoms. Found 21 (21 requested) and removed 29 (10 requested) atoms. Cycle 18: After refmac, R = 0.2035 (Rfree = 0.000) for 3880 atoms. Found 21 (21 requested) and removed 31 (10 requested) atoms. Cycle 19: After refmac, R = 0.1542 (Rfree = 0.000) for 3860 atoms. Found 7 (21 requested) and removed 14 (10 requested) atoms. Cycle 20: After refmac, R = 0.1375 (Rfree = 0.000) for 3844 atoms. Found 9 (21 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.38 3.82 Search for helices and strands: 0 residues in 0 chains, 3999 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 4013 seeds are put forward Round 1: 185 peptides, 39 chains. Longest chain 8 peptides. Score 0.275 Round 2: 208 peptides, 37 chains. Longest chain 12 peptides. Score 0.382 Round 3: 217 peptides, 34 chains. Longest chain 13 peptides. Score 0.450 Round 4: 205 peptides, 36 chains. Longest chain 10 peptides. Score 0.386 Round 5: 208 peptides, 36 chains. Longest chain 9 peptides. Score 0.395 Taking the results from Round 3 Chains 34, Residues 183, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4921 reflections ( 99.17 % complete ) and 9511 restraints for refining 3951 atoms. 8813 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2147 (Rfree = 0.000) for 3951 atoms. Found 21 (21 requested) and removed 30 (10 requested) atoms. Cycle 22: After refmac, R = 0.2099 (Rfree = 0.000) for 3929 atoms. Found 21 (21 requested) and removed 32 (10 requested) atoms. Cycle 23: After refmac, R = 0.1961 (Rfree = 0.000) for 3907 atoms. Found 21 (21 requested) and removed 20 (10 requested) atoms. Cycle 24: After refmac, R = 0.1744 (Rfree = 0.000) for 3896 atoms. Found 21 (21 requested) and removed 20 (10 requested) atoms. Cycle 25: After refmac, R = 0.1322 (Rfree = 0.000) for 3891 atoms. Found 7 (21 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.36 3.79 Search for helices and strands: 0 residues in 0 chains, 4007 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 4026 seeds are put forward Round 1: 168 peptides, 37 chains. Longest chain 8 peptides. Score 0.243 Round 2: 189 peptides, 34 chains. Longest chain 11 peptides. Score 0.362 Round 3: 200 peptides, 34 chains. Longest chain 12 peptides. Score 0.398 Round 4: 196 peptides, 32 chains. Longest chain 13 peptides. Score 0.413 Round 5: 204 peptides, 33 chains. Longest chain 14 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 9558 restraints for refining 3951 atoms. 8907 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2081 (Rfree = 0.000) for 3951 atoms. Found 15 (21 requested) and removed 28 (10 requested) atoms. Cycle 27: After refmac, R = 0.2020 (Rfree = 0.000) for 3920 atoms. Found 21 (21 requested) and removed 17 (10 requested) atoms. Cycle 28: After refmac, R = 0.1624 (Rfree = 0.000) for 3915 atoms. Found 7 (21 requested) and removed 17 (10 requested) atoms. Cycle 29: After refmac, R = 0.1698 (Rfree = 0.000) for 3903 atoms. Found 11 (21 requested) and removed 14 (10 requested) atoms. Cycle 30: After refmac, R = 0.1526 (Rfree = 0.000) for 3897 atoms. Found 3 (21 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, 4022 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 4039 seeds are put forward Round 1: 152 peptides, 31 chains. Longest chain 10 peptides. Score 0.277 Round 2: 178 peptides, 34 chains. Longest chain 9 peptides. Score 0.324 Round 3: 176 peptides, 29 chains. Longest chain 13 peptides. Score 0.390 Round 4: 200 peptides, 32 chains. Longest chain 14 peptides. Score 0.425 Round 5: 187 peptides, 29 chains. Longest chain 15 peptides. Score 0.426 Taking the results from Round 5 Chains 29, Residues 158, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4921 reflections ( 99.17 % complete ) and 9633 restraints for refining 3951 atoms. 9030 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2024 (Rfree = 0.000) for 3951 atoms. Found 21 (21 requested) and removed 19 (10 requested) atoms. Cycle 32: After refmac, R = 0.2144 (Rfree = 0.000) for 3939 atoms. Found 21 (21 requested) and removed 25 (10 requested) atoms. Cycle 33: After refmac, R = 0.2142 (Rfree = 0.000) for 3924 atoms. Found 21 (21 requested) and removed 24 (10 requested) atoms. Cycle 34: After refmac, R = 0.2090 (Rfree = 0.000) for 3910 atoms. Found 21 (21 requested) and removed 24 (10 requested) atoms. Cycle 35: After refmac, R = 0.1486 (Rfree = 0.000) for 3897 atoms. Found 7 (21 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.37 3.80 Search for helices and strands: 0 residues in 0 chains, 4024 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 4047 seeds are put forward Round 1: 153 peptides, 33 chains. Longest chain 10 peptides. Score 0.249 Round 2: 166 peptides, 31 chains. Longest chain 11 peptides. Score 0.327 Round 3: 186 peptides, 31 chains. Longest chain 12 peptides. Score 0.395 Round 4: 186 peptides, 31 chains. Longest chain 12 peptides. Score 0.395 Round 5: 183 peptides, 31 chains. Longest chain 12 peptides. Score 0.385 Taking the results from Round 4 Chains 31, Residues 155, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4921 reflections ( 99.17 % complete ) and 9581 restraints for refining 3944 atoms. 8992 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2113 (Rfree = 0.000) for 3944 atoms. Found 21 (21 requested) and removed 27 (10 requested) atoms. Cycle 37: After refmac, R = 0.2080 (Rfree = 0.000) for 3923 atoms. Found 21 (21 requested) and removed 32 (10 requested) atoms. Failed to save intermediate PDB Cycle 38: After refmac, R = 0.1532 (Rfree = 0.000) for 3907 atoms. Found 4 (21 requested) and removed 16 (10 requested) atoms. Cycle 39: After refmac, R = 0.1555 (Rfree = 0.000) for 3891 atoms. Found 3 (21 requested) and removed 15 (10 requested) atoms. Cycle 40: After refmac, R = 0.1392 (Rfree = 0.000) for 3879 atoms. Found 6 (21 requested) and removed 13 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.37 3.80 Search for helices and strands: 0 residues in 0 chains, 3994 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 4011 seeds are put forward Round 1: 144 peptides, 31 chains. Longest chain 10 peptides. Score 0.247 Round 2: 162 peptides, 27 chains. Longest chain 14 peptides. Score 0.373 Round 3: 159 peptides, 28 chains. Longest chain 15 peptides. Score 0.348 Round 4: 177 peptides, 29 chains. Longest chain 16 peptides. Score 0.394 Round 5: 181 peptides, 30 chains. Longest chain 16 peptides. Score 0.392 Taking the results from Round 4 Chains 30, Residues 148, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 4921 reflections ( 99.17 % complete ) and 9434 restraints for refining 3951 atoms. 8833 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1982 (Rfree = 0.000) for 3951 atoms. Found 21 (21 requested) and removed 30 (10 requested) atoms. Cycle 42: After refmac, R = 0.2011 (Rfree = 0.000) for 3929 atoms. Found 21 (21 requested) and removed 25 (10 requested) atoms. Cycle 43: After refmac, R = 0.1482 (Rfree = 0.000) for 3918 atoms. Found 14 (21 requested) and removed 16 (10 requested) atoms. Cycle 44: After refmac, R = 0.1458 (Rfree = 0.000) for 3909 atoms. Found 12 (21 requested) and removed 21 (10 requested) atoms. Cycle 45: After refmac, R = 0.1365 (Rfree = 0.000) for 3900 atoms. Found 5 (21 requested) and removed 14 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.37 3.80 Search for helices and strands: 0 residues in 0 chains, 4027 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 4047 seeds are put forward Round 1: 143 peptides, 31 chains. Longest chain 10 peptides. Score 0.243 Round 2: 163 peptides, 30 chains. Longest chain 12 peptides. Score 0.331 Round 3: 148 peptides, 27 chains. Longest chain 13 peptides. Score 0.324 Round 4: 159 peptides, 29 chains. Longest chain 13 peptides. Score 0.333 Round 5: 159 peptides, 28 chains. Longest chain 14 peptides. Score 0.348 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 28, Residues 131, 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 9641 restraints for refining 3951 atoms. 9145 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1866 (Rfree = 0.000) for 3951 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 47: After refmac, R = 0.1575 (Rfree = 0.000) for 3928 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 48: After refmac, R = 0.1553 (Rfree = 0.000) for 3913 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 49: After refmac, R = 0.1403 (Rfree = 0.000) for 3902 atoms. TimeTaking 39.73