Mon 24 Dec 07:30:24 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-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vkh-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vkh-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkh-3.2-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-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkh-3.2-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 07:30:28 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-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkh-3.2-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 395 and 0 Target number of residues in the AU: 395 Target solvent content: 0.5757 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-3.2-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-3.2-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 3.200 Wilson plot Bfac: 43.34 8219 reflections ( 99.49 % complete ) and 0 restraints for refining 4840 atoms. Observations/parameters ratio is 0.42 ------------------------------------------------------ Starting model: R = 0.3302 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2804 (Rfree = 0.000) for 4840 atoms. Found 43 (43 requested) and removed 92 (21 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.85 3.22 Search for helices and strands: 0 residues in 0 chains, 4915 seeds are put forward NCS extension: 0 residues added, 4915 seeds are put forward Round 1: 252 peptides, 47 chains. Longest chain 10 peptides. Score 0.387 Round 2: 315 peptides, 49 chains. Longest chain 14 peptides. Score 0.542 Round 3: 329 peptides, 44 chains. Longest chain 18 peptides. Score 0.626 Round 4: 344 peptides, 45 chains. Longest chain 25 peptides. Score 0.649 Round 5: 347 peptides, 45 chains. Longest chain 20 peptides. Score 0.655 Taking the results from Round 5 Chains 47, Residues 302, Estimated correctness of the model 55.0 % 2 chains (24 residues) have been docked in sequence ------------------------------------------------------ 8219 reflections ( 99.49 % complete ) and 8180 restraints for refining 3983 atoms. 6912 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2399 (Rfree = 0.000) for 3983 atoms. Found 33 (35 requested) and removed 30 (17 requested) atoms. Cycle 2: After refmac, R = 0.2149 (Rfree = 0.000) for 3953 atoms. Found 9 (35 requested) and removed 24 (17 requested) atoms. Cycle 3: After refmac, R = 0.2080 (Rfree = 0.000) for 3921 atoms. Found 12 (35 requested) and removed 19 (17 requested) atoms. Cycle 4: After refmac, R = 0.1993 (Rfree = 0.000) for 3907 atoms. Found 8 (35 requested) and removed 18 (17 requested) atoms. Cycle 5: After refmac, R = 0.1940 (Rfree = 0.000) for 3893 atoms. Found 6 (34 requested) and removed 21 (17 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.89 3.26 Search for helices and strands: 0 residues in 0 chains, 4054 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 4075 seeds are put forward Round 1: 287 peptides, 44 chains. Longest chain 14 peptides. Score 0.525 Round 2: 336 peptides, 41 chains. Longest chain 17 peptides. Score 0.669 Round 3: 351 peptides, 41 chains. Longest chain 26 peptides. Score 0.697 Round 4: 347 peptides, 43 chains. Longest chain 26 peptides. Score 0.673 Round 5: 346 peptides, 39 chains. Longest chain 30 peptides. Score 0.705 Taking the results from Round 5 Chains 40, Residues 307, Estimated correctness of the model 66.2 % 2 chains (40 residues) have been docked in sequence Building loops using Loopy2018 40 chains (307 residues) following loop building 2 chains (40 residues) in sequence following loop building ------------------------------------------------------ 8219 reflections ( 99.49 % complete ) and 8237 restraints for refining 3987 atoms. 6885 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2406 (Rfree = 0.000) for 3987 atoms. Found 28 (35 requested) and removed 29 (17 requested) atoms. Cycle 7: After refmac, R = 0.2228 (Rfree = 0.000) for 3970 atoms. Found 14 (34 requested) and removed 24 (17 requested) atoms. Cycle 8: After refmac, R = 0.2168 (Rfree = 0.000) for 3953 atoms. Found 8 (34 requested) and removed 19 (17 requested) atoms. Cycle 9: After refmac, R = 0.2136 (Rfree = 0.000) for 3940 atoms. Found 9 (33 requested) and removed 17 (17 requested) atoms. Cycle 10: After refmac, R = 0.2057 (Rfree = 0.000) for 3930 atoms. Found 5 (32 requested) and removed 17 (17 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.86 3.23 Search for helices and strands: 0 residues in 0 chains, 4040 seeds are put forward NCS extension: 14 residues added (7 deleted due to clashes), 4054 seeds are put forward Round 1: 282 peptides, 42 chains. Longest chain 13 peptides. Score 0.535 Round 2: 315 peptides, 45 chains. Longest chain 16 peptides. Score 0.584 Round 3: 325 peptides, 42 chains. Longest chain 20 peptides. Score 0.637 Round 4: 326 peptides, 45 chains. Longest chain 19 peptides. Score 0.610 Round 5: 339 peptides, 42 chains. Longest chain 17 peptides. Score 0.666 Taking the results from Round 5 Chains 42, Residues 297, Estimated correctness of the model 57.6 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 8219 reflections ( 99.49 % complete ) and 8676 restraints for refining 3987 atoms. 7506 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2289 (Rfree = 0.000) for 3987 atoms. Found 21 (31 requested) and removed 23 (17 requested) atoms. Cycle 12: After refmac, R = 0.2158 (Rfree = 0.000) for 3981 atoms. Found 12 (31 requested) and removed 18 (17 requested) atoms. Cycle 13: After refmac, R = 0.2104 (Rfree = 0.000) for 3971 atoms. Found 5 (31 requested) and removed 17 (17 requested) atoms. Cycle 14: After refmac, R = 0.2100 (Rfree = 0.000) for 3958 atoms. Found 5 (31 requested) and removed 17 (17 requested) atoms. Cycle 15: After refmac, R = 0.2051 (Rfree = 0.000) for 3945 atoms. Found 5 (31 requested) and removed 17 (17 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.88 3.25 Search for helices and strands: 0 residues in 0 chains, 4062 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 4079 seeds are put forward Round 1: 292 peptides, 44 chains. Longest chain 16 peptides. Score 0.538 Round 2: 301 peptides, 40 chains. Longest chain 22 peptides. Score 0.603 Round 3: 314 peptides, 40 chains. Longest chain 19 peptides. Score 0.633 Round 4: 330 peptides, 40 chains. Longest chain 25 peptides. Score 0.666 Round 5: 339 peptides, 40 chains. Longest chain 24 peptides. Score 0.683 Taking the results from Round 5 Chains 40, Residues 299, Estimated correctness of the model 61.5 % 1 chains (23 residues) have been docked in sequence ------------------------------------------------------ 8219 reflections ( 99.49 % complete ) and 8531 restraints for refining 3987 atoms. 7276 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2414 (Rfree = 0.000) for 3987 atoms. Found 26 (31 requested) and removed 22 (17 requested) atoms. Cycle 17: After refmac, R = 0.2270 (Rfree = 0.000) for 3987 atoms. Found 14 (31 requested) and removed 17 (17 requested) atoms. Cycle 18: After refmac, R = 0.2216 (Rfree = 0.000) for 3981 atoms. Found 8 (31 requested) and removed 17 (17 requested) atoms. Cycle 19: After refmac, R = 0.2163 (Rfree = 0.000) for 3971 atoms. Found 3 (31 requested) and removed 17 (17 requested) atoms. Cycle 20: After refmac, R = 0.2140 (Rfree = 0.000) for 3957 atoms. Found 2 (31 requested) and removed 17 (17 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.89 3.26 Search for helices and strands: 0 residues in 0 chains, 4067 seeds are put forward NCS extension: 38 residues added (2 deleted due to clashes), 4105 seeds are put forward Round 1: 257 peptides, 43 chains. Longest chain 17 peptides. Score 0.453 Round 2: 293 peptides, 42 chains. Longest chain 18 peptides. Score 0.563 Round 3: 307 peptides, 37 chains. Longest chain 21 peptides. Score 0.646 Round 4: 299 peptides, 39 chains. Longest chain 24 peptides. Score 0.609 Round 5: 304 peptides, 39 chains. Longest chain 19 peptides. Score 0.620 Taking the results from Round 3 Chains 37, Residues 270, Estimated correctness of the model 52.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8219 reflections ( 99.49 % complete ) and 8957 restraints for refining 3987 atoms. 7914 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2239 (Rfree = 0.000) for 3987 atoms. Found 18 (31 requested) and removed 17 (17 requested) atoms. Cycle 22: After refmac, R = 0.2099 (Rfree = 0.000) for 3983 atoms. Found 9 (31 requested) and removed 17 (17 requested) atoms. Cycle 23: After refmac, R = 0.2033 (Rfree = 0.000) for 3974 atoms. Found 5 (31 requested) and removed 18 (17 requested) atoms. Cycle 24: After refmac, R = 0.1991 (Rfree = 0.000) for 3959 atoms. Found 5 (31 requested) and removed 17 (17 requested) atoms. Cycle 25: After refmac, R = 0.1970 (Rfree = 0.000) for 3946 atoms. Found 6 (31 requested) and removed 17 (17 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.90 3.27 Search for helices and strands: 0 residues in 0 chains, 4031 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 4046 seeds are put forward Round 1: 292 peptides, 44 chains. Longest chain 16 peptides. Score 0.538 Round 2: 320 peptides, 43 chains. Longest chain 24 peptides. Score 0.616 Round 3: 310 peptides, 42 chains. Longest chain 18 peptides. Score 0.604 Round 4: 322 peptides, 42 chains. Longest chain 20 peptides. Score 0.631 Round 5: 307 peptides, 44 chains. Longest chain 18 peptides. Score 0.576 Taking the results from Round 4 Chains 42, Residues 280, Estimated correctness of the model 49.1 % 2 chains (19 residues) have been docked in sequence ------------------------------------------------------ 8219 reflections ( 99.49 % complete ) and 8603 restraints for refining 3987 atoms. 7451 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2143 (Rfree = 0.000) for 3987 atoms. Found 18 (31 requested) and removed 21 (17 requested) atoms. Cycle 27: After refmac, R = 0.2024 (Rfree = 0.000) for 3979 atoms. Found 6 (31 requested) and removed 18 (17 requested) atoms. Cycle 28: After refmac, R = 0.1949 (Rfree = 0.000) for 3964 atoms. Found 7 (31 requested) and removed 17 (17 requested) atoms. Cycle 29: After refmac, R = 0.1903 (Rfree = 0.000) for 3952 atoms. Found 2 (31 requested) and removed 18 (17 requested) atoms. Cycle 30: After refmac, R = 0.1900 (Rfree = 0.000) for 3934 atoms. Found 9 (31 requested) and removed 18 (17 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.91 3.28 Search for helices and strands: 0 residues in 0 chains, 4036 seeds are put forward NCS extension: 12 residues added (3 deleted due to clashes), 4048 seeds are put forward Round 1: 260 peptides, 45 chains. Longest chain 14 peptides. Score 0.437 Round 2: 288 peptides, 42 chains. Longest chain 15 peptides. Score 0.550 Round 3: 297 peptides, 42 chains. Longest chain 16 peptides. Score 0.573 Round 4: 301 peptides, 39 chains. Longest chain 17 peptides. Score 0.614 Round 5: 303 peptides, 43 chains. Longest chain 16 peptides. Score 0.577 Taking the results from Round 4 Chains 39, Residues 262, Estimated correctness of the model 44.8 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 8219 reflections ( 99.49 % complete ) and 8844 restraints for refining 3987 atoms. 7778 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2139 (Rfree = 0.000) for 3987 atoms. Found 15 (31 requested) and removed 22 (17 requested) atoms. Cycle 32: After refmac, R = 0.2011 (Rfree = 0.000) for 3973 atoms. Found 8 (31 requested) and removed 17 (17 requested) atoms. Cycle 33: After refmac, R = 0.1964 (Rfree = 0.000) for 3959 atoms. Found 10 (31 requested) and removed 17 (17 requested) atoms. Cycle 34: After refmac, R = 0.1903 (Rfree = 0.000) for 3948 atoms. Found 5 (31 requested) and removed 17 (17 requested) atoms. Cycle 35: After refmac, R = 0.1884 (Rfree = 0.000) for 3934 atoms. Found 8 (31 requested) and removed 17 (17 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.90 3.27 Search for helices and strands: 0 residues in 0 chains, 4046 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 4059 seeds are put forward Round 1: 250 peptides, 41 chains. Longest chain 15 peptides. Score 0.458 Round 2: 276 peptides, 39 chains. Longest chain 17 peptides. Score 0.553 Round 3: 288 peptides, 40 chains. Longest chain 16 peptides. Score 0.572 Round 4: 284 peptides, 38 chains. Longest chain 17 peptides. Score 0.584 Round 5: 285 peptides, 40 chains. Longest chain 17 peptides. Score 0.565 Taking the results from Round 4 Chains 38, Residues 246, Estimated correctness of the model 36.7 % 1 chains (16 residues) have been docked in sequence ------------------------------------------------------ 8219 reflections ( 99.49 % complete ) and 8843 restraints for refining 3986 atoms. 7825 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2131 (Rfree = 0.000) for 3986 atoms. Found 25 (31 requested) and removed 23 (17 requested) atoms. Cycle 37: After refmac, R = 0.1965 (Rfree = 0.000) for 3985 atoms. Found 8 (31 requested) and removed 17 (17 requested) atoms. Cycle 38: After refmac, R = 0.1915 (Rfree = 0.000) for 3976 atoms. Found 2 (31 requested) and removed 17 (17 requested) atoms. Cycle 39: After refmac, R = 0.1905 (Rfree = 0.000) for 3955 atoms. Found 3 (31 requested) and removed 17 (17 requested) atoms. Cycle 40: After refmac, R = 0.1918 (Rfree = 0.000) for 3939 atoms. Found 5 (31 requested) and removed 17 (17 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.91 3.28 Search for helices and strands: 0 residues in 0 chains, 4055 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 4070 seeds are put forward Round 1: 233 peptides, 39 chains. Longest chain 17 peptides. Score 0.433 Round 2: 270 peptides, 38 chains. Longest chain 17 peptides. Score 0.549 Round 3: 287 peptides, 37 chains. Longest chain 17 peptides. Score 0.602 Round 4: 249 peptides, 34 chains. Longest chain 17 peptides. Score 0.541 Round 5: 254 peptides, 35 chains. Longest chain 13 peptides. Score 0.542 Taking the results from Round 3 Chains 38, Residues 250, Estimated correctness of the model 41.6 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 8219 reflections ( 99.49 % complete ) and 8755 restraints for refining 3972 atoms. 7736 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2144 (Rfree = 0.000) for 3972 atoms. Found 20 (31 requested) and removed 21 (17 requested) atoms. Cycle 42: After refmac, R = 0.2010 (Rfree = 0.000) for 3970 atoms. Found 5 (31 requested) and removed 17 (17 requested) atoms. Cycle 43: After refmac, R = 0.1970 (Rfree = 0.000) for 3954 atoms. Found 7 (31 requested) and removed 17 (17 requested) atoms. Cycle 44: After refmac, R = 0.1882 (Rfree = 0.000) for 3942 atoms. Found 8 (31 requested) and removed 17 (17 requested) atoms. Cycle 45: After refmac, R = 0.1870 (Rfree = 0.000) for 3931 atoms. Found 8 (31 requested) and removed 17 (17 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.90 3.27 Search for helices and strands: 0 residues in 0 chains, 4039 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 4053 seeds are put forward Round 1: 212 peptides, 34 chains. Longest chain 15 peptides. Score 0.435 Round 2: 235 peptides, 32 chains. Longest chain 16 peptides. Score 0.527 Round 3: 226 peptides, 31 chains. Longest chain 15 peptides. Score 0.515 Round 4: 227 peptides, 30 chains. Longest chain 16 peptides. Score 0.530 Round 5: 240 peptides, 33 chains. Longest chain 16 peptides. Score 0.529 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 30, Residues 197, Estimated correctness of the model 20.8 % 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. 8219 reflections ( 99.49 % complete ) and 9288 restraints for refining 3960 atoms. 8530 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1993 (Rfree = 0.000) for 3960 atoms. Found 0 (31 requested) and removed 17 (17 requested) atoms. Cycle 47: After refmac, R = 0.1914 (Rfree = 0.000) for 3942 atoms. Found 0 (31 requested) and removed 8 (17 requested) atoms. Cycle 48: After refmac, R = 0.1904 (Rfree = 0.000) for 3934 atoms. Found 0 (31 requested) and removed 3 (17 requested) atoms. Cycle 49: After refmac, R = 0.1894 (Rfree = 0.000) for 3931 atoms. TimeTaking 41.85