Mon 24 Dec 00:21:35 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-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vkh-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vkh-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkh-4.0-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-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkh-4.0-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 ============================================================ Mon 24 Dec 00:21:40 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-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkh-4.0-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 344 and 0 Target number of residues in the AU: 344 Target solvent content: 0.6305 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-4.0-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-4.0-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 4.000 Wilson plot Bfac: 66.32 4226 reflections ( 99.04 % complete ) and 0 restraints for refining 4837 atoms. Observations/parameters ratio is 0.22 ------------------------------------------------------ Starting model: R = 0.3378 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3352 (Rfree = 0.000) for 4837 atoms. Found 22 (22 requested) and removed 62 (11 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.46 3.91 Search for helices and strands: 0 residues in 0 chains, 4918 seeds are put forward NCS extension: 0 residues added, 4918 seeds are put forward Round 1: 129 peptides, 29 chains. Longest chain 7 peptides. Score 0.220 Round 2: 172 peptides, 36 chains. Longest chain 8 peptides. Score 0.273 Round 3: 203 peptides, 39 chains. Longest chain 8 peptides. Score 0.337 Round 4: 216 peptides, 39 chains. Longest chain 13 peptides. Score 0.380 Round 5: 224 peptides, 38 chains. Longest chain 11 peptides. Score 0.419 Taking the results from Round 5 Chains 38, Residues 186, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4226 reflections ( 99.04 % complete ) and 9563 restraints for refining 3943 atoms. 8857 conditional restraints added. Observations/parameters ratio is 0.27 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2833 (Rfree = 0.000) for 3943 atoms. Found 15 (18 requested) and removed 32 (9 requested) atoms. Cycle 2: After refmac, R = 0.2645 (Rfree = 0.000) for 3865 atoms. Found 18 (18 requested) and removed 32 (9 requested) atoms. Cycle 3: After refmac, R = 0.2469 (Rfree = 0.000) for 3814 atoms. Found 18 (18 requested) and removed 28 (9 requested) atoms. Cycle 4: After refmac, R = 0.2409 (Rfree = 0.000) for 3774 atoms. Found 18 (18 requested) and removed 23 (9 requested) atoms. Cycle 5: After refmac, R = 0.1705 (Rfree = 0.000) for 3760 atoms. Found 17 (17 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.51 3.96 Search for helices and strands: 0 residues in 0 chains, 3937 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 3949 seeds are put forward Round 1: 165 peptides, 35 chains. Longest chain 8 peptides. Score 0.263 Round 2: 219 peptides, 41 chains. Longest chain 11 peptides. Score 0.362 Round 3: 239 peptides, 43 chains. Longest chain 12 peptides. Score 0.399 Round 4: 232 peptides, 37 chains. Longest chain 12 peptides. Score 0.456 Round 5: 236 peptides, 37 chains. Longest chain 17 peptides. Score 0.468 Taking the results from Round 5 Chains 37, Residues 199, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4226 reflections ( 99.04 % complete ) and 8885 restraints for refining 3758 atoms. 8126 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2489 (Rfree = 0.000) for 3758 atoms. Found 17 (17 requested) and removed 29 (8 requested) atoms. Cycle 7: After refmac, R = 0.2243 (Rfree = 0.000) for 3713 atoms. Found 17 (17 requested) and removed 27 (8 requested) atoms. Cycle 8: After refmac, R = 0.1576 (Rfree = 0.000) for 3684 atoms. Found 5 (17 requested) and removed 15 (8 requested) atoms. Cycle 9: After refmac, R = 0.1456 (Rfree = 0.000) for 3660 atoms. Found 5 (17 requested) and removed 15 (8 requested) atoms. Cycle 10: After refmac, R = 0.1430 (Rfree = 0.000) for 3644 atoms. Found 3 (17 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.54 4.00 Search for helices and strands: 0 residues in 0 chains, 3754 seeds are put forward NCS extension: 27 residues added (0 deleted due to clashes), 3781 seeds are put forward Round 1: 186 peptides, 38 chains. Longest chain 10 peptides. Score 0.293 Round 2: 211 peptides, 37 chains. Longest chain 14 peptides. Score 0.391 Round 3: 226 peptides, 38 chains. Longest chain 14 peptides. Score 0.425 Round 4: 241 peptides, 38 chains. Longest chain 15 peptides. Score 0.470 Round 5: 236 peptides, 40 chains. Longest chain 13 peptides. Score 0.429 Taking the results from Round 4 Chains 38, Residues 203, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4226 reflections ( 99.04 % complete ) and 8539 restraints for refining 3698 atoms. 7765 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2059 (Rfree = 0.000) for 3698 atoms. Found 17 (17 requested) and removed 24 (8 requested) atoms. Cycle 12: After refmac, R = 0.2048 (Rfree = 0.000) for 3676 atoms. Found 17 (17 requested) and removed 31 (8 requested) atoms. Cycle 13: After refmac, R = 0.1972 (Rfree = 0.000) for 3649 atoms. Found 17 (17 requested) and removed 27 (8 requested) atoms. Cycle 14: After refmac, R = 0.1960 (Rfree = 0.000) for 3622 atoms. Found 17 (17 requested) and removed 19 (8 requested) atoms. Cycle 15: After refmac, R = 0.1563 (Rfree = 0.000) for 3607 atoms. Found 8 (17 requested) and removed 14 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.54 4.00 Search for helices and strands: 0 residues in 0 chains, 3729 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 3749 seeds are put forward Round 1: 205 peptides, 42 chains. Longest chain 10 peptides. Score 0.301 Round 2: 236 peptides, 42 chains. Longest chain 11 peptides. Score 0.403 Round 3: 229 peptides, 40 chains. Longest chain 10 peptides. Score 0.408 Round 4: 241 peptides, 40 chains. Longest chain 17 peptides. Score 0.444 Round 5: 243 peptides, 39 chains. Longest chain 17 peptides. Score 0.463 Taking the results from Round 5 Chains 39, Residues 204, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4226 reflections ( 99.04 % complete ) and 8975 restraints for refining 3794 atoms. 8198 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2583 (Rfree = 0.000) for 3794 atoms. Found 18 (18 requested) and removed 96 (9 requested) atoms. Cycle 17: After refmac, R = 0.2193 (Rfree = 0.000) for 3690 atoms. Found 17 (17 requested) and removed 29 (8 requested) atoms. Cycle 18: After refmac, R = 0.1681 (Rfree = 0.000) for 3671 atoms. Found 5 (17 requested) and removed 25 (8 requested) atoms. Cycle 19: After refmac, R = 0.1605 (Rfree = 0.000) for 3642 atoms. Found 4 (17 requested) and removed 14 (8 requested) atoms. Cycle 20: After refmac, R = 0.1593 (Rfree = 0.000) for 3630 atoms. Found 2 (17 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.55 4.01 Search for helices and strands: 0 residues in 0 chains, 3756 seeds are put forward NCS extension: 28 residues added (3 deleted due to clashes), 3784 seeds are put forward Round 1: 191 peptides, 41 chains. Longest chain 10 peptides. Score 0.267 Round 2: 233 peptides, 44 chains. Longest chain 10 peptides. Score 0.366 Round 3: 232 peptides, 41 chains. Longest chain 11 peptides. Score 0.404 Round 4: 237 peptides, 43 chains. Longest chain 11 peptides. Score 0.393 Round 5: 240 peptides, 41 chains. Longest chain 13 peptides. Score 0.428 Taking the results from Round 5 Chains 41, Residues 199, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4226 reflections ( 99.04 % complete ) and 9311 restraints for refining 3885 atoms. 8556 conditional restraints added. Observations/parameters ratio is 0.27 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2498 (Rfree = 0.000) for 3885 atoms. Found 18 (18 requested) and removed 45 (9 requested) atoms. Cycle 22: After refmac, R = 0.2467 (Rfree = 0.000) for 3830 atoms. Found 18 (18 requested) and removed 39 (9 requested) atoms. Cycle 23: After refmac, R = 0.2335 (Rfree = 0.000) for 3789 atoms. Found 18 (18 requested) and removed 28 (9 requested) atoms. Cycle 24: After refmac, R = 0.2116 (Rfree = 0.000) for 3770 atoms. Found 13 (17 requested) and removed 18 (8 requested) atoms. Cycle 25: After refmac, R = 0.2023 (Rfree = 0.000) for 3758 atoms. Found 9 (17 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.59 4.05 Search for helices and strands: 0 residues in 0 chains, 3883 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 3901 seeds are put forward Round 1: 182 peptides, 39 chains. Longest chain 8 peptides. Score 0.264 Round 2: 218 peptides, 42 chains. Longest chain 9 peptides. Score 0.345 Round 3: 217 peptides, 36 chains. Longest chain 11 peptides. Score 0.424 Round 4: 206 peptides, 34 chains. Longest chain 12 peptides. Score 0.417 Round 5: 209 peptides, 32 chains. Longest chain 18 peptides. Score 0.453 Taking the results from Round 5 Chains 32, Residues 177, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4226 reflections ( 99.04 % complete ) and 9521 restraints for refining 3892 atoms. 8845 conditional restraints added. Observations/parameters ratio is 0.27 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2423 (Rfree = 0.000) for 3892 atoms. Found 18 (18 requested) and removed 44 (9 requested) atoms. Cycle 27: After refmac, R = 0.2416 (Rfree = 0.000) for 3859 atoms. Found 18 (18 requested) and removed 37 (9 requested) atoms. Cycle 28: After refmac, R = 0.2211 (Rfree = 0.000) for 3826 atoms. Found 18 (18 requested) and removed 32 (9 requested) atoms. Cycle 29: After refmac, R = 0.1787 (Rfree = 0.000) for 3806 atoms. Found 14 (18 requested) and removed 20 (9 requested) atoms. Cycle 30: After refmac, R = 0.1553 (Rfree = 0.000) for 3787 atoms. Found 6 (18 requested) and removed 13 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.57 4.03 Search for helices and strands: 0 residues in 0 chains, 3911 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 3927 seeds are put forward Round 1: 157 peptides, 36 chains. Longest chain 7 peptides. Score 0.217 Round 2: 174 peptides, 35 chains. Longest chain 12 peptides. Score 0.295 Round 3: 183 peptides, 34 chains. Longest chain 12 peptides. Score 0.341 Round 4: 180 peptides, 35 chains. Longest chain 11 peptides. Score 0.316 Round 5: 181 peptides, 32 chains. Longest chain 12 peptides. Score 0.364 Taking the results from Round 5 Chains 32, Residues 149, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 4226 reflections ( 99.04 % complete ) and 9650 restraints for refining 3944 atoms. 9062 conditional restraints added. Observations/parameters ratio is 0.27 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2505 (Rfree = 0.000) for 3944 atoms. Found 18 (18 requested) and removed 52 (9 requested) atoms. Cycle 32: After refmac, R = 0.2706 (Rfree = 0.000) for 3890 atoms. Found 18 (18 requested) and removed 29 (9 requested) atoms. Cycle 33: After refmac, R = 0.2260 (Rfree = 0.000) for 3862 atoms. Found 18 (18 requested) and removed 56 (9 requested) atoms. Cycle 34: After refmac, R = 0.1719 (Rfree = 0.000) for 3811 atoms. Found 11 (18 requested) and removed 15 (9 requested) atoms. Cycle 35: After refmac, R = 0.1607 (Rfree = 0.000) for 3795 atoms. Found 9 (18 requested) and removed 19 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.54 4.00 Search for helices and strands: 0 residues in 0 chains, 3894 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 3908 seeds are put forward Round 1: 125 peptides, 30 chains. Longest chain 7 peptides. Score 0.188 Round 2: 147 peptides, 30 chains. Longest chain 12 peptides. Score 0.274 Round 3: 177 peptides, 36 chains. Longest chain 11 peptides. Score 0.291 Round 4: 162 peptides, 31 chains. Longest chain 11 peptides. Score 0.313 Round 5: 165 peptides, 32 chains. Longest chain 11 peptides. Score 0.308 Taking the results from Round 4 Chains 31, Residues 131, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4226 reflections ( 99.04 % complete ) and 9225 restraints for refining 3752 atoms. 8732 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2423 (Rfree = 0.000) for 3752 atoms. Found 17 (17 requested) and removed 30 (8 requested) atoms. Cycle 37: After refmac, R = 0.2459 (Rfree = 0.000) for 3722 atoms. Found 17 (17 requested) and removed 28 (8 requested) atoms. Cycle 38: After refmac, R = 0.1867 (Rfree = 0.000) for 3697 atoms. Found 17 (17 requested) and removed 25 (8 requested) atoms. Cycle 39: After refmac, R = 0.1529 (Rfree = 0.000) for 3677 atoms. Found 11 (17 requested) and removed 13 (8 requested) atoms. Cycle 40: After refmac, R = 0.1510 (Rfree = 0.000) for 3673 atoms. Found 4 (17 requested) and removed 16 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.53 3.98 Search for helices and strands: 0 residues in 0 chains, 3767 seeds are put forward NCS extension: 0 residues added, 3767 seeds are put forward Round 1: 135 peptides, 30 chains. Longest chain 8 peptides. Score 0.228 Round 2: 162 peptides, 32 chains. Longest chain 12 peptides. Score 0.298 Round 3: 159 peptides, 32 chains. Longest chain 10 peptides. Score 0.287 Round 4: 158 peptides, 32 chains. Longest chain 11 peptides. Score 0.283 Round 5: 157 peptides, 30 chains. Longest chain 10 peptides. Score 0.310 Taking the results from Round 5 Chains 30, Residues 127, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4226 reflections ( 99.04 % complete ) and 9160 restraints for refining 3724 atoms. 8682 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2577 (Rfree = 0.000) for 3724 atoms. Found 17 (17 requested) and removed 21 (8 requested) atoms. Cycle 42: After refmac, R = 0.2308 (Rfree = 0.000) for 3706 atoms. Found 17 (17 requested) and removed 22 (8 requested) atoms. Cycle 43: After refmac, R = 0.2176 (Rfree = 0.000) for 3692 atoms. Found 17 (17 requested) and removed 24 (8 requested) atoms. Cycle 44: After refmac, R = 0.2123 (Rfree = 0.000) for 3678 atoms. Found 17 (17 requested) and removed 19 (8 requested) atoms. Cycle 45: After refmac, R = 0.1901 (Rfree = 0.000) for 3668 atoms. Found 17 (17 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.47 3.92 Search for helices and strands: 0 residues in 0 chains, 3771 seeds are put forward NCS extension: 0 residues added, 3771 seeds are put forward Round 1: 118 peptides, 27 chains. Longest chain 6 peptides. Score 0.209 Round 2: 161 peptides, 32 chains. Longest chain 9 peptides. Score 0.294 Round 3: 144 peptides, 26 chains. Longest chain 9 peptides. Score 0.326 Round 4: 152 peptides, 30 chains. Longest chain 8 peptides. Score 0.292 Round 5: 150 peptides, 27 chains. Longest chain 9 peptides. Score 0.331 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 27, Residues 123, 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-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4226 reflections ( 99.04 % complete ) and 9128 restraints for refining 3747 atoms. 8663 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2292 (Rfree = 0.000) for 3747 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2060 (Rfree = 0.000) for 3728 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.1949 (Rfree = 0.000) for 3714 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.2010 (Rfree = 0.000) for 3700 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Writing output files ... TimeTaking 45.58