null Tue 25 Dec 19:27:57 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2gb5-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2gb5-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2gb5-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gb5-3.2-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/2gb5-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gb5-3.2-parrot-hancs ############### 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 ============================================================ Tue 25 Dec 19:28:07 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/hancs/ArpWArp/wArpResults/WorkingDir/2gb5-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gb5-3.2-parrot-hancs/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 413 and 0 Target number of residues in the AU: 413 Target solvent content: 0.6204 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: 2gb5-3.2-parrot-hancs.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: 2gb5-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 4304 target number of atoms Had to go as low as 0.75 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 3.200 Wilson plot Bfac: 61.35 10184 reflections ( 99.58 % complete ) and 0 restraints for refining 4742 atoms. Observations/parameters ratio is 0.54 ------------------------------------------------------ Starting model: R = 0.3203 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2710 (Rfree = 0.000) for 4742 atoms. Found 29 (42 requested) and removed 35 (21 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.17 3.13 Search for helices and strands: 0 residues in 0 chains, 4818 seeds are put forward NCS extension: 0 residues added, 4818 seeds are put forward Round 1: 281 peptides, 53 chains. Longest chain 10 peptides. Score 0.372 Round 2: 325 peptides, 50 chains. Longest chain 13 peptides. Score 0.515 Round 3: 351 peptides, 48 chains. Longest chain 21 peptides. Score 0.591 Round 4: 379 peptides, 42 chains. Longest chain 25 peptides. Score 0.691 Round 5: 378 peptides, 46 chains. Longest chain 24 peptides. Score 0.658 Taking the results from Round 4 Chains 45, Residues 337, Estimated correctness of the model 63.2 % 5 chains (63 residues) have been docked in sequence ------------------------------------------------------ 10184 reflections ( 99.58 % complete ) and 7581 restraints for refining 3925 atoms. 6024 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2713 (Rfree = 0.000) for 3925 atoms. Found 31 (35 requested) and removed 24 (17 requested) atoms. Cycle 2: After refmac, R = 0.2616 (Rfree = 0.000) for 3884 atoms. Found 10 (35 requested) and removed 24 (17 requested) atoms. Cycle 3: After refmac, R = 0.2587 (Rfree = 0.000) for 3851 atoms. Found 10 (34 requested) and removed 19 (17 requested) atoms. Cycle 4: After refmac, R = 0.2531 (Rfree = 0.000) for 3832 atoms. Found 9 (34 requested) and removed 18 (17 requested) atoms. Cycle 5: After refmac, R = 0.2509 (Rfree = 0.000) for 3816 atoms. Found 8 (34 requested) and removed 17 (17 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.14 3.10 Search for helices and strands: 0 residues in 0 chains, 3911 seeds are put forward NCS extension: 18 residues added (5 deleted due to clashes), 3929 seeds are put forward Round 1: 338 peptides, 46 chains. Longest chain 20 peptides. Score 0.582 Round 2: 375 peptides, 42 chains. Longest chain 37 peptides. Score 0.684 Round 3: 374 peptides, 41 chains. Longest chain 38 peptides. Score 0.690 Round 4: 371 peptides, 38 chains. Longest chain 29 peptides. Score 0.707 Round 5: 370 peptides, 43 chains. Longest chain 24 peptides. Score 0.668 Taking the results from Round 4 Chains 42, Residues 333, Estimated correctness of the model 66.7 % 6 chains (110 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 126 A and 133 A 40 chains (337 residues) following loop building 5 chains (116 residues) in sequence following loop building ------------------------------------------------------ 10184 reflections ( 99.58 % complete ) and 7145 restraints for refining 3929 atoms. 5302 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2667 (Rfree = 0.000) for 3929 atoms. Found 35 (35 requested) and removed 26 (17 requested) atoms. Cycle 7: After refmac, R = 0.2501 (Rfree = 0.000) for 3916 atoms. Found 13 (34 requested) and removed 18 (17 requested) atoms. Cycle 8: After refmac, R = 0.2478 (Rfree = 0.000) for 3903 atoms. Found 7 (34 requested) and removed 17 (17 requested) atoms. Cycle 9: After refmac, R = 0.2370 (Rfree = 0.000) for 3882 atoms. Found 11 (32 requested) and removed 17 (17 requested) atoms. Cycle 10: After refmac, R = 0.2312 (Rfree = 0.000) for 3867 atoms. Found 6 (31 requested) and removed 17 (17 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.19 3.15 Search for helices and strands: 0 residues in 0 chains, 3949 seeds are put forward NCS extension: 52 residues added (3 deleted due to clashes), 4001 seeds are put forward Round 1: 304 peptides, 43 chains. Longest chain 19 peptides. Score 0.537 Round 2: 330 peptides, 43 chains. Longest chain 24 peptides. Score 0.593 Round 3: 340 peptides, 37 chains. Longest chain 28 peptides. Score 0.664 Round 4: 353 peptides, 40 chains. Longest chain 27 peptides. Score 0.663 Round 5: 361 peptides, 38 chains. Longest chain 29 peptides. Score 0.692 Taking the results from Round 5 Chains 40, Residues 323, Estimated correctness of the model 63.5 % 5 chains (93 residues) have been docked in sequence ------------------------------------------------------ 10184 reflections ( 99.58 % complete ) and 7611 restraints for refining 3929 atoms. 5953 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2610 (Rfree = 0.000) for 3929 atoms. Found 31 (31 requested) and removed 26 (17 requested) atoms. Cycle 12: After refmac, R = 0.2466 (Rfree = 0.000) for 3909 atoms. Found 11 (31 requested) and removed 18 (17 requested) atoms. Cycle 13: After refmac, R = 0.2312 (Rfree = 0.000) for 3895 atoms. Found 4 (31 requested) and removed 18 (17 requested) atoms. Cycle 14: After refmac, R = 0.2284 (Rfree = 0.000) for 3869 atoms. Found 13 (31 requested) and removed 17 (17 requested) atoms. Cycle 15: After refmac, R = 0.2328 (Rfree = 0.000) for 3865 atoms. Found 7 (31 requested) and removed 17 (17 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.18 3.14 Search for helices and strands: 0 residues in 0 chains, 3938 seeds are put forward NCS extension: 25 residues added (7 deleted due to clashes), 3963 seeds are put forward Round 1: 309 peptides, 45 chains. Longest chain 19 peptides. Score 0.529 Round 2: 334 peptides, 39 chains. Longest chain 32 peptides. Score 0.636 Round 3: 353 peptides, 45 chains. Longest chain 20 peptides. Score 0.621 Round 4: 353 peptides, 42 chains. Longest chain 28 peptides. Score 0.646 Round 5: 352 peptides, 43 chains. Longest chain 29 peptides. Score 0.636 Taking the results from Round 4 Chains 43, Residues 311, Estimated correctness of the model 52.9 % 6 chains (94 residues) have been docked in sequence ------------------------------------------------------ 10184 reflections ( 99.58 % complete ) and 7428 restraints for refining 3929 atoms. 5798 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2557 (Rfree = 0.000) for 3929 atoms. Found 19 (31 requested) and removed 29 (17 requested) atoms. Cycle 17: After refmac, R = 0.2469 (Rfree = 0.000) for 3911 atoms. Found 7 (31 requested) and removed 21 (17 requested) atoms. Cycle 18: After refmac, R = 0.2437 (Rfree = 0.000) for 3895 atoms. Found 9 (31 requested) and removed 17 (17 requested) atoms. Cycle 19: After refmac, R = 0.2308 (Rfree = 0.000) for 3880 atoms. Found 4 (31 requested) and removed 17 (17 requested) atoms. Cycle 20: After refmac, R = 0.2280 (Rfree = 0.000) for 3863 atoms. Found 4 (31 requested) and removed 17 (17 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.20 3.16 Search for helices and strands: 0 residues in 0 chains, 3923 seeds are put forward NCS extension: 58 residues added (4 deleted due to clashes), 3981 seeds are put forward Round 1: 281 peptides, 42 chains. Longest chain 19 peptides. Score 0.494 Round 2: 294 peptides, 39 chains. Longest chain 21 peptides. Score 0.555 Round 3: 334 peptides, 38 chains. Longest chain 29 peptides. Score 0.645 Round 4: 341 peptides, 39 chains. Longest chain 31 peptides. Score 0.649 Round 5: 348 peptides, 33 chains. Longest chain 32 peptides. Score 0.708 Taking the results from Round 5 Chains 36, Residues 315, Estimated correctness of the model 66.9 % 5 chains (97 residues) have been docked in sequence Building loops using Loopy2018 36 chains (315 residues) following loop building 5 chains (97 residues) in sequence following loop building ------------------------------------------------------ 10184 reflections ( 99.58 % complete ) and 7368 restraints for refining 3929 atoms. 5672 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2505 (Rfree = 0.000) for 3929 atoms. Found 16 (31 requested) and removed 21 (17 requested) atoms. Cycle 22: After refmac, R = 0.2456 (Rfree = 0.000) for 3907 atoms. Found 12 (31 requested) and removed 19 (17 requested) atoms. Cycle 23: After refmac, R = 0.2405 (Rfree = 0.000) for 3891 atoms. Found 9 (30 requested) and removed 17 (17 requested) atoms. Cycle 24: After refmac, R = 0.2345 (Rfree = 0.000) for 3881 atoms. Found 8 (29 requested) and removed 17 (17 requested) atoms. Cycle 25: After refmac, R = 0.2309 (Rfree = 0.000) for 3862 atoms. Found 4 (28 requested) and removed 17 (17 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.15 3.11 Search for helices and strands: 0 residues in 0 chains, 3937 seeds are put forward NCS extension: 44 residues added (4 deleted due to clashes), 3981 seeds are put forward Round 1: 306 peptides, 42 chains. Longest chain 28 peptides. Score 0.552 Round 2: 310 peptides, 34 chains. Longest chain 29 peptides. Score 0.635 Round 3: 323 peptides, 39 chains. Longest chain 27 peptides. Score 0.615 Round 4: 326 peptides, 36 chains. Longest chain 27 peptides. Score 0.647 Round 5: 306 peptides, 39 chains. Longest chain 23 peptides. Score 0.581 Taking the results from Round 4 Chains 40, Residues 290, Estimated correctness of the model 53.1 % 4 chains (66 residues) have been docked in sequence ------------------------------------------------------ 10184 reflections ( 99.58 % complete ) and 7954 restraints for refining 3928 atoms. 6555 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2410 (Rfree = 0.000) for 3928 atoms. Found 24 (28 requested) and removed 24 (17 requested) atoms. Cycle 27: After refmac, R = 0.2344 (Rfree = 0.000) for 3921 atoms. Found 10 (28 requested) and removed 18 (17 requested) atoms. Cycle 28: After refmac, R = 0.2226 (Rfree = 0.000) for 3911 atoms. Found 7 (28 requested) and removed 17 (17 requested) atoms. Cycle 29: After refmac, R = 0.2196 (Rfree = 0.000) for 3893 atoms. Found 6 (28 requested) and removed 17 (17 requested) atoms. Cycle 30: After refmac, R = 0.2116 (Rfree = 0.000) for 3881 atoms. Found 7 (27 requested) and removed 17 (17 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.17 3.13 Search for helices and strands: 0 residues in 0 chains, 3951 seeds are put forward NCS extension: 34 residues added (0 deleted due to clashes), 3985 seeds are put forward Round 1: 316 peptides, 46 chains. Longest chain 29 peptides. Score 0.535 Round 2: 340 peptides, 43 chains. Longest chain 27 peptides. Score 0.613 Round 3: 331 peptides, 39 chains. Longest chain 28 peptides. Score 0.631 Round 4: 323 peptides, 45 chains. Longest chain 21 peptides. Score 0.560 Round 5: 334 peptides, 36 chains. Longest chain 31 peptides. Score 0.662 Taking the results from Round 5 Chains 39, Residues 298, Estimated correctness of the model 56.7 % 4 chains (77 residues) have been docked in sequence ------------------------------------------------------ 10184 reflections ( 99.58 % complete ) and 7691 restraints for refining 3929 atoms. 6174 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2461 (Rfree = 0.000) for 3929 atoms. Found 24 (28 requested) and removed 24 (17 requested) atoms. Cycle 32: After refmac, R = 0.2314 (Rfree = 0.000) for 3921 atoms. Found 10 (28 requested) and removed 17 (17 requested) atoms. Cycle 33: After refmac, R = 0.2268 (Rfree = 0.000) for 3906 atoms. Found 11 (28 requested) and removed 17 (17 requested) atoms. Cycle 34: After refmac, R = 0.2236 (Rfree = 0.000) for 3899 atoms. Found 4 (28 requested) and removed 17 (17 requested) atoms. Cycle 35: After refmac, R = 0.2207 (Rfree = 0.000) for 3879 atoms. Found 8 (27 requested) and removed 17 (17 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.18 3.14 Search for helices and strands: 0 residues in 0 chains, 3950 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 3969 seeds are put forward Round 1: 291 peptides, 44 chains. Longest chain 21 peptides. Score 0.497 Round 2: 311 peptides, 39 chains. Longest chain 29 peptides. Score 0.591 Round 3: 337 peptides, 42 chains. Longest chain 25 peptides. Score 0.616 Round 4: 334 peptides, 40 chains. Longest chain 28 peptides. Score 0.628 Round 5: 327 peptides, 40 chains. Longest chain 25 peptides. Score 0.614 Taking the results from Round 4 Chains 42, Residues 294, Estimated correctness of the model 48.4 % 4 chains (45 residues) have been docked in sequence ------------------------------------------------------ 10184 reflections ( 99.58 % complete ) and 8139 restraints for refining 3929 atoms. 6815 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2404 (Rfree = 0.000) for 3929 atoms. Found 24 (28 requested) and removed 24 (17 requested) atoms. Cycle 37: After refmac, R = 0.2293 (Rfree = 0.000) for 3922 atoms. Found 12 (28 requested) and removed 18 (17 requested) atoms. Cycle 38: After refmac, R = 0.2304 (Rfree = 0.000) for 3909 atoms. Found 11 (28 requested) and removed 17 (17 requested) atoms. Cycle 39: After refmac, R = 0.2178 (Rfree = 0.000) for 3901 atoms. Found 8 (28 requested) and removed 17 (17 requested) atoms. Cycle 40: After refmac, R = 0.2148 (Rfree = 0.000) for 3891 atoms. Found 4 (27 requested) and removed 17 (17 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.17 3.13 Search for helices and strands: 0 residues in 0 chains, 3952 seeds are put forward NCS extension: 44 residues added (5 deleted due to clashes), 3996 seeds are put forward Round 1: 257 peptides, 42 chains. Longest chain 19 peptides. Score 0.434 Round 2: 304 peptides, 40 chains. Longest chain 27 peptides. Score 0.567 Round 3: 307 peptides, 40 chains. Longest chain 18 peptides. Score 0.573 Round 4: 300 peptides, 38 chains. Longest chain 28 peptides. Score 0.578 Round 5: 293 peptides, 34 chains. Longest chain 29 peptides. Score 0.601 Taking the results from Round 5 Chains 34, Residues 259, Estimated correctness of the model 41.3 % 1 chains (25 residues) have been docked in sequence ------------------------------------------------------ 10184 reflections ( 99.58 % complete ) and 8419 restraints for refining 3929 atoms. 7300 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2303 (Rfree = 0.000) for 3929 atoms. Found 19 (28 requested) and removed 21 (17 requested) atoms. Cycle 42: After refmac, R = 0.2203 (Rfree = 0.000) for 3922 atoms. Found 4 (28 requested) and removed 17 (17 requested) atoms. Cycle 43: After refmac, R = 0.2173 (Rfree = 0.000) for 3907 atoms. Found 5 (28 requested) and removed 17 (17 requested) atoms. Cycle 44: After refmac, R = 0.2188 (Rfree = 0.000) for 3891 atoms. Found 6 (27 requested) and removed 17 (17 requested) atoms. Cycle 45: After refmac, R = 0.2112 (Rfree = 0.000) for 3879 atoms. Found 3 (27 requested) and removed 17 (17 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.20 3.16 Search for helices and strands: 0 residues in 0 chains, 3932 seeds are put forward NCS extension: 53 residues added (1 deleted due to clashes), 3985 seeds are put forward Round 1: 244 peptides, 35 chains. Longest chain 22 peptides. Score 0.479 Round 2: 265 peptides, 41 chains. Longest chain 14 peptides. Score 0.465 Round 3: 283 peptides, 39 chains. Longest chain 25 peptides. Score 0.530 Round 4: 285 peptides, 40 chains. Longest chain 17 peptides. Score 0.524 Round 5: 275 peptides, 38 chains. Longest chain 26 peptides. Score 0.522 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 39, Residues 244, Estimated correctness of the model 20.8 % 1 chains (15 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 2gb5-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 10184 reflections ( 99.58 % complete ) and 8738 restraints for refining 3929 atoms. 7748 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2241 (Rfree = 0.000) for 3929 atoms. Found 0 (28 requested) and removed 10 (17 requested) atoms. Cycle 47: After refmac, R = 0.2212 (Rfree = 0.000) for 3914 atoms. Found 0 (28 requested) and removed 2 (17 requested) atoms. Cycle 48: After refmac, R = 0.2177 (Rfree = 0.000) for 3910 atoms. Found 0 (28 requested) and removed 10 (17 requested) atoms. Cycle 49: After refmac, R = 0.2139 (Rfree = 0.000) for 3896 atoms. Found 0 (28 requested) and removed 3 (17 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:35:03 GMT 2018 Job finished. TimeTaking 67.1 Used memory is bytes: 6813080