Mon 24 Dec 01:12:55 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 2gb5-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2gb5-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2gb5-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2gb5-3.4-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/2gb5-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2gb5-3.4-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 01:13:00 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/2gb5-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2gb5-3.4-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 404 and 0 Target number of residues in the AU: 404 Target solvent content: 0.6287 Checking the provided sequence file Detected sequence length: 269 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 538 Adjusted target solvent content: 0.51 Input MTZ file: 2gb5-3.4-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: 18 Cell parameters: 99.287 103.553 57.270 90.000 90.000 90.000 Input sequence file: 2gb5-3.4-parrot-mrncs.fasta_lf Building free atoms model in initial map for 4304 target number of atoms Had to go as low as 0.80 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: 49.644 3.400 Wilson plot Bfac: 65.77 8528 reflections ( 99.50 % complete ) and 0 restraints for refining 4791 atoms. Observations/parameters ratio is 0.45 ------------------------------------------------------ Starting model: R = 0.3195 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2939 (Rfree = 0.000) for 4791 atoms. Found 23 (36 requested) and removed 26 (18 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.30 3.26 Search for helices and strands: 0 residues in 0 chains, 4847 seeds are put forward NCS extension: 0 residues added, 4847 seeds are put forward Round 1: 212 peptides, 43 chains. Longest chain 11 peptides. Score 0.295 Round 2: 293 peptides, 48 chains. Longest chain 25 peptides. Score 0.459 Round 3: 325 peptides, 43 chains. Longest chain 22 peptides. Score 0.583 Round 4: 338 peptides, 39 chains. Longest chain 27 peptides. Score 0.644 Round 5: 344 peptides, 40 chains. Longest chain 24 peptides. Score 0.646 Taking the results from Round 5 Chains 41, Residues 304, Estimated correctness of the model 43.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 8528 reflections ( 99.50 % complete ) and 8602 restraints for refining 3912 atoms. 7394 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2809 (Rfree = 0.000) for 3912 atoms. Found 23 (29 requested) and removed 24 (14 requested) atoms. Cycle 2: After refmac, R = 0.2665 (Rfree = 0.000) for 3841 atoms. Found 15 (29 requested) and removed 23 (14 requested) atoms. Cycle 3: After refmac, R = 0.2344 (Rfree = 0.000) for 3816 atoms. Found 12 (28 requested) and removed 21 (14 requested) atoms. Cycle 4: After refmac, R = 0.2492 (Rfree = 0.000) for 3795 atoms. Found 15 (28 requested) and removed 16 (14 requested) atoms. Cycle 5: After refmac, R = 0.2245 (Rfree = 0.000) for 3787 atoms. Found 7 (28 requested) and removed 16 (14 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.30 3.26 Search for helices and strands: 0 residues in 0 chains, 3874 seeds are put forward NCS extension: 28 residues added (1 deleted due to clashes), 3902 seeds are put forward Round 1: 304 peptides, 45 chains. Longest chain 21 peptides. Score 0.517 Round 2: 330 peptides, 45 chains. Longest chain 18 peptides. Score 0.575 Round 3: 335 peptides, 41 chains. Longest chain 26 peptides. Score 0.621 Round 4: 336 peptides, 39 chains. Longest chain 26 peptides. Score 0.640 Round 5: 343 peptides, 38 chains. Longest chain 27 peptides. Score 0.661 Taking the results from Round 5 Chains 38, Residues 305, Estimated correctness of the model 47.3 % 1 chains (26 residues) have been docked in sequence ------------------------------------------------------ 8528 reflections ( 99.50 % complete ) and 8423 restraints for refining 3914 atoms. 7136 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2626 (Rfree = 0.000) for 3914 atoms. Found 28 (29 requested) and removed 29 (14 requested) atoms. Cycle 7: After refmac, R = 0.2477 (Rfree = 0.000) for 3895 atoms. Found 9 (29 requested) and removed 22 (14 requested) atoms. Cycle 8: After refmac, R = 0.2506 (Rfree = 0.000) for 3874 atoms. Found 9 (29 requested) and removed 18 (14 requested) atoms. Cycle 9: After refmac, R = 0.2428 (Rfree = 0.000) for 3861 atoms. Found 9 (29 requested) and removed 18 (14 requested) atoms. Cycle 10: After refmac, R = 0.2375 (Rfree = 0.000) for 3845 atoms. Found 11 (29 requested) and removed 17 (14 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.29 3.25 Search for helices and strands: 0 residues in 0 chains, 3925 seeds are put forward NCS extension: 37 residues added (1 deleted due to clashes), 3962 seeds are put forward Round 1: 287 peptides, 41 chains. Longest chain 18 peptides. Score 0.519 Round 2: 313 peptides, 40 chains. Longest chain 22 peptides. Score 0.586 Round 3: 338 peptides, 43 chains. Longest chain 19 peptides. Score 0.609 Round 4: 321 peptides, 43 chains. Longest chain 17 peptides. Score 0.575 Round 5: 326 peptides, 38 chains. Longest chain 26 peptides. Score 0.630 Taking the results from Round 5 Chains 42, Residues 288, Estimated correctness of the model 38.2 % 4 chains (34 residues) have been docked in sequence ------------------------------------------------------ 8528 reflections ( 99.50 % complete ) and 8497 restraints for refining 3914 atoms. 7253 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2701 (Rfree = 0.000) for 3914 atoms. Found 11 (29 requested) and removed 26 (14 requested) atoms. Cycle 12: After refmac, R = 0.2506 (Rfree = 0.000) for 3876 atoms. Found 13 (29 requested) and removed 24 (14 requested) atoms. Cycle 13: After refmac, R = 0.2385 (Rfree = 0.000) for 3852 atoms. Found 8 (29 requested) and removed 19 (14 requested) atoms. Cycle 14: After refmac, R = 0.2331 (Rfree = 0.000) for 3834 atoms. Found 13 (29 requested) and removed 17 (14 requested) atoms. Cycle 15: After refmac, R = 0.2095 (Rfree = 0.000) for 3825 atoms. Found 1 (28 requested) and removed 17 (14 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.31 3.27 Search for helices and strands: 0 residues in 0 chains, 3892 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 3910 seeds are put forward Round 1: 290 peptides, 46 chains. Longest chain 12 peptides. Score 0.473 Round 2: 332 peptides, 41 chains. Longest chain 24 peptides. Score 0.615 Round 3: 325 peptides, 40 chains. Longest chain 24 peptides. Score 0.610 Round 4: 334 peptides, 39 chains. Longest chain 30 peptides. Score 0.636 Round 5: 336 peptides, 38 chains. Longest chain 26 peptides. Score 0.649 Taking the results from Round 5 Chains 44, Residues 298, Estimated correctness of the model 43.8 % 4 chains (42 residues) have been docked in sequence ------------------------------------------------------ 8528 reflections ( 99.50 % complete ) and 8250 restraints for refining 3914 atoms. 6926 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2481 (Rfree = 0.000) for 3914 atoms. Found 17 (29 requested) and removed 27 (14 requested) atoms. Cycle 17: After refmac, R = 0.2322 (Rfree = 0.000) for 3887 atoms. Found 9 (29 requested) and removed 18 (14 requested) atoms. Cycle 18: After refmac, R = 0.2296 (Rfree = 0.000) for 3868 atoms. Found 9 (29 requested) and removed 19 (14 requested) atoms. Cycle 19: After refmac, R = 0.2235 (Rfree = 0.000) for 3851 atoms. Found 9 (29 requested) and removed 20 (14 requested) atoms. Cycle 20: After refmac, R = 0.2182 (Rfree = 0.000) for 3837 atoms. Found 11 (28 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.34 3.30 Search for helices and strands: 0 residues in 0 chains, 3933 seeds are put forward NCS extension: 25 residues added (3 deleted due to clashes), 3958 seeds are put forward Round 1: 295 peptides, 48 chains. Longest chain 19 peptides. Score 0.464 Round 2: 313 peptides, 41 chains. Longest chain 22 peptides. Score 0.577 Round 3: 310 peptides, 38 chains. Longest chain 17 peptides. Score 0.598 Round 4: 325 peptides, 44 chains. Longest chain 18 peptides. Score 0.574 Round 5: 324 peptides, 43 chains. Longest chain 18 peptides. Score 0.581 Taking the results from Round 3 Chains 38, Residues 272, Estimated correctness of the model 28.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8528 reflections ( 99.50 % complete ) and 8695 restraints for refining 3913 atoms. 7645 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2382 (Rfree = 0.000) for 3913 atoms. Found 21 (29 requested) and removed 19 (14 requested) atoms. Cycle 22: After refmac, R = 0.2252 (Rfree = 0.000) for 3912 atoms. Found 18 (29 requested) and removed 16 (14 requested) atoms. Cycle 23: After refmac, R = 0.2135 (Rfree = 0.000) for 3913 atoms. Found 14 (29 requested) and removed 14 (14 requested) atoms. Cycle 24: After refmac, R = 0.2095 (Rfree = 0.000) for 3908 atoms. Found 8 (29 requested) and removed 14 (14 requested) atoms. Cycle 25: After refmac, R = 0.2050 (Rfree = 0.000) for 3902 atoms. Found 11 (29 requested) and removed 15 (14 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.28 3.24 Search for helices and strands: 0 residues in 0 chains, 3978 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 3995 seeds are put forward Round 1: 278 peptides, 50 chains. Longest chain 14 peptides. Score 0.398 Round 2: 306 peptides, 43 chains. Longest chain 15 peptides. Score 0.542 Round 3: 321 peptides, 42 chains. Longest chain 25 peptides. Score 0.584 Round 4: 293 peptides, 39 chains. Longest chain 18 peptides. Score 0.553 Round 5: 306 peptides, 42 chains. Longest chain 22 peptides. Score 0.552 Taking the results from Round 3 Chains 42, Residues 279, Estimated correctness of the model 23.4 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 8528 reflections ( 99.50 % complete ) and 8648 restraints for refining 3914 atoms. 7546 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2409 (Rfree = 0.000) for 3914 atoms. Found 17 (29 requested) and removed 15 (14 requested) atoms. Cycle 27: After refmac, R = 0.2279 (Rfree = 0.000) for 3903 atoms. Found 11 (29 requested) and removed 16 (14 requested) atoms. Cycle 28: After refmac, R = 0.2226 (Rfree = 0.000) for 3892 atoms. Found 16 (29 requested) and removed 16 (14 requested) atoms. Cycle 29: After refmac, R = 0.2131 (Rfree = 0.000) for 3884 atoms. Found 11 (29 requested) and removed 14 (14 requested) atoms. Cycle 30: After refmac, R = 0.2095 (Rfree = 0.000) for 3877 atoms. Found 9 (29 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.32 3.28 Search for helices and strands: 0 residues in 0 chains, 3957 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 3982 seeds are put forward Round 1: 269 peptides, 45 chains. Longest chain 13 peptides. Score 0.431 Round 2: 282 peptides, 40 chains. Longest chain 25 peptides. Score 0.517 Round 3: 285 peptides, 42 chains. Longest chain 15 peptides. Score 0.504 Round 4: 294 peptides, 44 chains. Longest chain 18 peptides. Score 0.504 Round 5: 287 peptides, 43 chains. Longest chain 18 peptides. Score 0.498 Taking the results from Round 2 Chains 40, Residues 242, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8528 reflections ( 99.50 % complete ) and 8989 restraints for refining 3914 atoms. 8061 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2334 (Rfree = 0.000) for 3914 atoms. Found 15 (29 requested) and removed 15 (14 requested) atoms. Cycle 32: After refmac, R = 0.2316 (Rfree = 0.000) for 3912 atoms. Found 15 (29 requested) and removed 14 (14 requested) atoms. Cycle 33: After refmac, R = 0.2245 (Rfree = 0.000) for 3909 atoms. Found 10 (29 requested) and removed 15 (14 requested) atoms. Cycle 34: After refmac, R = 0.2180 (Rfree = 0.000) for 3900 atoms. Found 5 (29 requested) and removed 14 (14 requested) atoms. Cycle 35: After refmac, R = 0.2165 (Rfree = 0.000) for 3887 atoms. Found 2 (29 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.28 3.24 Search for helices and strands: 0 residues in 0 chains, 3954 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 3972 seeds are put forward Round 1: 237 peptides, 42 chains. Longest chain 14 peptides. Score 0.380 Round 2: 262 peptides, 34 chains. Longest chain 19 peptides. Score 0.533 Round 3: 274 peptides, 37 chains. Longest chain 16 peptides. Score 0.530 Round 4: 276 peptides, 38 chains. Longest chain 16 peptides. Score 0.524 Round 5: 274 peptides, 34 chains. Longest chain 26 peptides. Score 0.561 Taking the results from Round 5 Chains 34, Residues 240, Estimated correctness of the model 15.4 % 2 chains (29 residues) have been docked in sequence ------------------------------------------------------ 8528 reflections ( 99.50 % complete ) and 8569 restraints for refining 3914 atoms. 7533 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2360 (Rfree = 0.000) for 3914 atoms. Found 12 (29 requested) and removed 24 (14 requested) atoms. Cycle 37: After refmac, R = 0.2269 (Rfree = 0.000) for 3897 atoms. Found 13 (29 requested) and removed 18 (14 requested) atoms. Cycle 38: After refmac, R = 0.2149 (Rfree = 0.000) for 3890 atoms. Found 18 (29 requested) and removed 15 (14 requested) atoms. Cycle 39: After refmac, R = 0.2093 (Rfree = 0.000) for 3891 atoms. Found 7 (29 requested) and removed 17 (14 requested) atoms. Cycle 40: After refmac, R = 0.2019 (Rfree = 0.000) for 3879 atoms. Found 4 (29 requested) and removed 15 (14 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.27 3.23 Search for helices and strands: 0 residues in 0 chains, 3940 seeds are put forward NCS extension: 39 residues added (1 deleted due to clashes), 3979 seeds are put forward Round 1: 224 peptides, 36 chains. Longest chain 14 peptides. Score 0.415 Round 2: 262 peptides, 40 chains. Longest chain 18 peptides. Score 0.469 Round 3: 271 peptides, 39 chains. Longest chain 23 peptides. Score 0.502 Round 4: 273 peptides, 37 chains. Longest chain 24 peptides. Score 0.528 Round 5: 265 peptides, 38 chains. Longest chain 26 peptides. Score 0.498 Taking the results from Round 4 Chains 37, Residues 236, Estimated correctness of the model 3.4 % 3 chains (18 residues) have been docked in sequence ------------------------------------------------------ 8528 reflections ( 99.50 % complete ) and 8781 restraints for refining 3914 atoms. 7813 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2218 (Rfree = 0.000) for 3914 atoms. Found 14 (29 requested) and removed 16 (14 requested) atoms. Cycle 42: After refmac, R = 0.2236 (Rfree = 0.000) for 3906 atoms. Found 22 (29 requested) and removed 15 (14 requested) atoms. Cycle 43: After refmac, R = 0.2131 (Rfree = 0.000) for 3907 atoms. Found 13 (29 requested) and removed 15 (14 requested) atoms. Cycle 44: After refmac, R = 0.2134 (Rfree = 0.000) for 3901 atoms. Found 9 (29 requested) and removed 14 (14 requested) atoms. Cycle 45: After refmac, R = 0.2047 (Rfree = 0.000) for 3893 atoms. Found 9 (29 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.33 3.29 Search for helices and strands: 0 residues in 0 chains, 3956 seeds are put forward NCS extension: 26 residues added (0 deleted due to clashes), 3982 seeds are put forward Round 1: 238 peptides, 41 chains. Longest chain 15 peptides. Score 0.394 Round 2: 278 peptides, 38 chains. Longest chain 33 peptides. Score 0.529 Round 3: 270 peptides, 38 chains. Longest chain 19 peptides. Score 0.510 Round 4: 274 peptides, 39 chains. Longest chain 20 peptides. Score 0.509 Round 5: 254 peptides, 37 chains. Longest chain 15 peptides. Score 0.482 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 38, Residues 240, Estimated correctness of the model 3.8 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2gb5-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8528 reflections ( 99.50 % complete ) and 8766 restraints for refining 3914 atoms. 7844 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2183 (Rfree = 0.000) for 3914 atoms. Found 0 (29 requested) and removed 14 (14 requested) atoms. Cycle 47: After refmac, R = 0.2186 (Rfree = 0.000) for 3893 atoms. Found 0 (29 requested) and removed 14 (14 requested) atoms. Cycle 48: After refmac, R = 0.2171 (Rfree = 0.000) for 3876 atoms. Found 0 (29 requested) and removed 14 (14 requested) atoms. Cycle 49: After refmac, R = 0.2150 (Rfree = 0.000) for 3856 atoms. TimeTaking 42.62