null Mon 24 Dec 00:33:18 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 1vqr-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vqr-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vqr-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vqr-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/1vqr-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vqr-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 00:33:23 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/1vqr-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vqr-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 802 and 0 Target number of residues in the AU: 802 Target solvent content: 0.6539 Checking the provided sequence file Detected sequence length: 297 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1188 Adjusted target solvent content: 0.49 Input MTZ file: 1vqr-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: 5 Cell parameters: 123.141 122.090 96.897 90.000 120.583 90.000 Input sequence file: 1vqr-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 9504 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: 83.418 4.000 Wilson plot Bfac: 80.47 9486 reflections ( 90.22 % complete ) and 0 restraints for refining 10536 atoms. Observations/parameters ratio is 0.23 ------------------------------------------------------ Starting model: R = 0.3704 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3369 (Rfree = 0.000) for 10536 atoms. Found 50 (50 requested) and removed 312 (25 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.66 3.71 Search for helices and strands: 0 residues in 0 chains, 10344 seeds are put forward NCS extension: 0 residues added, 10344 seeds are put forward Round 1: 204 peptides, 47 chains. Longest chain 7 peptides. Score 0.198 Round 2: 248 peptides, 51 chains. Longest chain 9 peptides. Score 0.246 Round 3: 280 peptides, 59 chains. Longest chain 10 peptides. Score 0.243 Round 4: 298 peptides, 60 chains. Longest chain 10 peptides. Score 0.265 Round 5: 303 peptides, 59 chains. Longest chain 9 peptides. Score 0.280 Taking the results from Round 5 Chains 59, Residues 244, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9486 reflections ( 90.22 % complete ) and 22346 restraints for refining 8583 atoms. 21429 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2904 (Rfree = 0.000) for 8583 atoms. Found 37 (40 requested) and removed 80 (20 requested) atoms. Cycle 2: After refmac, R = 0.2721 (Rfree = 0.000) for 8443 atoms. Found 38 (40 requested) and removed 87 (20 requested) atoms. Cycle 3: After refmac, R = 0.2579 (Rfree = 0.000) for 8327 atoms. Found 35 (39 requested) and removed 57 (19 requested) atoms. Cycle 4: After refmac, R = 0.2482 (Rfree = 0.000) for 8244 atoms. Found 25 (39 requested) and removed 59 (19 requested) atoms. Cycle 5: After refmac, R = 0.2433 (Rfree = 0.000) for 8158 atoms. Found 33 (39 requested) and removed 41 (19 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.61 3.66 Search for helices and strands: 0 residues in 0 chains, 8301 seeds are put forward NCS extension: 0 residues added, 8301 seeds are put forward Round 1: 282 peptides, 65 chains. Longest chain 7 peptides. Score 0.205 Round 2: 364 peptides, 78 chains. Longest chain 8 peptides. Score 0.250 Round 3: 371 peptides, 73 chains. Longest chain 10 peptides. Score 0.292 Round 4: 367 peptides, 72 chains. Longest chain 10 peptides. Score 0.292 Round 5: 363 peptides, 69 chains. Longest chain 16 peptides. Score 0.305 Taking the results from Round 5 Chains 69, Residues 294, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9486 reflections ( 90.22 % complete ) and 18898 restraints for refining 7696 atoms. 17791 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2371 (Rfree = 0.000) for 7696 atoms. Found 36 (36 requested) and removed 56 (18 requested) atoms. Cycle 7: After refmac, R = 0.2296 (Rfree = 0.000) for 7593 atoms. Found 35 (36 requested) and removed 47 (18 requested) atoms. Cycle 8: After refmac, R = 0.2148 (Rfree = 0.000) for 7541 atoms. Found 27 (36 requested) and removed 38 (18 requested) atoms. Cycle 9: After refmac, R = 0.1748 (Rfree = 0.000) for 7499 atoms. Found 8 (35 requested) and removed 28 (17 requested) atoms. Cycle 10: After refmac, R = 0.1701 (Rfree = 0.000) for 7464 atoms. Found 8 (35 requested) and removed 25 (17 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.64 3.69 Search for helices and strands: 0 residues in 0 chains, 7607 seeds are put forward NCS extension: 35 residues added (0 deleted due to clashes), 7642 seeds are put forward Round 1: 354 peptides, 78 chains. Longest chain 10 peptides. Score 0.234 Round 2: 400 peptides, 75 chains. Longest chain 12 peptides. Score 0.322 Round 3: 409 peptides, 77 chains. Longest chain 10 peptides. Score 0.322 Round 4: 395 peptides, 72 chains. Longest chain 12 peptides. Score 0.333 Round 5: 389 peptides, 66 chains. Longest chain 13 peptides. Score 0.361 Taking the results from Round 5 Chains 66, Residues 323, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9486 reflections ( 90.22 % complete ) and 18028 restraints for refining 7562 atoms. 16802 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2219 (Rfree = 0.000) for 7562 atoms. Found 34 (35 requested) and removed 50 (17 requested) atoms. Cycle 12: After refmac, R = 0.2051 (Rfree = 0.000) for 7487 atoms. Found 28 (35 requested) and removed 48 (17 requested) atoms. Cycle 13: After refmac, R = 0.2071 (Rfree = 0.000) for 7428 atoms. Found 35 (35 requested) and removed 39 (17 requested) atoms. Cycle 14: After refmac, R = 0.1936 (Rfree = 0.000) for 7393 atoms. Found 34 (35 requested) and removed 34 (17 requested) atoms. Cycle 15: After refmac, R = 0.2017 (Rfree = 0.000) for 7370 atoms. Found 35 (35 requested) and removed 33 (17 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.61 3.66 Search for helices and strands: 0 residues in 0 chains, 7558 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 7578 seeds are put forward Round 1: 339 peptides, 77 chains. Longest chain 9 peptides. Score 0.217 Round 2: 412 peptides, 82 chains. Longest chain 12 peptides. Score 0.296 Round 3: 396 peptides, 77 chains. Longest chain 12 peptides. Score 0.304 Round 4: 396 peptides, 76 chains. Longest chain 13 peptides. Score 0.310 Round 5: 406 peptides, 71 chains. Longest chain 17 peptides. Score 0.354 Taking the results from Round 5 Chains 72, Residues 335, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 9486 reflections ( 90.22 % complete ) and 18229 restraints for refining 7752 atoms. 16913 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2103 (Rfree = 0.000) for 7752 atoms. Found 36 (36 requested) and removed 60 (18 requested) atoms. Cycle 17: After refmac, R = 0.2019 (Rfree = 0.000) for 7670 atoms. Found 36 (36 requested) and removed 46 (18 requested) atoms. Cycle 18: After refmac, R = 0.1968 (Rfree = 0.000) for 7636 atoms. Found 36 (36 requested) and removed 45 (18 requested) atoms. Cycle 19: After refmac, R = 0.1837 (Rfree = 0.000) for 7604 atoms. Found 36 (36 requested) and removed 32 (18 requested) atoms. Cycle 20: After refmac, R = 0.1835 (Rfree = 0.000) for 7590 atoms. Found 36 (36 requested) and removed 29 (18 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.64 3.69 Search for helices and strands: 0 residues in 0 chains, 7740 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 7758 seeds are put forward Round 1: 352 peptides, 77 chains. Longest chain 8 peptides. Score 0.238 Round 2: 387 peptides, 76 chains. Longest chain 10 peptides. Score 0.297 Round 3: 389 peptides, 77 chains. Longest chain 10 peptides. Score 0.293 Round 4: 373 peptides, 69 chains. Longest chain 16 peptides. Score 0.320 Round 5: 379 peptides, 70 chains. Longest chain 9 peptides. Score 0.322 Taking the results from Round 5 Chains 70, Residues 309, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 9486 reflections ( 90.22 % complete ) and 18843 restraints for refining 7878 atoms. 17655 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2058 (Rfree = 0.000) for 7878 atoms. Found 36 (37 requested) and removed 59 (18 requested) atoms. Cycle 22: After refmac, R = 0.2020 (Rfree = 0.000) for 7830 atoms. Found 37 (37 requested) and removed 36 (18 requested) atoms. Cycle 23: After refmac, R = 0.1934 (Rfree = 0.000) for 7812 atoms. Found 37 (37 requested) and removed 41 (18 requested) atoms. Cycle 24: After refmac, R = 0.1605 (Rfree = 0.000) for 7785 atoms. Found 6 (37 requested) and removed 26 (18 requested) atoms. Cycle 25: After refmac, R = 0.1588 (Rfree = 0.000) for 7754 atoms. Found 7 (36 requested) and removed 26 (18 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.67 3.72 Search for helices and strands: 0 residues in 0 chains, 7893 seeds are put forward NCS extension: 0 residues added, 7893 seeds are put forward Round 1: 281 peptides, 62 chains. Longest chain 8 peptides. Score 0.224 Round 2: 336 peptides, 61 chains. Longest chain 11 peptides. Score 0.317 Round 3: 349 peptides, 67 chains. Longest chain 10 peptides. Score 0.297 Round 4: 346 peptides, 60 chains. Longest chain 12 peptides. Score 0.338 Round 5: 343 peptides, 63 chains. Longest chain 17 peptides. Score 0.314 Taking the results from Round 4 Chains 60, Residues 286, Estimated correctness of the model 0.0 % 3 chains (12 residues) have been docked in sequence ------------------------------------------------------ 9486 reflections ( 90.22 % complete ) and 18954 restraints for refining 7891 atoms. 17824 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2044 (Rfree = 0.000) for 7891 atoms. Found 37 (37 requested) and removed 53 (18 requested) atoms. Cycle 27: After refmac, R = 0.2020 (Rfree = 0.000) for 7841 atoms. Found 32 (37 requested) and removed 38 (18 requested) atoms. Cycle 28: After refmac, R = 0.1910 (Rfree = 0.000) for 7809 atoms. Found 37 (37 requested) and removed 33 (18 requested) atoms. Cycle 29: After refmac, R = 0.1490 (Rfree = 0.000) for 7799 atoms. Found 5 (37 requested) and removed 24 (18 requested) atoms. Cycle 30: After refmac, R = 0.1437 (Rfree = 0.000) for 7765 atoms. Found 4 (36 requested) and removed 21 (18 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.66 3.71 Search for helices and strands: 0 residues in 0 chains, 7923 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 7935 seeds are put forward Round 1: 320 peptides, 71 chains. Longest chain 7 peptides. Score 0.227 Round 2: 366 peptides, 70 chains. Longest chain 12 peptides. Score 0.304 Round 3: 371 peptides, 65 chains. Longest chain 13 peptides. Score 0.342 Round 4: 377 peptides, 66 chains. Longest chain 14 peptides. Score 0.344 Round 5: 362 peptides, 63 chains. Longest chain 16 peptides. Score 0.342 Taking the results from Round 4 Chains 66, Residues 311, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9486 reflections ( 90.22 % complete ) and 18982 restraints for refining 7909 atoms. 17804 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1939 (Rfree = 0.000) for 7909 atoms. Found 33 (37 requested) and removed 43 (18 requested) atoms. Cycle 32: After refmac, R = 0.1937 (Rfree = 0.000) for 7871 atoms. Found 35 (37 requested) and removed 41 (18 requested) atoms. Cycle 33: After refmac, R = 0.1969 (Rfree = 0.000) for 7846 atoms. Found 31 (37 requested) and removed 34 (18 requested) atoms. Cycle 34: After refmac, R = 0.1905 (Rfree = 0.000) for 7827 atoms. Found 37 (37 requested) and removed 39 (18 requested) atoms. Cycle 35: After refmac, R = 0.1875 (Rfree = 0.000) for 7820 atoms. Found 35 (37 requested) and removed 35 (18 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.64 3.69 Search for helices and strands: 0 residues in 0 chains, 7987 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 8004 seeds are put forward Round 1: 287 peptides, 61 chains. Longest chain 9 peptides. Score 0.241 Round 2: 302 peptides, 62 chains. Longest chain 9 peptides. Score 0.258 Round 3: 316 peptides, 60 chains. Longest chain 10 peptides. Score 0.293 Round 4: 321 peptides, 57 chains. Longest chain 13 peptides. Score 0.320 Round 5: 324 peptides, 59 chains. Longest chain 10 peptides. Score 0.312 Taking the results from Round 4 Chains 57, Residues 264, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9486 reflections ( 90.22 % complete ) and 19557 restraints for refining 7961 atoms. 18558 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2112 (Rfree = 0.000) for 7961 atoms. Found 33 (37 requested) and removed 46 (18 requested) atoms. Cycle 37: After refmac, R = 0.2038 (Rfree = 0.000) for 7919 atoms. Found 37 (37 requested) and removed 39 (18 requested) atoms. Cycle 38: After refmac, R = 0.1568 (Rfree = 0.000) for 7895 atoms. Found 9 (37 requested) and removed 25 (18 requested) atoms. Cycle 39: After refmac, R = 0.1485 (Rfree = 0.000) for 7861 atoms. Found 3 (37 requested) and removed 22 (18 requested) atoms. Cycle 40: After refmac, R = 0.1509 (Rfree = 0.000) for 7837 atoms. Found 5 (37 requested) and removed 25 (18 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.66 3.71 Search for helices and strands: 0 residues in 0 chains, 7977 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 7990 seeds are put forward Round 1: 275 peptides, 61 chains. Longest chain 8 peptides. Score 0.221 Round 2: 326 peptides, 60 chains. Longest chain 15 peptides. Score 0.308 Round 3: 314 peptides, 62 chains. Longest chain 10 peptides. Score 0.277 Round 4: 327 peptides, 61 chains. Longest chain 13 peptides. Score 0.303 Round 5: 330 peptides, 60 chains. Longest chain 10 peptides. Score 0.314 Taking the results from Round 5 Chains 60, Residues 270, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 9486 reflections ( 90.22 % complete ) and 19046 restraints for refining 7890 atoms. 18000 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2045 (Rfree = 0.000) for 7890 atoms. Found 26 (37 requested) and removed 41 (18 requested) atoms. Cycle 42: After refmac, R = 0.2162 (Rfree = 0.000) for 7849 atoms. Found 37 (37 requested) and removed 42 (18 requested) atoms. Cycle 43: After refmac, R = 0.2007 (Rfree = 0.000) for 7828 atoms. Found 29 (37 requested) and removed 34 (18 requested) atoms. Cycle 44: After refmac, R = 0.1955 (Rfree = 0.000) for 7805 atoms. Found 24 (37 requested) and removed 34 (18 requested) atoms. Cycle 45: After refmac, R = 0.2034 (Rfree = 0.000) for 7778 atoms. Found 30 (37 requested) and removed 34 (18 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.65 3.70 Search for helices and strands: 0 residues in 0 chains, 7929 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 7941 seeds are put forward Round 1: 249 peptides, 57 chains. Longest chain 7 peptides. Score 0.205 Round 2: 295 peptides, 59 chains. Longest chain 11 peptides. Score 0.267 Round 3: 287 peptides, 56 chains. Longest chain 10 peptides. Score 0.275 Round 4: 285 peptides, 57 chains. Longest chain 11 peptides. Score 0.265 Round 5: 301 peptides, 58 chains. Longest chain 10 peptides. Score 0.283 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 58, Residues 243, 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 1vqr-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 9486 reflections ( 90.22 % complete ) and 18619 restraints for refining 7719 atoms. 17705 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2090 (Rfree = 0.000) for 7719 atoms. Found 0 (36 requested) and removed 18 (18 requested) atoms. Cycle 47: After refmac, R = 0.2098 (Rfree = 0.000) for 7681 atoms. Found 0 (36 requested) and removed 18 (18 requested) atoms. Cycle 48: After refmac, R = 0.2018 (Rfree = 0.000) for 7646 atoms. Found 0 (36 requested) and removed 18 (18 requested) atoms. Cycle 49: After refmac, R = 0.1885 (Rfree = 0.000) for 7613 atoms. Found 0 (36 requested) and removed 18 (18 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 02:06:53 GMT 2018 Job finished. TimeTaking 93.59 Used memory is bytes: 9422528